1
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Jahdkaran M, Asri N, Esmaily H, Rostami-Nejad M. Potential of nutraceuticals in celiac disease. Tissue Barriers 2024:2374628. [PMID: 38944818 DOI: 10.1080/21688370.2024.2374628] [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: 04/10/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024] Open
Abstract
Celiac Disease (CD) is the most common hereditarily-based food intolerance worldwide and a chronic inflammatory condition. The current standard treatment for CD involves strict observance and compliance with a gluten-free diet (GFD). However, maintaining a complete GFD poses challenges, necessitating the exploration of alternative therapeutic approaches. Nutraceuticals, bioactive products bridging nutrition and pharmaceuticals, have emerged as potential candidates to regulate pathways associated with CD and offer therapeutic benefits. Despite extensive research on nutraceuticals in various diseases, their role in CD has been relatively overlooked. This review proposes comprehensively assessing the potential of different nutraceuticals, including phytochemicals, fatty acids, vitamins, minerals, plant-based enzymes, and dietary amino acids, in managing CD. Nutraceuticals exhibit the ability to modulate crucial CD pathways, such as regulating gluten fragment accessibility and digestion, intestinal barrier function, downregulation of tissue transglutaminase (TG2), intestinal epithelial morphology, regulating innate and adaptive immune responses, inflammation, oxidative stress, and gut microbiota composition. However, further investigation is necessary to fully elucidate the underlying cellular and molecular mechanisms behind the therapeutic and prophylactic effects of nutraceuticals for CD. Emphasizing such research would contribute to future developments in CD therapies and interventions.
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Affiliation(s)
- Mahtab Jahdkaran
- Department of Clinical Pharmacy, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Celiac Disease and Gluten Related Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nastaran Asri
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hadi Esmaily
- Department of Clinical Pharmacy, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Rostami-Nejad
- Celiac Disease and Gluten Related Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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2
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Olazagoitia‐Garmendia A, Rojas‐Márquez H, Sebastian‐delaCruz M, Agirre‐Lizaso A, Ochoa A, Mendoza‐Gomez LM, Perugorria MJ, Bujanda L, Madrigal AH, Santin I, Castellanos‐Rubio A. m 6A Methylated Long Noncoding RNA LOC339803 Regulates Intestinal Inflammatory Response. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307928. [PMID: 38273714 PMCID: PMC10987157 DOI: 10.1002/advs.202307928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/20/2023] [Indexed: 01/27/2024]
Abstract
Cytokine mediated sustained inflammation increases the risk to develop different complex chronic inflammatory diseases, but the implicated mechanisms remain unclear. Increasing evidence shows that long noncoding RNAs (lncRNAs) play key roles in the pathogenesis of inflammatory disorders, while inflammation associated variants are described to affect their function or essential RNA modifications as N6-methyladenosine (m6A) methylation, increasing predisposition to inflammatory diseases. Here, the functional implication of the intestinal inflammation associated lncRNA LOC339803 in the production of cytokines by intestinal epithelial cells is described. Allele-specific m6A methylation is found to affect YTHDC1 mediated protein binding affinity. LOC339803-YTHDC1 interaction dictates chromatin localization of LOC339803 ultimately inducing the expression of NFκB mediated proinflammatory cytokines and contributing to the development of intestinal inflammation. These findings are confirmed using human intestinal biopsy samples from different intestinal inflammatory conditions and controls. Additionally, it is demonstrated that LOC339803 targeting can be a useful strategy for the amelioration of intestinal inflammation in vitro and ex vivo. Overall, the results support the importance of the methylated LOC339803 lncRNA as a mediator of intestinal inflammation, explaining genetic susceptibility and presenting this lncRNA as a potential novel therapeutic target for the treatment of inflammatory intestinal disorders.
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Affiliation(s)
- Ane Olazagoitia‐Garmendia
- Department of Biochemistry and Molecular BiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
| | - Henar Rojas‐Márquez
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
| | - Maialen Sebastian‐delaCruz
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
| | - Aloña Agirre‐Lizaso
- Department of Liver and Gastrointestinal DiseasesBiogipuzkoa Health Research InstituteDonostia University HospitalDonostia‐San Sebastian20014Spain
| | - Anne Ochoa
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
| | - Luis Manuel Mendoza‐Gomez
- Department of Biochemistry and Molecular BiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Biobizkaia Health Research InstituteBarakaldo48903Spain
| | - Maria J Perugorria
- Department of Liver and Gastrointestinal DiseasesBiogipuzkoa Health Research InstituteDonostia University HospitalDonostia‐San Sebastian20014Spain
- Department of MedicineFaculty of Medicine and NursingUniversity of the Basque CountryUPV/EHUDonostia‐San Sebastián20014Spain
- CIBERehdInstituto de Salud Carlos III (ISCIII)Madrid28029Spain
| | - Luis Bujanda
- Department of Liver and Gastrointestinal DiseasesBiogipuzkoa Health Research InstituteDonostia University HospitalDonostia‐San Sebastian20014Spain
- Department of MedicineFaculty of Medicine and NursingUniversity of the Basque CountryUPV/EHUDonostia‐San Sebastián20014Spain
- CIBERehdInstituto de Salud Carlos III (ISCIII)Madrid28029Spain
| | - Alain Huerta Madrigal
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of MedicineMedicine FacultyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Gastroenterology DepartmentHospital Universitario de GaldakaoGaldakao48960Spain
| | - Izortze Santin
- Department of Biochemistry and Molecular BiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas CIBERDEMInstituto de Salud Carlos IIIMadrid28029Spain
| | - Ainara Castellanos‐Rubio
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas CIBERDEMInstituto de Salud Carlos IIIMadrid28029Spain
- IkerbasqueBasque Foundation for ScienceBilbao48011Spain
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3
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Shin JJ, Park J, Shin HS, Arab I, Suk K, Lee WH. Roles of lncRNAs in NF-κB-Mediated Macrophage Inflammation and Their Implications in the Pathogenesis of Human Diseases. Int J Mol Sci 2024; 25:2670. [PMID: 38473915 DOI: 10.3390/ijms25052670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Over the past century, molecular biology's focus has transitioned from proteins to DNA, and now to RNA. Once considered merely a genetic information carrier, RNA is now recognized as both a vital element in early cellular life and a regulator in complex organisms. Long noncoding RNAs (lncRNAs), which are over 200 bases long but do not code for proteins, play roles in gene expression regulation and signal transduction by inducing epigenetic changes or interacting with various proteins and RNAs. These interactions exhibit a range of functions in various cell types, including macrophages. Notably, some macrophage lncRNAs influence the activation of NF-κB, a crucial transcription factor governing immune and inflammatory responses. Macrophage NF-κB is instrumental in the progression of various pathological conditions including sepsis, atherosclerosis, cancer, autoimmune disorders, and hypersensitivity. It orchestrates gene expression related to immune responses, inflammation, cell survival, and proliferation. Consequently, its malfunction is a key contributor to the onset and development of these diseases. This review aims to summarize the function of lncRNAs in regulating NF-κB activity in macrophage activation and inflammation, with a particular emphasis on their relevance to human diseases and their potential as therapeutic targets. The insights gained from studies on macrophage lncRNAs, as discussed in this review, could provide valuable knowledge for the development of treatments for various pathological conditions involving macrophages.
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Affiliation(s)
- Jae-Joon Shin
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jeongkwang Park
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyeung-Seob Shin
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Imene Arab
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyoungho Suk
- Department of Pharmacology, Brain Science and Engineering Institute, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Won-Ha Lee
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
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4
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Chadwick C, Lehman H, Luebbert S, Abdul-Aziz R, Borowitz D. Autoimmunity in people with cystic fibrosis. J Cyst Fibros 2023; 22:969-979. [PMID: 36966037 DOI: 10.1016/j.jcf.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 03/27/2023]
Abstract
Cystic fibrosis (CF) clinicians may see patients who have difficult-to-manage symptoms that do not have a clear CF-related etiology, such as unusual gastrointestinal (GI) complaints, vasculitis, or arthritis. Alterations in immunity, inflammation and intraluminal dysbiosis create a milieu that may lead to autoimmunity, and the CF transmembrane regulator protein may have a direct role as well. While autoantibodies and other autoimmune markers may develop, these may or may not lead to organ involvement, therefore they are helpful but not sufficient to establish an autoimmune diagnosis. Autoimmune involvement of the GI tract is the best-established association. Next steps to understand autoimmunity in CF should include a more in-depth assessment of the community perspective on its impact. In addition, bringing together specialists in various fields including, but not limited to, pulmonology, gastroenterology, immunology, and rheumatology, would lead to cross-dissemination and help define the path forward in basic science and clinical practice.
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Affiliation(s)
| | - Heather Lehman
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
| | | | - Rabheh Abdul-Aziz
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
| | - Drucy Borowitz
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
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5
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Abdelrahman AH, Ibrahim AA, Eid OM, Hassan M, Eid MM, Nour El Din Abd El Baky AM, Ismail M, Abou-Zekri M, Abd El-Fattah SN. A pilot study on promoter methylation of MTHFR, MALT1 and MAP3K7 genes in pediatric celiac disease. HUMAN GENE 2023; 36:201180. [DOI: 10.1016/j.humgen.2023.201180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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6
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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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7
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Skoracka K, Hryhorowicz S, Rychter AM, Ratajczak AE, Szymczak-Tomczak A, Zawada A, Słomski R, Dobrowolska A, Krela-Kaźmierczak I. Why are western diet and western lifestyle pro-inflammatory risk factors of celiac disease? Front Nutr 2023; 9:1054089. [PMID: 36742009 PMCID: PMC9895111 DOI: 10.3389/fnut.2022.1054089] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/31/2022] [Indexed: 01/21/2023] Open
Abstract
The prevalence of celiac disease increased in recent years. In addition to the genetic and immunological factors, it appears that environmental determinants are also involved in the pathophysiology of celiac disease. Gastrointestinal infections impact the development of celiac disease. Current research does not directly confirm the protective effect of natural childbirth and breastfeeding on celiac disease. However, it seems that in genetically predisposed children, the amount of gluten introduced into the diet may have an impact on celiac disease development. Also western lifestyle, including western dietary patterns high in fat, sugar, and gliadin, potentially may increase the risk of celiac disease due to changes in intestinal microbiota, intestinal permeability, or mucosal inflammation. Further research is needed to expand the knowledge of the relationship between environmental factors and the development of celiac disease to define evidence-based preventive interventions against the development of celiac disease. The manuscript summarizes current knowledge on factors predisposing to the development of celiac disease including factors associated with the western lifestyle.
