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Fadaie M, Khalafiyan A, Ghafouri E, Ranjbarnejad T, Moein S. A Systems Biology Approach to the Pathogenesis of Celiac Disease: Identification of Potential Protective and Promoting Mechanisms. Adv Biomed Res 2024; 13:42. [PMID: 39224401 PMCID: PMC11368239 DOI: 10.4103/abr.abr_229_23] [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: 06/27/2023] [Revised: 01/01/2024] [Accepted: 01/20/2024] [Indexed: 09/04/2024] Open
Abstract
Background Celiac disease (CeD) is an autoimmune enteropathy triggered by dietary gluten. Almost 90% of CeD patients have HLA-DQ2 or -DQ8 haplotypes. As a high proportion of first-degree relatives (FDRs) of CeD patients have the same haplotype, it is assumed that they are at a higher risk of disease development than the general population. Nevertheless, the prevalence of CeD among FDRs is considerably low (7.5%). Materials and Methods In order to figure out this discrepancy, a microarray dataset of intestinal mucosal biopsies of CeD patients, FDRs, and control groups was reanalyzed, and a protein-protein interaction network was constructed. Results Principal component analysis showed that CeD and FDR groups are far away in terms of gene expression. Comparing differentially expressed genes of both networks demonstrated inverse expression of some genes mainly related to cell cycle mechanisms. Moreover, analysis of the modular structures of up- and downregulated gene networks determined activation of protein degradation mechanisms and inhibition of ribosome-related protein synthesis in celiac patients with an upside-down pattern in FDRs. Conclusions The top-down systems biology approach determined some regulatory pathways with inverse function in CeD and FDR groups. These genes and molecular mechanisms could be a matter of investigation as potential druggable targets or prognostic markers in CeD.
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Affiliation(s)
- Mahmood Fadaie
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Anis Khalafiyan
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elham Ghafouri
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Tayebeh Ranjbarnejad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shiva Moein
- Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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González-Castro AM, Fernández-Bañares F, Zabana Y, Farago-Pérez G, Ortega-Barrionuevo J, Expósito E, Guagnozzi D. Microscopic Colitis and Celiac Disease: Sharing More than a Diagnostic Overlap. Nutrients 2024; 16:2233. [PMID: 39064676 PMCID: PMC11279699 DOI: 10.3390/nu16142233] [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: 06/02/2024] [Revised: 07/01/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
Microscopic colitis (MC) is an emergent group of chronic inflammatory diseases of the colon, and celiac disease (CD) is a chronic gluten-induced immune-mediated enteropathy affecting the small bowel. We performed a narrative review to provide an overview regarding the relationship between both disorders, analyzing the most recent studies published at the epidemiological, clinical and pathophysiological levels. In fact, MC and CD are concomitantly prevalent in approximately 6% of the cases, mainly in the subset of refractory patients. Thus, physicians should screen refractory patients with CD against MC and vice versa. Both disorders share more than a simple epidemiological association, being multifactorial diseases involving innate and adaptive immune responses to known or unknown luminal factors based on a rather common genetic ground. Moreover, autoimmunity is a shared characteristic between the patients with MC and those with CD, with autoimmunity in the latter being quite well-established. Furthermore, CD and MC share some common clinical symptoms and risk factors and overlap with other gastrointestinal diseases, but some differences exist between both disorders. More studies are therefore needed to better understand the complex mechanisms involving the common pathogenetic ground contributing to the CD and MC epidemiological association.
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Affiliation(s)
- Ana María González-Castro
- Translational Mucosal Immunology Laboratory, Vall d’Hebron Institut de Recerca, 08035 Barcelona, Spain; (A.M.G.-C.); (E.E.)
- Neuro-Immuno-Gastroenterology Laboratory, Vall d’Hebron Institut de Recerca, 08035 Barcelona, Spain
| | - Fernando Fernández-Bañares
- Gastroenterology Department, University Hospital Mútua Terrassa, 08221 Terrassa, Spain (Y.Z.)
