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Hernangomez-Laderas A, Cilleros-Portet A, Martínez Velasco S, Marí S, Legarda M, González-García BP, Tutau C, García-Santisteban I, Irastorza I, Fernandez-Jimenez N, Bilbao JR. Sex bias in celiac disease: XWAS and monocyte eQTLs in women identify TMEM187 as a functional candidate gene. Biol Sex Differ 2023; 14:86. [PMID: 38072919 PMCID: PMC10712119 DOI: 10.1186/s13293-023-00572-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Celiac disease (CeD) is an immune-mediated disorder that develops in genetically predisposed individuals upon gluten consumption. HLA risk alleles explain 40% of the genetic component of CeD, so there have been continuing efforts to uncover non-HLA loci that can explain the remaining heritability. As in most autoimmune disorders, the prevalence of CeD is significantly higher in women. Here, we investigated the possible involvement of the X chromosome on the sex bias of CeD. METHODS We performed a X chromosome-wide association study (XWAS) and a gene-based association study in women from the CeD Immunochip (7062 cases, 5446 controls). We also constructed a database of X chromosome cis-expression quantitative trait loci (eQTLs) in monocytes from unstimulated (n = 226) and lipopolysaccharide (LPS)-stimulated (n = 130) female donors and performed a Summary-data-based MR (SMR) analysis to integrate XWAS and eQTL information. We interrogated the expression of the potentially causal gene (TMEM187) in peripheral blood mononuclear cells (PBMCs) from celiac patients at onset, on a gluten-free diet, potential celiac patients and non-celiac controls. RESULTS The XWAS and gene-based analyses identified 13 SNPs and 25 genes, respectively, 22 of which had not been previously associated with CeD. The X chromosome cis-eQTL analysis found 18 genes with at least one cis-eQTL in naïve female monocytes and 8 genes in LPS-stimulated female monocytes, 2 of which were common to both situations and 6 were unique to LPS stimulation. SMR identified a potentially causal association of TMEM187 expression in naïve monocytes with CeD in women, regulated by CeD-associated, eQTL-SNPs rs7350355 and rs5945386. The CeD-risk alleles were correlated with lower TMEM187 expression. These results were replicated using eQTLs from LPS-stimulated monocytes. We observed higher levels of TMEM187 expression in PBMCs from female CeD patients at onset compared to female non-celiac controls, but not in male CeD individuals. CONCLUSION Using X chromosome genotypes and gene expression data from female monocytes, SMR has identified TMEM187 as a potentially causal candidate in CeD. Further studies are needed to understand the implication of the X chromosome in the higher prevalence of CeD in women.
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Affiliation(s)
- Alba Hernangomez-Laderas
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Silvia Martínez Velasco
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, Spain
| | - Sergi Marí
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - María Legarda
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, Spain
| | - Bárbara Paola González-García
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Carlos Tutau
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, Spain
| | - Iraia García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Iñaki Irastorza
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain.
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain.
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain.
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain.
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain.
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Oras A, Kallionpää H, Suomi T, Koskinen S, Laiho A, Elo LL, Knip M, Lahesmaa R, Aints A, Uibo R. Profiling of peripheral blood B-cell transcriptome in children who developed coeliac disease in a prospective study. Heliyon 2023; 9:e13147. [PMID: 36718152 PMCID: PMC9883278 DOI: 10.1016/j.heliyon.2023.e13147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 12/20/2022] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
Background In coeliac disease (CoD), the role of B-cells has mainly been considered to be production of antibodies. The functional role of B-cells has not been analysed extensively in CoD. Methods We conducted a study to characterize gene expression in B-cells from children developing CoD early in life using samples collected before and at the diagnosis of the disease. Blood samples were collected from children at risk at 12, 18, 24 and 36 months of age. RNA from peripheral blood CD19+ cells was sequenced and differential gene expression was analysed using R package Limma. Findings Overall, we found one gene, HNRNPL, modestly downregulated in all patients (logFC -0·7; q = 0·09), and several others downregulated in those diagnosed with CoD already by the age of 2 years. Interpretation The data highlight the role of B-cells in CoD development. The role of HNRPL in suppressing enteroviral replication suggests that the predisposing factor for both CoD and enteroviral infections is the low level of HNRNPL expression. Funding EU FP7 grant no. 202063, EU Regional Developmental Fund and research grant PRG712, The Academy of Finland Centre of Excellence in Molecular Systems Immunology and Physiology Research (SyMMyS) 2012-2017, grant no. 250114) and, AoF Personalized Medicine Program (grant no. 292482), AoF grants 292335, 294337, 319280, 31444, 319280, 329277, 331790) and grants from the Sigrid Jusélius Foundation (SJF).
