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Kuijpers L, Hornung B, van den Hout-van Vroonhoven MCGN, van IJcken WFJ, Grosveld F, Mulugeta E. Split Pool Ligation-based Single-cell Transcriptome sequencing (SPLiT-seq) data processing pipeline comparison. BMC Genomics 2024; 25:361. [PMID: 38609853 PMCID: PMC11010347 DOI: 10.1186/s12864-024-10285-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Single-cell sequencing techniques are revolutionizing every field of biology by providing the ability to measure the abundance of biological molecules at a single-cell resolution. Although single-cell sequencing approaches have been developed for several molecular modalities, single-cell transcriptome sequencing is the most prevalent and widely applied technique. SPLiT-seq (split-pool ligation-based transcriptome sequencing) is one of these single-cell transcriptome techniques that applies a unique combinatorial-barcoding approach by splitting and pooling cells into multi-well plates containing barcodes. This unique approach required the development of dedicated computational tools to preprocess the data and extract the count matrices. Here we compare eight bioinformatic pipelines (alevin-fry splitp, LR-splitpipe, SCSit, splitpipe, splitpipeline, SPLiTseq-demultiplex, STARsolo and zUMI) that have been developed to process SPLiT-seq data. We provide an overview of the tools, their computational performance, functionality and impact on downstream processing of the single-cell data, which vary greatly depending on the tool used. RESULTS We show that STARsolo, splitpipe and alevin-fry splitp can all handle large amount of data within reasonable time. In contrast, the other five pipelines are slow when handling large datasets. When using smaller dataset, cell barcode results are similar with the exception of SPLiTseq-demultiplex and splitpipeline. LR-splitpipe that is originally designed for processing long-read sequencing data is the slowest of all pipelines. Alevin-fry produced different down-stream results that are difficult to interpret. STARsolo functions nearly identical to splitpipe and produce results that are highly similar to each other. However, STARsolo lacks the function to collapse random hexamer reads for which some additional coding is required. CONCLUSION Our comprehensive comparative analysis aids users in selecting the most suitable analysis tool for efficient SPLiT-seq data processing, while also detailing the specific prerequisites for each of these pipelines. From the available pipelines, we recommend splitpipe or STARSolo for SPLiT-seq data analysis.
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Affiliation(s)
- Lucas Kuijpers
- Department of Cell Biology, Erasmus University Medical Center Rotterdam (Erasmus MC), Wytemaweg 80, Rotterdam, 3015CN, The Netherlands.
| | - Bastian Hornung
- Center for Biomics, Erasmus University Medical Center Rotterdam (Erasmus MC), Rotterdam, The Netherlands
| | | | - Wilfred F J van IJcken
- Center for Biomics, Erasmus University Medical Center Rotterdam (Erasmus MC), Rotterdam, The Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus University Medical Center Rotterdam (Erasmus MC), Wytemaweg 80, Rotterdam, 3015CN, The Netherlands
| | - Eskeatnaf Mulugeta
- Department of Cell Biology, Erasmus University Medical Center Rotterdam (Erasmus MC), Wytemaweg 80, Rotterdam, 3015CN, The Netherlands.
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2
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Kaiser FK, Hernandez MG, Krüger N, Englund E, Du W, Mykytyn AZ, Raadsen MP, Lamers MM, Rodrigues Ianiski F, Shamorkina TM, Snijder J, Armando F, Beythien G, Ciurkiewicz M, Schreiner T, Gruber-Dujardin E, Bleyer M, Batura O, Erffmeier L, Hinkel R, Rocha C, Mirolo M, Drabek D, Bosch BJ, Emalfarb M, Valbuena N, Tchelet R, Baumgärtner W, Saloheimo M, Pöhlmann S, Grosveld F, Haagmans BL, Osterhaus ADME. Filamentous fungus-produced human monoclonal antibody provides protection against SARS-CoV-2 in hamster and non-human primate models. Nat Commun 2024; 15:2319. [PMID: 38485931 PMCID: PMC10940701 DOI: 10.1038/s41467-024-46443-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024] Open
Abstract
Monoclonal antibodies are an increasingly important tool for prophylaxis and treatment of acute virus infections like SARS-CoV-2 infection. However, their use is often restricted due to the time required for development, variable yields and high production costs, as well as the need for adaptation to newly emerging virus variants. Here we use the genetically modified filamentous fungus expression system Thermothelomyces heterothallica (C1), which has a naturally high biosynthesis capacity for secretory enzymes and other proteins, to produce a human monoclonal IgG1 antibody (HuMab 87G7) that neutralises the SARS-CoV-2 variants of concern (VOCs) Alpha, Beta, Gamma, Delta, and Omicron. Both the mammalian cell and C1 produced HuMab 87G7 broadly neutralise SARS-CoV-2 VOCs in vitro and also provide protection against VOC Omicron in hamsters. The C1 produced HuMab 87G7 is also able to protect against the Delta VOC in non-human primates. In summary, these findings show that the C1 expression system is a promising technology platform for the development of HuMabs in preventive and therapeutic medicine.
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Affiliation(s)
- Franziska K Kaiser
- Research Center for Emerging Infections and Zoonosis, University of Veterinary Medicine, Foundation, Hannover, Germany
| | - Mariana Gonzalez Hernandez
- Research Center for Emerging Infections and Zoonosis, University of Veterinary Medicine, Foundation, Hannover, Germany
| | - Nadine Krüger
- German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
| | - Ellinor Englund
- VTT Technical Research Centre of Finland Ltd, 02150, Espoo, Finland
| | - Wenjuan Du
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Anna Z Mykytyn
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mathijs P Raadsen
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mart M Lamers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Francine Rodrigues Ianiski
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Tatiana M Shamorkina
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Federico Armando
- Department of Pathology, University of Veterinary Medicine, Foundation, Hannover, Germany
| | - Georg Beythien
- Department of Pathology, University of Veterinary Medicine, Foundation, Hannover, Germany
| | - Malgorzata Ciurkiewicz
- Department of Pathology, University of Veterinary Medicine, Foundation, Hannover, Germany
| | - Tom Schreiner
- Department of Pathology, University of Veterinary Medicine, Foundation, Hannover, Germany
| | - Eva Gruber-Dujardin
- German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
| | - Martina Bleyer
- German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
| | - Olga Batura
- German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
| | - Lena Erffmeier
- German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
| | - Rabea Hinkel
- German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
| | - Cheila Rocha
- German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
| | - Monica Mirolo
- Research Center for Emerging Infections and Zoonosis, University of Veterinary Medicine, Foundation, Hannover, Germany
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands and Harbour BioMed, Rotterdam, the Netherlands
| | - Berend-Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | | | | | | | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine, Foundation, Hannover, Germany
| | - Markku Saloheimo
- VTT Technical Research Centre of Finland Ltd, 02150, Espoo, Finland
| | - Stefan Pöhlmann
- German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands and Harbour BioMed, Rotterdam, the Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands.
| | - Albert D M E Osterhaus
- Research Center for Emerging Infections and Zoonosis, University of Veterinary Medicine, Foundation, Hannover, Germany.
- Global Virus Network, Baltimore, MD, 21201, USA.
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3
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Slagboom J, Lewis AH, Schouten WM, van Haperen R, Veltman M, Bittenbinder MA, Vonk FJ, Casewell NR, Grosveld F, Drabek D, Kool J. High throughput identification of human monoclonal antibodies and heavy-chain-only antibodies to treat snakebite. Toxicon X 2024; 21:100185. [PMID: 38425752 PMCID: PMC10901844 DOI: 10.1016/j.toxcx.2024.100185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 12/12/2023] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Snakebite envenoming is a priority Neglected Tropical Disease that causes an estimated 81,000-135,000 fatalities each year. The development of a new generation of safer, affordable, and accessible antivenom therapies is urgently needed. With this goal in mind, rigorous characterisation of the specific toxins in snake venom is key to generating novel therapies for snakebite. Monoclonal antibodies directed against venom toxins are emerging as potentially strong candidates in the development of new snakebite diagnostics and treatment. Venoms comprise many different toxins of which several are responsible for their pathological effects. Due to the large variability of venoms within and between species, formulations of combinations of human antibodies are proposed as the next generation antivenoms. Here a high-throughput screening method employing antibody-based ligand fishing of venom toxins in 384 filter-well plate format has been developed to determine the antibody target/s The approach uses Protein G beads for antibody capture followed by exposure to a full venom or purified toxins to bind their respective ligand toxin(s). This is followed by a washing/centrifugation step to remove non-binding toxins and an in-well tryptic digest. Finally, peptides from each well are analysed by nanoLC-MS/MS and subsequent Mascot database searching to identify the bound toxin/s for each antibody under investigation. The approach was successfully validated to rapidly screen antibodies sourced from hybridomas, derived from venom-immunised mice expressing either regular human antibodies or heavy-chain-only human antibodies (HCAbs).
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Affiliation(s)
- Julien Slagboom
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081HV, the Netherlands
| | - Abigail H. Lewis
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081HV, the Netherlands
| | - Wietse M. Schouten
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081HV, the Netherlands
| | - Rien van Haperen
- Department of Cell Biology and Genetics, Faculty of Medicine, Erasmus Medical Center Rotterdam, 3000 DR, Rotterdam, the Netherlands
- Harbour BioMed, Erasmus Medical Center Rotterdam, 3000 DR, Rotterdam, the Netherlands
| | - Mieke Veltman
- Department of Cell Biology and Genetics, Faculty of Medicine, Erasmus Medical Center Rotterdam, 3000 DR, Rotterdam, the Netherlands
- Harbour BioMed, Erasmus Medical Center Rotterdam, 3000 DR, Rotterdam, the Netherlands
| | - Mátyás A. Bittenbinder
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081HV, the Netherlands
- Naturalis Biodiversity Center, 2333 CR, Leiden, the Netherlands
| | - Freek J. Vonk
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081HV, the Netherlands
- Naturalis Biodiversity Center, 2333 CR, Leiden, the Netherlands
| | - Nicholas R. Casewell
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Frank Grosveld
- Department of Cell Biology and Genetics, Faculty of Medicine, Erasmus Medical Center Rotterdam, 3000 DR, Rotterdam, the Netherlands
- Harbour BioMed, Erasmus Medical Center Rotterdam, 3000 DR, Rotterdam, the Netherlands
| | - Dubravka Drabek
- Department of Cell Biology and Genetics, Faculty of Medicine, Erasmus Medical Center Rotterdam, 3000 DR, Rotterdam, the Netherlands
- Harbour BioMed, Erasmus Medical Center Rotterdam, 3000 DR, Rotterdam, the Netherlands
| | - Jeroen Kool
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081HV, the Netherlands
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van Staalduinen J, van Staveren T, Grosveld F, Wendt KS. Live-cell imaging of chromatin contacts opens a new window into chromatin dynamics. Epigenetics Chromatin 2023; 16:27. [PMID: 37349773 PMCID: PMC10288748 DOI: 10.1186/s13072-023-00503-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023] Open
Abstract
Our understanding of the organization of the chromatin fiber within the cell nucleus has made great progress in the last few years. High-resolution techniques based on next-generation sequencing as well as optical imaging that can investigate chromatin conformations down to the single cell level have revealed that chromatin structure is highly heterogeneous at the level of the individual allele. While TAD boundaries and enhancer-promoter pairs emerge as hotspots of 3D proximity, the spatiotemporal dynamics of these different types of chromatin contacts remain largely unexplored. Investigation of chromatin contacts in live single cells is necessary to close this knowledge gap and further enhance the current models of 3D genome organization and enhancer-promoter communication. In this review, we first discuss the potential of single locus labeling to study architectural and enhancer-promoter contacts and provide an overview of the available single locus labeling techniques such as FROS, TALE, CRISPR-dCas9 and ANCHOR, and discuss the latest developments and applications of these systems.
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Affiliation(s)
- Jente van Staalduinen
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands
| | - Thomas van Staveren
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands
| | - Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands.
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5
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Du W, Janssens R, Mykytyn AZ, Li W, Drabek D, van Haperen R, Chatziandreou M, Rissmann M, van der Lee J, van Dortmondt M, Martin IS, van Kuppeveld FJM, Hurdiss DL, Haagmans BL, Grosveld F, Bosch BJ. Avidity engineering of human heavy-chain-only antibodies mitigates neutralization resistance of SARS-CoV-2 variants. Front Immunol 2023; 14:1111385. [PMID: 36895554 PMCID: PMC9990171 DOI: 10.3389/fimmu.2023.1111385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/31/2023] [Indexed: 02/23/2023] Open
Abstract
Emerging SARS-CoV-2 variants have accrued mutations within the spike protein rendering most therapeutic monoclonal antibodies against COVID-19 ineffective. Hence there is an unmet need for broad-spectrum mAb treatments for COVID-19 that are more resistant to antigenically drifted SARS-CoV-2 variants. Here we describe the design of a biparatopic heavy-chain-only antibody consisting of six antigen binding sites recognizing two distinct epitopes in the spike protein NTD and RBD. The hexavalent antibody showed potent neutralizing activity against SARS-CoV-2 and variants of concern, including the Omicron sub-lineages BA.1, BA.2, BA.4 and BA.5, whereas the parental components had lost Omicron neutralization potency. We demonstrate that the tethered design mitigates the substantial decrease in spike trimer affinity seen for escape mutations for the hexamer components. The hexavalent antibody protected against SARS-CoV-2 infection in a hamster model. This work provides a framework for designing therapeutic antibodies to overcome antibody neutralization escape of emerging SARS-CoV-2 variants.