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto Carlos III), 28029 Madrid, Spain
| | - Yamile Zabana
- Gastroenterology Department, University Hospital Mútua Terrassa, 08221 Terrassa, Spain (Y.Z.)
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto Carlos III), 28029 Madrid, Spain
| | - Georgina Farago-Pérez
- Translational Mucosal Immunology Laboratory, Vall d’Hebron Institut de Recerca, 08035 Barcelona, Spain; (A.M.G.-C.); (E.E.)
| | - Jonathan Ortega-Barrionuevo
- Translational Mucosal Immunology Laboratory, Vall d’Hebron Institut de Recerca, 08035 Barcelona, Spain; (A.M.G.-C.); (E.E.)
| | - Elba Expósito
- Translational Mucosal Immunology Laboratory, Vall d’Hebron Institut de Recerca, 08035 Barcelona, Spain; (A.M.G.-C.); (E.E.)
- Neuro-Immuno-Gastroenterology Laboratory, Vall d’Hebron Institut de Recerca, 08035 Barcelona, Spain
| | - Danila Guagnozzi
- Translational Mucosal Immunology Laboratory, Vall d’Hebron Institut de Recerca, 08035 Barcelona, Spain; (A.M.G.-C.); (E.E.)
- Neuro-Immuno-Gastroenterology Laboratory, Vall d’Hebron Institut de Recerca, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto Carlos III), 28029 Madrid, Spain
- Gastroenterology Department, University Hospital Vall d’Hebron, 08035 Barcelona, Spain
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3
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Ugolkov Y, Nikitich A, Leon C, Helmlinger G, Peskov K, Sokolov V, Volkova A. Mathematical modeling in autoimmune diseases: from theory to clinical application. Front Immunol 2024; 15:1371620. [PMID: 38550585 PMCID: PMC10973044 DOI: 10.3389/fimmu.2024.1371620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/29/2024] [Indexed: 04/02/2024] Open
Abstract
The research & development (R&D) of novel therapeutic agents for the treatment of autoimmune diseases is challenged by highly complex pathogenesis and multiple etiologies of these conditions. The number of targeted therapies available on the market is limited, whereas the prevalence of autoimmune conditions in the global population continues to rise. Mathematical modeling of biological systems is an essential tool which may be applied in support of decision-making across R&D drug programs to improve the probability of success in the development of novel medicines. Over the past decades, multiple models of autoimmune diseases have been developed. Models differ in the spectra of quantitative data used in their development and mathematical methods, as well as in the level of "mechanistic granularity" chosen to describe the underlying biology. Yet, all models strive towards the same goal: to quantitatively describe various aspects of the immune response. The aim of this review was to conduct a systematic review and analysis of mathematical models of autoimmune diseases focused on the mechanistic description of the immune system, to consolidate existing quantitative knowledge on autoimmune processes, and to outline potential directions of interest for future model-based analyses. Following a systematic literature review, 38 models describing the onset, progression, and/or the effect of treatment in 13 systemic and organ-specific autoimmune conditions were identified, most models developed for inflammatory bowel disease, multiple sclerosis, and lupus (5 models each). ≥70% of the models were developed as nonlinear systems of ordinary differential equations, others - as partial differential equations, integro-differential equations, Boolean networks, or probabilistic models. Despite covering a relatively wide range of diseases, most models described the same components of the immune system, such as T-cell response, cytokine influence, or the involvement of macrophages in autoimmune processes. All models were thoroughly analyzed with an emphasis on assumptions, limitations, and their potential applications in the development of novel medicines.