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Affiliation(s)
- Kinga Skoracka
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznań, Poland,Doctoral School, Poznan University of Medical Sciences, Poznań, Poland,*Correspondence: Kinga Skoracka ✉
| | | | - Anna Maria Rychter
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznań, Poland,Doctoral School, Poznan University of Medical Sciences, Poznań, Poland
| | - Alicja Ewa Ratajczak
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznań, Poland,Doctoral School, Poznan University of Medical Sciences, Poznań, Poland
| | - Aleksandra Szymczak-Tomczak
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznań, Poland
| | - Agnieszka Zawada
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznań, Poland
| | - Ryszard Słomski
- Institute of Human Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Agnieszka Dobrowolska
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznań, Poland
| | - Iwona Krela-Kaźmierczak
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznań, Poland
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8
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Olazagoitia-Garmendia A. Pepsin-trypsin digested gliadin treatment in intestinal cells. Methods Cell Biol 2022; 179:1-11. [PMID: 37625867 DOI: 10.1016/bs.mcb.2022.11.002] [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: 12/23/2022]
Abstract
Celiac disease (CD) is an intestinal autoimmune disorder developed in genetically susceptible individuals upon gluten ingestion. Gliadin is known to be the most immunogenic gluten component, which can activate the host immune response represented by NFkB activation and release of proinflammatory cytokines as IL8. However, many aspects of the involvement of gliadin in CD pathophysiology is not well understood yet. Lack of a CD animal model increases difficulty elucidating key steps in CD development, what increases the importance of in vitro experiments. Here we present a protocol for in vitro pepsin-trypsin digested gliadin (PTG) treatment for long term studies in HCT116 intestinal cell line.
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Affiliation(s)
- Ane Olazagoitia-Garmendia
- University of the Basque Country, UPV/EHU, Leioa, Spain; Biocruces Bizkaia, Health Research Institute, Barakaldo, Spain.
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9
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Zhang L, He C. Ex vivo gliadin stimulation of intestinal cells. Methods Cell Biol 2022; 179:13-20. [PMID: 37625871 DOI: 10.1016/bs.mcb.2022.09.018] [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: 11/06/2022]
Abstract
Celiac disease is an autoimmune response to gluten proteins. While causes for celiac disease have been identified, there is no effective treatment other than diet control. In vitro models for celiac disease are important for quickly gaining understanding of the disease mechanism and testing potential treatments. Here we describe an ex vivo stimulation of intestinal epithelial cells with gliadin peptides as a method to induce celiac disease features in vitro.
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Affiliation(s)
- Linda Zhang
- Department of Chemistry, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, United States; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States; Howard Hughes Medical Institute, University of Chicago, Chicago, IL, United States
| | - Chuan He
- Department of Chemistry, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, United States; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States; Howard Hughes Medical Institute, University of Chicago, Chicago, IL, United States.
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10
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Barone MV, Auricchio R, Nanayakkara M, Greco L, Troncone R, Auricchio S. Pivotal Role of Inflammation in Celiac Disease. Int J Mol Sci 2022; 23:ijms23137177. [PMID: 35806180 PMCID: PMC9266393 DOI: 10.3390/ijms23137177] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 01/27/2023] Open
Abstract
Celiac disease (CD) is an immune-mediated enteropathy triggered in genetically susceptible individuals by gluten-containing cereals. A central role in the pathogenesis of CD is played by the HLA-restricted gliadin-specific intestinal T cell response generated in a pro-inflammatory environment. The mechanisms that generate this pro-inflammatory environment in CD is now starting to be addressed. In vitro study on CD cells and organoids, shows that constant low-grade inflammation is present also in the absence of gluten. In vivo studies on a population at risk, show before the onset of the disease and before the introduction of gluten in the diet, cellular and metabolic alterations in the absence of a T cell-mediated response. Gluten exacerbates these constitutive alterations in vitro and in vivo. Inflammation, may have a main role in CD, adding this disease tout court to the big family of chronic inflammatory diseases. Nutrients can have pro-inflammatory or anti-inflammatory effects, also mediated by intestinal microbiota. The intestine function as a crossroad for the control of inflammation both locally and at distance. The aim of this review is to discuss the recent literature on the main role of inflammation in the natural history of CD, supported by cellular fragility with increased sensitivity to gluten and other pro-inflammatory agents.
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Affiliation(s)
- Maria Vittoria Barone
- Department of Translational Medical Science, University Federico II, Via S. Pansini 5, 80131 Naples, Italy; (R.A.); (M.N.); (L.G.); (R.T.)
- European Laboratory for the Investigation of Food Induced Disease (ELFID), University Federico II, Via S. Pansini 5, 80131 Naples, Italy;
- Correspondence:
| | - Renata Auricchio
- Department of Translational Medical Science, University Federico II, Via S. Pansini 5, 80131 Naples, Italy; (R.A.); (M.N.); (L.G.); (R.T.)
- European Laboratory for the Investigation of Food Induced Disease (ELFID), University Federico II, Via S. Pansini 5, 80131 Naples, Italy;
| | - Merlin Nanayakkara
- Department of Translational Medical Science, University Federico II, Via S. Pansini 5, 80131 Naples, Italy; (R.A.); (M.N.); (L.G.); (R.T.)
- European Laboratory for the Investigation of Food Induced Disease (ELFID), University Federico II, Via S. Pansini 5, 80131 Naples, Italy;
| | - Luigi Greco
- Department of Translational Medical Science, University Federico II, Via S. Pansini 5, 80131 Naples, Italy; (R.A.); (M.N.); (L.G.); (R.T.)
- European Laboratory for the Investigation of Food Induced Disease (ELFID), University Federico II, Via S. Pansini 5, 80131 Naples, Italy;
| | - Riccardo Troncone
- Department of Translational Medical Science, University Federico II, Via S. Pansini 5, 80131 Naples, Italy; (R.A.); (M.N.); (L.G.); (R.T.)
- European Laboratory for the Investigation of Food Induced Disease (ELFID), University Federico II, Via S. Pansini 5, 80131 Naples, Italy;
| | - Salvatore Auricchio
- European Laboratory for the Investigation of Food Induced Disease (ELFID), University Federico II, Via S. Pansini 5, 80131 Naples, Italy;
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11
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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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12
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Ramírez-Sánchez AD, Chu X, Modderman R, Kooy-Winkelaar Y, Koletzko S, Korponay-Szabó IR, Troncone R, Wijmenga C, Mearin L, Withoff S, Jonkers IH, Li Y. Single-Cell RNA Sequencing of Peripheral Blood Mononuclear Cells From Pediatric Coeliac Disease Patients Suggests Potential Pre-Seroconversion Markers. Front Immunol 2022; 13:843086. [PMID: 35371081 PMCID: PMC8964997 DOI: 10.3389/fimmu.2022.843086] [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: 12/24/2021] [Accepted: 02/22/2022] [Indexed: 11/30/2022] Open
Abstract
Celiac Disease (CeD) is a complex immune disorder involving villous atrophy in the small intestine that is triggered by gluten intake. Current CeD diagnosis is based on late-stage pathophysiological parameters such as detection of specific antibodies in blood and histochemical detection of villus atrophy and lymphocyte infiltration in intestinal biopsies. To date, no early onset biomarkers are available that would help prevent widespread villous atrophy and severe symptoms and co-morbidities. To search for novel CeD biomarkers, we used single-cell RNA sequencing (scRNAseq) to investigate PBMC samples from 11 children before and after seroconversion for CeD and 10 control individuals matched for age, sex and HLA-genotype. We generated scRNAseq profiles of 9559 cells and identified the expected major cellular lineages. Cell proportions remained stable across the different timepoints and health conditions, but we observed differences in gene expression profiles in specific cell types when comparing patient samples before and after disease development and comparing patients with controls. Based on the time when transcripts were differentially expressed, we could classify the deregulated genes as biomarkers for active CeD or as potential pre-diagnostic markers. Pathway analysis showed that active CeD biomarkers display a transcriptional profile associated with antigen activation in CD4+ T cells, whereas NK cells express a subset of biomarker genes even before CeD diagnosis. Intersection of biomarker genes with CeD-associated genetic risk loci pinpointed genetic factors that might play a role in CeD onset. Investigation of potential cellular interaction pathways of PBMC cell subpopulations highlighted the importance of TNF pathways in CeD. Altogether, our results pinpoint genes and pathways that are altered prior to and during CeD onset, thereby identifying novel potential biomarkers for CeD diagnosis in blood.
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Affiliation(s)
- Aarón D Ramírez-Sánchez
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Xiaojing Chu
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.,Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine (CiiM) & TWINCORE, Joint Ventures Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Rutger Modderman
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Yvonne Kooy-Winkelaar
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Sibylle Koletzko
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München (LMU) Klinikum Munich, Munich, Germany.,Department of Pediatric Gastroenterology and Nutrition, School of Medicine Collegium Medicum University of Warmia and Mazury, Olsztyn, Poland
| | - Ilma R Korponay-Szabó
- Coeliac Disease Center, Heim Pál National Paediatric Institute, Budapest, Hungary.,Department of Paediatrics, Faculty of Medicine and Clinical Center, University of Debrecen, Debrecen, Hungary
| | - Riccardo Troncone
- Department of Medical Translational Sciences and European Laboratory for the Investigation of Food Induced Diseases, University Federico II, Naples, Italy
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Luisa Mearin
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Sebo Withoff
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Iris H Jonkers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Yang Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.,Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine (CiiM) & TWINCORE, Joint Ventures Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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13
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Porpora M, Conte M, Lania G, Bellomo C, Rapacciuolo L, Chirdo FG, Auricchio R, Troncone R, Auricchio S, Barone MV, Nanayakkara M. Inflammation Is Present, Persistent and More Sensitive to Proinflammatory Triggers in Celiac Disease Enterocytes. Int J Mol Sci 2022. [PMID: 35216089 DOI: 10.3390/ijms23041973.pmid:35216089;pmcid:pmc8880034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Celiac disease (CD) is a chronic inflammatory disease caused by a genetic predisposition to an abnormal T cell-mediated immune response to the gluten in the diet. Different environmental proinflammatory factors can influence and amplify the T cell-mediated response to gluten. The aim of this manuscript was to study the role of enterocytes in CD intestinal inflammation and their response to different proinflammatory factors, such as gliadin and viruses. Intestinal biopsies from CD patients on a gluten-containing (GCD-CD) or a gluten-free diet (GFD-CD) as well as biopsies from potential CD patients (Pot-CD) before the onset of intestinal lesions and controls (CTR) were used to investigate IL-1β and IL-6 mRNA levels in situ. Organoids from CD patients were used to test the levels of NF-κB, ERK, IL-6, and IL-1β by Western blot (WB), ELISA, and quantitative PCR. The Toll-like receptor ligand loxoribine (Lox) and gliadin peptide P31-43 were used as proinflammatory stimuli. In CD biopsies inflammation markers IL-1β and IL-6 were increased in the enterocytes, and also in Pot-CD before the onset of the intestinal lesion and in GFD-CD. The inflammatory markers pNF-κB, pERK, IL-1β, and IL-6 were increased and persistent in CD organoids; these organoids were more sensitive to P31-43 and Lox stimuli compared with CTR organoids. Taken together, these observations point to constitutive inflammation in CD enterocytes, which are more sensitive to inflammatory stimuli such as food components and viruses.