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Affiliation(s)
- Wenjuan Du
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Rick Janssens
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands.,Harbour BioMed, Rotterdam, Netherlands
| | - Anna Z Mykytyn
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Wentao Li
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands.,Harbour BioMed, Rotterdam, Netherlands
| | - Rien van Haperen
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands.,Harbour BioMed, Rotterdam, Netherlands
| | - Marianthi Chatziandreou
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Melanie Rissmann
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Joline van der Lee
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Melissa van Dortmondt
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Itziar Serna Martin
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Frank J M van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Daniel L Hurdiss
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands.,Harbour BioMed, Rotterdam, Netherlands
| | - Berend-Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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6
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Cruz LJ, Rezaei S, Grosveld F, Philipsen S, Eich C. Nanoparticles targeting hematopoietic stem and progenitor cells: Multimodal carriers for the treatment of hematological diseases. Front Genome Ed 2022; 4:1030285. [PMID: 36407494 PMCID: PMC9666682 DOI: 10.3389/fgeed.2022.1030285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/10/2022] [Indexed: 10/03/2023] Open
Abstract
Modern-day hematopoietic stem cell (HSC) therapies, such as gene therapy, modify autologous HSCs prior to re-infusion into myelo-conditioned patients and hold great promise for treatment of hematological disorders. While this approach has been successful in numerous clinical trials, it relies on transplantation of ex vivo modified patient HSCs, which presents several limitations. It is a costly and time-consuming procedure, which includes only few patients so far, and ex vivo culturing negatively impacts on the viability and stem cell-properties of HSCs. If viral vectors are used, this carries the additional risk of insertional mutagenesis. A therapy delivered to HSCs in vivo, with minimal disturbance of the HSC niche, could offer great opportunities for novel treatments that aim to reverse disease symptoms for hematopoietic disorders and could bring safe, effective and affordable genetic therapies to all parts of the world. However, substantial unmet needs exist with respect to the in vivo delivery of therapeutics to HSCs. In the last decade, in particular with the development of gene editing technologies such as CRISPR/Cas9, nanoparticles (NPs) have become an emerging platform to facilitate the manipulation of cells and organs. By employing surface modification strategies, different types of NPs can be designed to target specific tissues and cell types in vivo. HSCs are particularly difficult to target due to the lack of unique cell surface markers that can be utilized for cell-specific delivery of therapeutics, and their shielded localization in the bone marrow (BM). Recent advances in NP technology and genetic engineering have resulted in the development of advanced nanocarriers that can deliver therapeutics and imaging agents to hematopoietic stem- and progenitor cells (HSPCs) in the BM niche. In this review we provide a comprehensive overview of NP-based approaches targeting HSPCs to control and monitor HSPC activity in vitro and in vivo, and we discuss the potential of NPs for the treatment of malignant and non-malignant hematological disorders, with a specific focus on the delivery of gene editing tools.
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Affiliation(s)
- Luis J. Cruz
- Translational Nanobiomaterials and Imaging, Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | - Somayeh Rezaei
- Translational Nanobiomaterials and Imaging, Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | - Frank Grosveld
- Erasmus University Medical Center, Department of Cell Biology, Rotterdam, Netherlands
| | - Sjaak Philipsen
- Erasmus University Medical Center, Department of Cell Biology, Rotterdam, Netherlands
| | - Christina Eich
- Translational Nanobiomaterials and Imaging, Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
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7
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Du W, Hurdiss DL, Drabek D, Mykytyn AZ, Kaiser FK, González-Hernández M, Muñoz-Santos D, Lamers MM, van Haperen R, Li W, Drulyte I, Wang C, Sola I, Armando F, Beythien G, Ciurkiewicz M, Baumgärtner W, Guilfoyle K, Smits T, van der Lee J, van Kuppeveld FJM, van Amerongen G, Haagmans BL, Enjuanes L, Osterhaus ADME, Grosveld F, Bosch BJ. An ACE2-blocking antibody confers broad neutralization and protection against Omicron and other SARS-CoV-2 variants of concern. Sci Immunol 2022; 7:eabp9312. [PMID: 35471062 DOI: 10.1101/2022.02.17.480751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The ongoing evolution of SARS-CoV-2 has resulted in the emergence of Omicron, which displays notable immune escape potential through mutations at key antigenic sites on the spike protein. Many of these mutations localize to the spike protein ACE2 receptor binding domain, annulling the neutralizing activity of therapeutic antibodies that were effective against other variants of concern (VOCs) earlier in the pandemic. Here, we identified a receptor-blocking human monoclonal antibody, 87G7, that retained potent in vitro neutralizing activity against SARS-CoV-2 variants including the Alpha, Beta, Gamma, Delta, and Omicron (BA.1/BA.2) VOCs. Using cryo-electron microscopy and site-directed mutagenesis experiments, we showed that 87G7 targets a patch of hydrophobic residues in the ACE2-binding site that are highly conserved in SARS-CoV-2 variants, explaining its broad neutralization capacity. 87G7 protected mice and hamsters prophylactically against challenge with all current SARS-CoV-2 VOCs and showed therapeutic activity against SARS-CoV-2 challenge in both animal models. Our findings demonstrate that 87G7 holds promise as a prophylactic or therapeutic agent for COVID-19 that is more resilient to SARS-CoV-2 antigenic diversity.
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Affiliation(s)
- Wenjuan Du
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Daniel L Hurdiss
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands
- Harbour BioMed, Rotterdam, Netherlands
| | - Anna Z Mykytyn
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Franziska K Kaiser
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Mariana González-Hernández
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Diego Muñoz-Santos
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Mart M Lamers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Rien van Haperen
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands
- Harbour BioMed, Rotterdam, Netherlands
| | - Wentao Li
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Ieva Drulyte
- Thermo Fisher Scientific, Materials and Structural Analysis, Eindhoven, Netherlands
| | - Chunyan Wang
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Isabel Sola
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Federico Armando
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Georg Beythien
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Malgorzata Ciurkiewicz
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | | | - Tony Smits
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Joline van der Lee
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Frank J M van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | | | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Albert D M E Osterhaus
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Global Virus Network, Center of Excellence, Baltimore, MD, USA
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands
- Harbour BioMed, Rotterdam, Netherlands
| | - Berend-Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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8
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Wang C, Hesketh EL, Shamorkina TM, Li W, Franken PJ, Drabek D, van Haperen R, Townend S, van Kuppeveld FJM, Grosveld F, Ranson NA, Snijder J, de Groot RJ, Hurdiss DL, Bosch BJ. Antigenic structure of the human coronavirus OC43 spike reveals exposed and occluded neutralizing epitopes. Nat Commun 2022; 13:2921. [PMID: 35614127 PMCID: PMC9132891 DOI: 10.1038/s41467-022-30658-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/09/2022] [Indexed: 12/14/2022] Open
Abstract
Human coronavirus OC43 is a globally circulating common cold virus sustained by recurrent reinfections. How it persists in the population and defies existing herd immunity is unknown. Here we focus on viral glycoprotein S, the target for neutralizing antibodies, and provide an in-depth analysis of its antigenic structure. Neutralizing antibodies are directed to the sialoglycan-receptor binding site in S1A domain, but, remarkably, also to S1B. The latter block infection yet do not prevent sialoglycan binding. While two distinct neutralizing S1B epitopes are readily accessible in the prefusion S trimer, other sites are occluded such that their accessibility must be subject to conformational changes in S during cell-entry. While non-neutralizing antibodies were broadly reactive against a collection of natural OC43 variants, neutralizing antibodies generally displayed restricted binding breadth. Our data provide a structure-based understanding of protective immunity and adaptive evolution for this endemic coronavirus which emerged in humans long before SARS-CoV-2. Human coronavirus OC43 causes respiratory disease and is maintained in the human population through recurring infections. Here, by extensive structural analyses, the authors provide insights into the binding sites and breadth of neutralizing antibodies against this endemic coronavirus.
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Affiliation(s)
- Chunyan Wang
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Emma L Hesketh
- Astbury Centre Structural Molecular Biology, School Molecular and Cellular Biology, Faculty Biological Sciences, University of Leeds, Leeds, UK
| | - Tatiana M Shamorkina
- Biomolecular Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Wentao Li
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P.R. China
| | - Peter J Franken
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands.,Harbour BioMed, Rotterdam, The Netherlands
| | - Rien van Haperen
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands.,Harbour BioMed, Rotterdam, The Netherlands
| | - Sarah Townend
- Astbury Centre Structural Molecular Biology, School Molecular and Cellular Biology, Faculty Biological Sciences, University of Leeds, Leeds, UK
| | - Frank J M van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands.,Harbour BioMed, Rotterdam, The Netherlands
| | - Neil A Ranson
- Astbury Centre Structural Molecular Biology, School Molecular and Cellular Biology, Faculty Biological Sciences, University of Leeds, Leeds, UK
| | - Joost Snijder
- Biomolecular Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Raoul J de Groot
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Daniel L Hurdiss
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
| | - Berend-Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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9
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Du W, Hurdiss DL, Drabek D, Mykytyn AZ, Kaiser FK, González-Hernández M, Muñoz-Santos D, Lamers MM, van Haperen R, Li W, Drulyte I, Wang C, Sola I, Armando F, Beythien G, Ciurkiewicz M, Baumgärtner W, Guilfoyle K, Smits T, van der Lee J, van Kuppeveld FJM, van Amerongen G, Haagmans BL, Enjuanes L, Osterhaus ADME, Grosveld F, Bosch BJ. An ACE2-blocking antibody confers broad neutralization and protection against Omicron and other SARS-CoV-2 variants of concern. Sci Immunol 2022; 7:eabp9312. [PMID: 35471062 PMCID: PMC9097884 DOI: 10.1126/sciimmunol.abp9312] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The ongoing evolution of SARS-CoV-2 has resulted in the emergence of Omicron, which displays striking immune escape potential through mutations at key antigenic sites on the spike protein. Many of these mutations localize to the spike protein ACE2 receptor-binding domain, annulling the neutralizing activity of therapeutic antibodies that were effective against other Variants of Concern (VOCs) earlier in the pandemic. Here, we identified a receptor-blocking human monoclonal antibody, 87G7, that retained potent in vitro neutralizing activity against SARS-CoV-2 variants including the Alpha, Beta, Gamma, Delta and Omicron (BA.1/BA.2) VOCs. Using cryo-electron microscopy and site-directed mutagenesis experiments, we showed that 87G7 targets a patch of hydrophobic residues in the ACE2-binding site that are highly conserved in SARS-CoV-2 variants, explaining its broad neutralization capacity. 87G7 protected mice and/or hamsters prophylactically against challenge with all current SARS-CoV-2 VOCs, and showed therapeutic activity against SARS-CoV-2 challenge in both animal models. Our findings demonstrate that 87G7 holds promise as a prophylactic or therapeutic agent for COVID-19 that is more resilient to SARS-CoV-2 antigenic diversity.
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Affiliation(s)
- Wenjuan Du
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Daniel L Hurdiss
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands.,Harbour BioMed, Rotterdam, the Netherlands
| | - Anna Z Mykytyn
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Franziska K Kaiser
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Mariana González-Hernández
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Diego Muñoz-Santos
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Mart M Lamers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Rien van Haperen
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands.,Harbour BioMed, Rotterdam, the Netherlands
| | - Wentao Li
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Ieva Drulyte
- Thermo Fisher Scientific, Materials and Structural Analysis, Eindhoven, the Netherlands
| | - Chunyan Wang
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Isabel Sola
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Federico Armando
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Georg Beythien
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Malgorzata Ciurkiewicz
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | | | - Tony Smits
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Joline van der Lee
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Frank J M van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | | | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Albert D M E Osterhaus
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany.,Global Virus Network, Center of Excellence
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands.,Harbour BioMed, Rotterdam, the Netherlands
| | - Berend-Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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10
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Abstract
Chromatin domains and loops are important elements of chromatin structure and dynamics, but much remains to be learned about their exact biological role and nature. Topological associated domains and functional loops are key to gene expression and hold the answer to many questions regarding developmental decisions and diseases. Here, we discuss new findings, which have linked chromatin conformation with development, differentiation and diseases and hypothesized on various models while integrating all recent findings on how chromatin architecture affects gene expression during development, evolution and disease.
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Affiliation(s)
- Ilias Boltsis
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Guillaume Giraud
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
- Cancer Research Center of Lyon – INSERM U1052, Lyon, France
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
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11
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Haagmans BL, Noack D, Okba NMA, Li W, Wang C, Bestebroer T, de Vries R, Herfst S, de Meulder D, Verveer E, van Run P, Lamers MM, Rijnders B, Rokx C, van Kuppeveld F, Grosveld F, Drabek D, Geurts van Kessel C, Koopmans M, Bosch BJ, Kuiken T, Rockx B. SARS-CoV-2 Neutralizing Human Antibodies Protect Against Lower Respiratory Tract Disease in a Hamster Model. J Infect Dis 2021; 223:2020-2028. [PMID: 34043806 PMCID: PMC8243397 DOI: 10.1093/infdis/jiab289] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/25/2021] [Indexed: 01/08/2023] Open
Abstract
Effective clinical intervention strategies for COVID-19 are urgently needed.
