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Toledo-Stuardo K, Ribeiro CH, Campos I, Tello S, Latorre Y, Altamirano C, Dubois-Camacho K, Molina MC. Impact of MICA 3'UTR allelic variability on miRNA binding prediction, a bioinformatic approach. Front Genet 2023; 14:1273296. [PMID: 38146340 PMCID: PMC10749337 DOI: 10.3389/fgene.2023.1273296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 11/13/2023] [Indexed: 12/27/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that participate as powerful genetic regulators. MiRNAs can interfere with cellular processes by interacting with a broad spectrum of target genes under physiological and pathological states, including cancer development and progression. Major histocompatibility complex major histocompatibility complex class I-related chain A (MICA) belongs to a family of proteins that bind the natural-killer group 2, member D (NKG2D) receptor on Natural Killer cells and other cytotoxic lymphocytes. MICA plays a crucial role in the host's innate immune response to several disease settings, including cancer. MICA harbors various single nucleotide polymorphisms (SNPs) located in its 3'-untranslated region (3'UTR), a characteristic that increases the complexity of MICA regulation, favoring its post-transcriptional modulation by miRNAs under physiological and pathological conditions. Here, we conducted an in-depth analysis of MICA 3'UTR sequences according to each MICA allele described to date using NCBI database. We also systematically evaluated interactions between miRNAs and their putative targets on MICA 3'UTR containing SNPs using in silico analysis. Our in silico results showed that MICA SNPs rs9266829, rs 1880, and rs9266825, located in the target sequence of miRNAs hsa-miR-106a-5p, hsa-miR-17-5p, hsa-miR-20a-5p, hsa-miR-20b-5p, hsa-miR-93, hsa-miR-1207.5p, and hsa-miR-711 could modify the binding free energy between -8.62 and -18.14 kcal/mol, which may affect the regulation of MICA expression. We believe that our results may provide a starting point for further exploration of miRNA regulatory effects depending on MICA allelic variability; they may also be a guide to conduct miRNA in silico analysis for other highly polymorphic genes.
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Affiliation(s)
- Karen Toledo-Stuardo
- Faculty of Medicine, Immunology Program, Institute of Biomedical Sciences (ICBM), Universidad de Chile, Santiago, Chile
| | - Carolina H. Ribeiro
- Faculty of Medicine, Immunology Program, Institute of Biomedical Sciences (ICBM), Universidad de Chile, Santiago, Chile
| | - Ivo Campos
- Faculty of Medicine, Immunology Program, Institute of Biomedical Sciences (ICBM), Universidad de Chile, Santiago, Chile
| | - Samantha Tello
- Faculty of Medicine, Immunology Program, Institute of Biomedical Sciences (ICBM), Universidad de Chile, Santiago, Chile
| | - Yesenia Latorre
- Faculty of Medicine, Immunology Program, Institute of Biomedical Sciences (ICBM), Universidad de Chile, Santiago, Chile
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Claudia Altamirano
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Karen Dubois-Camacho
- Faculty of Medicine, Immunology Program, Institute of Biomedical Sciences (ICBM), Universidad de Chile, Santiago, Chile
- Faculty of Medicine, Clinical and Molecular Pharmacology Program, Institute of Biomedical Sciences (ICBM), Universidad de Chile, Santiago, Chile
- Gastroenterology and Hepatology Department, University Medical Center Groningen, Groningen, Netherlands
| | - Maria Carmen Molina
- Faculty of Medicine, Immunology Program, Institute of Biomedical Sciences (ICBM), Universidad de Chile, Santiago, Chile
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2
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Koskela S, Tammi S, Clancy J, Lucas JAM, Turner TR, Hyvärinen K, Ritari J, Partanen J. MICA and MICB allele assortment in Finland. HLA 2023. [PMID: 36919857 DOI: 10.1111/tan.15023] [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: 12/30/2021] [Revised: 02/01/2023] [Accepted: 03/04/2023] [Indexed: 03/16/2023]
Abstract
Genetic variation in the MICA and MICB genes located within the major histocompatibility complex region has been reported to be associated with transplantation outcome and susceptibility to autoimmune diseases and infections. Only limited data of polymorphism in these genes in different populations are available. We here report allelic variation at 2-field resolution and the haplotypes of the MICA and MICB genes in Finland (n = 1032 individuals), a north European population with historical bottleneck and founder effects. Altogether 24 MICA and 18 MICB alleles were found, forming 70 estimated MICA-MICB haplotypes. As compared to other populations frequency differences were found, for example, MICA*010:01 was found to be at an allele frequency of 0.133 in Finland which is higher than in other European populations (0.021-0.077), but close to Asian populations (0.151-0.220). Three novel alleles with amino acid change are described. The results demonstrate a relatively high level of polymorphism and population differences in MICA and MICB allele distribution.