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Affiliation(s)
- Monia Porpora
- ELFID (European Laboratory for the Investigation of Food Induced Diseases), Department of Translational Medical Science, Section of Paediatrics, University Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Mariangela Conte
- ELFID (European Laboratory for the Investigation of Food Induced Diseases), Department of Translational Medical Science, Section of Paediatrics, University Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Giuliana Lania
- ELFID (European Laboratory for the Investigation of Food Induced Diseases), Department of Translational Medical Science, Section of Paediatrics, University Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Claudia Bellomo
- ELFID (European Laboratory for the Investigation of Food Induced Diseases), Department of Translational Medical Science, Section of Paediatrics, University Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Luciano Rapacciuolo
- ELFID (European Laboratory for the Investigation of Food Induced Diseases), Department of Translational Medical Science, Section of Paediatrics, University Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Fernando Gabriel Chirdo
- Departamento de Ciencias Biologicas, Facultad de Ciencias Exactas, Instituto de Estudios Inmunologicos y Fisiopatologicos-IIFP (UNLP-CONICET), Bv. 120 1489, La Plata 1900, Argentina
| | - Renata Auricchio
- ELFID (European Laboratory for the Investigation of Food Induced Diseases), Department of Translational Medical Science, Section of Paediatrics, University Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Riccardo Troncone
- ELFID (European Laboratory for the Investigation of Food Induced Diseases), Department of Translational Medical Science, Section of Paediatrics, University Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Salvatore Auricchio
- ELFID (European Laboratory for the Investigation of Food Induced Diseases), Department of Translational Medical Science, Section of Paediatrics, University Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Maria Vittoria Barone
- ELFID (European Laboratory for the Investigation of Food Induced Diseases), Department of Translational Medical Science, Section of Paediatrics, University Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Merlin Nanayakkara
- ELFID (European Laboratory for the Investigation of Food Induced Diseases), Department of Translational Medical Science, Section of Paediatrics, University Federico II, Via S. Pansini 5, 80131 Naples, Italy
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14
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Inflammation Is Present, Persistent and More Sensitive to Proinflammatory Triggers in Celiac Disease Enterocytes. Int J Mol Sci 2022; 23:ijms23041973. [PMID: 35216089 PMCID: PMC8880034 DOI: 10.3390/ijms23041973] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/21/2022] [Accepted: 02/02/2022] [Indexed: 12/21/2022] Open
Abstract
Celiac disease (CD) is a chronic inflammatory disease caused by a genetic predisposition to an abnormal T cell-mediated immune response to the gluten in the diet. Different environmental proinflammatory factors can influence and amplify the T cell-mediated response to gluten. The aim of this manuscript was to study the role of enterocytes in CD intestinal inflammation and their response to different proinflammatory factors, such as gliadin and viruses. Intestinal biopsies from CD patients on a gluten-containing (GCD-CD) or a gluten-free diet (GFD-CD) as well as biopsies from potential CD patients (Pot-CD) before the onset of intestinal lesions and controls (CTR) were used to investigate IL-1β and IL-6 mRNA levels in situ. Organoids from CD patients were used to test the levels of NF-κB, ERK, IL-6, and IL-1β by Western blot (WB), ELISA, and quantitative PCR. The Toll-like receptor ligand loxoribine (Lox) and gliadin peptide P31-43 were used as proinflammatory stimuli. In CD biopsies inflammation markers IL-1β and IL-6 were increased in the enterocytes, and also in Pot-CD before the onset of the intestinal lesion and in GFD-CD. The inflammatory markers pNF-κB, pERK, IL-1β, and IL-6 were increased and persistent in CD organoids; these organoids were more sensitive to P31-43 and Lox stimuli compared with CTR organoids. Taken together, these observations point to constitutive inflammation in CD enterocytes, which are more sensitive to inflammatory stimuli such as food components and viruses.
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15
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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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16
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Olazagoitia-Garmendia A, Zhang L, Mera P, Godbout JK, Sebastian-DelaCruz M, Garcia-Santisteban I, Mendoza LM, Huerta A, Irastorza I, Bhagat G, Green PH, Herrero L, Serra D, Rodriguez JA, Verdu EF, He C, Bilbao JR, Castellanos-Rubio A. Gluten-induced RNA methylation changes regulate intestinal inflammation via allele-specific XPO1 translation in epithelial cells. Gut 2022; 71:68-76. [PMID: 33526437 PMCID: PMC8666699 DOI: 10.1136/gutjnl-2020-322566] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 12/23/2020] [Accepted: 01/17/2021] [Indexed: 12/16/2022]
Abstract
OBJECTIVES Coeliac disease (CD) is a complex autoimmune disorder that develops in genetically susceptible individuals. Dietary gluten triggers an immune response for which the only available treatment so far is a strict, lifelong gluten free diet. Human leucocyte antigen (HLA) genes and several non-HLA regions have been associated with the genetic susceptibility to CD, but their role in the pathogenesis of the disease is still essentially unknown, making it complicated to develop much needed non-dietary treatments. Here, we describe the functional involvement of a CD-associated single-nucleotide polymorphism (SNP) located in the 5'UTR of XPO1 in the inflammatory environment characteristic of the coeliac intestinal epithelium. DESIGN The function of the CD-associated SNP was investigated using an intestinal cell line heterozygous for the SNP, N6-methyladenosine (m6A)-related knock-out and HLA-DQ2 mice, and human samples from patients with CD. RESULTS Individuals harbouring the risk allele had higher m6A methylation in the 5'UTR of XPO1 RNA, rendering greater XPO1 protein amounts that led to downstream nuclear factor kappa B (NFkB) activity and subsequent inflammation. Furthermore, gluten exposure increased overall m6A methylation in humans as well as in in vitro and in vivo models. CONCLUSION We identify a novel m6A-XPO1-NFkB pathway that is activated in CD patients. The findings will prompt the development of new therapeutic approaches directed at m6A proteins and XPO1, a target under evaluation for the treatment of intestinal disorders.
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Affiliation(s)
- Ane Olazagoitia-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Linda Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, USA
| | - Paula Mera
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Julie K Godbout
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Maialen Sebastian-DelaCruz
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Iraia Garcia-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
| | - Luis Manuel Mendoza
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
| | - Alain Huerta
- Enfermedades Digestivas, Hospital de Galdakao-Usansolo, Galdacano, Spain
| | - Iñaki Irastorza
- Department of Pediatrics, University of the Basque Country (UPV-EHU), Leioa, Spain
| | - Govind Bhagat
- Celiac Disease Center, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Peter H Green
- Celiac Disease Center, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Laura Herrero
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Dolors Serra
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose Antonio Rodriguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
| | - Elena F Verdu
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, USA
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Ainara Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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17
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A Novel Regulatory Player in the Innate Immune System: Long Non-Coding RNAs. Int J Mol Sci 2021; 22:ijms22179535. [PMID: 34502451 PMCID: PMC8430513 DOI: 10.3390/ijms22179535] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) represent crucial transcriptional and post-transcriptional gene regulators during antimicrobial responses in the host innate immune system. Studies have shown that lncRNAs are expressed in a highly tissue- and cell-specific- manner and are involved in the differentiation and function of innate immune cells, as well as inflammatory and antiviral processes, through versatile molecular mechanisms. These lncRNAs function via the interactions with DNA, RNA, or protein in either cis or trans pattern, relying on their specific sequences or their transcriptions and processing. The dysregulation of lncRNA function is associated with various human non-infectious diseases, such as inflammatory bowel disease, cardiovascular diseases, and diabetes mellitus. Here, we provide an overview of the regulation and mechanisms of lncRNA function in the development and differentiation of innate immune cells, and during the activation or repression of innate immune responses. These elucidations might be beneficial for the development of therapeutic strategies targeting inflammatory and innate immune-mediated diseases.
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18
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Voisine J, Abadie V. Interplay Between Gluten, HLA, Innate and Adaptive Immunity Orchestrates the Development of Coeliac Disease. Front Immunol 2021; 12:674313. [PMID: 34149709 PMCID: PMC8206552 DOI: 10.3389/fimmu.2021.674313] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/18/2021] [Indexed: 12/26/2022] Open
Abstract
Several environmental, genetic, and immune factors create a "perfect storm" for the development of coeliac disease: the antigen gluten, the strong association of coeliac disease with HLA, the deamidation of gluten peptides by the enzyme transglutaminase 2 (TG2) generating peptides that bind strongly to the predisposing HLA-DQ2 or HLA-DQ8 molecules, and the ensuing unrestrained T cell response. T cell immunity is at the center of the disease contributing to the inflammatory process through the loss of tolerance to gluten and the differentiation of HLA-DQ2 or HLA-DQ8-restricted anti-gluten inflammatory CD4+ T cells secreting pro-inflammatory cytokines and to the killing of intestinal epithelial cells by cytotoxic intraepithelial CD8+ lymphocytes. However, recent studies emphasize that the individual contribution of each of these cell subsets is not sufficient and that interactions between these different populations of T cells and the simultaneous activation of innate and adaptive immune pathways in distinct gut compartments are required to promote disease immunopathology. In this review, we will discuss how tissue destruction in the context of coeliac disease results from the complex interactions between gluten, HLA molecules, TG2, and multiple innate and adaptive immune components.
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Affiliation(s)
- Jordan Voisine
- Department of Medicine, The University of Chicago, Chicago, IL, United States.,Committee on Immunology, The University of Chicago, Chicago, IL, United States
| | - Valérie Abadie
- Department of Medicine, The University of Chicago, Chicago, IL, United States.,Section of Gastroenterology, Nutrition and Hepatology, The University of Chicago, Chicago, IL, United States
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19
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Bakker OB, Ramírez-Sánchez AD, Borek ZA, de Klein N, Li Y, Modderman R, Kooy-Winkelaar Y, Johannesen MK, Matarese F, Martens JHA, Kumar V, van Bergen J, Qiao SW, Lundin KEA, Sollid LM, Koning F, Wijmenga C, Withoff S, Jonkers IH. Potential impact of celiac disease genetic risk factors on T cell receptor signaling in gluten-specific CD4+ T cells. Sci Rep 2021; 11:9252. [PMID: 33927210 PMCID: PMC8085175 DOI: 10.1038/s41598-021-86612-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/18/2021] [Indexed: 02/08/2023] Open
Abstract
Celiac disease is an auto-immune disease in which an immune response to dietary gluten leads to inflammation and subsequent atrophy of small intestinal villi, causing severe bowel discomfort and malabsorption of nutrients. The major instigating factor for the immune response in celiac disease is the activation of gluten-specific CD4+ T cells expressing T cell receptors that recognize gluten peptides presented in the context of HLA-DQ2 and DQ8. Here we provide an in-depth characterization of 28 gluten-specific T cell clones. We assess their transcriptional and epigenetic response to T cell receptor stimulation and link this to genetic factors associated with celiac disease. Gluten-specific T cells have a distinct transcriptional profile that mostly resembles that of Th1 cells but also express cytokines characteristic of other types of T-helper cells. This transcriptional response appears not to be regulated by changes in chromatin state, but rather by early upregulation of transcription factors and non-coding RNAs that likely orchestrate the subsequent activation of genes that play a role in immune pathways. Finally, integration of chromatin and transcription factor binding profiles suggest that genes activated by T cell receptor stimulation of gluten‑specific T cells may be impacted by genetic variation at several genetic loci associated with celiac disease.