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Affiliation(s)
- Astrid Oras
- Department of Immunology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia
| | - Henna Kallionpää
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Finland
| | - Tomi Suomi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Finland,InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Satu Koskinen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Finland,InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Laura L. Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Finland,InFLAMES Research Flagship Center, University of Turku, Turku, Finland,Institute of Biomedicine, University of Turku, Finland
| | - Mikael Knip
- Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland,Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Finland,InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Alar Aints
- Department of Immunology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia,Corresponding author. Department of Immunology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, EE50411, Tartu, Estonia.
| | - Raivo Uibo
- Department of Immunology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia
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3
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Alim MA, Njenda D, Lundmark A, Kaminska M, Jansson L, Eriksson K, Kats A, Johannsen G, Arvidsson CK, Mydel PM, Yucel-Lindberg T. Pleckstrin Levels Are Increased in Patients with Chronic Periodontitis and Regulated via the MAP Kinase-p38α Signaling Pathway in Gingival Fibroblasts. Front Immunol 2022; 12:801096. [PMID: 35087525 PMCID: PMC8787058 DOI: 10.3389/fimmu.2021.801096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022] Open
Abstract
Chronic periodontitis (CP) is a bacteria-driven inflammatory disease characterized by the breakdown of gingival tissue, the periodontal ligament, and alveolar bone, leading ultimately to tooth loss. We previously reported the pleckstrin gene (PLEK) to be highly upregulated in gingival tissue of patients with CP and the only gene concurrently upregulated in other inflammatory diseases including rheumatoid arthritis and cardiovascular diseases. Using saliva from 169 individuals diagnosed with CP and healthy controls, we investigated whether pleckstrin could serve as a novel biomarker of periodontitis. Additionally, we explored signal pathways involved in the regulation of PLEK using human gingival fibroblasts (HGFs). Pleckstrin levels were significantly higher (p < 0.001) in the saliva samples of patients with CP compared to controls and closely associated with CP severity. Immunohistochemical analysis revealed the expression of pleckstrin in inflammatory cells and gingival fibroblasts of CP patients. To explore the signal pathways involved in pleckstrin regulation, we stimulated HGFs with either interleukin-1β (IL-1β) or lipopolysaccharides (LPS) alone, or in combination with inhibitors targeting c-Jun N-terminal kinase, tyrosine kinase, protein kinase C, or p38 MAP kinase. Results showed that IL-1β and LPS significantly increased PLEK mRNA and pleckstrin protein levels. VX-745, the p38 MAP kinase inhibitor significantly decreased IL-1β- and LPS-induced pleckstrin levels at both the mRNA and the protein level. Together, these findings show that pleckstrin could serve as a salivary biomarker for the chronic inflammatory disease periodontitis and a regulator of inflammation via the p38 MAP kinase pathway.
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Affiliation(s)
- M Abdul Alim
- Department of Dental Medicine, Division of Pediatric Dentistry, Karolinska Institutet, Huddinge, Sweden
| | - Duncan Njenda
- Department of Dental Medicine, Division of Periodontology, Karolinska Institutet, Huddinge, Sweden
| | - Anna Lundmark
- Department of Dental Medicine, Division of Pediatric Dentistry, Karolinska Institutet, Huddinge, Sweden.,Department of Dental Medicine, Division of Periodontology, Karolinska Institutet, Huddinge, Sweden
| | - Marta Kaminska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Leif Jansson
- Department of Dental Medicine, Division of Periodontology, Karolinska Institutet, Huddinge, Sweden.,Department of Periodontology, Folktandvården Stockholms län AB, Folktandvården Eastmaninstitutet, Stockholm, Sweden
| | - Kaja Eriksson
- Department of Dental Medicine, Division of Pediatric Dentistry, Karolinska Institutet, Huddinge, Sweden.,Department of Dental Medicine, Division of Periodontology, Karolinska Institutet, Huddinge, Sweden
| | - Anna Kats
- Department of Dental Medicine, Division of Periodontology, Karolinska Institutet, Huddinge, Sweden
| | - Gunnar Johannsen
- Department of Dental Medicine, Division of Periodontology, Karolinska Institutet, Huddinge, Sweden
| | - Catalin Koro Arvidsson
- Department of Dental Medicine, Division of Periodontology, Karolinska Institutet, Huddinge, Sweden
| | - Piotr M Mydel
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.,Department of Clinical Science, Broegelmann Laboratory, University of Bergen, Bergen, Norway
| | - Tülay Yucel-Lindberg
- Department of Dental Medicine, Division of Pediatric Dentistry, Karolinska Institutet, Huddinge, Sweden
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4
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Rodrigues D, de Souza T, Coyle L, Di Piazza M, Herpers B, Ferreira S, Zhang M, Vappiani J, Sévin DC, Gabor A, Lynch A, Chung SW, Saez-Rodriguez J, Jennen DGJ, Kleinjans JCS, de Kok TM. New insights into the mechanisms underlying 5-fluorouracil-induced intestinal toxicity based on transcriptomic and metabolomic responses in human intestinal organoids. Arch Toxicol 2021; 95:2691-2718. [PMID: 34151400 PMCID: PMC8298376 DOI: 10.1007/s00204-021-03092-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/15/2021] [Indexed: 12/13/2022]