Although several clinical trials have evaluated the use of convalescent plasma
containing virus-neutralizing antibodies, the levels of neutralizing antibodies
are usually not assessed and the effectiveness has not been proven. We show that
hamsters treated prophylactically with a 1:2560 titer of human convalescent
plasma or a 1:5260 titer of monoclonal antibody were protected against weight
loss, had a significant reduction of virus replication in the lungs and showed
reduced pneumonia . Interestingly, this protective effect was lost with a titer
of 1:320 of convalescent plasma. These data highlight the importance of
screening plasma donors for high levels of neutralizing antibodies. Our data show that prophylactic administration of high levels of neutralizing
antibody, either monoclonal or from convalescent plasma, prevent severe
SARS-CoV-2 pneumonia in a hamster model, and could be used as an alternative or
complementary to other antiviral treatments for COVID-19.
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Affiliation(s)
- Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Danny Noack
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Nisreen M A Okba
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Wentao Li
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Chunyan Wang
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Theo Bestebroer
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Rory de Vries
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Sander Herfst
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Dennis de Meulder
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Elwin Verveer
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Peter van Run
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mart M Lamers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Bart Rijnders
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Casper Rokx
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Frank van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands.,Harbour BioMed, Rotterdam, the Netherlands
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands.,Harbour BioMed, Rotterdam, the Netherlands
| | | | - Marion Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Berend Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Thijs Kuiken
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Barry Rockx
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
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12
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Abstract
Accurate control of gene expression in the right cell at the right moment is of fundamental importance to animal development and homeostasis. At the heart of gene regulation lie the enhancers, a class of gene regulatory elements that ensures precise spatiotemporal activation of gene transcription. Mammalian genomes are littered with enhancers, which are frequently organized in cooperative clusters such as locus control regions and superenhancers. Here, we discuss our current knowledge of enhancer biology, including an overview of the discovery of the various enhancer subsets and the mechanistic models used to explain their gene regulatory function.
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Affiliation(s)
- Frank Grosveld
- Department of Cell Biology, Erasmus MC, 3000 CA Rotterdam, The Netherlands; ,
| | | | - Ralph Stadhouders
- Department of Cell Biology, Erasmus MC, 3000 CA Rotterdam, The Netherlands; , .,Department of Pulmonary Medicine, Erasmus MC, 3000 CA Rotterdam, The Netherlands
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13
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Giraud G, Kolovos P, Boltsis I, van Staalduinen J, Guyot B, Weiss-Gayet M, IJcken WV, Morlé F, Grosveld F. Interplay between FLI-1 and the LDB1 complex in murine erythroleukemia cells and during megakaryopoiesis. iScience 2021; 24:102210. [PMID: 33733070 PMCID: PMC7940982 DOI: 10.1016/j.isci.2021.102210] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/22/2020] [Accepted: 02/17/2021] [Indexed: 11/29/2022] Open
Abstract
Transcription factors are key players in a broad range of cellular processes such as cell-fate decision. Understanding how they act to control these processes is of critical importance for therapy purposes. FLI-1 controls several hematopoietic lineage differentiation including megakaryopoiesis and erythropoiesis. Its aberrant expression is often observed in cancer and is associated with poor prognosis. We showed that FLI-1 interacts with the LDB1 complex, which also plays critical roles in erythropoiesis and megakaryopoiesis. In this study, we aimed to unravel how FLI-1 and the LDB1 complex act together in murine erythroleukemia cells and in megakaryocyte. Combining omics techniques, we show that FLI-1 enables the recruitment of the LDB1 complex to regulatory sequences of megakaryocytic genes and to enhancers. We show as well for the first time that FLI-1 is able to modulate the 3D chromatin organization by promoting chromatin looping between enhancers and promoters most likely through the LDB1 complex. FLI-1 is important for the recruitment of the LDB1 complex FLI-1 is important for chromatin looping FLI-1 and the LDB1 complex co-regulate megakaryopoiesis
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Affiliation(s)
- Guillaume Giraud
- Department of Cell Biology, Erasmus Medical Centre, 3015CN Rotterdam, the Netherlands
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis 68100, Greece
| | - Ilias Boltsis
- Department of Cell Biology, Erasmus Medical Centre, 3015CN Rotterdam, the Netherlands
| | - Jente van Staalduinen
- Department of Cell Biology, Erasmus Medical Centre, 3015CN Rotterdam, the Netherlands
| | - Boris Guyot
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Department of Immunity, Virus and Microenvironment, Lyon, France
| | - Michele Weiss-Gayet
- Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217 - Université de Lyon - Université Claude Bernard Lyon 1, Lyon, France
| | - Wilfred van IJcken
- Biomics Center, Erasmus University Medical Center, 3015CN Rotterdam, the Netherlands
| | - François Morlé
- Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217 - Université de Lyon - Université Claude Bernard Lyon 1, Lyon, France
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Centre, 3015CN Rotterdam, the Netherlands
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14
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Wang C, van Haperen R, Gutiérrez-Álvarez J, Li W, Okba NMA, Albulescu I, Widjaja I, van Dieren B, Fernandez-Delgado R, Sola I, Hurdiss DL, Daramola O, Grosveld F, van Kuppeveld FJM, Haagmans BL, Enjuanes L, Drabek D, Bosch BJ. A conserved immunogenic and vulnerable site on the coronavirus spike protein delineated by cross-reactive monoclonal antibodies. Nat Commun 2021; 12:1715. [PMID: 33731724 PMCID: PMC7969777 DOI: 10.1038/s41467-021-21968-w] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/15/2021] [Indexed: 01/31/2023] Open
Abstract
The coronavirus spike glycoprotein, located on the virion surface, is the key mediator of cell entry and the focus for development of protective antibodies and vaccines. Structural studies show exposed sites on the spike trimer that might be targeted by antibodies with cross-species specificity. Here we isolated two human monoclonal antibodies from immunized humanized mice that display a remarkable cross-reactivity against distinct spike proteins of betacoronaviruses including SARS-CoV, SARS-CoV-2, MERS-CoV and the endemic human coronavirus HCoV-OC43. Both cross-reactive antibodies target the stem helix in the spike S2 fusion subunit which, in the prefusion conformation of trimeric spike, forms a surface exposed membrane-proximal helical bundle. Both antibodies block MERS-CoV infection in cells and provide protection to mice from lethal MERS-CoV challenge in prophylactic and/or therapeutic models. Our work highlights an immunogenic and vulnerable site on the betacoronavirus spike protein enabling elicitation of antibodies with unusual binding breadth.
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MESH Headings
- Animals
- Antibodies, Monoclonal, Humanized/immunology
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Viral/immunology
- Betacoronavirus/classification
- Betacoronavirus/immunology
- Camelus
- Coronavirus Infections/drug therapy
- Coronavirus Infections/virology
- Cross Reactions
- Epitopes/chemistry
- Epitopes/genetics
- Epitopes/immunology
- Humans
- Mice
- Protein Conformation
- Protein Subunits
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- Chunyan Wang
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Rien van Haperen
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands
- Harbour BioMed, Rotterdam, the Netherlands
| | - Javier Gutiérrez-Álvarez
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Wentao Li
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Nisreen M A Okba
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Irina Albulescu
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Ivy Widjaja
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Merus N.V., Utrecht, the Netherlands
| | - Brenda van Dieren
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Raul Fernandez-Delgado
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Isabel Sola
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Daniel L Hurdiss
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Olalekan Daramola
- Cell Culture and Fermentation Sciences, Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands
- Harbour BioMed, Rotterdam, the Netherlands
| | - Frank J M van Kuppeveld
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands
- Harbour BioMed, Rotterdam, the Netherlands
| | - Berend-Jan Bosch
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
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15
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Cruz LJ, van Dijk T, Vepris O, Li TMWY, Schomann T, Baldazzi F, Kurita R, Nakamura Y, Grosveld F, Philipsen S, Eich C. PLGA-Nanoparticles for Intracellular Delivery of the CRISPR-Complex to Elevate Fetal Globin Expression in Erythroid Cells. Biomaterials 2020; 268:120580. [PMID: 33321292 DOI: 10.1016/j.biomaterials.2020.120580] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 12/16/2022]
Abstract
Ex vivo gene editing of CD34+ hematopoietic stem and progenitor cells (HSPCs) offers great opportunities to develop new treatments for a number of malignant and non-malignant diseases. Efficient gene-editing in HSPCs has been achieved using electroporation and/or viral transduction to deliver the CRISPR-complex, but cellular toxicity is a drawback of currently used methods. Nanoparticle (NP)-based gene-editing strategies can further enhance the gene-editing potential of HSPCs and provide a delivery system for in vivo application. Here, we developed CRISPR/Cas9-PLGA-NPs efficiently encapsulating Cas9 protein, single gRNA and a fluorescent probe. The initial 'burst' of Cas9 and gRNA release was followed by a sustained release pattern. CRISPR/Cas9-PLGA-NPs were taken up and processed by human HSPCs, without inducing cellular cytotoxicity. Upon escape from the lysosomal compartment, CRISPR/Cas9-PLGA-NPs-mediated gene editing of the γ-globin gene locus resulted in elevated expression of fetal hemoglobin (HbF) in primary erythroid cells. The development of CRISPR/Cas9-PLGA-NPs provides an attractive tool for the delivery of the CRISPR components to target HSPCs, and could provide the basis for in vivo treatment of hemoglobinopathies and other genetic diseases.
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Affiliation(s)
- Luis J Cruz
- Translational Nanobiomaterials and Imaging, Department of Radiology, Leiden University Medical Center, the Netherlands
| | - Thamar van Dijk
- Erasmus University Medical Center, Department of Cell Biology, Rotterdam, the Netherlands
| | - Olena Vepris
- Translational Nanobiomaterials and Imaging, Department of Radiology, Leiden University Medical Center, the Netherlands
| | - Tracy M W Y Li
- Translational Nanobiomaterials and Imaging, Department of Radiology, Leiden University Medical Center, the Netherlands
| | - Timo Schomann
- Translational Nanobiomaterials and Imaging, Department of Radiology, Leiden University Medical Center, the Netherlands; Percuros B.V, Leiden, the Netherlands
| | - Fabio Baldazzi
- Translational Nanobiomaterials and Imaging, Department of Radiology, Leiden University Medical Center, the Netherlands
| | - Ryo Kurita
- Central Blood Institute, Research and Development Department, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- RIKEN BioResource Research Center, Cell Engineering Division, National Research and Development Corporation, Tsukuba, Japan
| | - Frank Grosveld
- Erasmus University Medical Center, Department of Cell Biology, Rotterdam, the Netherlands
| | - Sjaak Philipsen
- Erasmus University Medical Center, Department of Cell Biology, Rotterdam, the Netherlands
| | - Christina Eich
- Translational Nanobiomaterials and Imaging, Department of Radiology, Leiden University Medical Center, the Netherlands.
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16
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Wang C, Li W, Drabek D, Okba NMA, van Haperen R, Osterhaus ADME, van Kuppeveld FJM, Haagmans BL, Grosveld F, Bosch BJ. Publisher Correction: A human monoclonal antibody blocking SARS-CoV-2 infection. Nat Commun 2020; 11:2511. [PMID: 32409714 PMCID: PMC7224291 DOI: 10.1038/s41467-020-16452-w] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Chunyan Wang
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Wentao Li
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands.,Harbour BioMed, Rotterdam, the Netherlands
| | - Nisreen M A Okba
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Rien van Haperen
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands.,Harbour BioMed, Rotterdam, the Netherlands
| | | | - Frank J M van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands.,Harbour BioMed, Rotterdam, the Netherlands
| | - Berend-Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
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17
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Wichgers Schreur PJ, van de Water S, Harmsen M, Bermúdez-Méndez E, Drabek D, Grosveld F, Wernike K, Beer M, Aebischer A, Daramola O, Rodriguez Conde S, Brennan K, Kozub D, Søndergaard Kristiansen M, Mistry KK, Deng Z, Hellert J, Guardado-Calvo P, Rey FA, van Keulen L, Kortekaas J. Multimeric single-domain antibody complexes protect against bunyavirus infections. eLife 2020; 9:52716. [PMID: 32314955 PMCID: PMC7173960 DOI: 10.7554/elife.52716] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 04/11/2020] [Indexed: 12/25/2022] Open
Abstract
The World Health Organization has included three bunyaviruses posing an increasing threat to human health on the Blueprint list of viruses likely to cause major epidemics and for which no, or insufficient countermeasures exist. Here, we describe a broadly applicable strategy, based on llama-derived single-domain antibodies (VHHs), for the development of bunyavirus biotherapeutics. The method was validated using the zoonotic Rift Valley fever virus (RVFV) and Schmallenberg virus (SBV), an emerging pathogen of ruminants, as model pathogens. VHH building blocks were assembled into highly potent neutralizing complexes using bacterial superglue technology. The multimeric complexes were shown to reduce and prevent virus-induced morbidity and mortality in mice upon prophylactic administration. Bispecific molecules engineered to present two different VHHs fused to an Fc domain were further shown to be effective upon therapeutic administration. The presented VHH-based technology holds great promise for the development of bunyavirus antiviral therapies.