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Affiliation(s)
- Satu Koskela
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland.,Finnish Red Cross Blood Service Biobank, Helsinki, Finland
| | - Silja Tammi
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland.,Finnish Red Cross Blood Service Biobank, Helsinki, Finland
| | - Jonna Clancy
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland.,Finnish Red Cross Blood Service Biobank, Helsinki, Finland
| | | | - Thomas R Turner
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
| | - Kati Hyvärinen
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland
| | - Jarmo Ritari
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland
| | - Jukka Partanen
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland.,Finnish Red Cross Blood Service Biobank, Helsinki, Finland
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3
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Toledo-Stuardo K, Ribeiro CH, Canals A, Morales M, Gárate V, Rodríguez-Siza J, Tello S, Bustamante M, Armisen R, Matthies DJ, Zapata-Torres G, González-Hormazabal P, Molina MC. Major Histocompatibility Complex Class I-Related Chain A (MICA) Allelic Variants Associate With Susceptibility and Prognosis of Gastric Cancer. Front Immunol 2021; 12:645528. [PMID: 33868281 PMCID: PMC8045969 DOI: 10.3389/fimmu.2021.645528] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/23/2021] [Indexed: 12/14/2022] Open
Abstract
Gastric cancer (GC) is the fifth most prevalent type of cancer worldwide. Gastric tumor cells express MICA protein, a ligand to NKG2D receptor that triggers natural killer (NK) cells effector functions for early tumor elimination. MICA gene is highly polymorphic, thus originating alleles that encode protein variants with a controversial role in cancer. The main goal of this work was to study MICA gene polymorphisms and their relationship with the susceptibility and prognosis of GC. Fifty patients with GC and 50 healthy volunteers were included in this study. MICA alleles were identified using Sanger sequencing methods. The analysis of MICA gene sequence revealed 13 MICA sequences and 5 MICA-short tandem repeats (STR) alleles in the studied cohorts We identified MICA*002 (*A9) as the most frequent allele in both, patients and controls, followed by MICA*008 allele (*A5.1). MICA*009/049 allele was significantly associated with increased risk of GC (OR: 5.11 [95% CI: 1.39–18.74], p = 0.014). The analysis of MICA-STR alleles revealed a higher frequency of MICA*A5 in healthy individuals than GC patients (OR = 0.34 [95% CI: 0.12–0.98], p = 0.046). Survival analysis after gastrectomy showed that patients with MICA*002/002 or MICA*002/004 alleles had significantly higher survival rates than those patients bearing MICA*002/008 (p = 0.014) or MICA*002/009 (MICA*002/049) alleles (p = 0.040). The presence of threonine in the position MICA-181 (MICA*009/049 allele) was more frequent in GC patients than controls (p = 0.023). Molecular analysis of MICA-181 showed that the presence of threonine provides greater mobility to the protein than arginine in the same position (MICA*004), which could explain, at least in part, some immune evasion mechanisms developed by the tumor. In conclusion, our findings suggest that the study of MICA alleles is crucial to search for new therapeutic approaches and may be useful for the evaluation of risk and prognosis of GC and personalized therapy.
