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Develtere W, Decaestecker W, Rombaut D, Anders C, Clicque E, Vuylsteke M, Jacobs TB. Continual improvement of CRISPR-induced multiplex mutagenesis in Arabidopsis. Plant J 2024. [PMID: 38713824 DOI: 10.1111/tpj.16785] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 05/09/2024]
Abstract
CRISPR/Cas9 is currently the most powerful tool to generate mutations in plant genomes and more efficient tools are needed as the scale of experiments increases. In the model plant Arabidopsis, the choice of the promoter driving Cas9 expression is critical to generate germline mutations. Several optimal promoters have been reported. However, it is unclear which promoter is ideal as they have not been thoroughly tested side by side. Furthermore, most plant vectors still use one of the two Cas9 nuclear localization sequence (NLS) configurations initially reported. We genotyped more than 6000 Arabidopsis T2 plants to test seven promoters and six types of NLSs across 14 targets to systematically improve the generation of single and multiplex inheritable mutations. We found that the RPS5A promoter and bipartite NLS were individually the most efficient components. When combined, 99% of T2 plants contained at least one knockout (KO) mutation and 84% contained 4- to 7-plex KOs, the highest multiplexing KO rate in Arabidopsis to date. These optimizations will be useful to generate higher-order KOs in the germline of Arabidopsis and will likely be applicable to other CRISPR systems as well.
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Affiliation(s)
- Ward Develtere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Ward Decaestecker
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Debbie Rombaut
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Chantal Anders
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Elke Clicque
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | | | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
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2
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Bruggeman A, Vandendriessche C, Hamerlinck H, De Looze D, Tate DJ, Vuylsteke M, De Commer L, Devolder L, Raes J, Verhasselt B, Laukens D, Vandenbroucke RE, Santens P. Safety and efficacy of faecal microbiota transplantation in patients with mild to moderate Parkinson's disease (GUT-PARFECT): a double-blind, placebo-controlled, randomised, phase 2 trial. EClinicalMedicine 2024; 71:102563. [PMID: 38686220 PMCID: PMC11056595 DOI: 10.1016/j.eclinm.2024.102563] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 05/02/2024] Open
Abstract
Background Dysregulation of the gut microbiome has been implicated in Parkinson's disease (PD). This study aimed to evaluate the clinical effects and safety of a single faecal microbiota transplantation (FMT) in patients with early-stage PD. Methods The GUT-PARFECT trial, a single-centre randomised, double-blind, placebo-controlled trial was conducted at Ghent University Hospital between December 01, 2020 and December 12, 2022. Participants (aged 50-65 years, Hoehn and Yahr stage 2) were randomly assigned to receive nasojejunal FMT with either healthy donor stool or their own stool. Computer-generated randomisation was done in a 1:1 ratio through permutated-block scheduling. Treatment allocation was concealed for participants and investigators. The primary outcome measure at 12 months was the change in the Movement Disorders Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) motor score obtained during off-medication evaluations. Intention-to-treat analysis was performed using a mixed model for repeated measures analysis. This completed trial is registered on ClinicalTrials.gov (NCT03808389). Findings Between December 2020 and December 2021, FMT procedures were conducted on 46 patients with PD: 22 in the healthy donor group and 24 in the placebo group. Clinical evaluations were performed at baseline, 3, 6, and 12 months post-FMT. Full data analysis was possible for 21 participants in the healthy donor group and 22 in the placebo group. After 12 months, the MDS-UPDRS motor score significantly improved by a mean of 5.8 points (95% CI -11.4 to -0.2) in the healthy donor group and by 2.7 points (-8.3 to 2.9) in the placebo group (p = 0.0235). Adverse events were limited to temporary abdominal discomfort. Interpretation Our findings suggested a single FMT induced mild, but long-lasting beneficial effects on motor symptoms in patients with early-stage PD. These findings highlight the potential of modulating the gut microbiome as a therapeutic approach and warrant a further exploration of FMT in larger cohorts of patients with PD in various disease stages. Funding Flemish PD patient organizations (VPL and Parkili), Research Foundation Flanders (FWO), Biocodex Microbiota Foundation.