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Affiliation(s)
| | - Sandra van de Water
- Department of Virology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Michiel Harmsen
- Department of Virology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Erick Bermúdez-Méndez
- Department of Virology, Wageningen Bioveterinary Research, Lelystad, Netherlands.,Laboratory of Virology, Wageningen University, Wageningen, Netherlands
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus MC, Rotterdam, Netherlands.,Harbour Antibodies B.V, Rotterdam, Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus MC, Rotterdam, Netherlands.,Harbour Antibodies B.V, Rotterdam, Netherlands
| | - Kerstin Wernike
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Andrea Aebischer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Olalekan Daramola
- Biopharmaceutical Development, R&D BioPharmaceuticals, AstraZeneca, Cambridge, United Kingdom
| | - Sara Rodriguez Conde
- Biopharmaceutical Development, R&D BioPharmaceuticals, AstraZeneca, Cambridge, United Kingdom
| | - Karen Brennan
- Biopharmaceutical Development, R&D BioPharmaceuticals, AstraZeneca, Cambridge, United Kingdom
| | - Dorota Kozub
- Biopharmaceutical Development, R&D BioPharmaceuticals, AstraZeneca, Cambridge, United Kingdom
| | | | - Kieran K Mistry
- Biopharmaceutical Development, R&D BioPharmaceuticals, AstraZeneca, Cambridge, United Kingdom
| | - Ziyan Deng
- Biopharmaceutical Development, R&D BioPharmaceuticals, AstraZeneca, Cambridge, United Kingdom
| | - Jan Hellert
- Structural Virology Unit, Virology Department, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Pablo Guardado-Calvo
- Structural Virology Unit, Virology Department, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Félix A Rey
- Structural Virology Unit, Virology Department, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Lucien van Keulen
- Department of Virology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Jeroen Kortekaas
- Department of Virology, Wageningen Bioveterinary Research, Lelystad, Netherlands.,Laboratory of Virology, Wageningen University, Wageningen, Netherlands
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18
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Grigorieva IV, Oszwald A, Grigorieva EF, Schachner H, Neudert B, Ostendorf T, Floege J, Lindenmeyer MT, Cohen CD, Panzer U, Aigner C, Schmidt A, Grosveld F, Thakker RV, Rees AJ, Kain R. A Novel Role for GATA3 in Mesangial Cells in Glomerular Development and Injury. J Am Soc Nephrol 2019; 30:1641-1658. [PMID: 31405951 DOI: 10.1681/asn.2018111143] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/01/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND GATA3 is a dual-zinc finger transcription factor that regulates gene expression in many developing tissues. In the kidney, GATA3 is essential for ureteric bud branching, and mice without it fail to develop kidneys. In humans, autosomal dominant GATA3 mutations can cause renal aplasia as part of the hypoparathyroidism, renal dysplasia, deafness (HDR) syndrome that includes mesangioproliferative GN. This suggests that GATA3 may have a previously unrecognized role in glomerular development or injury. METHODS To determine GATA3's role in glomerular development or injury, we assessed GATA3 expression in developing and mature kidneys from Gata3 heterozygous (+/-) knockout mice, as well as injured human and rodent kidneys. RESULTS We show that GATA3 is expressed by FOXD1 lineage stromal progenitor cells, and a subset of these cells mature into mesangial cells (MCs) that continue to express GATA3 in adult kidneys. In mice, we uncover that GATA3 is essential for normal glomerular development, and mice with haploinsufficiency of Gata3 have too few MC precursors and glomerular abnormalities. Expression of GATA3 is maintained in MCs of adult kidneys and is markedly increased in rodent models of mesangioproliferative GN and in IgA nephropathy, suggesting that GATA3 plays a critical role in the maintenance of glomerular homeostasis. CONCLUSIONS These results provide new insights on the role GATA3 plays in MC development and response to injury. It also shows that GATA3 may be a novel and robust nuclear marker for identifying MCs in tissue sections.
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Affiliation(s)
| | | | | | | | | | - Tammo Ostendorf
- Division of Nephrology and Clinical Immunology, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany
| | - Jürgen Floege
- Division of Nephrology and Clinical Immunology, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany
| | - Maja T Lindenmeyer
- Nephrological Center, Medical Clinic and Policlinic IV, University of Munich, Munich, Germany
| | - Clemens D Cohen
- Nephrological Center, Medical Clinic and Policlinic IV, University of Munich, Munich, Germany
| | - Ulf Panzer
- III. Medical Clinic, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christof Aigner
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, Vienna, Austria
| | - Alice Schmidt
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, Vienna, Austria
| | - Frank Grosveld
- Department of Cell Biology, Dr. Molewaterplein 50, Rotterdam, The Netherlands; and
| | - Rajesh V Thakker
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, University of Oxford, Oxford, UK
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19
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Widjaja I, Wang C, van Haperen R, Gutiérrez-Álvarez J, van Dieren B, Okba NMA, Raj VS, Li W, Fernandez-Delgado R, Grosveld F, van Kuppeveld FJM, Haagmans BL, Enjuanes L, Drabek D, Bosch BJ. Towards a solution to MERS: protective human monoclonal antibodies targeting different domains and functions of the MERS-coronavirus spike glycoprotein. Emerg Microbes Infect 2019; 8:516-530. [PMID: 30938227 PMCID: PMC6455120 DOI: 10.1080/22221751.2019.1597644] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The Middle-East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic virus that causes severe and often fatal respiratory disease in humans. Efforts to develop antibody-based therapies have focused on neutralizing antibodies that target the receptor binding domain of the viral spike protein thereby blocking receptor binding. Here, we developed a set of human monoclonal antibodies that target functionally distinct domains of the MERS-CoV spike protein. These antibodies belong to six distinct epitope groups and interfere with the three critical entry functions of the MERS-CoV spike protein: sialic acid binding, receptor binding and membrane fusion. Passive immunization with potently as well as with poorly neutralizing antibodies protected mice from lethal MERS-CoV challenge. Collectively, these antibodies offer new ways to gain humoral protection in humans against the emerging MERS-CoV by targeting different spike protein epitopes and functions.
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Affiliation(s)
- Ivy Widjaja
- a Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine , Utrecht University , Utrecht , Netherlands
| | - Chunyan Wang
- a Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine , Utrecht University , Utrecht , Netherlands
| | - Rien van Haperen
- b Department of Cell Biology , Erasmus MC , Rotterdam , Netherlands.,c Harbour Antibodies B.V. , Rotterdam , Netherlands
| | - Javier Gutiérrez-Álvarez
- d Department of Molecular and Cell Biology , National Center for Biotechnology-Spanish National Research Council (CNB-CSIC) , Madrid , Spain
| | - Brenda van Dieren
- a Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine , Utrecht University , Utrecht , Netherlands
| | - Nisreen M A Okba
- e Department of Viroscience , Erasmus Medical Center , Rotterdam , Netherlands
| | - V Stalin Raj
- e Department of Viroscience , Erasmus Medical Center , Rotterdam , Netherlands
| | - Wentao Li
- a Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine , Utrecht University , Utrecht , Netherlands
| | - Raul Fernandez-Delgado
- d Department of Molecular and Cell Biology , National Center for Biotechnology-Spanish National Research Council (CNB-CSIC) , Madrid , Spain
| | - Frank Grosveld
- b Department of Cell Biology , Erasmus MC , Rotterdam , Netherlands.,c Harbour Antibodies B.V. , Rotterdam , Netherlands
| | - Frank J M van Kuppeveld
- a Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine , Utrecht University , Utrecht , Netherlands
| | - Bart L Haagmans
- e Department of Viroscience , Erasmus Medical Center , Rotterdam , Netherlands
| | - Luis Enjuanes
- d Department of Molecular and Cell Biology , National Center for Biotechnology-Spanish National Research Council (CNB-CSIC) , Madrid , Spain
| | - Dubravka Drabek
- b Department of Cell Biology , Erasmus MC , Rotterdam , Netherlands.,c Harbour Antibodies B.V. , Rotterdam , Netherlands
| | - Berend-Jan Bosch
- a Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine , Utrecht University , Utrecht , Netherlands
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20
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Cantú I, van de Werken HJG, Gillemans N, Stadhouders R, Heshusius S, Maas A, Esteghamat F, Ozgur Z, van IJcken WFJ, Grosveld F, von Lindern M, Philipsen S, van Dijk TB. The mouse KLF1 Nan variant impairs nuclear condensation and erythroid maturation. PLoS One 2019; 14:e0208659. [PMID: 30921348 PMCID: PMC6438607 DOI: 10.1371/journal.pone.0208659] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/11/2019] [Indexed: 12/13/2022] Open
Abstract
Krüppel-like factor 1 (KLF1) is an essential transcription factor for erythroid development, as demonstrated by Klf1 knockout mice which die around E14 due to severe anemia. In humans, >140 KLF1 variants, causing different erythroid phenotypes, have been described. The KLF1 Nan variant, a single amino acid substitution (p.E339D) in the DNA binding domain, causes hemolytic anemia and is dominant over wildtype KLF1. Here we describe the effects of the KLF1 Nan variant during fetal development. We show that Nan embryos have defects in erythroid maturation. RNA-sequencing of the KLF1 Nan fetal liver cells revealed that Exportin 7 (Xpo7) was among the 782 deregulated genes. This nuclear exportin is implicated in terminal erythroid differentiation; in particular it is involved in nuclear condensation. Indeed, KLF1 Nan fetal liver cells had larger nuclei and reduced chromatin condensation. Knockdown of XPO7 in wildtype erythroid cells caused a similar phenotype. We propose that reduced expression of XPO7 is partially responsible for the erythroid defects observed in KLF1 Nan erythroid cells.
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Affiliation(s)
- Ileana Cantú
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Nynke Gillemans
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Steven Heshusius
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
- Department of Hematopoiesis, Sanquin Research, Amsterdam, The Netherlands
| | - Alex Maas
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Zeliha Ozgur
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
| | | | - Frank Grosveld
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Sjaak Philipsen
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
- * E-mail:
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21
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Kolovos P, Brouwer RWW, Kockx CEM, Lesnussa M, Kepper N, Zuin J, Imam AMA, van de Werken HJG, Wendt KS, Knoch TA, van IJcken WFJ, Grosveld F. Investigation of the spatial structure and interactions of the genome at sub-kilobase-pair resolution using T2C. Nat Protoc 2018; 13:459-477. [DOI: 10.1038/nprot.2017.132] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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22
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Cruz-Molina S, Respuela P, Tebartz C, Kolovos P, Nikolic M, Fueyo R, van Ijcken WF, Grosveld F, Frommolt P, Bazzi H, Rada-Iglesias A. PRC2 Facilitates the Regulatory Topology Required for Poised Enhancer Function during Pluripotent Stem Cell Differentiation. Cell Stem Cell 2017; 20:689-705.e9. [DOI: 10.1016/j.stem.2017.02.004] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 12/19/2016] [Accepted: 02/07/2017] [Indexed: 01/28/2023]
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23
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Drabek D, Janssens R, de Boer E, Rademaker R, Kloess J, Skehel J, Grosveld F. Expression Cloning and Production of Human Heavy-Chain-Only Antibodies from Murine Transgenic Plasma Cells. Front Immunol 2016; 7:619. [PMID: 28066429 PMCID: PMC5165034 DOI: 10.3389/fimmu.2016.00619] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/06/2016] [Indexed: 12/02/2022] Open
Abstract
Several technologies have been developed to isolate human antibodies against different target antigens as a source of potential therapeutics, including hybridoma technology, phage and yeast display systems. For conventional antibodies, this involves either random pairing of VH and variable light (VL) domains in combinatorial display libraries or isolation of cognate pairs of VH and VL domains from human B cells or from transgenic mice carrying human immunoglobulin loci followed by single-cell sorting, single-cell RT-PCR, and bulk cloning of isolated natural VH–VL pairs. Heavy-chain-only antibodies (HCAbs) that naturally occur in camelids require only heavy immunoglobulin chain cloning. Here, we present an automatable novel, high-throughput technology for rapid direct cloning and production of fully human HCAbs from sorted population of transgenic mouse plasma cells carrying a human HCAb locus. Utility of the technique is demonstrated by isolation of diverse sets of sequence unique, soluble, high-affinity influenza A strain X-31 hemagglutinin-specific HCAbs.
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Affiliation(s)
- Dubravka Drabek
- Department of Cell Biology, Erasmus MC , Rotterdam , Netherlands
| | - Rick Janssens
- Department of Cell Biology, Erasmus MC , Rotterdam , Netherlands
| | - Ernie de Boer
- Department of Cell Biology, Erasmus MC , Rotterdam , Netherlands
| | | | | | - John Skehel
- WHO Influenza Centre, Frances Crick Institute , London , UK
| | - Frank Grosveld
- Department of Cell Biology, Erasmus MC, Rotterdam, Netherlands; Harbour Antibodies BV, Rotterdam, Netherlands
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24
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Breton A, Theodorou A, Aktuna S, Sonzogni L, Darling D, Chan L, Menzel S, van der Spek PJ, Swagemakers SMA, Grosveld F, Philipsen S, Thein SL. ASH1L (a histone methyltransferase protein) is a novel candidate globin gene regulator revealed by genetic study of an English family with beta-thalassaemia unlinked to the beta-globin locus. Br J Haematol 2016; 175:525-530. [PMID: 27434206 DOI: 10.1111/bjh.14256] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 06/06/2016] [Indexed: 01/14/2023]
Abstract
In 1993, we described an English family with beta-thalassaemia that was not linked to the beta-globin locus. Whole genome sequence analyses revealed potential causative mutations in 15 different genes, of which 4 were consistently and uniquely associated with the phenotype in all 7 affected family members, also confirmed by genetic linkage analysis. Of the 4 genes, which are present in a centromeric region of chromosome 1, ASH1L was proposed as causative through functional mRNA knock-down and chromatin-immunoprecipitation studies in human erythroid progenitor cells. Our data suggest a putative role for ASH1L (Trithorax protein) in the regulation of globin genes.