Abstract
5-Fluorouracil (5-FU) is a widely used chemotherapeutical that induces acute toxicity in the small and large intestine of patients. Symptoms can be severe and lead to the interruption of cancer treatments. However, there is limited understanding of the molecular mechanisms underlying 5-FU-induced intestinal toxicity. In this study, well-established 3D organoid models of human colon and small intestine (SI) were used to characterize 5-FU transcriptomic and metabolomic responses. Clinically relevant 5-FU concentrations for in vitro testing in organoids were established using physiologically based pharmacokinetic simulation of dosing regimens recommended for cancer patients, resulting in exposures to 10, 100 and 1000 µM. After treatment, different measurements were performed: cell viability and apoptosis; image analysis of cell morphological changes; RNA sequencing; and metabolome analysis of supernatant from organoids cultures. Based on analysis of the differentially expressed genes, the most prominent molecular pathways affected by 5-FU included cell cycle, p53 signalling, mitochondrial ATP synthesis and apoptosis. Short time-series expression miner demonstrated tissue-specific mechanisms affected by 5-FU, namely biosynthesis and transport of small molecules, and mRNA translation for colon; cell signalling mediated by Rho GTPases and fork-head box transcription factors for SI. Metabolomic analysis showed that in addition to the effects on TCA cycle and oxidative stress in both organoids, tissue-specific metabolic alterations were also induced by 5-FU. Multi-omics integration identified transcription factor E2F1, a regulator of cell cycle and apoptosis, as the best key node across all samples. These results provide new insights into 5-FU toxicity mechanisms and underline the relevance of human organoid models in the safety assessment in drug development.
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Affiliation(s)
- Daniela Rodrigues
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands.
| | - Terezinha de Souza
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Luke Coyle
- Departmnet of Nonclinical Drug Safety, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
| | - Matteo Di Piazza
- Departmnet of Nonclinical Drug Safety, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
- F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Bram Herpers
- OcellO B.V., BioPartner Center, Leiden, the Netherlands
| | - Sofia Ferreira
- Certara UK Limited, Simcyp Division, Sheffield, S1 2BJ, UK
| | - Mian Zhang
- Certara UK Limited, Simcyp Division, Sheffield, S1 2BJ, UK
| | | | - Daniel C Sévin
- GSK Functional Genomics/Cellzome, 69117, Heidelberg, Germany
| | - Attila Gabor
- Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
| | | | - Seung-Wook Chung
- Departmnet of Nonclinical Drug Safety, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
| | - Julio Saez-Rodriguez
- GSK Non-Clinical Safety, Ware, SG12 0DP, UK
- Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, Heidelberg University, Heidelberg, Germany
| | - Danyel G J Jennen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Jos C S Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Theo M de Kok
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
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5
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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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Izadi F, Soheilifar MH, Keshmiri Neghab H, Soheilifar M, Esmaeeli Djavid G. Network Analysis of Common Genes and Transcriptional Factors between Celiac Disease and Inflammatory Bowel Diseases. Middle East J Dig Dis 2021; 12:257-264. [PMID: 33564383 PMCID: PMC7859603 DOI: 10.34172/mejdd.2020.191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Understanding the associations among different disorders remarkably improves their diagnosis and treatments. Celiac disease is the most complicated and prevalent form of immune-mediated diseases. On the other hand, inflammatory bowel diseases lead to inflammation of the intestine with an unknown cause. Although inflammatory bowel diseases have been often thought of as an autoimmune disorder, they can be triggered by whatever that can lead to the inflammation in the whole bowel. Henceforth, both aforementioned diseases are related to autoimmune attacks and cause a sort of inflammatory event, which exploring trade-off among them supposedly will lead to discovering important genes and, in turn, to the possible common therapeutic protocols. In the current study, we aimed to determine the correlation between the common genes in celiac disease and inflammatory bowel diseases. METHODS 314 and 851 genes correlated with celiac disease and inflammatory bowel diseases respectively extracted from DisGeNET were subjected to an in-silico data analysis framework to mine prognosticates genes and the associated pathways. RESULTS 149 shared genes between these diseases regulated by highlighted transcription factors NFKB1, IRF1, STAT1, HSF1, GATA3 were characterized as discriminating molecules, which by further screening were enriched in pathways mostly involved in apoptosis, T cell activation, and cytokine, chemokine, and interleukin signaling. CONCLUSION We observed that the identified common genes were associated with a wide range of pathogenic mechanisms underlying these diseases.