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Affiliation(s)
- Karen Toledo-Stuardo
- Immunology Program, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), University of Chile, Santiago, Chile
| | - Carolina H Ribeiro
- Immunology Program, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), University of Chile, Santiago, Chile
| | - Andrea Canals
- Biostatistics Program, School of Public Health, University of Chile, Santiago, Chile.,Academic Direction, Clínica Santa María, Santiago, Chile
| | - Marcela Morales
- Immunology Program, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), University of Chile, Santiago, Chile
| | - Valentina Gárate
- Immunology Program, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), University of Chile, Santiago, Chile
| | - Jose Rodríguez-Siza
- Immunology Program, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), University of Chile, Santiago, Chile
| | - Samantha Tello
- Immunology Program, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), University of Chile, Santiago, Chile
| | - Marco Bustamante
- Department of Surgery (Oriente), Hospital del Salvador, University of Chile, Santiago, Chile
| | - Ricardo Armisen
- Center of Genetics and Genomics, Faculty of Medicine Clínica Alemana, Institute for Sciences and Innovations in Medicine (ICIM), Universidad del Desarrollo, Santiago, Chile
| | - Douglas J Matthies
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical and Pharmaceutical Sciences, University of Chile, Santiago, Chile
| | - Gerald Zapata-Torres
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical and Pharmaceutical Sciences, University of Chile, Santiago, Chile
| | | | - María Carmen Molina
- Immunology Program, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), University of Chile, Santiago, Chile
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Askar M, Sobecks R, Wang T, Haagenson M, Majhail N, Madbouly A, Thomas D, Zhang A, Fleischhauer K, Hsu K, Verneris M, Lee SJ, Spellman SR, Fernández-Viña M. MHC Class I Chain-Related Gene A (MICA) Donor-Recipient Mismatches and MICA-129 Polymorphism in Unrelated Donor Hematopoietic Cell Transplantations Has No Impact on Outcomes in Acute Lymphoblastic Leukemia, Acute Myeloid Leukemia, or Myelodysplastic Syndrome: A Center for International Blood and Marrow Transplant Research Study. Biol Blood Marrow Transplant 2017; 23:436-444. [PMID: 27987385 PMCID: PMC5370205 DOI: 10.1016/j.bbmt.2016.11.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/24/2016] [Indexed: 11/26/2022]
Abstract
Single-center studies have previously reported associations of MHC Class I Chain-Related Gene A (MICA) polymorphisms and donor-recipient MICA mismatching with graft-versus-host disease (GVHD) after unrelated donor hematopoietic cell transplantation (HCT). In this study, we investigated the association of MICA polymorphism (MICA-129, MM versus MV versus VV) and MICA mismatches after HCT with 10/10 HLA-matched (n = 552) or 9/10 (n = 161) unrelated donors. Included were adult patients with a first unrelated bone marrow or peripheral blood HCT for acute lymphoblastic leukemia, acute myeloid leukemia, or myelodysplastic syndrome that were reported to the Center for International Blood and Marrow Transplant Research between 1999 and 2011. Our results showed that neither MICA mismatch nor MICA-129 polymorphism were associated with any transplantation outcome (P < .01), with the exception of a higher relapse in recipients of MICA-mismatched HLA 10/10 donors (hazard ratio [HR], 1.7; P = .003). There was a suggestion of association between MICA mismatches and a higher risk of acute GVHD grades II to IV (HR, 1.4; P = .013) There were no significant interactions between MICA mismatches and HLA matching (9/10 versus 10/10). In conclusion, the findings in this cohort did not confirm prior studies reporting that MICA polymorphism and MICA mismatches were associated with HCT outcomes.