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Affiliation(s)
- Amandine Breton
- Molecular Haematology, Division of Cancer Studies, King's College London Faculty of Life Sciences and Medicine, London, SE5 9NU, UK
| | - Andria Theodorou
- Molecular Haematology, Division of Cancer Studies, King's College London Faculty of Life Sciences and Medicine, London, SE5 9NU, UK
| | - Suleyman Aktuna
- Molecular Haematology, Division of Cancer Studies, King's College London Faculty of Life Sciences and Medicine, London, SE5 9NU, UK
| | - Laura Sonzogni
- Molecular Haematology, Division of Cancer Studies, King's College London Faculty of Life Sciences and Medicine, London, SE5 9NU, UK
| | - David Darling
- Department of Haematological Medicine, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK
| | - Lucas Chan
- Department of Haematological Medicine, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK
| | - Stephan Menzel
- Molecular Haematology, Division of Cancer Studies, King's College London Faculty of Life Sciences and Medicine, London, SE5 9NU, UK
| | | | | | - Frank Grosveld
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands.,Netherlands Consortium for Systems Biology, Erasmus MC, Rotterdam, The Netherlands.,Centre for Biomedical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Sjaak Philipsen
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands.,Netherlands Consortium for Systems Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Swee Lay Thein
- Molecular Haematology, Division of Cancer Studies, King's College London Faculty of Life Sciences and Medicine, London, SE5 9NU, UK. .,Department of Haematological Medicine, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK.
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25
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Bolkestein M, de Blois E, Koelewijn SJ, Eggermont AMM, Grosveld F, de Jong M, Koning GA. Investigation of Factors Determining the Enhanced Permeability and Retention Effect in Subcutaneous Xenografts. J Nucl Med 2015; 57:601-7. [PMID: 26719375 DOI: 10.2967/jnumed.115.166173] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/25/2015] [Indexed: 12/30/2022] Open
Abstract
Liposomal chemotherapy offers several advantages over conventional therapies, including high intratumoral drug delivery, reduced side effects, prolonged circulation time, and the possibility to dose higher. The efficient delivery of liposomal chemotherapeutics relies, however, on the enhanced permeability and retention (EPR) effect, which refers to the ability of macromolecules to extravasate leaky tumor vessels and accumulate in the tumor tissue. Using a panel of human xenograft tumors, we evaluated the influence of the EPR effect on liposomal distribution in vivo by injection of pegylated liposomes radiolabeled with (111)In. Liposomal accumulation in tumors and organs was followed over time by SPECT/CT imaging. We observed that fast-growing xenografts, which may be less representative of tumor development in patients, showed higher liposomal accumulation than slow-growing xenografts. Additionally, several other parameters known to influence the EPR effect were evaluated, such as blood and lymphatic vessel density, intratumoral hypoxia, and the presence of infiltrating macrophages. The investigation of various parameters showed a few correlations. Although hypoxia, proliferation, and macrophage presence were associated with tumor growth, no hard conclusions or predictions could be made regarding the EPR effect or liposomal uptake. However, liposomal uptake was significantly correlated with tumor growth, with fast-growing tumors showing a higher uptake, although no biological determinants could be elucidated to explain this correlation.
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Affiliation(s)
- Michiel Bolkestein
- Laboratory of Experimental Surgical Oncology, Department of Surgery, Erasmus MC, Rotterdam, The Netherlands
| | - Erik de Blois
- Departments of Nuclear Medicine and Radiology, Erasmus MC, Rotterdam, The Netherlands
| | - Stuart J Koelewijn
- Departments of Nuclear Medicine and Radiology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Frank Grosveld
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Marion de Jong
- Departments of Nuclear Medicine and Radiology, Erasmus MC, Rotterdam, The Netherlands
| | - Gerben A Koning
- Laboratory of Experimental Surgical Oncology, Department of Surgery, Erasmus MC, Rotterdam, The Netherlands
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26
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Stadhouders R, Cico A, Stephen T, Thongjuea S, Kolovos P, Baymaz HI, Yu X, Demmers J, Bezstarosti K, Maas A, Barroca V, Kockx C, Ozgur Z, van Ijcken W, Arcangeli ML, Andrieu-Soler C, Lenhard B, Grosveld F, Soler E. Control of developmentally primed erythroid genes by combinatorial co-repressor actions. Nat Commun 2015; 6:8893. [PMID: 26593974 PMCID: PMC4673834 DOI: 10.1038/ncomms9893] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 10/14/2015] [Indexed: 12/21/2022] Open
Abstract
How transcription factors (TFs) cooperate within large protein complexes to allow rapid modulation of gene expression during development is still largely unknown. Here we show that the key haematopoietic LIM-domain-binding protein-1 (LDB1) TF complex contains several activator and repressor components that together maintain an erythroid-specific gene expression programme primed for rapid activation until differentiation is induced. A combination of proteomics, functional genomics and in vivo studies presented here identifies known and novel co-repressors, most notably the ETO2 and IRF2BP2 proteins, involved in maintaining this primed state. The ETO2–IRF2BP2 axis, interacting with the NCOR1/SMRT co-repressor complex, suppresses the expression of the vast majority of archetypical erythroid genes and pathways until its decommissioning at the onset of terminal erythroid differentiation. Our experiments demonstrate that multimeric regulatory complexes feature a dynamic interplay between activating and repressing components that determines lineage-specific gene expression and cellular differentiation. Conserved sets of transcription factors (TFs) regulate hematopoiesis. Here, Stadhouders et al. show that IRF2BP2 is a component of the LDB1 TF complex and together with its co-repressor ETO2, enhances transcriptional repression, which plays a crucial role at the erythroid progenitor stage.
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Affiliation(s)
- Ralph Stadhouders
- Department of Cell Biology, Erasmus Medical Center, 3015CN Rotterdam, The Netherlands
| | - Alba Cico
- Inserm UMR967, CEA/DSV/iRCM, Laboratory of Molecular Hematopoiesis, Université Paris-Saclay, 92265 Fontenay-aux-Roses, France
| | - Tharshana Stephen
- Inserm UMR967, CEA/DSV/iRCM, Laboratory of Molecular Hematopoiesis, Université Paris-Saclay, 92265 Fontenay-aux-Roses, France
| | - Supat Thongjuea
- Computational Biology Unit, Bergen Center for Computational Science, N-5008 Bergen, Norway.,MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Petros Kolovos
- Department of Cell Biology, Erasmus Medical Center, 3015CN Rotterdam, The Netherlands
| | - H Irem Baymaz
- Department of Cell Biology, Erasmus Medical Center, 3015CN Rotterdam, The Netherlands
| | - Xiao Yu
- Department of Cell Biology, Erasmus Medical Center, 3015CN Rotterdam, The Netherlands
| | - Jeroen Demmers
- Department of Proteomics, Erasmus Medical Center, 3015CN Rotterdam, The Netherlands
| | - Karel Bezstarosti
- Department of Proteomics, Erasmus Medical Center, 3015CN Rotterdam, The Netherlands
| | - Alex Maas
- Department of Cell Biology, Erasmus Medical Center, 3015CN Rotterdam, The Netherlands
| | - Vilma Barroca
- CEA/DSV/iRCM/SCSR, Université Paris-Saclay, 92265 Fontenay-aux-Roses, France
| | - Christel Kockx
- Center for Biomics, Erasmus Medical Center, 3015CN Rotterdam, The Netherlands
| | - Zeliha Ozgur
- Center for Biomics, Erasmus Medical Center, 3015CN Rotterdam, The Netherlands
| | - Wilfred van Ijcken
- Center for Biomics, Erasmus Medical Center, 3015CN Rotterdam, The Netherlands
| | - Marie-Laure Arcangeli
- Inserm UMR967, CEA/DSV/iRCM, Laboratory of Hematopoietic and Leukemic Stem cells, Université Paris-Saclay, 92265 Fontenay-aux-Roses, France
| | - Charlotte Andrieu-Soler
- Inserm UMR967, CEA/DSV/iRCM, Laboratory of Molecular Hematopoiesis, Université Paris-Saclay, 92265 Fontenay-aux-Roses, France
| | - Boris Lenhard
- Department of Molecular Sciences, Faculty of Medicine, MRC Clinical Sciences Centre, Institute of Clinical Sciences, Imperial College London, London W12 0NN, UK
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, 3015CN Rotterdam, The Netherlands.,Cancer Genomics Center, Erasmus Medical Center, 3015CN Rotterdam, The Netherlands
| | - Eric Soler
- Department of Cell Biology, Erasmus Medical Center, 3015CN Rotterdam, The Netherlands.,Inserm UMR967, CEA/DSV/iRCM, Laboratory of Molecular Hematopoiesis, Université Paris-Saclay, 92265 Fontenay-aux-Roses, France.,Cancer Genomics Center, Erasmus Medical Center, 3015CN Rotterdam, The Netherlands.,Laboratory of Excellence GR-Ex, 75015 Paris, France
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27
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Caputo L, Witzel HR, Kolovos P, Cheedipudi S, Looso M, Mylona A, van IJcken WFJ, Laugwitz KL, Evans SM, Braun T, Soler E, Grosveld F, Dobreva G. The Isl1/Ldb1 Complex Orchestrates Genome-wide Chromatin Organization to Instruct Differentiation of Multipotent Cardiac Progenitors. Cell Stem Cell 2015; 17:287-99. [PMID: 26321200 DOI: 10.1016/j.stem.2015.08.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 07/08/2015] [Accepted: 08/06/2015] [Indexed: 01/21/2023]
Abstract
Cardiac stem/progenitor cells hold great potential for regenerative therapies; however, the mechanisms regulating their expansion and differentiation remain insufficiently defined. Here we show that Ldb1 is a central regulator of genome organization in cardiac progenitor cells, which is crucial for cardiac lineage differentiation and heart development. We demonstrate that Ldb1 binds to the key regulator of cardiac progenitors, Isl1, and protects it from degradation. Furthermore, the Isl1/Ldb1 complex promotes long-range enhancer-promoter interactions at the loci of the core cardiac transcription factors Mef2c and Hand2. Chromosome conformation capture followed by sequencing identified specific Ldb1-mediated interactions of the Isl1/Ldb1 responsive Mef2c anterior heart field enhancer with genes that play key roles in cardiac progenitor cell function and cardiovascular development. Importantly, the expression of these genes was downregulated upon Ldb1 depletion and Isl1/Ldb1 haplodeficiency. In conclusion, the Isl1/Ldb1 complex orchestrates a network for heart-specific transcriptional regulation and coordination in three-dimensional space during cardiogenesis.
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Affiliation(s)
- Luca Caputo
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Hagen R Witzel
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Petros Kolovos
- Department of Cell Biology, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Sirisha Cheedipudi
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Mario Looso
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Athina Mylona
- Department of Cell Biology, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands; School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, Kent CT1 1QU, UK
| | | | - Karl-Ludwig Laugwitz
- I. Medical Department, Cardiology, Klinikum rechts der Isar, Technical University, 81675 Munich, Germany
| | - Sylvia M Evans
- Department of Medicine, Skaggs School of Pharmacy, University of California, San Diego, La Jolla, CA 92093, USA
| | - Thomas Braun
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Eric Soler
- Department of Cell Biology, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands; Laboratory of Molecular Hematopoiesis, CEA/DSV/iRCM/LHM, INSERM UMR967, 92265 Fontenay-aux-Roses, France; Laboratory of Excellence GR-Ex, 75015, Paris, France
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Gergana Dobreva
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany; Medical Faculty, University of Frankfurt, 60590 Frankfurt am Main, Germany.
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28
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Gu W, Monteiro R, Zuo J, Simões FC, Martella A, Andrieu-Soler C, Grosveld F, Sauka-Spengler T, Patient R. A novel TGFβ modulator that uncouples R-Smad/I-Smad-mediated negative feedback from R-Smad/ligand-driven positive feedback. PLoS Biol 2015; 13:e1002051. [PMID: 25665164 PMCID: PMC4321984 DOI: 10.1371/journal.pbio.1002051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/17/2014] [Indexed: 01/17/2023] Open
Abstract
As some of the most widely utilised intercellular signalling molecules, transforming growth factor β (TGFβ) superfamily members play critical roles in normal development and become disrupted in human disease. Establishing appropriate levels of TGFβ signalling involves positive and negative feedback, which are coupled and driven by the same signal transduction components (R-Smad transcription factor complexes), but whether and how the regulation of the two can be distinguished are unknown. Genome-wide comparison of published ChIP-seq datasets suggests that LIM domain binding proteins (Ldbs) co-localise with R-Smads at a substantial subset of R-Smad target genes including the locus of inhibitory Smad7 (I-Smad7), which mediates negative feedback for TGFβ signalling. We present evidence suggesting that zebrafish Ldb2a binds and directly activates the I-Smad7 gene, whereas it binds and represses the ligand gene, Squint (Sqt), which drives positive feedback. Thus, the fine tuning of TGFβ signalling derives from positive and negative control by Ldb2a. Expression of ldb2a is itself activated by TGFβ signals, suggesting potential feed-forward loops that might delay the negative input of Ldb2a to the positive feedback, as well as the positive input of Ldb2a to the negative feedback. In this way, precise gene expression control by Ldb2a enables an initial build-up of signalling via a fully active positive feedback in the absence of buffering by the negative feedback. In Ldb2a-deficient zebrafish embryos, homeostasis of TGFβ signalling is perturbed and signalling is stably enhanced, giving rise to excess mesoderm and endoderm, an effect that can be rescued by reducing signalling by the TGFβ family members, Nodal and BMP. Thus, Ldb2a is critical to the homeostatic control of TGFβ signalling and thereby embryonic patterning.