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Affiliation(s)
- Olivier B Bakker
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Aarón D Ramírez-Sánchez
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Zuzanna A Borek
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Niek de Klein
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Yang Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Rutger Modderman
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Yvonne Kooy-Winkelaar
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Marie K Johannesen
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Filomena Matarese
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Vinod Kumar
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Nitte (Deemed to be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangaluru, 575018, India
| | - Jeroen van Bergen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Shuo-Wang Qiao
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Knut E A Lundin
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Ludvig M Sollid
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Sebo Withoff
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Iris H Jonkers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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20
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Bangarusamy DK, Lakshmanan AP, Al-Zaidan S, Alabduljabbar S, Terranegra A. Nutri-epigenetics: the effect of maternal diet and early nutrition on the pathogenesis of autoimmune diseases. Minerva Pediatr (Torino) 2021; 73:98-110. [PMID: 33880901 DOI: 10.23736/s2724-5276.20.06166-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Autoimmune diseases comprise a wide group of diseases involving a self-response of the immune system against the host. The etiopathogenesis is very complex involving disease-specific factors but also environmental factors, among which the diet. Maternal diet during pregnancy as well as early nutrition recently attracted the interest of the scientists as contributing to the immune programming. In this paper, we reviewed the most recent literature on the effect of maternal diet and early nutrition in modulating the immune system in a selected subset of autoimmune diseases: type 1 diabetes, celiac disease, inflammatory bowel disease, juvenile idiopathic arthritis and rheumatoid arthritis. Particularly, we focused our narrative on the role of maternal and perinatal nutrition in the epigenetic mechanisms underlying the auto-immune response. Maternal diet during pregnancy as well as breastfeeding and early nutrition play a big role in many epigenetic mechanisms. Most of the nutrients consumed by the mother and the infant are known exerting epigenetic functions, such as folate, methionine, zinc, vitamins B12 and D, fibers, casein and gliadin, and they were linked to gene expression changes in the immune pathways. Despite the common role of maternal diet, breastfeeding and early nutrition in almost all the autoimmune diseases, each disease seems to have specific diet-driver epigenetic mechanisms that require further investigations. The research in this field is opening new routes to establishing a precision nutrition approach to the auto-immune diseases.
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Affiliation(s)
- Dhinoth K Bangarusamy
- Unit of Maternal and Child Health, Department of Research, Sidra Medicine, Doha, Qatar
| | - Arun P Lakshmanan
- Unit of Maternal and Child Health, Department of Research, Sidra Medicine, Doha, Qatar
| | - Sara Al-Zaidan
- Unit of Maternal and Child Health, Department of Research, Sidra Medicine, Doha, Qatar
| | - Shaikha Alabduljabbar
- Unit of Maternal and Child Health, Department of Research, Sidra Medicine, Doha, Qatar
| | - Annalisa Terranegra
- Unit of Maternal and Child Health, Department of Research, Sidra Medicine, Doha, Qatar -
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21
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Wolf J, Willscher E, Loeffler-Wirth H, Schmidt M, Flemming G, Zurek M, Uhlig HH, Händel N, Binder H. Deciphering the Transcriptomic Heterogeneity of Duodenal Coeliac Disease Biopsies. Int J Mol Sci 2021; 22:ijms22052551. [PMID: 33806322 PMCID: PMC7961974 DOI: 10.3390/ijms22052551] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
Coeliac disease (CD) is a clinically heterogeneous autoimmune disease with variable presentation and progression triggered by gluten intake. Molecular or genetic factors contribute to disease heterogeneity, but the reasons for different outcomes are poorly understood. Transcriptome studies of tissue biopsies from CD patients are scarce. Here, we present a high-resolution analysis of the transcriptomes extracted from duodenal biopsies of 24 children and adolescents with active CD and 21 individuals without CD but with intestinal afflictions as controls. The transcriptomes of CD patients divide into three groups-a mixed group presenting the control cases, and CD-low and CD-high groups referring to lower and higher levels of CD severity. Persistence of symptoms was weakly associated with subgroup, but the highest marsh stages were present in subgroup CD-high, together with the highest cell cycle rates as an indicator of virtually complete villous atrophy. Considerable variation in inflammation-level between subgroups was further deciphered into immune cell types using cell type de-convolution. Self-organizing maps portrayal was applied to provide high-resolution landscapes of the CD-transcriptome. We find asymmetric patterns of miRNA and long non-coding RNA and discuss the effect of epigenetic regulation. Expression of genes involved in interferon gamma signaling represent suitable markers to distinguish CD from non-CD cases. Multiple pathways overlay in CD biopsies in different ways, giving rise to heterogeneous transcriptional patterns, which potentially provide information about etiology and the course of the disease.
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Affiliation(s)
- Johannes Wolf
- Department of Laboratory Medicine at Hospital “St. Georg” Leipzig, 04129 Leipzig, Germany;
- Immuno Deficiency Centre Leipzig (IDCL) at Hospital St. Georg Leipzig, Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiency Diseases, 04129 Leipzig, Germany
| | - Edith Willscher
- IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (E.W.); (H.L.-W.); (M.S.)
| | - Henry Loeffler-Wirth
- IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (E.W.); (H.L.-W.); (M.S.)
| | - Maria Schmidt
- IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (E.W.); (H.L.-W.); (M.S.)
| | - Gunter Flemming
- Paediatric Gastroenterology Unit, University Hospital for Children and Adolescents, 04103 Leipzig, Germany;
| | - Marlen Zurek
- Children’s Hospital of the Clinical Centre “Sankt Georg”, 04129 Leipzig, Germany; (M.Z.); (N.H.)
| | - Holm H. Uhlig
- Translational Gastroenterology Unit, Oxford NIHR Biomedical Research Centre, Experimental Medicine, Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Oxford OX4 2PG, UK;
| | - Norman Händel
- Children’s Hospital of the Clinical Centre “Sankt Georg”, 04129 Leipzig, Germany; (M.Z.); (N.H.)
| | - Hans Binder
- IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (E.W.); (H.L.-W.); (M.S.)
- Correspondence:
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22
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Barone MV, Auricchio S. A Cumulative Effect of Food and Viruses to Trigger Celiac Disease (CD): A Commentary on the Recent Literature. Int J Mol Sci 2021; 22:2027. [PMID: 33670760 PMCID: PMC7922374 DOI: 10.3390/ijms22042027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 12/27/2022] Open
Abstract
Celiac disease (CD) is a type of inflammatory chronic disease caused by nutrients such as gliadin that induce a TC (T cell)-mediated response in a partially known genetical background in an environment predisposed to inflammation, including viruses and food. Various experimental and clinical observations suggest that multiple agents such as viruses and bacteria have some common, inflammatory pathways predisposing individuals to chronic inflammatory diseases including celiac disease (CD). More recently, a Western diet and lifestyle have been linked to tissue inflammation and increase in chronic inflammatory diseases. In CD, the gliadin protein itself has been shown to be able to induce inflammation. A cooperation between viruses and gliadin is present in vitro and in vivo with common mechanisms to induce inflammation. Nutrients could have also a protective effect on CD, and in fact the anti-inflammatory Mediterranean diet has a protective effect on the development of CD in children. The possible impact of these observations on clinical practice is discussed.
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Affiliation(s)
- Maria Vittoria Barone
- Department of Translation Medical Science (DISMET), University Federico II, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University Federico II, 80131 Naples, Italy;
| | - Salvatore Auricchio
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University Federico II, 80131 Naples, Italy;
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23
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LncRNAs and Immunity: Coding the Immune System with Noncoding Oligonucleotides. Int J Mol Sci 2021; 22:ijms22041741. [PMID: 33572313 PMCID: PMC7916124 DOI: 10.3390/ijms22041741] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) represent key regulators of gene transcription during the inflammatory response. Recent findings showed lncRNAs to be dysregulated in human diseases, such as inflammatory bowel disease, diabetes, allergies, asthma, and cancer. These noncoding RNAs are crucial for immune mechanism, as they are involved in differentiation, cell migration and in the production of inflammatory mediators through regulating protein–protein interactions or their ability to assemble with RNA and DNA. The last interaction can occur in cis or trans and is responsible for all the possible lncRNAs biological effects. Our proposal is to provide an overview on lncRNAs roles and functions related to immunity and immune mediated diseases, since these elucidations could be beneficial to untangle the complex bond between them.
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24
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van der Graaf A, Zorro MM, Claringbould A, Võsa U, Aguirre-Gamboa R, Li C, Mooiweer J, Ricaño-Ponce I, Borek Z, Koning F, Kooy-Winkelaar Y, Sollid LM, Qiao SW, Kumar V, Li Y, Franke L, Withoff S, Wijmenga C, Sanna S, Jonkers I. Systematic Prioritization of Candidate Genes in Disease Loci Identifies TRAFD1 as a Master Regulator of IFNγ Signaling in Celiac Disease. Front Genet 2021; 11:562434. [PMID: 33569077 PMCID: PMC7868554 DOI: 10.3389/fgene.2020.562434] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/16/2020] [Indexed: 12/17/2022] Open
Abstract
Celiac disease (CeD) is a complex T cell-mediated enteropathy induced by gluten. Although genome-wide association studies have identified numerous genomic regions associated with CeD, it is difficult to accurately pinpoint which genes in these loci are most likely to cause CeD. We used four different in silico approaches-Mendelian randomization inverse variance weighting, COLOC, LD overlap, and DEPICT-to integrate information gathered from a large transcriptomics dataset. This identified 118 prioritized genes across 50 CeD-associated regions. Co-expression and pathway analysis of these genes indicated an association with adaptive and innate cytokine signaling and T cell activation pathways. Fifty-one of these genes are targets of known drug compounds or likely druggable genes, suggesting that our methods can be used to pinpoint potential therapeutic targets. In addition, we detected 172 gene combinations that were affected by our CeD-prioritized genes in trans. Notably, 41 of these trans-mediated genes appear to be under control of one master regulator, TRAF-type zinc finger domain containing 1 (TRAFD1), and were found to be involved in interferon (IFN)γ signaling and MHC I antigen processing/presentation. Finally, we performed in vitro experiments in a human monocytic cell line that validated the role of TRAFD1 as an immune regulator acting in trans. Our strategy confirmed the role of adaptive immunity in CeD and revealed a genetic link between CeD and IFNγ signaling as well as with MHC I antigen processing, both major players of immune activation and CeD pathogenesis.
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Affiliation(s)
- Adriaan van der Graaf
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Maria M. Zorro
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Annique Claringbould
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Urmo Võsa
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Raúl Aguirre-Gamboa
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Chan Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Joram Mooiweer
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Isis Ricaño-Ponce
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Zuzanna Borek
- Deutsches Rheumaforschungszentrum Berlin (DRFZ), An Institute of the Leibniz Association, Berlin, Germany
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gastroenterology, Infectious Diseases and Rheumatology, Berlin, Germany
| | - Frits Koning
- Department of Immunology, Leiden University, Leiden, Netherlands
| | | | - Ludvig M. Sollid
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Shuo-Wang Qiao
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Vinod Kumar
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
| | - Yang Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine, Helmholtz Centre for Infection Research, Hannover Medical School, Hanover, Germany
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Sebo Withoff
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Serena Sanna
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Istituto di Ricerca Genetica e Biomedica (IRGB) del Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Iris Jonkers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
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25
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Losso JN. Food Processing, Dysbiosis, Gastrointestinal Inflammatory Diseases, and Antiangiogenic Functional Foods or Beverages. Annu Rev Food Sci Technol 2021; 12:235-258. [PMID: 33467906 DOI: 10.1146/annurev-food-062520-090235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Foods and beverages provide nutrients and alter the gut microbiota, resulting in eubiosis or dysbiosis. Chronic consumption of a diet that is high in saturated or trans fats, meat proteins, reducing sugars, and salt and low in fiber induces dysbiosis. Dysbiosis, loss of redox homeostasis, mast cells, hypoxia, angiogenesis, the kynurenine pathway, transglutaminase 2, and/or the Janus kinase pathway are implicated in the pathogenesis and development of inflammatory bowel disease, celiac disease, and gastrointestinal malignancy. This review discusses the effects of oxidative, carbonyl, or glycative stress-inducing dietary ingredients or food processing-derived compounds on gut microbiota and gastrointestinal epithelial and mast cells as well as on the development of associated angiogenic diseases, including key signaling pathways. The preventive or therapeutic potential and the biochemical pathways of antiangiogenic or proangiogenic foods or beverages are also described. The outcomes of the interactions between disease pathways and components of food are critical for the design of foods and beverages for healthy lives.