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Affiliation(s)
- Fereshteh Izadi
- Research Center for Molecular Medicine, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | | | - Hoda Keshmiri Neghab
- Department of Photo Healing and Regeneration, Medical Laser Research Center, Yara Institute, ACECR, Tehran, Iran
| | - Mahya Soheilifar
- Department of Biology, Faculty of Sciences, Malayer University, Malayer, Iran
| | - Gholamreza Esmaeeli Djavid
- Department of Photo Healing and Regeneration, Medical Laser Research Center, Yara Institute, ACECR, Tehran, Iran
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7
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Chen Y, Li H, Lai L, Feng Q, Shen J. Identification of Common Differentially Expressed Genes and Potential Therapeutic Targets in Ulcerative Colitis and Rheumatoid Arthritis. Front Genet 2020; 11:572194. [PMID: 33262784 PMCID: PMC7686785 DOI: 10.3389/fgene.2020.572194] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Ulcerative colitis (UC) and rheumatoid arthritis (RA) are immune-mediated inflammatory diseases (IMIDs) with similar symptoms and common genomics. However, the relationship between UC and RA has not been investigated thoroughly. Therefore, this study aimed to establish the differentially expressed genes (DEGs) and potential therapeutic targets in UC and RA. Three microarray datasets (GSE38713, GSE1919, and GSE12251) were selected from the Gene Expression Omnibus (GEO) database for analysis. We used R software to identify the DEGs and performed enrichment analyses. Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Cytoscape software were used to construct the protein-protein interaction (PPI) network and identify the hub genes. A regulatory network based on the constructed PPI was generated using StarBase and PROMO databases. We identified a total of 1542 and 261 DEGs in UC and RA. There were 169 common DEGs identified in both UC and RA, including 63 upregulated genes (DEGs1) and nine downregulated genes (DEGs2). The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of DEGs1 and DEGs2 in the PPI network revealed that the genes enriched were involved in immunity. A total of 45 hub genes were selected based on high scores of correlation; three hub genes (SRGN, PLEK, and FCGR3B) were found to be upregulated in UC and RA, and downregulated in UC patients with response to infliximab treatment. The identification of novel DEGs and hub genes in the current study contributes to a novel perception for latent functional mechanisms and presents potential prognostic indicators and therapeutic targets in UC and RA.
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Affiliation(s)
- Yueying Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Hanyang Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Lijie Lai
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Qi Feng
- Department of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Shen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
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8
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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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9
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Kahlenberg JM, Kang I. Advances in Disease Mechanisms and Translational Technologies: Clinicopathologic Significance of Inflammasome Activation in Autoimmune Diseases. Arthritis Rheumatol 2020; 72:386-395. [PMID: 31562704 DOI: 10.1002/art.41127] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022]
Abstract
Autoimmune diseases are characterized by dysregulated immune tolerance to self and inflammatory damage to tissues and organs. The development of inflammation involves multiple innate and adaptive immune pathways. Inflammasomes are multimeric cytosolic protein complexes that form to mediate host immune responses upon recognizing pathogen- or damage-associated molecular patterns via pattern-recognition receptors (PRRs). The accelerating pace of inflammasome research has demonstrated important roles for inflammasome activation in many pathologic conditions, including infectious, metabolic, autoinflammatory, and autoimmune diseases. The inflammasome generally comprises a PRR, procaspase 1, and an adaptor molecule connecting the PRR and procaspase 1. Upon inflammasome activation, procaspase 1 becomes active caspase 1 that converts pro-interleukin-1β (proIL-1β) and proIL-18 into mature and active IL-1β and IL-18, respectively. The cytokines IL-1β and IL-18 have multipotent effects on immune and nonimmune cells and induce and promote systemic and local inflammatory responses. Human studies have shown increased levels of these cytokines, altered activation of inflammasome-related molecules, and/or the presence of inflammasome activators in rheumatic diseases, including systemic lupus erythematosus, rheumatoid arthritis, crystal-induced arthropathies, and Sjögren's syndrome. Such changes are found in the primary target organs, such as the kidneys, joints, and salivary glands, as well as in the cardiovascular system. In animal models of rheumatic diseases, inflammation and tissue damage improve upon genetic or pharmacologic targeting of the inflammasome, supporting its pathogenic role. Herein, we review the clinicopathologic significance and therapeutic targeting of inflammasome activation in rheumatic diseases and related conditions based on recent findings.