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Affiliation(s)
- Wenchao Gu
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Rui Monteiro
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- BHF Centre of Research Excellence, Oxford, United Kingdom
| | - Jie Zuo
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Filipa Costa Simões
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Andrea Martella
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Charlotte Andrieu-Soler
- INSERM U872, Université René Descartes Sorbonne Paris Cité, Team 17, Centre de Recherche des Cordeliers, Paris, France
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Tatjana Sauka-Spengler
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Roger Patient
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- BHF Centre of Research Excellence, Oxford, United Kingdom
- * E-mail:
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29
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Soler E, Grosveld F. Targeting epigenetics to speed up repair. Cell Stem Cell 2014; 14:553-4. [PMID: 24792110 DOI: 10.1016/j.stem.2014.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In this issue of Cell Stem Cell, Palii et al. reveal that TAL1 is a master regulator of adhesion and migration networks in human endothelial progenitors and that ex vivo treatment with the histone deacetylase inhibitor TSA enables their faster vascularization after ischemic injury.
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Affiliation(s)
- Eric Soler
- INSERM UMR967 CEA/DSV/iRCM, 92265 Fontenay-aux-Roses, France.
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands.
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30
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Diermeier S, Kolovos P, Heizinger L, Schwartz U, Georgomanolis T, Zirkel A, Wedemann G, Grosveld F, Knoch TA, Merkl R, Cook PR, Längst G, Papantonis A. TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning. Genome Biol 2014; 15:536. [PMID: 25608606 PMCID: PMC4268828 DOI: 10.1186/s13059-014-0536-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 11/07/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The rearrangement of nucleosomes along the DNA fiber profoundly affects gene expression, but little is known about how signalling reshapes the chromatin landscape, in three-dimensional space and over time, to allow establishment of new transcriptional programs. RESULTS Using micrococcal nuclease treatment and high-throughput sequencing, we map genome-wide changes in nucleosome positioning in primary human endothelial cells stimulated with tumour necrosis factor alpha (TNFα) - a proinflammatory cytokine that signals through nuclear factor kappa-B (NF-κB). Within 10 min, nucleosomes reposition at regions both proximal and distal to NF-κB binding sites, before the transcription factor quantitatively binds thereon. Similarly, in long TNFα-responsive genes, repositioning precedes transcription by pioneering elongating polymerases and appears to nucleate from intragenic enhancer clusters resembling super-enhancers. By 30 min, widespread repositioning throughout megabase pair-long chromosomal segments, with consequential effects on three-dimensional structure (detected using chromosome conformation capture), is seen. CONCLUSIONS Whilst nucleosome repositioning is viewed as a local phenomenon, our results point to effects occurring over multiple scales. Here, we present data in support of a TNFα-induced priming mechanism, mostly independent of NF-κB binding and/or elongating RNA polymerases, leading to a plastic network of interactions that affects DNA accessibility over large domains.
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Affiliation(s)
- Sarah Diermeier
- />Department of Biochemistry III, University of Regensburg, Universität Strasse 31, 93053 Regensburg, Germany
- />Present address: Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, 11724 NY USA
| | - Petros Kolovos
- />Cell Biology and Genetics, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
- />Biophysical Genomics, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Leonhard Heizinger
- />Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Uwe Schwartz
- />Department of Biochemistry III, University of Regensburg, Universität Strasse 31, 93053 Regensburg, Germany
| | - Theodore Georgomanolis
- />Centre for Molecular Medicine, University of Cologne, Robert-Koch-Strasse 21, 50931 Cologne, Germany
| | - Anne Zirkel
- />Centre for Molecular Medicine, University of Cologne, Robert-Koch-Strasse 21, 50931 Cologne, Germany
| | - Gero Wedemann
- />Institute for Applied Computer Science, University of Applied Sciences Stralsund, Zur Schwedenschanze 15, 18435 Stralsund, Germany
| | - Frank Grosveld
- />Cell Biology and Genetics, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Tobias A Knoch
- />Biophysical Genomics, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
- />BioQuant & German Cancer Research Center, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Rainer Merkl
- />Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Peter R Cook
- />Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, United Kingdom
| | - Gernot Längst
- />Department of Biochemistry III, University of Regensburg, Universität Strasse 31, 93053 Regensburg, Germany
| | - Argyris Papantonis
- />Centre for Molecular Medicine, University of Cologne, Robert-Koch-Strasse 21, 50931 Cologne, Germany
- />Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, United Kingdom
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31
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Visser M, Kayser M, Grosveld F, Palstra RJ. Genetic variation in regulatory DNA elements: the case of OCA2 transcriptional regulation. Pigment Cell Melanoma Res 2014; 27:169-77. [PMID: 24387780 DOI: 10.1111/pcmr.12210] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 12/20/2013] [Indexed: 12/16/2022]
Abstract
Mutations within the OCA2 gene or the complete absence of the OCA2 protein leads to oculocutaneous albinism type 2. The OCA2 protein plays a central role in melanosome biogenesis, and it is a strong determinant of the eumelanin content in melanocytes. Transcript levels of the OCA2 gene are strongly correlated with pigmentation intensities. Recent studies demonstrated that the transcriptional level of OCA2 is to a large extent determined by the noncoding SNP rs12913832 located 21.5 kb upstream of the OCA2 gene promoter. In this review, we discuss current hypotheses and the available data on the mechanism of OCA2 transcriptional regulation and how this is influenced by genetic variation. Finally, we will explore how future epigenetic studies can be used to advance our insight into the functional biology that connects genetic variation to human pigmentation.
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Affiliation(s)
- Mijke Visser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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32
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Kapere Ochieng J, Schilders K, Kool H, Buscop-van Kempen M, Boerema-De Munck A, Grosveld F, Wijnen R, Tibboel D, Rottier RJ. Differentiated type II pneumocytes can be reprogrammed by ectopic Sox2 expression. PLoS One 2014; 9:e107248. [PMID: 25210856 PMCID: PMC4161395 DOI: 10.1371/journal.pone.0107248] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 08/12/2014] [Indexed: 12/24/2022] Open
Abstract
The adult lung contains several distinct stem cells, although their properties and full potential are still being sorted out. We previously showed that ectopic Sox2 expression in the developing lung manipulated the fate of differentiating cells. Here, we addressed the question whether fully differentiated cells could be redirected towards another cell type. Therefore, we used transgenic mice to express an inducible Sox2 construct in type II pneumocytes, which are situated in the distal, respiratory areas of the lung. Within three days after the induction of the transgene, the type II cells start to proliferate and form clusters of cuboidal cells. Prolonged Sox2 expression resulted in the reversal of the type II cell towards a more embryonic, precursor-like cell, being positive for the stem cell markers Sca1 and Ssea1. Moreover, the cells started to co-express Spc and Cc10, characteristics of bronchioalveolar stem cells. We demonstrated that Sox2 directly regulates the expression of Sca1. Subsequently, these cells expressed Trp63, a marker for basal cells of the trachea. So, we show that the expression of one transcription factor in fully differentiated, distal lung cells changes their fate towards proximal cells through intermediate cell types. This may have implications for regenerative medicine, and repair of diseased and damaged lungs.
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Affiliation(s)
- Joshua Kapere Ochieng
- Department of Pediatric Surgery of the Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Kim Schilders
- Department of Pediatric Surgery of the Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Heleen Kool
- Department of Pediatric Surgery of the Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Marjon Buscop-van Kempen
- Department of Pediatric Surgery of the Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Anne Boerema-De Munck
- Department of Pediatric Surgery of the Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Frank Grosveld
- Department of Cell Biology of the Erasmus MC, Rotterdam, the Netherlands
| | - Rene Wijnen
- Department of Pediatric Surgery of the Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Dick Tibboel
- Department of Pediatric Surgery of the Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Robbert J. Rottier
- Department of Pediatric Surgery of the Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
- Department of Cell Biology of the Erasmus MC, Rotterdam, the Netherlands
- * E-mail:
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33
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Farahbakhshian E, Verstegen MM, Visser TP, Kheradmandkia S, Geerts D, Arshad S, Riaz N, Grosveld F, van Til NP, Meijerink JPP. Angiopoietin-like protein 3 promotes preservation of stemness during ex vivo expansion of murine hematopoietic stem cells. PLoS One 2014; 9:e105642. [PMID: 25170927 PMCID: PMC4149469 DOI: 10.1371/journal.pone.0105642] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 07/22/2014] [Indexed: 12/25/2022] Open
Abstract
Allogeneic hematopoietic stem cell (HSC) transplantations from umbilical cord blood or autologous HSCs for gene therapy purposes are hampered by limited number of stem cells. To test the ability to expand HSCs in vitro prior to transplantation, two growth factor cocktails containing stem cell factor, thrombopoietin, fms-related tyrosine kinase-3 ligand (STF) or stem cell factor, thrombopoietin, insulin-like growth factor-2, fibroblast growth factor-1 (STIF) either with or without the addition of angiopoietin-like protein-3 (Angptl3) were used. Culturing HSCs in STF and STIF media for 7 days expanded long-term repopulating stem cells content in vivo by ∼6-fold and ∼10-fold compared to freshly isolated stem cells. Addition of Angptl3 resulted in increased expansion of these populations by ∼17-fold and ∼32-fold, respectively, and was further supported by enforced expression of Angptl3 in HSCs through lentiviral transduction that also promoted HSC expansion. As expansion of highly purified lineage-negative, Sca-1+, c-Kit+ HSCs was less efficient than less pure lineage-negative HSCs, Angptl3 may have a direct effect on HCS but also an indirect effect on accessory cells that support HSC expansion. No evidence for leukemia or toxicity was found during long-term follow up of mice transplanted with ex vivo expanded HSCs or manipulated HSC populations that expressed Angptl3. We conclude that the cytokine combinations used in this study to expand HSCs ex vivo enhances the engraftment in vivo. This has important implications for allogeneic umbilical cord-blood derived HSC transplantations and autologous HSC applications including gene therapy.
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Affiliation(s)
- Elnaz Farahbakhshian
- The Department of Hematology, Erasmus Medical Center, Rotterdam, the Netherlands; The Department of Pediatric Oncology/Hematology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Monique M Verstegen
- The Department of Hematology, Erasmus Medical Center, Rotterdam, the Netherlands; The Department of Surgery, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Trudi P Visser
- The Department of Hematology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Sima Kheradmandkia
- The Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Dirk Geerts
- The Department of Pediatric Oncology/Hematology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Shazia Arshad
- The Department of Hematology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Noveen Riaz
- The Department of Hematology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Frank Grosveld
- The Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Niek P van Til
- The Department of Hematology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jules P P Meijerink
- The Department of Pediatric Oncology/Hematology, Erasmus Medical Center, Rotterdam, the Netherlands
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Kolovos P, van de Werken HJ, Kepper N, Zuin J, Brouwer RW, Kockx CE, Wendt KS, van IJcken WF, Grosveld F, Knoch TA. Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements. Epigenetics Chromatin 2014; 7:10. [PMID: 25031611 PMCID: PMC4100494 DOI: 10.1186/1756-8935-7-10] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 05/28/2014] [Indexed: 11/26/2022] Open
Abstract
Background Significant efforts have recently been put into the investigation of the spatial organization and the chromatin-interaction networks of genomes. Chromosome conformation capture (3C) technology and its derivatives are important tools used in this effort. However, many of these have limitations, such as being limited to one viewpoint, expensive with moderate to low resolution, and/or requiring a large sequencing effort. Techniques like Hi-C provide a genome-wide analysis. However, it requires massive sequencing effort with considerable costs. Here we describe a new technique termed Targeted Chromatin Capture (T2C), to interrogate large selected regions of the genome. T2C provides an unbiased view of the spatial organization of selected loci at superior resolution (single restriction fragment resolution, from 2 to 6 kbp) at much lower costs than Hi-C due to the lower sequencing effort. Results We applied T2C on well-known model regions, the mouse β-globin locus and the human H19/IGF2 locus. In both cases we identified all known chromatin interactions. Furthermore, we compared the human H19/IGF2 locus data obtained from different chromatin conformation capturing methods with T2C data. We observed the same compartmentalization of the locus, but at a much higher resolution (single restriction fragments vs. the common 40 kbp bins) and higher coverage. Moreover, we compared the β-globin locus in two different biological samples (mouse primary erythroid cells and mouse fetal brain), where it is either actively transcribed or not, to identify possible transcriptional dependent interactions. We identified the known interactions in the β-globin locus and the same topological domains in both mouse primary erythroid cells and in mouse fetal brain with the latter having fewer interactions probably due to the inactivity of the locus. Furthermore, we show that interactions due to the important chromatin proteins, Ldb1 and Ctcf, in both tissues can be analyzed easily to reveal their role on transcriptional interactions and genome folding. Conclusions T2C is an efficient, easy, and affordable with high (restriction fragment) resolution tool to address both genome compartmentalization and chromatin-interaction networks for specific genomic regions at high resolution for both clinical and non-clinical research.