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Affiliation(s)
- Arnout Bruggeman
- Department of Neurology, University Hospital Ghent, Ghent, Belgium
- Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium
- Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Charysse Vandendriessche
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium
- Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Hannelore Hamerlinck
- Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Danny De Looze
- Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of Gastroenterology, University Hospital Ghent, Ghent, Belgium
| | - David J. Tate
- Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of Gastroenterology, University Hospital Ghent, Ghent, Belgium
| | - Marnik Vuylsteke
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium
- Statistics for Biosciences, Gnomixx, Melle, Belgium
| | - Lindsey De Commer
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, VIB, Leuven, Belgium
| | - Lindsay Devolder
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, VIB, Leuven, Belgium
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, VIB, Leuven, Belgium
| | - Bruno Verhasselt
- Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Debby Laukens
- Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Roosmarijn E. Vandenbroucke
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium
- Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Patrick Santens
- Department of Neurology, University Hospital Ghent, Ghent, Belgium
- Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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3
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Bogaert A, Fijalkowska D, Staes A, Van de Steene T, Vuylsteke M, Stadler C, Eyckerman S, Spirohn K, Hao T, Calderwood MA, Gevaert K. N-terminal proteoforms may engage in different protein complexes. Life Sci Alliance 2023; 6:e202301972. [PMID: 37316325 PMCID: PMC10267514 DOI: 10.26508/lsa.202301972] [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: 02/06/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023] Open
Abstract
Alternative translation initiation and alternative splicing may give rise to N-terminal proteoforms, proteins that differ at their N-terminus compared with their canonical counterparts. Such proteoforms can have altered localizations, stabilities, and functions. Although proteoforms generated from splice variants can be engaged in different protein complexes, it remained to be studied to what extent this applies to N-terminal proteoforms. To address this, we mapped the interactomes of several pairs of N-terminal proteoforms and their canonical counterparts. First, we generated a catalogue of N-terminal proteoforms found in the HEK293T cellular cytosol from which 22 pairs were selected for interactome profiling. In addition, we provide evidence for the expression of several N-terminal proteoforms, identified in our catalogue, across different human tissues, as well as tissue-specific expression, highlighting their biological relevance. Protein-protein interaction profiling revealed that the overlap of the interactomes for both proteoforms is generally high, showing their functional relation. We also showed that N-terminal proteoforms can be engaged in new interactions and/or lose several interactions compared with their canonical counterparts, thus further expanding the functional diversity of proteomes.
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Affiliation(s)
- Annelies Bogaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Daria Fijalkowska
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - An Staes
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tessa Van de Steene
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Charlotte Stadler
- Department of Protein Science, KTH Royal Institute of Technology and Science for Life Laboratories, Stockholm, Sweden
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kerstin Spirohn
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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4
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Ferreira A, Timmerman E, Staes A, Vuylsteke M, De Muynck L, Gevaert K. Protein interactors of 3-O sulfated heparan sulfates in human MCI and age-matched control cerebrospinal fluid. Sci Data 2023; 10:121. [PMID: 36879013 PMCID: PMC9986659 DOI: 10.1038/s41597-023-02009-1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/07/2023] [Indexed: 03/08/2023] Open
Abstract
Heparan sulfates (HS) proteoglycans are commonly found on the cell surface and mediate many processes. Binding of HS ligands is determined by the sulfation code on the HS chain that can be N-/2-O/6-O- or 3-O-sulfated, generating heterogenous sulfation patterns. 3-O sulfated HS (3S-HS) play a role in several (patho)physiological processes such as blood coagulation, viral pathogenesis and binding and internalization of tau in Alzheimer's disease. However, few 3S-HS-specific interactors are known. Thus, our insight into the role of 3S-HS in health and disease is limited, especially in the central nervous system. Using human CSF, we determined the interactome of synthetic HS with defined sulfation patterns. Our affinity-enrichment mass spectrometry studies expand the repertoire of proteins that may interact with (3S-)HS. Validating our approach, ATIII, a known 3S-HS interactor, was found to require GlcA-GlcNS6S3S for binding, similar to what has been reported. Our dataset holds novel, potential HS and 3S-HS protein ligands, that can be explored in future studies focusing on molecular mechanisms that depend on 3S-HS in (patho)physiological conditions.