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10
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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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11
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Noori E, Kazemi B, Bandehpour M, Zali H, Khalesi B, Khalili S. Deciphering crucial genes in coeliac disease by bioinformatics analysis. Autoimmunity 2019; 53:102-113. [PMID: 31809599 DOI: 10.1080/08916934.2019.1698552] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Coeliac disease (CD) is a chronic autoimmune disease that is characterized by malabsorption in sensitive individuals. CD is triggered by the ingestion of grains containing gluten. CD is concomitant with several other disorders, including dermatitis herpetiformis, selective IgA deficiency, thyroid disorders, diabetes mellitus, various connective tissue disorders, inflammatory bowel disease, and rheumatoid arthritis. The advent of high throughput technologies has provided a massive wealth of data which are processed in various omics scale fields. These approaches have revolutionized the medical research and monitoring of the biological systems. In this regard, omics scaled analyses of CD by Comparative Toxicogenomics Database (CTD), DISEASES, and GeneCards databases have retrieved 2656 CD associated genes. Amongst, 54 genes were assigned by Venn Diagram of the intersection to be shared by these 3 databases for CD. These common genes were subjected to further analysis and screening. The Enrich database, GeneMANIA, Cytoscape, and WebGestalt (WEB-based GEne SeT AnaLysis Toolkit) were employed for functional analysis. These analyses indicated that the obtained genes are mainly involved in the immune system and signalling pathways related to autoimmune diseases. The STAT1, ALB, IL10, IL2, IL4, IL17A, TGFB1, IL1B, IL6, TNF, IFNG hub genes were particularly indicated to have significant roles in CD. Functional analyses of these hub genes by GeneMANIA indicated that they are involved in immune systems regulation. Moreover, 25 out of 54 genes were identified to be seed genes by the WebGestalt database. Gene set analysis with GEO2R tool from Gene Expression Omnibus (GEO) showed that there were 15 significant genes in GSE76168, 29 significant genes in GSE87460, 12 significant genes in GSE87458, 9 significant genes in GSE87457, 3753 significant genes in GSE112102 and 1043 significant genes in GSE102991 with differential expression in coeliac patients compared to controls. The IRF1and STAT1 genes were common between the significant genes from GEO and the 54 CD related genes from three public databases. In the light these results, nine key genes, including IRF1, STAT1, IL17A, TGFB1, ALB, IL10, IL2, IL4, and IL1B, were identified to be associated with CD. These findings could be used to find novel diagnostic biomarkers, understand the pathology of disease, and devise more efficient treatments.
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Affiliation(s)
- Effat Noori
- Department of Biotechnology School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahram Kazemi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mojgan Bandehpour
- Department of Biotechnology School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hakimeh Zali
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahman Khalesi
- Department of Research and Production of Poultry Viral Vaccine, Razi Vaccine and Serum Research Institute Agriculture Research Education and Extension Organization(AREEO), Karaj, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
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12
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KhalKhal E, Razzaghi Z, Zali H, Bahadorimonfared A, Iranshahi M, Rostami-Nejad M. Comparison of cytokine and gene activities in tissue and blood samples of patients with celiac disease. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2019; 12:S108-S116. [PMID: 32099610 PMCID: PMC7011060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AIM The aim of this study is to explore the expression of genes associated to celiac disease (CD) in the target tissue and peripheral blood monocytes (PBMC) or serum to introduce possible potential biomarkers. BACKGROUND Celiac disease (CD) is an autoimmune disease induced by gluten ingestion in genetically predisposed individuals. Despite technological progress, small intestine biopsy is still the gold standard for diagnosis of CD. METHODS CD data were collected from public databases (proteomics and microarray-based techniques documents). Differentially expressed genes (DEGs) in PBMC or serum as well as small intestinal biopsies from celiac patients compared to normal were collected and analyzed to introduce common individuals. Gene ontology was done to identify the involved biological terms. RESULTS Among 598 CD genes in biopsies and 260 genes in PBMC or serum, 32 common genes with a similar expression pattern in both sources were identified. A total of 48 biological terms were introduced which were involved in the CD via the determined DEGs. "Cytokine activity" was the most expanded one of the biological terms. CONCLUSION In this analysis, it was concluded that 32 potential biomarkers of CD can be assessed by complementary research to introduce effective and available biomarkers in biopsy and blood.
