101
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Mochel JP, Jergens AE, Kingsbury D, Kim HJ, Martín MG, Allenspach K. Intestinal Stem Cells to Advance Drug Development, Precision, and Regenerative Medicine: A Paradigm Shift in Translational Research. AAPS JOURNAL 2017; 20:17. [PMID: 29234895 PMCID: PMC6044282 DOI: 10.1208/s12248-017-0178-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/21/2017] [Indexed: 12/23/2022]
Abstract
Recent advances in our understanding of the intestinal stem cell niche and the role of key signaling pathways on cell growth and maintenance have allowed the development of fully differentiated epithelial cells in 3D organoids. Stem cell-derived organoids carry significant levels of proteins that are natively expressed in the gut and have important roles in drug transport and metabolism. They are, therefore, particularly relevant to study the gastrointestinal (GI) absorption of oral medications. In addition, organoids have the potential to serve as a robust preclinical model for demonstrating the effectiveness of new drugs more rapidly, with more certainty, and at lower costs compared with live animal studies. Importantly, because they are derived from individuals with different genotypes, environmental risk factors and drug sensitivity profiles, organoids are a highly relevant screening system for personalized therapy in both human and veterinary medicine. Lastly, and in the context of patient-specific congenital diseases, orthotopic transplantation of engineered organoids could repair and/or replace damaged epithelial tissues reported in various GI diseases, such as inflammatory bowel disease, cystic fibrosis, and tuft enteropathy. Ongoing translational research on organoids derived from dogs with naturally occurring digestive disorders has the potential to improve the predictability of preclinical models used for optimizing the therapeutic management of severe chronic enteropathies in human patients.
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Affiliation(s)
- Jonathan P Mochel
- Department of Biomedical Sciences, Iowa State University College of Veterinary Medicine, 2448 Lloyd, 1809 S Riverside Dr., Ames, Iowa, 50011-1250, USA.
| | - Albert E Jergens
- Department of Veterinary Clinical Sciences, Iowa State University College of Veterinary Medicine, 50011-1250 Ames, Iowa, USA
| | - Dawn Kingsbury
- Department of Veterinary Clinical Sciences, Iowa State University College of Veterinary Medicine, 50011-1250 Ames, Iowa, USA
| | - Hyun Jung Kim
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, 78712, USA
| | - Martín G Martín
- Department of Pediatrics, University of California Los Angeles, California, Los Angeles, 90095-1782, USA
| | - Karin Allenspach
- Department of Veterinary Clinical Sciences, Iowa State University College of Veterinary Medicine, 50011-1250 Ames, Iowa, USA
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102
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Iakobachvili N, Peters PJ. Humans in a Dish: The Potential of Organoids in Modeling Immunity and Infectious Diseases. Front Microbiol 2017; 8:2402. [PMID: 29259597 PMCID: PMC5723307 DOI: 10.3389/fmicb.2017.02402] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/20/2017] [Indexed: 12/14/2022] Open
Abstract
For many decades, human infectious diseases have been studied in immortalized cell lines, isolated primary cells from blood and a range of animal hosts. This research has been of fundamental importance in advancing our understanding of host and pathogen responses but remains limited by the absence of multicellular context and inherent differences in animal immune systems that result in altered immune responses. Recent developments in stem cell biology have led to the in vitro growth of organoids that faithfully recapitulate a variety of human tissues including lung, intestine and brain amongst many others. Organoids are derived from human stem cells and retain the genomic background, cellular organization and functionality of their tissue of origin. Thus they have been widely used to characterize stem cell development, numerous cancers and genetic diseases. We believe organoid technology can be harnessed to study host–pathogen interactions resulting in a more physiologically relevant model that yields more predictive data of human infectious diseases than current systems. Here, we highlight recent work and discuss the potential of human stem cell-derived organoids in studying infectious diseases and immunity.