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Affiliation(s)
- Andreia Ferreira
- Janssen Research & Development, a Division of Janssen Pharmaceutica N.V., 2340, Beerse, Belgium
- VIB-UGent Center for Medical Biotechnology, B-9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9052, Ghent, Belgium
| | - Evy Timmerman
- VIB-UGent Center for Medical Biotechnology, B-9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9052, Ghent, Belgium
- VIB Proteomics Core, B-9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9000, Ghent, Belgium
| | - An Staes
- VIB-UGent Center for Medical Biotechnology, B-9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9052, Ghent, Belgium
| | | | - Louis De Muynck
- Janssen Research & Development, a Division of Janssen Pharmaceutica N.V., 2340, Beerse, Belgium.
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, B-9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9052, Ghent, Belgium.
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5
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Portela Catani JP, Ysenbaert T, Smet A, Vuylsteke M, Vogel TU, Saelens X. Anti-neuraminidase and anti-hemagglutinin immune serum can confer inter-lineage cross protection against recent influenza B. PLoS One 2023; 18:e0280825. [PMID: 36689429 PMCID: PMC9870131 DOI: 10.1371/journal.pone.0280825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
Influenza B viruses (IBV) are responsible for a considerable part of the burden caused by influenza virus infections. Since their emergence in the 1980s, the Yamagata and Victoria antigenic lineages of influenza B circulate in alternate patterns across the globe. Furthermore, their evolutionary divergence and the appearance of new IBV subclades complicates the prediction of future influenza vaccines compositions. It has been proposed that the addition of the neuraminidase (NA) antigen could potentially induce a broader protection and compensate for hemagglutinin (HA) mismatches in the current vaccines. Here we show that anti-NA and -HA sera against both Victoria and Yamagata lineages have limited inter-lineage cross-reactivity. When transferred to mice prior to infection with a panel of IBVs, anti-NA sera were as potent as anti-HA sera in conferring protection against homologous challenge and, in some cases, conferred superior protection against challenge with heterologous IBV strains.
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Affiliation(s)
- João Paulo Portela Catani
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Tine Ysenbaert
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Anouk Smet
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | | | - Thorsten U. Vogel
- Sanofi, Research North America, Cambridge, Massachusetts, United States of America
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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6
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Van Poelvoorde LAE, Delcourt T, Vuylsteke M, De Keersmaecker SCJ, Thomas I, Van Gucht S, Saelens X, Roosens N, Vanneste K. A general approach to identify low-frequency variants within influenza samples collected during routine surveillance. Microb Genom 2022; 8. [PMID: 36169645 DOI: 10.1099/mgen.0.000867] [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] [Indexed: 11/18/2022] Open
Abstract
Influenza viruses exhibit considerable diversity between hosts. Additionally, different quasispecies can be found within the same host. High-throughput sequencing technologies can be used to sequence a patient-derived virus population at sufficient depths to identify low-frequency variants (LFV) present in a quasispecies, but many challenges remain for reliable LFV detection because of experimental errors introduced during sample preparation and sequencing. High genomic copy numbers and extensive sequencing depths are required to differentiate false positive from real LFV, especially at low allelic frequencies (AFs). This study proposes a general approach for identifying LFV in patient-derived samples obtained during routine surveillance. Firstly, validated thresholds were determined for LFV detection, whilst balancing both the cost and feasibility of reliable LFV detection in clinical samples. Using a genetically well-defined population of influenza A viruses, thresholds of at least 104 genomes per microlitre and AF of ≥5 % were established as detection limits. Secondly, a subset of 59 retained influenza A (H3N2) samples from the 2016-2017 Belgian influenza season was composed. Thirdly, as a proof of concept for the added value of LFV for routine influenza monitoring, potential associations between patient data and whole genome sequencing data were investigated. A significant association was found between a high prevalence of LFV and disease severity. This study provides a general methodology for influenza LFV detection, which can also be adopted by other national influenza reference centres and for other viruses such as SARS-CoV-2. Additionally, this study suggests that the current relevance of LFV for routine influenza surveillance programmes might be undervalued.