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Affiliation(s)
- Ensieh KhalKhal
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Razzaghi
- Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Hakimeh Zali
- Proteomics Research Center, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Ayad Bahadorimonfared
- Department of Health & Community Medicine, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Majid Iranshahi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Rostami-Nejad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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13
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Del Prete E, Facchiano A, Liò P. Bioinformatics methodologies for coeliac disease and its comorbidities. Brief Bioinform 2018; 21:355-367. [PMID: 30452543 DOI: 10.1093/bib/bby109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/01/2018] [Accepted: 10/11/2018] [Indexed: 12/30/2022] Open
Abstract
Coeliac disease (CD) is a complex, multifactorial pathology caused by different factors, such as nutrition, immunological response and genetic factors. Many autoimmune diseases are comorbidities for CD, and a comprehensive and integrated analysis with bioinformatics approaches can help in evaluating the interconnections among all the selected pathologies. We first performed a detailed survey of gene expression data available in public repositories on CD and less commonly considered comorbidities. Then we developed an innovative pipeline that integrates gene expression, cell-type data and online resources (e.g. a list of comorbidities from the literature), using bioinformatics methods such as gene set enrichment analysis and semantic similarity. Our pipeline is written in R language, available at the following link: http://bioinformatica.isa.cnr.it/COELIAC_DISEASE/SCRIPTS/. We found a list of common differential expressed genes, gene ontology terms and pathways among CD and comorbidities and the closeness among the selected pathologies by means of disease ontology terms. Physicians and other researchers, such as molecular biologists, systems biologists and pharmacologists can use it to analyze pathology in detail, from differential expressed genes to ontologies, performing a comparison with the pathology comorbidities or with other diseases.
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Affiliation(s)
- Eugenio Del Prete
- Department of Sciences, University of Basilicata,Via dell'Ateneo Lucano, Potenza, Italy.,National Research Council, Institute of Food Science (CNR-ISA),Via Roma 64, Avellino, Italy.,Computer Laboratory, University of Cambridge, JJ Thomson Ave., Cambridge, UK
| | - Angelo Facchiano
- National Research Council, Institute of Food Science (CNR-ISA),Via Roma 64, Avellino, Italy
| | - Pietro Liò
- Computer Laboratory, University of Cambridge, JJ Thomson Ave., Cambridge, UK
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14
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Medrano LM, Pascual V, Bodas A, López-Palacios N, Salazar I, Espino-Paisán L, González-Pérez B, Urcelay E, Mendoza JL, Núñez C. Expression patterns common and unique to ulcerative colitis and celiac disease. Ann Hum Genet 2018; 83:86-94. [PMID: 30402962 DOI: 10.1111/ahg.12293] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 10/02/2018] [Accepted: 10/15/2018] [Indexed: 12/14/2022]
Abstract
Autoimmune diseases like celiac disease (CeD) and ulcerative colitis (UC) show a common genetic background defined by the existence of shared susceptibility loci. We aimed to go deeper into this common genetic background through performing a cross-disease study based on gene expression. We measured the expression of 21 genes located in 13 CeD-UC susceptibility regions, and 10 genes in five CeD risk regions. Determinations were carried out in colon/rectum samples from 13 UC patients (inflamed and uninflamed tissue) and four colon samples from controls. Duodenal samples from 19 CeD patients and 12 controls were used for comparisons. Differences were analyzed using the Bayesian method. The shared chromosomal regions containing TNFAIP3, PTPN2, ICOSLG, C1orf106, and IL21 showed similar results in both diseases. FASLG, PLEK, CCR4, and TAGAP, all located in CeD risk loci, were up-regulated in both CeD and UC patients. Finally, ZFP36L1, ZMIZ1, PUS10, UBE2L3, and BACH2 showed opposite results in CeD and UC. A high complexity underlies autoimmune common susceptibility loci, as the expression pattern of the studied genes does not always correlate with the one expected attending to the apparent genetic background. Differentially expressed genes such as ZFP36L1, ZMIZ1, PUS10, and BACH2 deserve further research in autoimmune diseases.