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Affiliation(s)
- Yaroslav Ugolkov
- Research Center of Model-Informed Drug Development, Ivan Mikhaylovich (I.M.) Sechenov First Moscow State Medical University, Moscow, Russia
- Marchuk Institute of Numerical Mathematics of the Russian Academy of Sciences (RAS), Moscow, Russia
| | - Antonina Nikitich
- Research Center of Model-Informed Drug Development, Ivan Mikhaylovich (I.M.) Sechenov First Moscow State Medical University, Moscow, Russia
- Marchuk Institute of Numerical Mathematics of the Russian Academy of Sciences (RAS), Moscow, Russia
| | - Cristina Leon
- Modeling and Simulation Decisions FZ - LLC, Dubai, United Arab Emirates
| | | | - Kirill Peskov
- Research Center of Model-Informed Drug Development, Ivan Mikhaylovich (I.M.) Sechenov First Moscow State Medical University, Moscow, Russia
- Marchuk Institute of Numerical Mathematics of the Russian Academy of Sciences (RAS), Moscow, Russia
- Modeling and Simulation Decisions FZ - LLC, Dubai, United Arab Emirates
- Sirius University of Science and Technology, Sirius, Russia
| | - Victor Sokolov
- Marchuk Institute of Numerical Mathematics of the Russian Academy of Sciences (RAS), Moscow, Russia
- Modeling and Simulation Decisions FZ - LLC, Dubai, United Arab Emirates
| | - Alina Volkova
- Marchuk Institute of Numerical Mathematics of the Russian Academy of Sciences (RAS), Moscow, Russia
- Modeling and Simulation Decisions FZ - LLC, Dubai, United Arab Emirates
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Leonov V, Mogilevskaya E, Gerasimuk E, Gizzatkulov N, Demin O. CYTOCON: The manually curated database of human in vivo cell and molecule concentrations. CPT Pharmacometrics Syst Pharmacol 2022; 12:41-49. [PMID: 36128761 PMCID: PMC9835118 DOI: 10.1002/psp4.12867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/08/2022] [Accepted: 09/05/2022] [Indexed: 01/19/2023] Open
Abstract
Cell and cYTOkine CONcentrations DataBase (CYTOCON DB) is a project undertaken by the InSysBio team and aimed at the development of a database that allows collecting, processing, and visualizing publicly available in vivo human data on baseline concentrations of cells, cytokines, chemokines, and other molecules. Besides manual curation, an important feature of CYTOCON is that most values found in papers are converted from a huge variety of original units (i.e., mg/ml and number of cells per mm2 of biopsy surface section) to unified units: "pM" for cytokine and "kcell/L" for cell concentration. These features of the database can help researchers facilitate the creation and calibration of quantitative systems pharmacology (QSP) models. Possible applications can be: estimation of the average value or variability of the cell, cytokine or chemokine concentrations for patient groups with different characteristics, such as age, gender, disease severity, disease subtype, etc.; and analysis of correlations among the cell, cytokine, or chemokine concentrations in patients with different characteristics, such as severity of the disease.
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Affiliation(s)
| | | | | | | | - Oleg Demin
- INSYSBIO UK LTD.EdinburghUK,INSYSBIO LLCMoscowRussia
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5
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Bai JPF, Schmidt BJ, Gadkar KG, Damian V, Earp JC, Friedrich C, van der Graaf PH, Madabushi R, Musante CJ, Naik K, Rogge M, Zhu H. FDA-Industry Scientific Exchange on assessing quantitative systems pharmacology models in clinical drug development: a meeting report, summary of challenges/gaps, and future perspective. AAPS JOURNAL 2021; 23:60. [PMID: 33931790 DOI: 10.1208/s12248-021-00585-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/23/2021] [Indexed: 02/07/2023]
Abstract
The pharmaceutical industry is actively applying quantitative systems pharmacology (QSP) to make internal decisions and guide drug development. To facilitate the eventual development of a common framework for assessing the credibility of QSP models for clinical drug development, scientists from US Food and Drug Administration and the pharmaceutical industry organized a full-day virtual Scientific Exchange on July 1, 2020. An assessment form was used to ensure consistency in the evaluation process. Among the cases presented, QSP was applied to various therapeutic areas. Applications mostly focused on phase 2 dose selection. Model transparency, including details on expert knowledge and data used for model development, was identified as a major factor for robust model assessment. The case studies demonstrated some commonalities in the workflow of QSP model development, calibration, and validation but differ in the size, scope, and complexity of QSP models, in the acceptance criteria for model calibration and validation, and in the algorithms/approaches used for creating virtual patient populations. Though efforts are being made to build the credibility of QSP models and the confidence is increasing in applying QSP for internal decisions at the clinical stages of drug development, there are still many challenges facing QSP application to late stage drug development. The QSP community needs a strategic plan that includes the ability and flexibility to Adapt, to establish Common expectations for model Credibility needed to inform drug Labeling and patient care, and to AIM to achieve the goal (ACCLAIM).