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Affiliation(s)
- Laura A E Van Poelvoorde
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium.,National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Thomas Delcourt
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | | | | | - Isabelle Thomas
- National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Steven Van Gucht
- National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Xavier Saelens
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Nancy Roosens
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
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Oltean T, Lippens L, Lemeire K, De Tender C, Vuylsteke M, Denys H, Vandecasteele K, Vandenabeele P, Adjemian S. Association of Cell Death Markers With Tumor Immune Cell Infiltrates After Chemo-Radiation in Cervical Cancer. Front Oncol 2022; 12:892813. [PMID: 35903697 PMCID: PMC9316180 DOI: 10.3389/fonc.2022.892813] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/08/2022] [Indexed: 11/20/2022] Open
Abstract
Irradiation induces distinct cellular responses such as apoptosis, necroptosis, iron-dependent cell death (a feature of ferroptosis), senescence, and mitotic catastrophe. Several of these outcomes are immunostimulatory and may represent a potential for immunogenic type of cell death (ICD) induced by radiotherapy triggering abscopal effects. The purpose of this study is to determine whether intra-tumoral ICD markers can serve as biomarkers for the prediction of patient's outcomes defined as the metastasis status and survival over a 5-year period. Thirty-eight patients with locally advanced cervical cancer, treated with neoadjuvant chemoradiotherapy using cisplatin were included in this study. Pre-treatment tumor biopsy and post-treatment hysterectomy samples were stained for cell death markers and danger associated molecular patterns (DAMPs): cleaved caspase-3 (apoptosis), phosphorylated mixed lineage kinase domain like pseudokinase (pMLKL; necroptosis), glutathione peroxidase 4 (GPX4; ferroptosis) and 4-hydroxy-2-noneal (4-HNE; ferroptosis), high mobility group box 1 (HMGB1) and calreticulin. Although these markers could not predict the patient's outcome in terms of relapse or survival, many significantly correlated with immune cell infiltration. For instance, inducing ferroptosis post-treatment seems to negatively impact immune cell recruitment. Measuring ICD markers could reflect the impact of treatment on the tumor microenvironment with regard to immune cell recruitment and infiltration. One Sentence Summary Cell death readouts during neoadjuvant chemoradiation in cervical cancer.