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Affiliation(s)
- Luz María Medrano
- Servicio de Inmunología Clínica, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Virginia Pascual
- Servicio de Inmunología Clínica, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Andrés Bodas
- Servicio de Pediatría, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain
| | - Natalia López-Palacios
- Servicio de Aparato Digestivo, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain
| | - Isabel Salazar
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Laura Espino-Paisán
- Laboratorio de Investigación en Genética de Enfermedades Complejas, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain
| | - Beatriz González-Pérez
- Departamento de Estadística e Investigación Operativa I, Facultad de Matemáticas, Universidad Complutense de Madrid, Madrid, Spain
| | - Elena Urcelay
- Laboratorio de Investigación en Genética de Enfermedades Complejas, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain
| | - Juan Luis Mendoza
- Servicio de Aparato Digestivo, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain
| | - Concepción Núñez
- Laboratorio de Investigación en Genética de Enfermedades Complejas, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain
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15
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Chua MMJ, Lee M, Dominguez I. Cancer-type dependent expression of CK2 transcripts. PLoS One 2017; 12:e0188854. [PMID: 29206231 PMCID: PMC5714396 DOI: 10.1371/journal.pone.0188854] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 11/14/2017] [Indexed: 01/31/2023] Open
Abstract
A multitude of proteins are aberrantly expressed in cancer cells, including the oncogenic serine-threonine kinase CK2. In a previous report, we found increases in CK2 transcript expression that could explain the increased CK2 protein levels found in tumors from lung and bronchus, prostate, breast, colon and rectum, ovarian and pancreatic cancers. We also found that, contrary to the current notions about CK2, some CK2 transcripts were downregulated in several cancers. Here, we investigate all other cancers using Oncomine to determine whether they also display significant CK2 transcript dysregulation. As anticipated from our previous analysis, we found cancers with all CK2 transcripts upregulated (e.g. cervical), and cancers where there was a combination of upregulation and/or downregulation of the CK2 transcripts (e.g. sarcoma). Unexpectedly, we found some cancers with significant downregulation of all CK2 transcripts (e.g. testicular cancer). We also found that, in some cases, CK2 transcript levels were already dysregulated in benign lesions (e.g. Barrett’s esophagus). We also found that CK2 transcript upregulation correlated with lower patient survival in most cases where data was significant. However, there were two cancer types, glioblastoma and renal cell carcinoma, where CK2 transcript upregulation correlated with higher survival. Overall, these data show that the expression levels of CK2 genes is highly variable in cancers and can lead to different patient outcomes.
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Affiliation(s)
- Melissa M. J. Chua
- Department of Medicine, Boston University School of Medicine, Boston MA, United States of America
| | - Migi Lee
- Department of Medicine, Boston University School of Medicine, Boston MA, United States of America
| | - Isabel Dominguez
- Department of Medicine, Boston University School of Medicine, Boston MA, United States of America
- * E-mail:
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16
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Efthymakis K, Serio M, Milano A, Laterza F, Bonitatibus A, Di Nicola M, Neri M. Application of the Biopsy-Sparing ESPGHAN Guidelines for Celiac Disease Diagnosis in Adults: A Real-Life Study. Dig Dis Sci 2017; 62:2433-2439. [PMID: 28717844 DOI: 10.1007/s10620-017-4672-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/04/2017] [Indexed: 12/19/2022]
Abstract
BACKGROUND Current adult celiac disease diagnosis requires histological confirmation. However, pediatric guidelines have proposed biopsy-sparing algorithms. AIMS To explore the applicability of the ESPGHAN criteria and assess the accuracy of serology in predicting disease in adults. METHODS We evaluated 234 consecutive adults showing elevated anti-tTG titers, EMA-positivity, and genetic susceptibility. Patients underwent upper endoscopy with duodenal biopsy. We determined optimal anti-tTG cutoff levels using ROC curves. RESULTS Mean anti-tTG levels were 71.1 ± 66.5 U/ml; mean normalized levels were 14.8 ± 14.1 × ULN (mean ± SD). Partial/total villous atrophy was present in 36%/55% of cases, respectively. Anti-tTG levels correlated with histology (r s = 0.397, p < 0.001). AUC was similar before and after normalization (0.803 vs 0.807). Applying the ESPGHAN criterion (≥10 × ULN), we calculated a 97.66% PPV. ROC curve analysis showed an optimal cutoff of ≥16 × ULN, with a PPV of 98.86%. Eleven different assays were used for anti-tTG titer determination: Two were prevalent, labeled A (n = 141) and B (n = 59). They performed differently regarding disease prediction (AUC = 0.689 vs 0.925, p < 0.01), showing distinct optimal cutoff values (14.3 × ULN vs 3.7 × ULN), even after standardization (-0.14 vs -1.2). CONCLUSION In adult symptomatic patients showing EMA-positivity and genetic susceptibility, anti-tTG titers correlated with histology. ESPGHAN criteria performed similarly to previous studies. However, a calculated 16 × ULN cutoff showed an improved PPV. Among prevalent assays, PPV peaked differently both after normalization and standardization, indicating intrinsic differences in performance, thus preventing uniform prediction of disease in a real-life setting. Assay-specific optimal cutoffs seem possible, but would complicate diagnostic criteria. However, biopsy-sparing strategies in adults could prove useful in challenging patients.