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Affiliation(s)
- Jack N Losso
- School of Nutrition and Food Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA;
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26
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Gliadin Sequestration as a Novel Therapy for Celiac Disease: A Prospective Application for Polyphenols. Int J Mol Sci 2021; 22:ijms22020595. [PMID: 33435615 PMCID: PMC7826989 DOI: 10.3390/ijms22020595] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/13/2022] Open
Abstract
Celiac disease is an autoimmune disorder characterized by a heightened immune response to gluten proteins in the diet, leading to gastrointestinal symptoms and mucosal damage localized to the small intestine. Despite its prevalence, the only treatment currently available for celiac disease is complete avoidance of gluten proteins in the diet. Ongoing clinical trials have focused on targeting the immune response or gluten proteins through methods such as immunosuppression, enhanced protein degradation and protein sequestration. Recent studies suggest that polyphenols may elicit protective effects within the celiac disease milieu by disrupting the enzymatic hydrolysis of gluten proteins, sequestering gluten proteins from recognition by critical receptors in pathogenesis and exerting anti-inflammatory effects on the system as a whole. This review highlights mechanisms by which polyphenols can protect against celiac disease, takes a critical look at recent works and outlines future applications for this potential treatment method.
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27
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Gupta KB, Mantha AK, Dhiman M. Mitigation of Gliadin-Induced Inflammation and Cellular Damage by Curcumin in Human Intestinal Cell Lines. Inflammation 2021; 44:873-889. [PMID: 33394186 DOI: 10.1007/s10753-020-01383-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/08/2020] [Accepted: 11/03/2020] [Indexed: 12/19/2022]
Abstract
Wheat is a major diet from many years; apart from its nutritious value, the wheat protein gliadin is responsible for many inflammatory diseases like celiac disease (CD), and non-celiac gluten sensitivity (NCGS). In this study, the gliadin-induced inflammation and associated cellular damage along with the protective role of curcumin was evaluated using human intestinal cell lines (HCT-116 and HT-29) as a model. Cells were cultured and exposed to 160 μg/ml of gliadin, 100 μM H2O2, and 10 μM curcumin (3 h pretreatment) followed by the assessment of inflammation. Spectrophotometric methods, real-time-PCR, ELISA, Western blotting, and confocal microscopy techniques were used to assess inflammatory markers such as advanced oxidation protein products (AOPPs) level, activity of myeloperoxidase (MPO) and NADPH oxidase (NOX), cytokines, and cell damage markers. The results show that gliadin increases the AOPPs level and the activity of MPO and NOX expression. It enhances inflammation by increasing expression of pro-inflammatory cytokines, altered expression of anti-inflammatory, and regulatory cytokines. It exacerbates the cellular damage by increasing MMP-2 and 9 and decreasing integrin α and β expression. Gliadin promotes disease pathogenesis by inducing the inflammation and cellular damage which further alter the cellular homeostasis. The pretreatment of curcumin counteracts the adverse effect of gliadin and protect the cells via diminishing the inflammation and help the cell to regain the cellular morphology suggesting phytochemical-based remedial interventions against wheat allergies.
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Affiliation(s)
- Kunj Bihari Gupta
- Department of Microbiology, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, Punjab, 151401, India
| | - Anil K Mantha
- Department of Zoology, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, Punjab, 151401, India
| | - Monisha Dhiman
- Department of Microbiology, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, Punjab, 151401, India.
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28
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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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29
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Chirdo FG, Auricchio S, Troncone R, Barone MV. The gliadin p31-43 peptide: Inducer of multiple proinflammatory effects. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 358:165-205. [PMID: 33707054 DOI: 10.1016/bs.ircmb.2020.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Coeliac disease (CD) is the prototype of an inflammatory chronic disease induced by food. In this context, gliadin p31-43 peptide comes into the spotlight as an important player of the inflammatory/innate immune response to gliadin in CD. The p31-43 peptide is part of the p31-55 peptide from α-gliadins that remains undigested for a long time, and can be present in the small intestine after ingestion of a gluten-containing diet. Different biophysical methods and molecular dynamic simulations have shown that p31-43 spontaneously forms oligomeric nanostructures, whereas experimental approaches using in vitro assays, mouse models, and human duodenal tissues have shown that p31-43 is able to induce different forms of cellular stress by driving multiple inflammatory pathways. Increased proliferative activity of the epithelial cells in the crypts, enterocyte stress, activation of TG2, induction of Ca2+, IL-15, and NFκB signaling, inhibition of CFTR, alteration of vesicular trafficking, and activation of the inflammasome platform are some of the biological effects of p31-43, which, in the presence of appropriate genetic susceptibility and environmental factors, may act together to drive CD.
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Affiliation(s)
- Fernando Gabriel Chirdo
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Estudios Inmunológicos y Fisiopatológicos-IIFP (UNLP-CONICET), La Plata, Argentina.
| | - Salvatore Auricchio
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University Federico II, Naples, Italy
| | - Riccardo Troncone
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University Federico II, Naples, Italy; Department of Translational Medical Science, University Federico II, Naples, Italy
| | - Maria Vittoria Barone
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University Federico II, Naples, Italy; Department of Translational Medical Science, University Federico II, Naples, Italy
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30
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Banaganapalli B, Mansour H, Mohammed A, Alharthi AM, Aljuaid NM, Nasser KK, Ahmad A, Saadah OI, Al-Aama JY, Elango R, Shaik NA. Exploring celiac disease candidate pathways by global gene expression profiling and gene network cluster analysis. Sci Rep 2020; 10:16290. [PMID: 33004927 PMCID: PMC7529771 DOI: 10.1038/s41598-020-73288-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 08/27/2020] [Indexed: 12/13/2022] Open
Abstract
Celiac disease (CeD) is a gastrointestinal autoimmune disorder, whose specific molecular basis is not yet fully interpreted. Therefore, in this study, we compared the global gene expression profile of duodenum tissues from CeD patients, both at the time of disease diagnosis and after two years of the gluten-free diet. A series of advanced systems biology approaches like differential gene expression, protein–protein interactions, gene network-cluster analysis were deployed to annotate the candidate pathways relevant to CeD pathogenesis. The duodenum tissues from CeD patients revealed the differential expression of 106 up- and 193 down-regulated genes. The pathway enrichment of differentially expressed genes (DEGs) highlights the involvement of biological pathways related to loss of cell division regulation (cell cycle, p53 signalling pathway), immune system processes (NOD-like receptor signalling pathway, Th1, and Th2 cell differentiation, IL-17 signalling pathway) and impaired metabolism and absorption (mineral and vitamin absorptions and drug metabolism) in celiac disease. The molecular dysfunctions of these 3 biological events tend to increase the number of intraepithelial lymphocytes (IELs) and villous atrophy of the duodenal mucosa promoting the development of CeD. For the first time, this study highlights the involvement of aberrant cell division, immune system, absorption, and metabolism pathways in CeD pathophysiology and presents potential novel therapeutic opportunities.
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Affiliation(s)
- Babajan Banaganapalli
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.,Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Haifa Mansour
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Arif Mohammed
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Arwa Mastoor Alharthi
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nada Mohammed Aljuaid
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khalidah Khalid Nasser
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Aftab Ahmad
- Department of Health Information Technology, Faculty of Applied Studies, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Omar I Saadah
- Pediatric Gastroenterology Unit, Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jumana Yousuf Al-Aama
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.,Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ramu Elango
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589, Saudi Arabia. .,Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Noor Ahmad Shaik
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589, Saudi Arabia. .,Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.
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31
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The expression levels of CHI3L1 and IL15Rα correlate with TGM2 in duodenum biopsies of patients with celiac disease. Inflamm Res 2020; 69:925-935. [PMID: 32500186 DOI: 10.1007/s00011-020-01371-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/13/2020] [Accepted: 06/02/2020] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE AND DESIGN Celiac disease (CD) is an intestinal inflammatory disorder of the small intestine. Gliadins are a component of gluten and there are three main types (α, γ, and ω). Recent studies indicate that gliadin peptides are able to activate an innate immune response. IL15 is a major mediator of the innate immune response and is involved in the early alteration of CD mucosa. The chitinase molecules are highly expressed by the innate immune cells during the inflammatory processes. MATERIAL OR SUBJECTS We analyzed several microarray datasets of PBMCs and duodenum biopsies of CD patients and healthy control subjects (HCs). We verified the modulation CHI3L1 in CD patients and correlated the expression levels to the IL15, IL15Rα, TGM2, IFNγ, and IFNGR1/2. Duodenal biopsy samples belonged to nine active and nine treated children patients (long-term effects of gliadin), and 17 adult CD patients and 10 adults HCs. We also selected 169 samples of PBMCs from 127 CD patients on adherence to a gluten-free diet (GFD) for at least 2 years and 44 HCs. RESULTS Our analysis showed that CHI3L1 and IL15Rα were significantly upregulated in adult and children's celiac duodenum biopsies. In addition, the two genes were correlated significantly both in children than in adults CD duodenum biopsies. No significant modulation was observed in PBMCs of adult CD patients compared to the HCs. The correlation analysis of the expression levels of CHI3L1 and IL15Rα compared to TGM showed significant values both in adults and in children duodenal biopsies. Furthermore, the IFNγ expression levels were positively correlated with CHI3L1 and IL15Rα. Receiver operating characteristic (ROC) analysis confirmed the diagnostic ability of CHI3L1 and IL15Rα to discriminate CD from HCs. CONCLUSION Our data suggest a role for CHI3L1 underlying the pathophysiology of CD and represent a starting point aiming to inspire new investigation that proves the possible use of CHI3L1 as a diagnostic factor and therapeutic target.