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Affiliation(s)
- Nino Iakobachvili
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Peter J Peters
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
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103
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Starr AE, Deeke SA, Li L, Zhang X, Daoud R, Ryan J, Ning Z, Cheng K, Nguyen LVH, Abou-Samra E, Lavallée-Adam M, Figeys D. Proteomic and Metaproteomic Approaches to Understand Host–Microbe Interactions. Anal Chem 2017; 90:86-109. [DOI: 10.1021/acs.analchem.7b04340] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Amanda E. Starr
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Shelley A. Deeke
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Leyuan Li
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Rachid Daoud
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - James Ryan
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kai Cheng
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Linh V. H. Nguyen
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Elias Abou-Samra
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research, Toronto, Ontario, M5G 1M1, Canada
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104
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Alnabulsi A, Murray GI. Proteomics for early detection of colorectal cancer: recent updates. Expert Rev Proteomics 2017; 15:55-63. [PMID: 29064727 DOI: 10.1080/14789450.2018.1396893] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Colorectal cancer (CRC) is a common type of cancer with a relatively poor survival rate. The survival rate of patients could be improved if CRC is detected early. Biomarkers associated with early stages of tumor development might provide useful tools for the early diagnosis of colorectal cancer. Areas covered: Online searches using PubMed and Google Scholar were performed using keywords and with a focus on recent proteomic studies. The aim of this review is to highlight the need for biomarkers to improve the detection rate of early CRC and provide an overview of proteomic technologies used for biomarker discovery and validation. This review will also discuss recent proteomic studies which focus on identifying biomarkers associated with the early stages of CRC development. Expert commentary: A large number of CRC biomarkers are increasingly being identified by proteomics using diverse approaches. However, the clinical relevance and introduction of these markers into clinical practice cannot be determined without a robust validation process. The size of validation cohorts remains a major limitation in many biomarker studies.
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Affiliation(s)
- Abdo Alnabulsi
- a Pathology, School of Medicine, Medical Sciences and Nutrition , University of Aberdeen , Aberdeen , UK
| | - Graeme I Murray
- a Pathology, School of Medicine, Medical Sciences and Nutrition , University of Aberdeen , Aberdeen , UK
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105
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Latosinska A, Frantzi M, Vlahou A, Merseburger AS, Mischak H. Clinical Proteomics for Precision Medicine: The Bladder Cancer Case. Proteomics Clin Appl 2017; 12. [DOI: 10.1002/prca.201700074] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/10/2017] [Indexed: 12/15/2022]
Affiliation(s)
| | | | - Antonia Vlahou
- Biotechnology Division; Biomedical Research Foundation; Academy of Athens; Athens Greece
| | - Axel S. Merseburger
- Department of Urology; Campus Lübeck; University Hospital Schleswig-Holstein; Lübeck Germany
| | - Harald Mischak
- Mosaiques Diagnostics GmbH; Hannover Germany
- BHF Glasgow Cardiovascular Research Centre; University of Glasgow; Glasgow UK
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106
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Lou YR, Leung AW. Next generation organoids for biomedical research and applications. Biotechnol Adv 2017; 36:132-149. [PMID: 29056474 DOI: 10.1016/j.biotechadv.2017.10.005] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 10/07/2017] [Accepted: 10/16/2017] [Indexed: 12/14/2022]
Abstract
Organoids are in vitro cultures of miniature fetal or adult organ-like structures. Their potentials for use in tissue and organ replacement, disease modeling, toxicology studies, and drug discovery are tremendous. Currently, major challenges facing human organoid technology include (i) improving the range of cellular heterogeneity for a particular organoid system, (ii) mimicking the native micro- and matrix-environment encountered by cells within organoids, and (iii) developing robust protocols for the in vitro maturation of organoids that remain mostly fetal-like in cultures. To tackle these challenges, we advocate the principle of reverse engineering that replicates the inner workings of in vivo systems with the goal of achieving functionality and maturation of the resulting organoid structures with the input of minimal intrinsic (cellular) and environmental (matrix and niche) constituents. Here, we present an overview of organoid technology development in several systems that employ cell materials derived from fetal and adult tissues and pluripotent stem cell cultures. We focus on key studies that exploit the self-organizing property of embryonic progenitors and the role of designer matrices and cell-free scaffolds in assisting organoid formation. We further explore the relationship between adult stem cells, niche factors, and other current developments that aim to enhance robust organoid maturation. From these works, we propose a standardized pipeline for the development of future protocols that would help generate more physiologically relevant human organoids for various biomedical applications.