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Affiliation(s)
- Petros Kolovos
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Harmen Jg van de Werken
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Nick Kepper
- Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Jessica Zuin
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Rutger Ww Brouwer
- Center for Biomics, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Christel Em Kockx
- Center for Biomics, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Wilfred Fj van IJcken
- Center for Biomics, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Tobias A Knoch
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
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35
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Stadhouders R, Aktuna S, Thongjuea S, Aghajanirefah A, Pourfarzad F, van Ijcken W, Lenhard B, Rooks H, Best S, Menzel S, Grosveld F, Thein SL, Soler E. HBS1L-MYB intergenic variants modulate fetal hemoglobin via long-range MYB enhancers. J Clin Invest 2014; 124:1699-710. [PMID: 24614105 DOI: 10.1172/jci71520] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 01/09/2014] [Indexed: 01/21/2023] Open
Abstract
Genetic studies have identified common variants within the intergenic region (HBS1L-MYB) between GTP-binding elongation factor HBS1L and myeloblastosis oncogene MYB on chromosome 6q that are associated with elevated fetal hemoglobin (HbF) levels and alterations of other clinically important human erythroid traits. It is unclear how these noncoding sequence variants affect multiple erythrocyte characteristics. Here, we determined that several HBS1L-MYB intergenic variants affect regulatory elements that are occupied by key erythroid transcription factors within this region. These elements interact with MYB, a critical regulator of erythroid development and HbF levels. We found that several HBS1L-MYB intergenic variants reduce transcription factor binding, affecting long-range interactions with MYB and MYB expression levels. These data provide a functional explanation for the genetic association of HBS1L-MYB intergenic polymorphisms with human erythroid traits and HbF levels. Our results further designate MYB as a target for therapeutic induction of HbF to ameliorate sickle cell and β-thalassemia disease severity.
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36
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Stadhouders R, de Bruijn MJW, Rother MB, Yuvaraj S, de Almeida CR, Kolovos P, Van Zelm MC, van Ijcken W, Grosveld F, Soler E, Hendriks RW. Pre-B cell receptor signaling induces immunoglobulin κ locus accessibility by functional redistribution of enhancer-mediated chromatin interactions. PLoS Biol 2014; 12:e1001791. [PMID: 24558349 PMCID: PMC3928034 DOI: 10.1371/journal.pbio.1001791] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 01/08/2014] [Indexed: 12/13/2022] Open
Abstract
Chromatin conformation analyses provide novel insights into how variable segments in the immunoglobulin light chain gene become accessible for recombination in precursor B lymphocytes. During B cell development, the precursor B cell receptor (pre-BCR) checkpoint is thought to increase immunoglobulin κ light chain (Igκ) locus accessibility to the V(D)J recombinase. Accordingly, pre-B cells lacking the pre-BCR signaling molecules Btk or Slp65 showed reduced germline Vκ transcription. To investigate whether pre-BCR signaling modulates Vκ accessibility through enhancer-mediated Igκ locus topology, we performed chromosome conformation capture and sequencing analyses. These revealed that already in pro-B cells the κ enhancers robustly interact with the ∼3.2 Mb Vκ region and its flanking sequences. Analyses in wild-type, Btk, and Slp65 single- and double-deficient pre-B cells demonstrated that pre-BCR signaling reduces interactions of both enhancers with Igκ locus flanking sequences and increases interactions of the 3′κ enhancer with Vκ genes. Remarkably, pre-BCR signaling does not significantly affect interactions between the intronic enhancer and Vκ genes, which are already robust in pro-B cells. Both enhancers interact most frequently with highly used Vκ genes, which are often marked by transcription factor E2a. We conclude that the κ enhancers interact with the Vκ region already in pro-B cells and that pre-BCR signaling induces accessibility through a functional redistribution of long-range chromatin interactions within the Vκ region, whereby the two enhancers play distinct roles. B lymphocyte development involves the generation of a functional antigen receptor, comprising two heavy chains and two light chains arranged in a characteristic “Y” shape. To do this, the receptor genes must first be assembled by ordered genomic recombination events, starting with the immunoglobulin heavy chain (IgH) gene segments. On successful rearrangement, the resulting IgH μ protein is presented on the cell surface as part of a preliminary version of the B cell receptor—the “pre-BCR.” Pre-BCR signaling then redirects recombination activity to the immunoglobulin κ light chain gene. The activity of two regulatory κ enhancer elements is known to be crucial for opening up the gene, but it remains largely unknown how the hundred or so Variable (V) segments in the κ locus gain access to the recombination system. Here, we studied a panel of pre-B cells from mice lacking specific signaling molecules, reflecting absent, partial, or complete pre-BCR signaling. We identify gene regulatory changes that are dependent on pre-BCR signaling and occur via long-range chromatin interactions between the κ enhancers and the V segments. Surprisingly the light chain gene initially contracts, but the interactions then become more functionally redistributed when pre-BCR signaling occurs. Interestingly, we find that the two enhancers play distinct roles in the process of coordinating chromatin interactions towards the V segments. Our study combines chromatin conformation techniques with data on transcription factor binding to gain unique insights into the functional role of chromatin dynamics.
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MESH Headings
- Animals
- Cells, Cultured
- Chromatin/genetics
- Chromatin/metabolism
- Chromatin Assembly and Disassembly
- Enhancer Elements, Genetic
- Epistasis, Genetic
- Histones/metabolism
- Immunoglobulin kappa-Chains/genetics
- Immunoglobulin kappa-Chains/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Precursor Cells, B-Lymphoid/metabolism
- Protein Processing, Post-Translational
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/metabolism
- Signal Transduction
- Transcriptome
- V(D)J Recombination
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Affiliation(s)
| | | | | | - Saravanan Yuvaraj
- Department of Pulmonary Medicine, Erasmus MC Rotterdam, The Netherlands
| | | | - Petros Kolovos
- Department of Cell Biology, Erasmus MC Rotterdam, The Netherlands
| | | | | | - Frank Grosveld
- Department of Cell Biology, Erasmus MC Rotterdam, The Netherlands
- The Cancer Genomics Center, Erasmus MC Rotterdam, The Netherlands
| | - Eric Soler
- Department of Cell Biology, Erasmus MC Rotterdam, The Netherlands
- The Cancer Genomics Center, Erasmus MC Rotterdam, The Netherlands
- INSERM UMR967 and French Alternative Energies and Atomic Energy Commission (CEA), Fontenay-aux-Roses, France
| | - Rudi W. Hendriks
- Department of Pulmonary Medicine, Erasmus MC Rotterdam, The Netherlands
- * E-mail:
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37
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Pourfarzad F, Aghajanirefah A, de Boer E, Ten Have S, Bryn van Dijk T, Kheradmandkia S, Stadhouders R, Thongjuea S, Soler E, Gillemans N, von Lindern M, Demmers J, Philipsen S, Grosveld F. Locus-specific proteomics by TChP: targeted chromatin purification. Cell Rep 2013; 4:589-600. [PMID: 23911284 DOI: 10.1016/j.celrep.2013.07.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/01/2013] [Accepted: 07/07/2013] [Indexed: 12/20/2022] Open
Abstract
Here, we show that transcription factors bound to regulatory sequences can be identified by purifying these unique sequences directly from mammalian cells in vivo. Using targeted chromatin purification (TChP), a double-pull-down strategy with a tetracycline-sensitive "hook" bound to a specific promoter, we identify transcription factors bound to the repressed γ-globin gene-associated regulatory regions. After validation of the binding, we show that, in human primary erythroid cells, knockdown of a number of these transcription factors induces γ-globin gene expression. Reactivation of γ-globin gene expression ameliorates the symptoms of β-thalassemia and sickle cell disease, and these factors provide potential targets for the development of therapeutics for treating these patients.
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Affiliation(s)
- Farzin Pourfarzad
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, the Netherlands; Center for Biomedical Genetics, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, the Netherlands
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38
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Price FD, Yin H, Jones A, van Ijcken W, Grosveld F, Rudnicki MA. Canonical Wnt Signaling Induces a Primitive Endoderm Metastable State in Mouse Embryonic Stem Cells. Stem Cells 2013; 31:752-64. [DOI: 10.1002/stem.1321] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 12/09/2012] [Indexed: 11/08/2022]
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39
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Abstract
On 11 to 13 March 2013, BioMed Central will be hosting its inaugural conference, Epigenetics & Chromatin: Interactions and Processes, at Harvard Medical School, Cambridge, MA, USA. Epigenetics & Chromatin has now launched a special article series based on the general themes of the conference.
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Affiliation(s)
- Steven Henikoff
- Howard Hughes Medical Institute and Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, WA, 98109-1024, Seattle, USA
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Dr. Molewaterplein 50, Rotterdam, The Netherlands
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40
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Huang Y, Kapere Ochieng J, Kempen MBV, Munck ABD, Swagemakers S, van IJcken W, Grosveld F, Tibboel D, Rottier RJ. Hypoxia inducible factor 3α plays a critical role in alveolarization and distal epithelial cell differentiation during mouse lung development. PLoS One 2013; 8:e57695. [PMID: 23451260 PMCID: PMC3581546 DOI: 10.1371/journal.pone.0057695] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 01/28/2013] [Indexed: 12/18/2022] Open
Abstract
Lung development occurs under relative hypoxia and the most important oxygen-sensitive response pathway is driven by Hypoxia Inducible Factors (HIF). HIFs are heterodimeric transcription factors of an oxygen-sensitive subunit, HIFα, and a constitutively expressed subunit, HIF1β. HIF1α and HIF2α, encoded by two separate genes, contribute to the activation of hypoxia inducible genes. A third HIFα gene, HIF3α, is subject to alternative promoter usage and splicing, leading to three major isoforms, HIF3α, NEPAS and IPAS. HIF3α gene products add to the complexity of the hypoxia response as they function as dominant negative inhibitors (IPAS) or weak transcriptional activators (HIF3α/NEPAS). Previously, we and others have shown the importance of the Hif1α and Hif2α factors in lung development, and here we investigated the role of Hif3α during pulmonary development. Therefore, HIF3α was conditionally expressed in airway epithelial cells during gestation and although HIF3α transgenic mice were born alive and appeared normal, their lungs showed clear abnormalities, including a post-pseudoglandular branching defect and a decreased number of alveoli. The HIF3α expressing lungs displayed reduced numbers of Clara cells, alveolar epithelial type I and type II cells. As a result of HIF3α expression, the level of Hif2α was reduced, but that of Hif1α was not affected. Two regulatory genes, Rarβ, involved in alveologenesis, and Foxp2, a transcriptional repressor of the Clara cell specific Ccsp gene, were significantly upregulated in the HIF3α expressing lungs. In addition, aberrant basal cells were observed distally as determined by the expression of Sox2 and p63. We show that Hif3α binds a conserved HRE site in the Sox2 promoter and weakly transactivated a reporter construct containing the Sox2 promoter region. Moreover, Hif3α affected the expression of genes not typically involved in the hypoxia response, providing evidence for a novel function of Hif3α beyond the hypoxia response.
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Affiliation(s)
- Yadi Huang
- Department of Pediatric Surgery, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Joshua Kapere Ochieng
- Department of Pediatric Surgery, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Marjon Buscop-van Kempen
- Department of Pediatric Surgery, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Anne Boerema-de Munck
- Department of Pediatric Surgery, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Sigrid Swagemakers
- Department of Bioinformatics, Erasmus MC, Rotterdam, The Netherlands
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | - Frank Grosveld
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Dick Tibboel
- Department of Pediatric Surgery, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Robbert J. Rottier
- Department of Pediatric Surgery, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
- * E-mail:
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41
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Stadhouders R, Kolovos P, Brouwer R, Zuin J, van den Heuvel A, Kockx C, Palstra RJ, Wendt KS, Grosveld F, van Ijcken W, Soler E. Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions. Nat Protoc 2013; 8:509-24. [PMID: 23411633 DOI: 10.1038/nprot.2013.018] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Chromosome conformation capture (3C) technology is a powerful and increasingly popular tool for analyzing the spatial organization of genomes. Several 3C variants have been developed (e.g., 4C, 5C, ChIA-PET, Hi-C), allowing large-scale mapping of long-range genomic interactions. Here we describe multiplexed 3C sequencing (3C-seq), a 4C variant coupled to next-generation sequencing, allowing genome-scale detection of long-range interactions with candidate regions. Compared with several other available techniques, 3C-seq offers a superior resolution (typically single restriction fragment resolution; approximately 1-8 kb on average) and can be applied in a semi-high-throughput fashion. It allows the assessment of long-range interactions of up to 192 genes or regions of interest in parallel by multiplexing library sequencing. This renders multiplexed 3C-seq an inexpensive, quick (total hands-on time of 2 weeks) and efficient method that is ideal for the in-depth analysis of complex genetic loci. The preparation of multiplexed 3C-seq libraries can be performed by any investigator with basic skills in molecular biology techniques. Data analysis requires basic expertise in bioinformatics and in Linux and Python environments. The protocol describes all materials, critical steps and bioinformatics tools required for successful application of 3C-seq technology.