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32
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Fernandez-Jimenez N, Bilbao JR. Mendelian randomization analysis of celiac GWAS reveals a blood expression signature with diagnostic potential in absence of gluten consumption. Hum Mol Genet 2020; 28:3037-3042. [PMID: 31127932 PMCID: PMC6737291 DOI: 10.1093/hmg/ddz113] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/10/2019] [Accepted: 05/20/2019] [Indexed: 12/26/2022] Open
Abstract
Celiac disease (CeD) is an immune-mediated enteropathy with a strong genetic component where the main environmental trigger is dietary gluten, and currently a correct diagnosis of the disease is impossible if gluten-free diet (GFD) has already been started. We hypothesized that merging different levels of genomic information through Mendelian randomization (MR) could help discover genetic biomarkers useful for CeD diagnosis. MR was performed using public databases of expression quantitative trait loci (QTL) and methylation QTL as exposures and the largest CeD genome-wide association study conducted to date as the outcome, in order to identify potential causal genes. As a result, we identified UBE2L3, an ubiquitin ligase located in a CeD-associated region. We interrogated the expression of UBE2L3 in an independent data set of peripheral blood mononuclear cells (PBMCs) and found that its expression is altered in CeD patients on GFD when compared to non-celiac controls. The relative expression of UBE2L3 isoforms predicts CeD with 100% specificity and sensitivity and could be used as a diagnostic marker, especially in the absence of gluten consumption. This approach could be applicable to other diseases where diagnosis of asymptomatic patients can be complicated.
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Affiliation(s)
- Nora Fernandez-Jimenez
- University of the Basque Country (UPV/EHU), BioCruces-Bizkaia Health Research Institute, Leioa, Basque Country, Spain
| | - Jose Ramon Bilbao
- University of the Basque Country (UPV/EHU), BioCruces-Bizkaia Health Research Institute, Leioa, Basque Country, Spain.,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM) Madrid, Spain
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Ricaño-Ponce I, Gutierrez-Achury J, Costa AF, Deelen P, Kurilshikov A, Zorro MM, Platteel M, van der Graaf A, Sanna S, Daffra O, Zhernakova A, Fu J, Trynka G, Smecuol E, Niveloni SI, Bai JC, Kumar V, Wijmenga C. Immunochip meta-analysis in European and Argentinian populations identifies two novel genetic loci associated with celiac disease. Eur J Hum Genet 2020; 28:313-323. [PMID: 31591516 PMCID: PMC7028987 DOI: 10.1038/s41431-019-0520-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 09/03/2019] [Accepted: 09/10/2019] [Indexed: 12/30/2022] Open
Abstract
Celiac disease (CeD) is a common immune-mediated disease of the small intestine that is triggered by exposure to dietary gluten. While the HLA locus plays a major role in disease susceptibility, 39 non-HLA loci were also identified in a study of 24,269 individuals. We now build on this earlier study by adding 4125 additional Caucasian samples including an Argentinian cohort. In doing so, we not only confirm the previous associations, we also identify two novel independent genome-wide significant associations at loci: 12p13.31 and 22q13.1. By applying a genomics approach and differential expression analysis in CeD intestinal biopsies, we prioritize potential causal genes at these novel loci, including LTBR, CYTH4, and RAC2. Nineteen prioritized causal genes are overlapping known drug targets. Pathway enrichment analysis and expression of these genes in CeD biopsies suggest that they have roles in regulating multiple pathways such as the tumor necrosis factor (TNF) mediated signaling pathway and positive regulation of I-κB kinase/NF-κB signaling.
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Affiliation(s)
- Isis Ricaño-Ponce
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Javier Gutierrez-Achury
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Ana Florencia Costa
- Small Bowel Section, Department of Medicine, Dr. C. Bonorino Udaondo Gastroenterology Hospital, Buenos Aires, Argentina
| | - Patrick Deelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Maria Magdalena Zorro
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Mathieu Platteel
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Adriaan van der Graaf
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Serena Sanna
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Oscar Daffra
- Gastroenterology Service, OSEP Mendoza, Mendoza, Argentina
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Gosia Trynka
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Edgardo Smecuol
- Small Bowel Section, Department of Medicine, Dr. C. Bonorino Udaondo Gastroenterology Hospital, Buenos Aires, Argentina
| | - Sonia Isabel Niveloni
- Small Bowel Section, Department of Medicine, Dr. C. Bonorino Udaondo Gastroenterology Hospital, Buenos Aires, Argentina
| | - Julio Cesar Bai
- Small Bowel Section, Department of Medicine, Dr. C. Bonorino Udaondo Gastroenterology Hospital, Buenos Aires, Argentina
| | - Vinod Kumar
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525GA, Nijmegen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands.
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.
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Hearn NL, Chiu CL, Lind JM. Comparison of DNA methylation profiles from saliva in Coeliac disease and non-coeliac disease individuals. BMC Med Genomics 2020; 13:16. [PMID: 32014011 PMCID: PMC6998322 DOI: 10.1186/s12920-020-0670-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 01/23/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Coeliac disease (CD) is a autoimmune disease characterised by mucosal inflammation in the small intestine in response to dietary gluten. Genetic factors play a key role with CD individuals carrying either the HLA-DQ2 or HLA-DQ8 haplotype, however these haplotypes are present in half the general population making them necessary but insufficient to cause CD. Epigenetic modifications, including DNA methylation that can change in response to environmental exposure could help to explain how interactions between genes and environmental factors combine to trigger disease development. Identifying changes in DNA methylation profiles in individuals with CD could help discover novel genomic regions involved in the onset and development of CD. METHODS The Illumina InfiniumMethylation450 Beadchip array (HM450) was used to compare DNA methylation profiles in saliva, in CD and non-CD affected individuals. CD individuals who had been diagnosed at least 2 years previously; were on a GFD; and who were currently asymptomatic; were compared to age and sex-matched non-CD affected healthy controls. Bisulphite pyrosequencing was used to validate regions found to be differentially methylated. These regions were also validated in a second larger cohort of CD and non-CD affected individuals. RESULTS Methylation differences within the HLA region at HLA-DQB1 were identified on HM450 but could not be confirmed with pyrosequencing. Significant methylation differences near the SLC17A3 gene were confirmed on pyrosequencing in the initial pilot cohort. Interestingly pyrosequencing sequencing of these same sites within a second cohort of CD and non-CD affected controls produced significant methylation differences in the opposite direction. CONCLUSION Altered DNA methylation profiles appear to be present in saliva in CD individuals. Further work to confirm whether these differences are truly associated with CD is needed.
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Affiliation(s)
- Nerissa L. Hearn
- Western Sydney University, School of Medicine, Sydney, Australia
| | - Christine L. Chiu
- Macquarie University, Faculty of Medicine and Health Sciences, Sydney, Australia
| | - Joanne M. Lind
- Western Sydney University, School of Medicine, Sydney, Australia
- Macquarie University, Faculty of Medicine and Health Sciences, Sydney, Australia
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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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Small-bowel carcinomas associated with celiac disease: transcriptomic profiling shows predominance of microsatellite instability-immune and mesenchymal subtypes. Virchows Arch 2019; 476:711-723. [DOI: 10.1007/s00428-019-02675-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/30/2019] [Accepted: 09/22/2019] [Indexed: 02/08/2023]
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Ochoa E, Zuber V, Fernandez-Jimenez N, Bilbao JR, Clark GR, Maher ER, Bottolo L. MethylCal: Bayesian calibration of methylation levels. Nucleic Acids Res 2019; 47:e81. [PMID: 31049595 PMCID: PMC6698668 DOI: 10.1093/nar/gkz325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/24/2019] [Accepted: 04/20/2019] [Indexed: 12/16/2022] Open
Abstract
Bisulfite amplicon sequencing has become the primary choice for single-base methylation quantification of multiple targets in parallel. The main limitation of this technology is a preferential amplification of an allele and strand in the PCR due to methylation state. This effect, known as 'PCR bias', causes inaccurate estimation of the methylation levels and calibration methods based on standard controls have been proposed to correct for it. Here, we present a Bayesian calibration tool, MethylCal, which can analyse jointly all CpGs within a CpG island (CGI) or a Differentially Methylated Region (DMR), avoiding 'one-at-a-time' CpG calibration. This enables more precise modeling of the methylation levels observed in the standard controls. It also provides accurate predictions of the methylation levels not considered in the controlled experiment, a feature that is paramount in the derivation of the corrected methylation degree. We tested the proposed method on eight independent assays (two CpG islands and six imprinting DMRs) and demonstrated its benefits, including the ability to detect outliers. We also evaluated MethylCal's calibration in two practical cases, a clinical diagnostic test on 18 patients potentially affected by Beckwith-Wiedemann syndrome, and 17 individuals with celiac disease. The calibration of the methylation levels obtained by MethylCal allows a clearer identification of patients undergoing loss or gain of methylation in borderline cases and could influence further clinical or treatment decisions.
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Affiliation(s)
- Eguzkine Ochoa
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
- Cambridge NIHR Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Verena Zuber
- Department of Epidemiology and Biostatistics, Imperial College London, London W2 1PG, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain
- CIBERDEM Diabetes and Associated Metabolic Diseases, Spain
| | - Graeme R Clark
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
- Cambridge NIHR Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
- Cambridge NIHR Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK
- The Alan Turing Institute, London NW1 2DB, UK
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Xie Y, Wang M, Tian J, Li X, Yang M, Zhang K, Tan S, Luo L, Luo C, Peng L, Tang A. Long non-coding RNA expressed in macrophage co-varies with the inflammatory phenotype during macrophage development and polarization. J Cell Mol Med 2019; 23:6530-6542. [PMID: 31419045 PMCID: PMC6787567 DOI: 10.1111/jcmm.14557] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/19/2019] [Accepted: 07/02/2019] [Indexed: 12/13/2022] Open
Abstract
Advances in microarray, RNA‐seq and omics techniques, thousands of long non‐coding RNAs (lncRNAs) with unknown functions have been discovered. LncRNAs have presented a diverse perspective on gene regulation in diverse biological processes, especially in human immune response. Macrophages participate in the whole phase of immune inflammatory response. They are able to shape their phenotype and arouse extensive functional activation after receiving physiological and pathological stimuli. Emerging studies indicated that lncRNAs participated in the gene regulatory network during complex biological processes of macrophage, including macrophage‐induced inflammatory responses. Here, we reviewed the existing knowledges of lncRNAs in the processes of macrophage development and polarization, and their roles in several different inflammatory diseases. Specifically, we focused on how lncRNAs function in macrophage, which might help to discover some potential therapeutic targets and diagnostic biomarkers.
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Affiliation(s)
- Yixin Xie
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Urological Organ Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Min Wang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jingjing Tian
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xianping Li
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Min Yang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Kan Zhang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shan Tan
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lingli Luo
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Can Luo
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Longkai Peng
- Department of Urological Organ Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Aiguo Tang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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Jeong YJ, Oh HK, Choi HR. Methylation of the RELA Gene is Associated with Expression of NF-κB1 in Response to TNF-α in Breast Cancer. Molecules 2019; 24:E2834. [PMID: 31382678 PMCID: PMC6696039 DOI: 10.3390/molecules24152834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/28/2019] [Accepted: 08/01/2019] [Indexed: 11/16/2022] Open
Abstract
The nuclear factor (NF)-κB family of transcriptional factors plays a critical role in inflammation, immunoregulation, cell differentiation, and tumorigenesis. This study aims to investigate the role of methylation of genes encoding for the NF-κB family in breast cancer. We analyze the DNA methylation status of the NFKB1 gene and the RELA gene in breast cancer using pyrosequencing. The expression of NF-κB1 and RELA proteins is assessed and the level of RNA transcripts in frozen tissue is determined using RT-PCR. There is no statistically significant difference in the methylation status of the NFKB1 and the RELA genes between tumors and normal tissues. The methylation status of the NFKB1 gene and the RELA gene is not significantly associated with the levels of NF-κB1 transcripts in tumor tissues. However, the methylation level of the RELA gene is significantly associated with the level of tumor necrosis factor (TNF)-α. In addition, the level of NF-κB1 transcripts was associated with the levels of TNF-α and IL-4. In tumors with positive TNF-α, the increased methylation level of the RELA gene is significantly associated with the positive expression of NF-κB1 transcripts. These results demonstrate that the level of the RELA gene methylation is related to the levels of NF-κB1 transcripts under the influence of TNF-α. Further study is needed to determine how TNF-α is involved in the methylation of the RELA gene and the subsequent expression of NF-κB1.