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Affiliation(s)
- Jane P F Bai
- Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, 20903, USA.
| | - Brian J Schmidt
- Quantitative Clinical Pharmacology, Bristol Myers Squibb, Princeton, New Jersey, USA.
| | - Kapil G Gadkar
- Development Sciences, Genentech Inc., South San Francisco, California, 94080, USA. .,Denali Therapeutics, San Francisco, California, USA.
| | - Valeriu Damian
- GSK R&D - Upper Providence, 1250 S Collegeville Rd, Collegeville, Pennsylvania, 19426, USA
| | - Justin C Earp
- Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, 20903, USA
| | | | - Piet H van der Graaf
- Certara, Canterbury, CT2 7FG, UK.,Leiden Academic Centre for Drug Research, Leiden, 2333, CC, the Netherlands
| | - Rajanikanth Madabushi
- Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, 20903, USA
| | - Cynthia J Musante
- Early Clinical Development, Pfizer Worldwide Research, Development, & Medical, 1 Portland Street, Cambridge, Massachusetts, 02139, USA
| | - Kunal Naik
- Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, 20903, USA
| | - Mark Rogge
- Quantitative Translational Science, Takeda Pharmaceuticals International Co, 40 Landsdowne Street, Cambridge, Massachusetts, 02139, USA
| | - Hao Zhu
- Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, 20903, USA
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Helmlinger G, Sokolov V, Peskov K, Hallow KM, Kosinsky Y, Voronova V, Chu L, Yakovleva T, Azarov I, Kaschek D, Dolgun A, Schmidt H, Boulton DW, Penland RC. Quantitative Systems Pharmacology: An Exemplar Model-Building Workflow With Applications in Cardiovascular, Metabolic, and Oncology Drug Development. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2019; 8:380-395. [PMID: 31087533 PMCID: PMC6617832 DOI: 10.1002/psp4.12426] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/03/2019] [Indexed: 12/13/2022]
Abstract
Quantitative systems pharmacology (QSP), a mechanistically oriented form of drug and disease modeling, seeks to address a diverse set of problems in the discovery and development of therapies. These problems bring a considerable amount of variability and uncertainty inherent in the nonclinical and clinical data. Likewise, the available modeling techniques and related software tools are manifold. Appropriately, the development, qualification, application, and impact of QSP models have been similarly varied. In this review, we describe the progressive maturation of a QSP modeling workflow: a necessary step for the efficient, reproducible development and qualification of QSP models, which themselves are highly iterative and evolutive. Furthermore, we describe three applications of QSP to impact drug development; one supporting new indications for an approved antidiabetic clinical asset through mechanistic hypothesis generation, one highlighting efficacy and safety differentiation within the sodium‐glucose cotransporter‐2 inhibitor drug class, and one enabling rational selection of immuno‐oncology drug combinations.