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Affiliation(s)
- Teodora Oltean
- Cell Death and Inflammation Unit, Vlaams Instituut voor Biotechnologie (VIB)-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lien Lippens
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Medical Oncology, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium
| | - Kelly Lemeire
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie (VIB)-UGent Center for Inflammation Research (IRC) Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
| | - Caroline De Tender
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | | | - Hannelore Denys
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Medical Oncology, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium
| | - Katrien Vandecasteele
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium
- Radiation Oncology, Ghent University Hospital, Ghent, Belgium
| | - Peter Vandenabeele
- Cell Death and Inflammation Unit, Vlaams Instituut voor Biotechnologie (VIB)-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Methusalem Program, Ghent University, Ghent, Belgium
| | - Sandy Adjemian
- Cell Death and Inflammation Unit, Vlaams Instituut voor Biotechnologie (VIB)-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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8
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Uwimana B, Mwanje G, Batte M, Akech V, Shah T, Vuylsteke M, Swennen R. Continuous Mapping Identifies Loci Associated With Weevil Resistance [ Cosmopolites sordidus (Germar)] in a Triploid Banana Population. Front Plant Sci 2021; 12:753241. [PMID: 34912355 PMCID: PMC8667469 DOI: 10.3389/fpls.2021.753241] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/14/2021] [Indexed: 06/14/2023]
Abstract
The first step toward marker-assisted selection is linking the phenotypes to molecular markers through quantitative trait loci (QTL) analysis. While the process is straightforward in self-pollinating diploid (2x) species, QTL analysis in polyploids requires unconventional methods. In this study, we have identified markers associated with weevil Cosmopolites sordidus (Germar) resistance in bananas using 138 triploid (2n = 3x) hybrids derived from a cross between a tetraploid "Monyet" (2n = 4x) and a 2x "Kokopo" (2n = 2x) banana genotypes. The population was genotyped by Diversity Arrays Technology Sequencing (DArTSeq), resulting in 18,009 polymorphic single nucleotide polymorphisms (SNPs) between the two parents. Marker-trait association was carried out by continuous mapping where the adjusted trait means for the corm peripheral damage (PD) and total cross-section damage (TXD), both on the logit scale, were regressed on the marker allele frequencies. Forty-four SNPs that were associated with corm PD were identified on the chromosomes 5, 6, and 8, with 41 of them located on chromosome 6 and segregated in "Kokopo." Eleven SNPs associated with corm total TXD were identified on chromosome 6 and segregated in "Monyet." The additive effect of replacing one reference allele with the alternative allele was determined at each marker position. The PD QTL was confirmed using conventional QTL linkage analysis in the simplex markers segregating in "Kokopo" (AAAA × RA). We also identified 43 putative genes in the vicinity of the markers significantly associated with the two traits. The identified loci associated with resistance to weevil damage will be used in the efforts of developing molecular tools for marker-assisted breeding in bananas.
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Affiliation(s)
- Brigitte Uwimana
- International Institute of Tropical Agriculture (IITA), Kampala, Uganda
| | - Gerald Mwanje
- International Institute of Tropical Agriculture (IITA), Kampala, Uganda
| | - Michael Batte
- International Institute of Tropical Agriculture (IITA), Kampala, Uganda
| | - Violet Akech
- International Institute of Tropical Agriculture (IITA), Kampala, Uganda
| | - Trushar Shah
- International Institute of Tropical Agriculture (IITA), International Livestock Research Institute Campus, Nairobi, Kenya
| | | | - Rony Swennen
- International Institute of Tropical Agriculture (IITA), Kampala, Uganda
- Department of Crop Biosystems, KU Leuven, Heverlee, Belgium
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9
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De Vos S, Rombauts S, Coussement L, Dermauw W, Vuylsteke M, Sorgeloos P, Clegg JS, Nambu Z, Van Nieuwerburgh F, Norouzitallab P, Van Leeuwen T, De Meyer T, Van Stappen G, Van de Peer Y, Bossier P. The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments. BMC Genomics 2021; 22:635. [PMID: 34465293 PMCID: PMC8406910 DOI: 10.1186/s12864-021-07937-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 08/14/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Brine shrimp Artemia have an unequalled ability to endure extreme salinity and complete anoxia. This study aims to elucidate its strategies to cope with these stressors. RESULTS AND DISCUSSION Here, we present the genome of an inbred A. franciscana Kellogg, 1906. We identified 21,828 genes of which, under high salinity, 674 genes and under anoxia, 900 genes were differentially expressed (42%, respectively 30% were annotated). Under high salinity, relevant stress genes and pathways included several Heat Shock Protein and Leaf Embryogenesis Abundant genes, as well as the trehalose metabolism. In addition, based on differential gene expression analysis, it can be hypothesized that a high oxidative stress response and endocytosis/exocytosis are potential salt management strategies, in addition to the expression of major facilitator superfamily genes responsible for transmembrane ion transport. Under anoxia, genes involved in mitochondrial function, mTOR signalling and autophagy were differentially expressed. Both high salt and anoxia enhanced degradation of erroneous proteins and protein chaperoning. Compared with other branchiopod genomes, Artemia had 0.03% contracted and 6% expanded orthogroups, in which 14% of the genes were differentially expressed under high salinity or anoxia. One phospholipase D gene family, shown to be important in plant stress response, was uniquely present in both extremophiles Artemia and the tardigrade Hypsibius dujardini, yet not differentially expressed under the described experimental conditions. CONCLUSIONS A relatively complete genome of Artemia was assembled, annotated and analysed, facilitating research on its extremophile features, and providing a reference sequence for crustacean research.