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Affiliation(s)
- Young Ju Jeong
- Department of Surgery, School of Medicine, Catholic University of Daegu, Daegu 42472, Korea.
| | - Hoon Kyu Oh
- Department of Pathology, School of Medicine, Catholic University of Daegu, Daegu 42472, Korea
| | - Hye Ryeon Choi
- Department of Surgery, School of Medicine, Catholic University of Daegu, Daegu 42472, Korea
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Cielo D, Galatola M, Fernandez-Jimenez N, De Leo L, Garcia-Etxebarria K, Loganes C, Tommasini A, Not T, Auricchio R, Greco L, Bilbao JR. Combined Analysis of Methylation and Gene Expression Profiles in Separate Compartments of Small Bowel Mucosa Identified Celiac Disease Patients' Signatures. Sci Rep 2019; 9:10020. [PMID: 31292504 PMCID: PMC6620355 DOI: 10.1038/s41598-019-46468-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 06/14/2019] [Indexed: 02/07/2023] Open
Abstract
By GWAS studies on celiac disease, gene expression was studied at the level of the whole intestinal mucosa, composed by two different compartments: epithelium and lamina propria. Our aim is to analyse the gene-expression and DNA methylation of candidate genes in each of these compartments. Epithelium was separated from lamina propria in biopsies of CeD patients and CTRs using magnetic beads. Gene-expression was analysed by RT-PC; methylation analysis required bisulfite conversion and NGS. Reverse modulation of gene-expression and methylation in the same cellular compartment was observed for the IL21 and SH2B3 genes in CeD patients relative to CTRs. Bioinformatics analysis highlighted the regulatory elements in the genomic region of SH2B3 that altered methylation levels. The cREL and TNFAIP3 genes showed methylation patterns that were significantly different between CeD patients and CTRs. In CeD, the genes linked to inflammatory processes are up-regulated, whereas the genes involved in the cell adhesion/integrity of the intestinal barrier are down-regulated. These findings suggest a correlation between gene-expression and methylation profile for the IL21 and SH2B3 genes. We identified a “gene-expression phenotype” of CeD and showed that the abnormal response to dietary antigens in CeD might be related not to abnormalities of gene structure but to the regulation of molecular pathways.
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Affiliation(s)
- D Cielo
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy.,European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples "Federico II", Naples, Italy
| | - M Galatola
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy. .,European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples "Federico II", Naples, Italy.
| | - N Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Health Research Institute, Leioa, Spain
| | - L De Leo
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
| | - K Garcia-Etxebarria
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Health Research Institute, Leioa, Spain
| | - C Loganes
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
| | - A Tommasini
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
| | - T Not
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Health Research Institute, Leioa, Spain.,Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
| | - R Auricchio
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy.,European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples "Federico II", Naples, Italy
| | - L Greco
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy.,European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples "Federico II", Naples, Italy
| | - J R Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Health Research Institute, Leioa, Spain
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Kramer K, Yeboah-Awudzi M, Magazine N, King JM, Xu Z, Losso JN. Procyanidin B2 rich cocoa extracts inhibit inflammation in Caco-2 cell model of in vitro celiac disease by down-regulating interferon-gamma- or gliadin peptide 31-43-induced transglutaminase-2 and interleukin-15. J Funct Foods 2019. [DOI: 10.1016/j.jff.2019.03.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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42
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Lania G, Nanayakkara M, Maglio M, Auricchio R, Porpora M, Conte M, De Matteis MA, Rizzo R, Luini A, Discepolo V, Troncone R, Auricchio S, Barone MV. Constitutive alterations in vesicular trafficking increase the sensitivity of cells from celiac disease patients to gliadin. Commun Biol 2019; 2:190. [PMID: 31123714 PMCID: PMC6527696 DOI: 10.1038/s42003-019-0443-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 04/19/2019] [Indexed: 02/06/2023] Open
Abstract
Celiac Disease (CD) is an autoimmune disease characterized by inflammation of the intestinal mucosa due to an immune response to wheat gliadins. Some gliadin peptides (e.g., A-gliadin P57-68) induce an adaptive Th1 pro-inflammatory response. Other gliadin peptides (e.g., A-gliadin P31-43) induce a stress/innate immune response involving interleukin 15 (IL15) and interferon α (IFN-α). In the present study, we describe a stressed/inflamed celiac cellular phenotype in enterocytes and fibroblasts probably due to an alteration in the early-recycling endosomal system. Celiac cells are more sensitive to the gliadin peptide P31-43 and IL15 than controls. This phenotype is reproduced in control cells by inducing a delay in early vesicular trafficking. This constitutive lesion might mediate the stress/innate immune response to gliadin, which can be one of the triggers of the gliadin-specific T-cell response.
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Affiliation(s)
- Giuliana Lania
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Merlin Nanayakkara
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Mariantonia Maglio
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Renata Auricchio
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Monia Porpora
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Mariangela Conte
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Maria Antonietta De Matteis
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Via S. Pansini 5, 80131 Naples, Italy
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Riccardo Rizzo
- Institute of Protein Biochemistry—IBP-CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Alberto Luini
- Institute of Protein Biochemistry—IBP-CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Valentina Discepolo
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Riccardo Troncone
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Salvatore Auricchio
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Maria Vittoria Barone
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
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Castellanos-Rubio A, Ghosh S. Disease-Associated SNPs in Inflammation-Related lncRNAs. Front Immunol 2019; 10:420. [PMID: 30906297 PMCID: PMC6418042 DOI: 10.3389/fimmu.2019.00420] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 02/18/2019] [Indexed: 02/06/2023] Open
Abstract
Immune-mediated diseases, such as celiac disease, type 1 diabetes or multiple sclerosis, are a clinically heterogeneous group of diseases that share many key genetic triggers. Although the pathogenic mechanisms responsible for the development of immune mediated disorders is not totally understood, high-throughput genomic studies, such as GWAS and Immunochip, performed in the past few years have provided intriguing hints about underlying mechanisms and pathways that lead to disease. More than a hundred gene variants associated with disease susceptibility have been identified through such studies, but the progress toward understanding the underlying mechanisms has been slow. The majority of the identified risk variants are located in non-coding regions of the genome making it difficult to assign a molecular function to the SNPs. However, recent studies have revealed that many of the non-coding regions bearing disease-associated SNPs generate long non-coding RNAs (lncRNAs). LncRNAs have been implicated in several inflammatory diseases, and many of them have been shown to function as regulators of gene expression. Many of the disease associated SNPs located in lncRNAs modify their secondary structure, or influence expression levels, thereby affecting their regulatory function, hence contributing to the development of disease.
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Affiliation(s)
- Ainara Castellanos-Rubio
- Immunogenetics Research Laboratory, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain.,Functional Studies in Celiac Disease Group, BioCruces Health Research Institute, Barakaldo, Spain
| | - Sankar Ghosh
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
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Fernandez-Jimenez N, Garcia-Etxebarria K, Plaza-Izurieta L, Romero-Garmendia I, Jauregi-Miguel A, Legarda M, Ecsedi S, Castellanos-Rubio A, Cahais V, Cuenin C, Degli Esposti D, Irastorza I, Hernandez-Vargas H, Herceg Z, Bilbao JR. The methylome of the celiac intestinal epithelium harbours genotype-independent alterations in the HLA region. Sci Rep 2019; 9:1298. [PMID: 30718669 PMCID: PMC6362130 DOI: 10.1038/s41598-018-37746-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/13/2018] [Indexed: 12/12/2022] Open
Abstract
The Human Leucocyte Antigen (HLA) locus and other DNA sequence variants identified in Genome-Wide Association (GWA) studies explain around 50% of the heritability of celiac disease (CD). However, the pathogenesis of CD could be driven by other layers of genomic information independent from sequence variation, such as DNA methylation, and it is possible that allele-specific methylation explains part of the SNP associations. Since the DNA methylation landscape is expected to be different among cell types, we analyzed the methylome of the epithelial and immune cell populations of duodenal biopsies in CD patients and controls separately. We found a cell type-specific methylation signature that includes genes mapping to the HLA region, namely TAP1 and HLA-B. We also performed Immunochip SNP genotyping of the same samples and interrogated the expression of some of the affected genes. Our analysis revealed that the epithelial methylome is characterized by the loss of CpG island (CGI) boundaries, often associated to altered gene expression, and by the increased variability of the methylation across the samples. The overlap between differentially methylated positions (DMPs) and CD-associated SNPs or variants contributing to methylation quantitative trait loci (mQTLs) is minimal. In contrast, there is a notable enrichment of mQTLs among the most significant CD-associated SNPs. Our results support the notion that DNA methylation alterations constitute a genotype-independent event and confirm its role in the HLA region (apart from the well-known, DQ allele-specific effect). Finally, we find that a fraction of the CD-associated variants could exert its phenotypic effect through DNA methylation.
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Affiliation(s)
- Nora Fernandez-Jimenez
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain
| | - Koldo Garcia-Etxebarria
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain
- Department of Gastrointestinal and Liver Diseases, Biodonostia Health Research Institute, Donostia, Basque Country, Spain
| | - Leticia Plaza-Izurieta
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain
| | - Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain
| | - Amaia Jauregi-Miguel
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain
| | - Maria Legarda
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, 48903, Spain
| | - Szilvia Ecsedi
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
- Universite Côte d'Azur, INSERM, CNRS, iBV, Nice, France
| | - Ainara Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain
- Spanish Biomedical Research Center in Diabetes and associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
| | - Cyrille Cuenin
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
| | - Davide Degli Esposti
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
- Irstea - Laboratoire d'écotoxicologie, UR "Milieux aquatiques, écologie et pollutions", Villeurbanne, France
| | - Iñaki Irastorza
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, 48903, Spain
| | - Hector Hernandez-Vargas
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
- Department of Immunology, Virology and Inflammation; TGF beta and Immune Evasion Group; Cancer Research Center of Lyon; INSERM, CNRS, Centre Léon Bérard Hospital, Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain.
- Spanish Biomedical Research Center in Diabetes and associated Metabolic Disorders (CIBERDEM), Madrid, Spain.