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Affiliation(s)
- Medhat Askar
- Department of Pathology, Baylor University Medical Center, Dallas, Texas.
| | - Ronald Sobecks
- Blood and Marrow Transplant Program, Cleveland Clinic Foundation, Cleveland, Ohio
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research, Milwaukee, Wisconsin
| | - Mike Haagenson
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | - Navneet Majhail
- Blood and Marrow Transplant Program, Cleveland Clinic Foundation, Cleveland, Ohio
| | - Abeer Madbouly
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | - Dawn Thomas
- Blood and Marrow Transplant Program, Cleveland Clinic Foundation, Cleveland, Ohio
| | - Aiwen Zhang
- Blood and Marrow Transplant Program, Cleveland Clinic Foundation, Cleveland, Ohio
| | | | - Katharine Hsu
- Division of Hematologic Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center-Adults, New York, New York
| | - Michael Verneris
- Division of Hematology, Oncology, and Transplantation, Department of Pediatrics, University of Minnesota Medical Center, Minneapolis, Minnesota
| | - Stephanie J Lee
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
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Abstract
Human and mouse NKG2D ligands (NKG2DLs) are absent or only poorly expressed by most normal cells but are upregulated by cell stress, hence, alerting the immune system in case of malignancy or infection. Although these ligands are numerous and highly variable (at genetic, genomic, structural, and biochemical levels), they all belong to the major histocompatibility complex class I gene superfamily and bind to a single, invariant, receptor: NKG2D. NKG2D (CD314) is an activating receptor expressed on NK cells and subsets of T cells that have a key role in the recognition and lysis of infected and tumor cells. Here, we review the molecular diversity of NKG2DLs, discuss the increasing appreciation of their roles in a variety of medical conditions, and propose several explanations for the evolutionary force(s) that seem to drive the multiplicity and diversity of NKG2DLs while maintaining their interaction with a single invariant receptor.
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Affiliation(s)
- Raphael Carapito
- ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx TRANSPLANTEX, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,Laboratoire International Associé (LIA) INSERM, Strasbourg (France) - Nagano (Japan), Strasbourg, France.,Fédération Hospitalo-Universitaire (FHU) OMICARE, Strasbourg, France
| | - Seiamak Bahram
- ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx TRANSPLANTEX, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,Laboratoire International Associé (LIA) INSERM, Strasbourg (France) - Nagano (Japan), Strasbourg, France.,Fédération Hospitalo-Universitaire (FHU) OMICARE, Strasbourg, France.,Laboratoire Central d'Immunologie, Pôle de Biologie, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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6
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Nunes JM. Using uniformat and gene[rate] to Analyze Data with Ambiguities in Population Genetics. Evol Bioinform Online 2016; 11:19-26. [PMID: 26917942 PMCID: PMC4762493 DOI: 10.4137/ebo.s32415] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/28/2015] [Accepted: 12/31/2015] [Indexed: 01/13/2023] Open
Abstract
Some genetic systems frequently present ambiguous data that cannot be straightforwardly analyzed with common methods of population genetics. Two possibilities arise to analyze such data: one is the arbitrary simplification of the data and the other is the development of methods adapted to such ambiguous data. In this article, we present an attempt at such a development, the uniformat grammar and The gene[rate] tools, highlighting the specific aspects and the adaptations required to analyze ambiguous nominal data in population genetics.