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Affiliation(s)
- Gabriel Helmlinger
- Quantitative Clinical Pharmacology, Early Clinical Development, IMED Biotech Unit, AstraZeneca Pharmaceuticals, Boston, Massachusetts, USA
| | | | - Kirill Peskov
- M&S Decisions LLC, Moscow, Russia.,Computational Oncology Group, I.M. Sechenov First Moscow State Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Karen M Hallow
- School of Chemical, Materials, and Biomedical Engineering, University of Georgia, Athens, Georgia, USA.,Department of Epidemiology and Biostatistics, University of Georgia, Athens, Georgia, USA
| | | | | | - Lulu Chu
- Quantitative Clinical Pharmacology, Early Clinical Development, IMED Biotech Unit, AstraZeneca Pharmaceuticals, Boston, Massachusetts, USA
| | | | | | | | | | | | - David W Boulton
- Quantitative Clinical Pharmacology, Early Clinical Development, IMED Biotech Unit, AstraZeneca Pharmaceuticals, Gaithersburg, Maryland, USA
| | - Robert C Penland
- Quantitative Clinical Pharmacology, Early Clinical Development, IMED Biotech Unit, AstraZeneca Pharmaceuticals, Boston, Massachusetts, USA
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Agarwal S, Kovilam O, Zach TL, Agrawal DK. Immunopathogenesis and therapeutic approaches in pediatric celiac disease. Expert Rev Clin Immunol 2016; 12:857-69. [PMID: 26999328 PMCID: PMC4975578 DOI: 10.1586/1744666x.2016.1168294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/16/2016] [Indexed: 01/06/2023]
Abstract
Celiac Disease is an autoimmune enteropathy with increasing incidence worldwide in both adults and children. It occurs as an inflammatory condition with destruction of the normal architecture of villi on consumption of gluten and related protein products found in wheat, barley and rye. However, the exact pathogenesis is not yet fully understood. A gluten-free diet remains the main modality of therapy to date. While some patients continue to have symptoms even on a gluten-free diet, adherence to this diet is also difficult, especially for the children. Hence, there is continued interest in novel methods of therapy and the current research focus is on the promising novel non-dietary modalities of treatment. Here, we critically reviewed the existing literature regarding the pathogenesis of celiac disease in children including the role of in-utero exposure leading to neonatal and infant sensitization and its application for the development of new therapeutic approaches for these patients.
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Affiliation(s)
- Shreya Agarwal
- Department of Clinical & Translational Science, Creighton University School of Medicine, Omaha, NE, USA
| | - Oormila Kovilam
- Department of Obstetrics and Gynecology, Creighton University School of Medicine, Omaha, NE, USA
| | - Terence L. Zach
- Department of Pediatrics, Creighton University School of Medicine, Omaha, NE, USA
| | - Devendra K. Agrawal
- Department of Clinical & Translational Science, Creighton University School of Medicine, Omaha, NE, USA
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Khaleghi S, Ju JM, Lamba A, Murray JA. The potential utility of tight junction regulation in celiac disease: focus on larazotide acetate. Therap Adv Gastroenterol 2016; 9:37-49. [PMID: 26770266 PMCID: PMC4699279 DOI: 10.1177/1756283x15616576] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Celiac disease (CD) is a common chronic immune disease triggered by gluten. Gliadin peptides pass through the epithelial layers, either paracellularly or transcellularly, to launch a potent adaptive immune response in the lamina propria. This aberrant immune response leads to diverse gastrointestinal and extra-gastrointestinal symptoms. Currently, the only treatment for CD is a strict lifelong adherence to a gluten-free diet (GFD), which can be challenging. An early effect of gluten in CD is an increase in gut permeability. Larazotide acetate, also known as AT-1001, is a synthetic peptide developed as a permeability regulator primarily targeting CD. In vitro studies indicate that larazotide acetate is capable of inhibiting the actin rearrangement caused by gliadin and clinical studies have been conducted using this peptide as a therapy for CD.
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Affiliation(s)
- Shahryar Khaleghi
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 1st St SW, Rochester, MN 55905, USA
| | - Josephine M. Ju
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 1st St SW, Rochester, MN 55905, USA
| | - Abhinav Lamba
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 1st St SW, Rochester, MN 55905, USA
| | - Joseph A. Murray
- Professor of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, 200 1st St SW, Rochester, MN 55905, USA
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