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Affiliation(s)
- Yan-Ru Lou
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.
| | - Alan W Leung
- Yale Stem Cell Center, Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, United States.
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107
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Abstract
The development of 3D cell cultures into self-organizing organ-like structures named organoids provides a model that better reflects in vivo organ physiology and their functional properties. Organoids have been established from several organs, such as the intestine, prostate, brain, liver, kidney and pancreas. With recent advances in high-throughput and -omics profiling technologies, it is now possible to study the mechanisms of cellular organisation at the systems level. It is therefore not surprising that these methods are now used to characterize organoids at the transcriptomic, proteomic, chromatin state and transcription factor DNA-binding levels. These approaches can therefore provide a wealth of information regarding both the mechanisms involved in different diseases, and those involved in cell responses to different conditions, in a more in vivo setting. The authors provide an overview of the potential applications of quantitative mass spectrometry with organoid culture, and how the use of large-scale proteome measurements is emerging in different organoid systems.
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Affiliation(s)
- Alexis Gonneaud
- Department of Anatomy and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Claude Asselin
- Department of Anatomy and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - François Boudreau
- Department of Anatomy and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
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108
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Abazova N, Krijgsveld J. Advances in stem cell proteomics. Curr Opin Genet Dev 2017; 46:149-155. [PMID: 28806595 DOI: 10.1016/j.gde.2017.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 07/14/2017] [Accepted: 07/20/2017] [Indexed: 12/15/2022]
Abstract
Stem cells are at the basis of organismal development, characterized by their potential to differentiate towards specific lineages upon receiving proper signals. To understand the molecular principles underlying gain and loss of pluripotency, proteomics plays an increasingly important role owing to technical developments in mass spectrometry and implementation of innovative biochemical approaches. Here we review how quantitative proteomics has been used to investigate protein expression, localization, interaction and modification in stem cells both in vitro and in vivo, thereby complementing other omics approaches to study fundamental properties of stem cell plasticity.
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Affiliation(s)
- Nade Abazova
- German Cancer Research Center (DKFZ), Heidelberg, Germany; Excellence Cluster CellNetworks, Heidelberg University, Heidelberg, Germany; European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Heidelberg, Germany; Excellence Cluster CellNetworks, Heidelberg University, Heidelberg, Germany.
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109
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Finnberg NK, Gokare P, Lev A, Grivennikov SI, MacFarlane AW, Campbell KS, Winters RM, Kaputa K, Farma JM, Abbas AES, Grasso L, Nicolaides NC, El-Deiry WS. Application of 3D tumoroid systems to define immune and cytotoxic therapeutic responses based on tumoroid and tissue slice culture molecular signatures. Oncotarget 2017; 8:66747-66757. [PMID: 28977993 PMCID: PMC5620133 DOI: 10.18632/oncotarget.19965] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 07/20/2017] [Indexed: 12/16/2022] Open
Abstract
We have developed 3D-tumoroids and tumor slice in vitro culture systems from surgical tumor specimens derived from patients with colorectal cancer (CRC) or lung cancer to evaluate immune cell populations infiltrating cultured tissues. The system incorporates patient's peripherally and tumor-derived immune cells into tumoroid in vitro cultures to evaluate the ability of the culture to mimic an immunosuppressive tumor microenvironment (ITM). This system enables analysis of tumor response to standard therapy within weeks of surgical resection. Here we show that tumoroid cultures from a CRC patient are highly sensitive to the thymidylate synthase inhibitor 5-fluorouracil (adrucil) but less sensitive to the combination of nucleoside analog trifluridine and thymidine phosphorylase inhibitor tipiracil (Lonsurf). Moreover, re-introduction of isolated immune cells derived from surrounding and infiltrating tumor tissue as well as CD45+ tumor infiltrating hematopoietic cells displayed prolonged (>10 days) survival in co-culture. Established tumor slice cultures were found to contain both an outer epithelial and inner stromal cell compartment mimicking tumor structure in vivo. Collectively, these data suggest that, 3D-tumoroid and slice culture assays may provide a feasible in vitro approach to assess efficacy of novel therapeutics in the context of heterogeneous tumor-associated cell types including immune and non-transformed stromal cells. In addition, delineating the impact of therapeutics on immune cells, and cell types involved in therapeutic resistance mechanisms may be possible in general or for patient-specific responses.