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Affiliation(s)
- Konstantinos Efthymakis
- Department of Medicine and Ageing Sciences and Center for Excellence On Ageing and Translational Medicine (CeSI-MeT), "G. D'Annunzio" University and Foundation, Chieti, Italy
| | - Mariaelena Serio
- Department of Medicine and Ageing Sciences and Center for Excellence On Ageing and Translational Medicine (CeSI-MeT), "G. D'Annunzio" University and Foundation, Chieti, Italy
| | - Angelo Milano
- Department of Medicine and Ageing Sciences and Center for Excellence On Ageing and Translational Medicine (CeSI-MeT), "G. D'Annunzio" University and Foundation, Chieti, Italy
| | - Francesco Laterza
- Department of Medicine and Ageing Sciences and Center for Excellence On Ageing and Translational Medicine (CeSI-MeT), "G. D'Annunzio" University and Foundation, Chieti, Italy
| | - Antonella Bonitatibus
- Department of Medicine and Ageing Sciences and Center for Excellence On Ageing and Translational Medicine (CeSI-MeT), "G. D'Annunzio" University and Foundation, Chieti, Italy
| | - Marta Di Nicola
- Department of Medical, Oral and Biotechnological Sciences, "G. D'Annunzio" University and Foundation, Chieti, Italy
| | - Matteo Neri
- Department of Medicine and Ageing Sciences and Center for Excellence On Ageing and Translational Medicine (CeSI-MeT), "G. D'Annunzio" University and Foundation, Chieti, Italy.
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17
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Izadi F, Rezaei Tavirani M, Honarkar Z, Rostami-Nejad M. Celiac disease and hepatitis C relationships in transcriptional regulatory networks. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2017; 10:303-310. [PMID: 29379596 PMCID: PMC5758739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
AIM we mainly aimed to elucidate potential comorbidities between celiac disease and hepatitis c by means of data and network analysis approaches. BACKGROUND understanding the association among the disorders evidently has important impact on the diagnosis and therapeutic approaches. Celiac disease is the most challenging, common types of autoimmune disorders. On the other hand, hepatitis c virus genome products like some proteins are supposed to be resemble to gliadin types that in turn activates gluten intolerance in people with inclined to gluten susceptibilities. Moreover, a firm support of association between chronic hepatitis and celiac disease remains largely unclear. Henceforth exploring cross-talk among these diseases will apparently lead to the promising discoveries concerning important genes and regulators. METHODS 321 and 1032 genes associated with celiac disease and hepatitis c retrieved from DisGeNET were subjected to build a gene regulatory network. Afterward a network-driven integrative analysis was performed to exploring prognosticates genes and related pathways. RESULTS 105 common genes between these diseases included 11 transcription factors were identified as hallmark molecules where by further screening enriched in biological GO terms and pathways chiefly in immune systems and signaling pathways such as chemokines, cytokines and interleukins. CONCLUSION in silico data analysis approaches indicated that the identified selected combinations of genes covered a wide range of known functions triggering the inflammation implicated in these diseases.
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Affiliation(s)
- Fereshteh Izadi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Zahra Honarkar
- Gastroenterology Unit, Modares Hospital, Shahid beheshti University of Medical Sciences, Tehran, Iran ,Gastroenterology Department, Atiyeh Hospital, Tehran, Iran
| | - Mohammad Rostami-Nejad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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