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Charlesworth RPG, Agnew LL, Scott DR, Andronicos NM. Celiac disease gene expression data can be used to classify biopsies along the Marsh score severity scale. J Gastroenterol Hepatol 2019; 34:169-177. [PMID: 29972865 DOI: 10.1111/jgh.14369] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/19/2018] [Accepted: 06/19/2018] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND AIM The diagnosis of celiac disease autoimmune pathology relies on the subjective histological assignment of biopsies into Marsh score categories. It is hypothesized that Marsh score categories have unique gene expression signatures. The aims were as follows: first, to develop a celiac disease quantitative reverse transcription-polymerase chain reaction (RT-PCR) array; second, define gene expression signatures associated with Marsh score categories; and third, develop equations that classify biopsies into Marsh score categories and to monitor the efficacy of patient treatment. METHODS Gene targets for inclusion in the celiac RT-PCR (qRT-PCR) array were identified using systematic analysis of published celiac transcriptomic data. The array was used to assess the gene expression associated with histological changes in duodenal biopsies obtained from adult patients. Finally, Marsh score classification equations were defined using discriminant analysis. RESULTS The array contained 87 genes. The expression of 26 genes were significantly (p < 0.06) associated with the discrete Marsh score categories. As the Marsh score pathology of biopsies increased, there was a progression of innate immune gene expression through adaptive Th1-specific gene expression with a concurrent decrease in intestinal structural gene expression in high Marsh score samples. These 26 genes were used to define classification equations that accounted for 99% of the observed experimental variation and which could classify biopsies into Marsh score categories and monitor patient treatment progression. CONCLUSIONS This proof-of-concept study successfully developed a celiac RT-PCR array and has provided evidence that discriminant equations defined using gene expression data can objectively and accurately classify duodenal biopsies into Marsh score categories.
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Affiliation(s)
- Richard P G Charlesworth
- Discipline of Biomedical Sciences, School of Science and Technology, University of New England, Armidale, New South Wales, Australia
| | - Linda L Agnew
- Discipline of Biomedical Sciences, School of Science and Technology, University of New England, Armidale, New South Wales, Australia
| | - David R Scott
- Hunter New England Area Health Service, Tamworth, New South Wales, Australia
| | - Nicholas M Andronicos
- Discipline of Biomedical Sciences, School of Science and Technology, University of New England, Armidale, New South Wales, Australia
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Celiac Diasease-associated lncRNA Named HCG14 Regulates NOD1 Expression in Intestinal Cells. J Pediatr Gastroenterol Nutr 2018; 67:225-231. [PMID: 29601440 DOI: 10.1097/mpg.0000000000001970] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
OBJECTIVE The aim of the study is to identify additional celiac disease associated loci in the major histocompatibility complex (MHC) independent from classical HLA risk alleles (HLA-DR3-DQ2) and to characterize their potential functional impact in celiac disease pathogenesis at the intestinal level. METHODS We performed a high-resolution single-nucleotide polymorphism (SNP) genotyping of the MHC region, comparing HLA-DR3 homozygous celiac patients and non-celiac controls carrying a single copy of the B8-DR3-DQ2 conserved extended haplotype. Expression level of potential novel risk genes was determined by RT-PCR in intestinal biopsies and in intestinal and immune cells isolated from control and celiac individuals. Small interfering RNA-driven silencing of selected genes was performed in the intestinal cell line T84. RESULTS MHC genotyping revealed 2 associated SNPs, one located in TRIM27 gene and another in the non-coding gene HCG14. After stratification analysis, only HCG14 showed significant association independent from HLA-DR-DQ loci. Expression of HCG14 was slightly downregulated in epithelial cells isolated from duodenal biopsies of celiac patients, and eQTL analysis revealed that polymorphisms in HCG14 region were associated with decreased NOD1 expression in duodenal intestinal cells. CONCLUSIONS We have successfully employed a conserved extended haplotype-matching strategy and identified a novel additional celiac disease risk variant in the lncRNA HCG14. This lncRNA seems to regulate the expression of NOD1 in an allele-specific manner. Further functional studies are needed to clarify the role of HCG14 in the regulation of gene expression and to determine the molecular mechanisms by which the risk variant in HCG14 contributes to celiac disease pathogenesis.
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van Dam S, Võsa U, van der Graaf A, Franke L, de Magalhães JP. Gene co-expression analysis for functional classification and gene-disease predictions. Brief Bioinform 2018; 19:575-592. [PMID: 28077403 PMCID: PMC6054162 DOI: 10.1093/bib/bbw139] [Citation(s) in RCA: 430] [Impact Index Per Article: 71.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/01/2016] [Indexed: 01/06/2023] Open
Abstract
Gene co-expression networks can be used to associate genes of unknown function with biological processes, to prioritize candidate disease genes or to discern transcriptional regulatory programmes. With recent advances in transcriptomics and next-generation sequencing, co-expression networks constructed from RNA sequencing data also enable the inference of functions and disease associations for non-coding genes and splice variants. Although gene co-expression networks typically do not provide information about causality, emerging methods for differential co-expression analysis are enabling the identification of regulatory genes underlying various phenotypes. Here, we introduce and guide researchers through a (differential) co-expression analysis. We provide an overview of methods and tools used to create and analyse co-expression networks constructed from gene expression data, and we explain how these can be used to identify genes with a regulatory role in disease. Furthermore, we discuss the integration of other data types with co-expression networks and offer future perspectives of co-expression analysis.
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Affiliation(s)
- Sipko van Dam
- Department of Genetics, UMCG HPC CB50, RB Groningen, Netherlands
| | - Urmo Võsa
- Department of Genetics, UMCG HPC CB50, RB Groningen, Netherlands
| | | | - Lude Franke
- Department of Genetics, UMCG HPC CB50, RB Groningen, Netherlands
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Herrera MG, Pizzuto M, Lonez C, Rott K, Hütten A, Sewald N, Ruysschaert JM, Dodero VI. Large supramolecular structures of 33-mer gliadin peptide activate toll-like receptors in macrophages. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2018; 14:1417-1427. [DOI: 10.1016/j.nano.2018.04.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/23/2018] [Accepted: 04/16/2018] [Indexed: 02/08/2023]
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Sangineto M, Graziano G, D’Amore S, Salvia R, Palasciano G, Sabbà C, Vacca M, Cariello M. Identification of peculiar gene expression profile in peripheral blood mononuclear cells (PBMC) of celiac patients on gluten free diet. PLoS One 2018; 13:e0197915. [PMID: 29795662 PMCID: PMC5967809 DOI: 10.1371/journal.pone.0197915] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/10/2018] [Indexed: 12/26/2022] Open
Abstract
Celiac disease (CD) is a systemic disorder characterized by an immune-mediated reaction to gluten and a wide spectrum of clinical manifestations. Currently, the main treatment of CD is represented by adherence to a gluten-free diet (GFD) which determines the resolution of symptoms, and the normalization of the serology and of the duodenal villous atrophy. In the present study, we aimed to identify changes in gene expression in peripheral blood mononuclear cells (PBMCs) of celiac patients on GFD for at least 2 years, in order to identify novel disease biomarkers and candidate targets for putative therapeutic approaches. Microarray analysis was performed on PBMCs from 17 celiac patients on long-term GFD and 20 healthy controls. We identified 517 annotated genes that were significantly modulated between celiac patients and controls. Significant biological pathways were functionally clustered using the Core Function of Ingenuity System Pathway Analysis (IPA). Intriguingly, despite being on a GFD, celiac patients exhibited a peculiar PBMC profile characterized by an aberrant expression of genes involved in the regulation of immunity, inflammatory response, metabolism, and cell proliferation. Random forest algorithm was then used to validate the prediction ability of core genes as classifiers of the "celiac status". In conclusion, our study identified a characteristic PBMCs signature profile in clinically asymptomatic celiac patient.
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Affiliation(s)
- Moris Sangineto
- Department of Interdisciplinary Medicine, “Aldo Moro” University of Bari, Bari, Italy
| | - Giusi Graziano
- National Cancer Research Center, IRCCS Oncologico Giovanni Paolo II, Bari, Italy
| | - Simona D’Amore
- Department of Interdisciplinary Medicine, “Aldo Moro” University of Bari, Bari, Italy
| | - Roberto Salvia
- Department of Interdisciplinary Medicine, “Aldo Moro” University of Bari, Bari, Italy
| | - Giuseppe Palasciano
- Department of Biomedical Sciences and Human Oncology, Clinica Medica “A. Murri”, “Aldo Moro” University of Bari, Bari, Italy
| | - Carlo Sabbà
- Department of Interdisciplinary Medicine, “Aldo Moro” University of Bari, Bari, Italy
| | - Michele Vacca
- Department of Interdisciplinary Medicine, “Aldo Moro” University of Bari, Bari, Italy
| | - Marica Cariello
- Department of Interdisciplinary Medicine, “Aldo Moro” University of Bari, Bari, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome, Italy
- * E-mail:
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50
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Romero-Garmendia I, Garcia-Etxebarria K, Hernandez-Vargas H, Santin I, Jauregi-Miguel A, Plaza-Izurieta L, Cros MP, Legarda M, Irastorza I, Herceg Z, Fernandez-Jimenez N, Bilbao JR. Transcription Factor Binding Site Enrichment Analysis in Co-Expression Modules in Celiac Disease. Genes (Basel) 2018; 9:E245. [PMID: 29748492 PMCID: PMC5977185 DOI: 10.3390/genes9050245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 12/12/2022] Open
Abstract
The aim of this study was to construct celiac co-expression patterns at a whole genome level and to identify transcription factors (TFs) that could drive the gliadin-related changes in coordination of gene expression observed in celiac disease (CD). Differential co-expression modules were identified in the acute and chronic responses to gliadin using expression data from a previous microarray study in duodenal biopsies. Transcription factor binding site (TFBS) and Gene Ontology (GO) annotation enrichment analyses were performed in differentially co-expressed genes (DCGs) and selection of candidate regulators was performed. Expression of candidates was measured in clinical samples and the activation of the TFs was further characterized in C2BBe1 cells upon gliadin challenge. Enrichment analyses of the DCGs identified 10 TFs and five were selected for further investigation. Expression changes related to active CD were detected in four TFs, as well as in several of their in silico predicted targets. The activation of TFs was further characterized in C2BBe1 cells upon gliadin challenge, and an increase in nuclear translocation of CAMP Responsive Element Binding Protein 1 (CREB1) and IFN regulatory factor-1 (IRF1) in response to gliadin was observed. Using transcriptome-wide co-expression analyses we are able to propose novel genes involved in CD pathogenesis that respond upon gliadin stimulation, also in non-celiac models.
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Affiliation(s)
- Irati Romero-Garmendia
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
| | - Koldo Garcia-Etxebarria
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
| | - Hector Hernandez-Vargas
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, France.
| | - Izortze Santin
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), 28029 Madrid, Spain.
| | - Amaia Jauregi-Miguel
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
| | - Leticia Plaza-Izurieta
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
| | - Marie-Pierre Cros
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, France.
| | - Maria Legarda
- Pediatric Gastroenterology Unit, Cruces University Hospital, University of the Basque Country-(UPV/EHU) and Biocruces Health Research Institute, 48903 Barakaldo, Spain.
| | - Iñaki Irastorza
- Pediatric Gastroenterology Unit, Cruces University Hospital, University of the Basque Country-(UPV/EHU) and Biocruces Health Research Institute, 48903 Barakaldo, Spain.
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, France.
| | - Nora Fernandez-Jimenez
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, France.
| | - Jose Ramon Bilbao
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), 28029 Madrid, Spain.
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