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Affiliation(s)
- Niklas K Finnberg
- Department of Hematology/Oncology and Molecular Therapeutics Program, Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Prashanth Gokare
- Department of Hematology/Oncology and Molecular Therapeutics Program, Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Avital Lev
- Department of Hematology/Oncology and Molecular Therapeutics Program, Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Sergei I Grivennikov
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | | | - Kerry S Campbell
- Division of Basic Science, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Ryan M Winters
- Biosample Repository Facility, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Karen Kaputa
- Biosample Repository Facility, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Jeffrey M Farma
- Division of General Surgery, Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Abbas El-Sayed Abbas
- Division of Thoracic Surgery, Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | | | | | - Wafik S El-Deiry
- Department of Hematology/Oncology and Molecular Therapeutics Program, Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA
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110
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Bartfeld S, Clevers H. Stem cell-derived organoids and their application for medical research and patient treatment. J Mol Med (Berl) 2017; 95:729-738. [PMID: 28391362 DOI: 10.1007/s00109-017-1531-7] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/28/2017] [Accepted: 04/03/2017] [Indexed: 12/14/2022]
Abstract
3D culture has allowed the initiation and expansion of organ-like structures, called organoids, from either tissue-resident adult stem cells or pluripotent stem cells. Today, organoids can be grown to resemble a wide variety of organs, exhibiting remarkable similarity to their in vivo counterparts. As successful organoid generation is possible from virtually every patient, organoids hold a great promise for medical research and the development of new treatments. They have already found their way into the clinic, enabling personalized medicine in small patient trials. In this review, we provide an update on current organoid technology and summarize their application in basic research, disease modelling, drug development, personalized treatment and regenerative medicine.
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Affiliation(s)
- Sina Bartfeld
- Research Center for Infectious Diseases, ZINF, Institute for Molecular Infection Biology, IMIB, University of Würzburg, Josef-Schneider-Str 2/D15, 97080, Würzburg, Germany.
| | - Hans Clevers
- Hubrecht Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.,Princess Máxima Center for Pediatric Oncology, 3584 CT, Utrecht, The Netherlands
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111
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van Ooijen MP, Jong VL, Eijkemans MJC, Heck AJR, Andeweg AC, Binai NA, van den Ham HJ. Identification of differentially expressed peptides in high-throughput proteomics data. Brief Bioinform 2017; 19:971-981. [DOI: 10.1093/bib/bbx031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Indexed: 12/25/2022] Open
Affiliation(s)
| | - Victor L Jong
- Department of Biostatistics and Research Support, Julius Center, UMC Utrecht, Netherlands
| | - Marinus J C Eijkemans
- Julius Center for Health Sciences and Primary Care of the University Medical Center Utrecht, Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Utrecht University, Netherlands
| | - Arno C Andeweg
- Department of Viroscience, Erasmus MC, CA Rotterdam, Netherlands
| | - Nadine A Binai
- Biomolecular Mass Spectrometry Group, Utrecht University, Netherlands
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