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Affiliation(s)
- José Manuel Nunes
- Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland
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7
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Varicella-Zoster Virus and Herpes Simplex Virus 1 Differentially Modulate NKG2D Ligand Expression during Productive Infection. J Virol 2015; 89:7932-43. [PMID: 25995251 DOI: 10.1128/jvi.00292-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 05/15/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Natural killer (NK) cell-deficient patients are particularly susceptible to severe infection with herpesviruses, especially varicella-zoster virus (VZV) and herpes simplex virus 1 (HSV-1). The critical role that NK cells play in controlling these infections denotes an intricate struggle for dominance between virus and NK cell antiviral immunity; however, research in this area has remained surprisingly limited. Our study addressed this absence of knowledge and found that infection with VZV was not associated with enhanced NK cell activation, suggesting that the virus uses specific mechanisms to limit NK cell activity. Analysis of viral regulation of ligands for NKG2D, a potent activating receptor ubiquitously expressed on NK cells, revealed that VZV differentially modulates expression of the NKG2D ligands MICA, ULBP2, and ULBP3 by upregulating MICA expression while reducing ULBP2 and ULBP3 expression on the surface of infected cells. Despite being closely related to VZV, infection with HSV-1 produced a remarkably different effect on NKG2D ligand expression. A significant decrease in MICA, ULBP2, and ULBP3 was observed with HSV-1 infection at a total cellular protein level, as well as on the cell surface. We also demonstrate that HSV-1 differentially regulates expression of an additional NKG2D ligand, ULBP1, by reducing cell surface expression while total protein levels are unchanged. Our findings illustrate both a striking point of difference between two closely related alphaherpesviruses, as well as suggest a powerful capacity for VZV and HSV-1 to evade antiviral NK cell activity through novel modulation of NKG2D ligand expression. IMPORTANCE Patients with deficiencies in NK cell function experience an extreme susceptibility to infection with herpesviruses, in particular, VZV and HSV-1. Despite this striking correlation, research into understanding how these two alphaherpesviruses interact with NK cells is surprisingly limited. Through examination of viral regulation of ligands to the activating NK cell receptor NKG2D, we reveal patterns of modulation by VZV, which were unexpectedly varied in response to regulation by HSV-1 infection. Our study begins to unravel the undoubtedly complex interactions that occur between NK cells and alphaherpesvirus infection by providing novel insights into how VZV and HSV-1 manipulate NKG2D ligand expression to modulate NK cell activity, while also illuminating a distinct variation between two closely related alphaherpesviruses.
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Piancatelli D, Oumhani K, Benelbarhdadi I, Del Beato T, Colanardi A, Sebastiani P, Tessitore A, El Aouad R, Essaid A. MICA∗078: A novel allele identified in a Moroccan individual affected by celiac disease. Hum Immunol 2015; 76:438-41. [PMID: 25797203 DOI: 10.1016/j.humimm.2015.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/10/2015] [Accepted: 03/11/2015] [Indexed: 10/23/2022]
Abstract
A novel MICA allele, MICA(∗)078, has been identified during HLA/MICA high resolution typing of Moroccan patients with celiac disease. MICA(∗)078 shows an uncommon variation at a highly conserved nucleotide position (nt 493, G → A), resulting in one amino acid change at codon 142 (V → I) of MICA gene (compared to MICA(∗)002:01), located in the α2-domain, in which V142 is the common residue.
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Affiliation(s)
- Daniela Piancatelli
- National Research Council (CNR), Institute of Translational Pharmacology, U.O.S. L'Aquila, Italy.
| | | | - Imane Benelbarhdadi
- Medicine C, Dep. of Gastroenterology, Ibn Sina Hospital, Mohammed V-Souissi University, Rabat, Morocco
| | - Tiziana Del Beato
- National Research Council (CNR), Institute of Translational Pharmacology, U.O.S. L'Aquila, Italy
| | - Alessia Colanardi
- National Research Council (CNR), Institute of Translational Pharmacology, U.O.S. L'Aquila, Italy
| | - Pierluigi Sebastiani
- National Research Council (CNR), Institute of Translational Pharmacology, U.O.S. L'Aquila, Italy
| | | | - Rajae El Aouad
- Hassan II Academy of Science and Technology, Rabat, Morocco
| | - Abdellah Essaid
- Medicine C, Dep. of Gastroenterology, Ibn Sina Hospital, Mohammed V-Souissi University, Rabat, Morocco
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