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Affiliation(s)
- Ralph Stadhouders
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
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42
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Yin H, Pasut A, Soleimani VD, Bentzinger CF, Antoun G, Thorn S, Seale P, Fernando P, van Ijcken W, Grosveld F, Dekemp RA, Boushel R, Harper ME, Rudnicki MA. MicroRNA-133 controls brown adipose determination in skeletal muscle satellite cells by targeting Prdm16. Cell Metab 2013; 17:210-24. [PMID: 23395168 PMCID: PMC3641657 DOI: 10.1016/j.cmet.2013.01.004] [Citation(s) in RCA: 223] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 08/18/2012] [Accepted: 01/11/2013] [Indexed: 12/17/2022]
Abstract
Brown adipose tissue (BAT) is an energy-dispensing thermogenic tissue that plays an important role in balancing energy metabolism. Lineage-tracing experiments indicate that brown adipocytes are derived from myogenic progenitors during embryonic development. However, adult skeletal muscle stem cells (satellite cells) have long been considered uniformly determined toward the myogenic lineage. Here, we report that adult satellite cells give rise to brown adipocytes and that microRNA-133 regulates the choice between myogenic and brown adipose determination by targeting the 3'UTR of Prdm16. Antagonism of microRNA-133 during muscle regeneration increases uncoupled respiration, glucose uptake, and thermogenesis in local treated muscle and augments whole-body energy expenditure, improves glucose tolerance, and impedes the development of diet-induced obesity. Finally, we demonstrate that miR-133 levels are downregulated in mice exposed to cold, resulting in de novo generation of satellite cell-derived brown adipocytes. Therefore, microRNA-133 represents an important therapeutic target for the treatment of obesity.
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Affiliation(s)
- Hang Yin
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
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43
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Papadopoulos P, Gutiérrez L, van der Linden R, Kong-A-San J, Maas A, Drabek D, Patrinos GP, Philipsen S, Grosveld F. A dual reporter mouse model of the human β-globin locus: applications and limitations. PLoS One 2012; 7:e51272. [PMID: 23272095 PMCID: PMC3522686 DOI: 10.1371/journal.pone.0051272] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2012] [Accepted: 10/30/2012] [Indexed: 12/27/2022] Open
Abstract
The human β-globin locus contains the β-like globin genes (i.e. fetal γ-globin and adult β-globin), which heterotetramerize with α-globin subunits to form fetal or adult hemoglobin. Thalassemia is one of the commonest inherited disorders in the world, which results in quantitative defects of the globins, based on a number of genome variations found in the globin gene clusters. Hereditary persistence of fetal hemoglobin (HPFH) also caused by similar types of genomic alterations can compensate for the loss of adult hemoglobin. Understanding the regulation of the human γ-globin gene expression is a challenge for the treatment of thalassemia. A mouse model that facilitates high-throughput assays would simplify such studies. We have generated a transgenic dual reporter mouse model by tagging the γ- and β-globin genes with GFP and DsRed fluorescent proteins respectively in the endogenous human β-globin locus. Erythroid cell lines derived from this mouse model were tested for their capacity to reactivate the γ-globin gene. Here, we discuss the applications and limitations of this fluorescent reporter model to study the genetic basis of red blood cell disorders and the potential use of such model systems in high-throughput screens for hemoglobinopathies therapeutics.
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Affiliation(s)
| | - Laura Gutiérrez
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | | | - John Kong-A-San
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Alex Maas
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - George P. Patrinos
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
- Department of Pharmacy, University of Patras, Patras, Greece
| | - Sjaak Philipsen
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
- * E-mail:
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44
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Wright S, DeBoer E, Rosenthal A, Flavell RA, Grosveld F. Notice of redundant publicationDNA sequences required for regulated expression of β-globin genes in murine erythroleukaemia cells. Philos Trans R Soc Lond B Biol Sci 2012. [DOI: 10.1098/rstb.2012.0385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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45
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Pourfarzad F, von Lindern M, Azarkeivan A, Hou J, Kia SK, Esteghamat F, van Ijcken W, Philipsen S, Najmabadi H, Grosveld F. Hydroxyurea responsiveness in β-thalassemic patients is determined by the stress response adaptation of erythroid progenitors and their differentiation propensity. Haematologica 2012; 98:696-704. [PMID: 23100274 DOI: 10.3324/haematol.2012.074492] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
β-thalassemia is caused by mutations in the β-globin locus resulting in loss of, or reduced, hemoglobin A (adult hemoglobin, HbA, α2β2) production. Hydroxyurea treatment increases fetal γ-globin (fetal hemoglobin, HbF, α2γ2) expression in postnatal life substituting for the missing adult β-globin and is, therefore, an attractive therapeutic approach. Patients treated with hydroxyurea fall into three categories: i) 'responders' who increase hemoglobin to therapeutic levels; (ii) 'moderate-responders' who increase hemoglobin levels but still need transfusions at longer intervals; and (iii) 'non-responders' who do not reach adequate hemoglobin levels and remain transfusion-dependent. The mechanisms underlying these differential responses remain largely unclear. We generated RNA expression profiles from erythroblast progenitors of 8 responder and 8 non-responder β-thalassemia patients. These profiles revealed that hydroxyurea treatment induced differential expression of many genes in cells from non-responders while it had little impact on cells from responders. Part of the gene program up-regulated by hydroxyurea in non-responders was already highly expressed in responders before hydroxyurea treatment. Baseline HbF expression was low in non-responders, and hydroxyurea treatment induced significant cell death. We conclude that cells from responders have adapted well to constitutive stress conditions and display a propensity to proceed to the erythroid differentiation program.
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46
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Palstra RJ, Grosveld F. Transcription factor binding at enhancers: shaping a genomic regulatory landscape in flux. Front Genet 2012; 3:195. [PMID: 23060900 PMCID: PMC3460357 DOI: 10.3389/fgene.2012.00195] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 09/12/2012] [Indexed: 12/26/2022] Open
Abstract
The mammalian genome is packed tightly in the nucleus of the cell. This packing is primarily facilitated by histone proteins and results in an ordered organization of the genome in chromosome territories that can be roughly divided in heterochromatic and euchromatic domains. On top of this organization several distinct gene regulatory elements on the same chromosome or other chromosomes are thought to dynamically communicate via chromatin looping. Advances in genome-wide technologies have revealed the existence of a plethora of these regulatory elements in various eukaryotic genomes. These regulatory elements are defined by particular in vitro assays as promoters, enhancers, insulators, and boundary elements. However, recent studies indicate that the in vivo distinction between these elements is often less strict. Regulatory elements are bound by a mixture of common and lineage-specific transcription factors which mediate the long-range interactions between these elements. Inappropriate modulation of the binding of these transcription factors can alter the interactions between regulatory elements, which in turn leads to aberrant gene expression with disease as an ultimate consequence. Here we discuss the bi-modal behavior of regulatory elements that act in cis (with a focus on enhancers), how their activity is modulated by transcription factor binding and the effect this has on gene regulation.
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Affiliation(s)
- Robert-Jan Palstra
- Department of Cell Biology, Erasmus MC University Medical Center Rotterdam, Netherlands
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47
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Fanis P, Gillemans N, Aghajanirefah A, Pourfarzad F, Demmers J, Esteghamat F, Vadlamudi RK, Grosveld F, Philipsen S, van Dijk TB. Five friends of methylated chromatin target of protein-arginine-methyltransferase[prmt]-1 (chtop), a complex linking arginine methylation to desumoylation. Mol Cell Proteomics 2012; 11:1263-73. [PMID: 22872859 DOI: 10.1074/mcp.m112.017194] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chromatin target of Prmt1 (Chtop) is a vertebrate-specific chromatin-bound protein that plays an important role in transcriptional regulation. As its mechanism of action remains unclear, we identified Chtop-interacting proteins using a biotinylation-proteomics approach. Here we describe the identification and initial characterization of Five Friends of Methylated Chtop (5FMC). 5FMC is a nuclear complex that can only be recruited by Chtop when the latter is arginine-methylated by Prmt1. It consists of the co-activator Pelp1, the Sumo-specific protease Senp3, Wdr18, Tex10, and Las1L. Pelp1 functions as the core of 5FMC, as the other components become unstable in the absence of Pelp1. We show that recruitment of 5FMC to Zbp-89, a zinc-finger transcription factor, affects its sumoylation status and transactivation potential. Collectively, our data provide a mechanistic link between arginine methylation and (de)sumoylation in the control of transcriptional activity.
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Affiliation(s)
- Pavlos Fanis
- Department of Cell Biology, Erasmus MC, 3000 CA, Rotterdam, The Netherlands
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48
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Stadhouders R, van den Heuvel A, Kolovos P, Jorna R, Leslie K, Grosveld F, Soler E. Transcription regulation by distal enhancers: who's in the loop? Transcription 2012; 3:181-6. [PMID: 22771987 DOI: 10.4161/trns.20720] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genome-wide chromatin profiling efforts have shown that enhancers are often located at large distances from gene promoters within the noncoding genome. Whereas enhancers can stimulate transcription initiation by communicating with promoters via chromatin looping mechanisms, we propose that enhancers may also stimulate transcription elongation by physical interactions with intronic elements. We review here recent findings derived from the study of the hematopoietic system.
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Affiliation(s)
- Ralph Stadhouders
- Department of Cell Biology; Erasmus Medical Center, Rotterdam, The Netherlands
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49
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Carvalho RH, Haberle V, Hou J, van Gent T, Thongjuea S, van Ijcken W, Kockx C, Brouwer R, Rijkers E, Sieuwerts A, Foekens J, van Vroonhoven M, Aerts J, Grosveld F, Lenhard B, Philipsen S. Genome-wide DNA methylation profiling of non-small cell lung carcinomas. Epigenetics Chromatin 2012; 5:9. [PMID: 22726460 PMCID: PMC3407794 DOI: 10.1186/1756-8935-5-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 06/22/2012] [Indexed: 12/15/2022] Open
Abstract
Background Non-small cell lung carcinoma (NSCLC) is a complex malignancy that owing to its heterogeneity and poor prognosis poses many challenges to diagnosis, prognosis and patient treatment. DNA methylation is an important mechanism of epigenetic regulation involved in normal development and cancer. It is a very stable and specific modification and therefore in principle a very suitable marker for epigenetic phenotyping of tumors. Here we present a genome-wide DNA methylation analysis of NSCLC samples and paired lung tissues, where we combine MethylCap and next generation sequencing (MethylCap-seq) to provide comprehensive DNA methylation maps of the tumor and paired lung samples. The MethylCap-seq data were validated by bisulfite sequencing and methyl-specific polymerase chain reaction of selected regions. Results Analysis of the MethylCap-seq data revealed a strong positive correlation between replicate experiments and between paired tumor/lung samples. We identified 57 differentially methylated regions (DMRs) present in all NSCLC tumors analyzed by MethylCap-seq. While hypomethylated DMRs did not correlate to any particular functional category of genes, the hypermethylated DMRs were strongly associated with genes encoding transcriptional regulators. Furthermore, subtelomeric regions and satellite repeats were hypomethylated in the NSCLC samples. We also identified DMRs that were specific to two of the major subtypes of NSCLC, adenocarcinomas and squamous cell carcinomas. Conclusions Collectively, we provide a resource containing genome-wide DNA methylation maps of NSCLC and their paired lung tissues, and comprehensive lists of known and novel DMRs and associated genes in NSCLC.
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Affiliation(s)
- Rejane Hughes Carvalho
- Department of Cell Biology, ErasmusMC, PO Box 2040, Rotterdam, CA, 3000, The Netherlands.
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50
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Sleutels F, Soochit W, Bartkuhn M, Heath H, Dienstbach S, Bergmaier P, Franke V, Rosa-Garrido M, van de Nobelen S, Caesar L, van der Reijden M, Bryne JC, van Ijcken W, Grootegoed JA, Delgado MD, Lenhard B, Renkawitz R, Grosveld F, Galjart N. The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner. Epigenetics Chromatin 2012; 5:8. [PMID: 22709888 PMCID: PMC3418201 DOI: 10.1186/1756-8935-5-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 06/18/2012] [Indexed: 11/20/2022] Open
Abstract
Background CTCF is a highly conserved and essential zinc finger protein expressed in virtually all cell types. In conjunction with cohesin, it organizes chromatin into loops, thereby regulating gene expression and epigenetic events. The function of CTCFL or BORIS, the testis-specific paralog of CTCF, is less clear. Results Using immunohistochemistry on testis sections and fluorescence-based microscopy on intact live seminiferous tubules, we show that CTCFL is only transiently present during spermatogenesis, prior to the onset of meiosis, when the protein co-localizes in nuclei with ubiquitously expressed CTCF. CTCFL distribution overlaps completely with that of Stra8, a retinoic acid-inducible protein essential for the propagation of meiosis. We find that absence of CTCFL in mice causes sub-fertility because of a partially penetrant testicular atrophy. CTCFL deficiency affects the expression of a number of testis-specific genes, including Gal3st1 and Prss50. Combined, these data indicate that CTCFL has a unique role in spermatogenesis. Genome-wide RNA expression studies in ES cells expressing a V5- and GFP-tagged form of CTCFL show that genes that are downregulated in CTCFL-deficient testis are upregulated in ES cells. These data indicate that CTCFL is a male germ cell gene regulator. Furthermore, genome-wide DNA-binding analysis shows that CTCFL binds a consensus sequence that is very similar to that of CTCF. However, only ~3,700 out of the ~5,700 CTCFL- and ~31,000 CTCF-binding sites overlap. CTCFL binds promoters with loosely assembled nucleosomes, whereas CTCF favors consensus sites surrounded by phased nucleosomes. Finally, an ES cell-based rescue assay shows that CTCFL is functionally different from CTCF. Conclusions Our data suggest that nucleosome composition specifies the genome-wide binding of CTCFL and CTCF. We propose that the transient expression of CTCFL in spermatogonia and preleptotene spermatocytes serves to occupy a subset of promoters and maintain the expression of male germ cell genes.
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Affiliation(s)
- Frank Sleutels
- Department of Cell Biology Erasmus Medical Center, Rotterdam, The Netherlands.
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