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Affiliation(s)
- Stephanie De Vos
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Department of Plant Systems Biology, VIB, Department of Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Stephane Rombauts
- Department of Plant Systems Biology, VIB, Department of Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Louis Coussement
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Wannes Dermauw
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | | | - Patrick Sorgeloos
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - James S Clegg
- Coastal and Marine Sciences Institute, University of California, Bodega Bay, Davis, CA, USA
| | - Ziro Nambu
- Department of Medical Technology, School of Health Sciences, University of Occupational and Environmental Health, Japan, Kitakyushu, Fukuoka, Japan
| | - Filip Van Nieuwerburgh
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Parisa Norouzitallab
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Laboratory for Immunology and Animal Biotechnology, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Thomas Van Leeuwen
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Gilbert Van Stappen
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Department of Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Peter Bossier
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
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10
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Pannecoucke E, Van Trimpont M, Desmet J, Pieters T, Reunes L, Demoen L, Vuylsteke M, Loverix S, Vandenbroucke K, Alard P, Henderikx P, Deroo S, Baatz F, Lorent E, Thiolloy S, Somers K, McGrath Y, Van Vlierberghe P, Lasters I, Savvides SN. Cell-penetrating Alphabody protein scaffolds for intracellular drug targeting. Sci Adv 2021; 7:7/13/eabe1682. [PMID: 33771865 PMCID: PMC7997521 DOI: 10.1126/sciadv.abe1682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 02/05/2021] [Indexed: 05/02/2023]
Abstract
The therapeutic scope of antibody and nonantibody protein scaffolds is still prohibitively limited against intracellular drug targets. Here, we demonstrate that the Alphabody scaffold can be engineered into a cell-penetrating protein antagonist against induced myeloid leukemia cell differentiation protein MCL-1, an intracellular target in cancer, by grafting the critical B-cell lymphoma 2 homology 3 helix of MCL-1 onto the Alphabody and tagging the scaffold's termini with designed cell-penetration polypeptides. Introduction of an albumin-binding moiety extended the serum half-life of the engineered Alphabody to therapeutically relevant levels, and administration thereof in mouse tumor xenografts based on myeloma cell lines reduced tumor burden. Crystal structures of such a designed Alphabody in complex with MCL-1 and serum albumin provided the structural blueprint of the applied design principles. Collectively, we provide proof of concept for the use of Alphabodies against intracellular disease mediators, which, to date, have remained in the realm of small-molecule therapeutics.
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Affiliation(s)
- Erwin Pannecoucke
- VIB Center for Inflammation Research, 9052 Ghent, Belgium
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, 9052 Ghent, Belgium
| | - Maaike Van Trimpont
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | | | - Tim Pieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lindy Reunes
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lisa Demoen
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | | | | | | | | | | | | | | | | | | | | | | | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | | | - Savvas N Savvides
- VIB Center for Inflammation Research, 9052 Ghent, Belgium.
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, 9052 Ghent, Belgium
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11
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Adjemian S, Oltean T, Martens S, Wiernicki B, Goossens V, Vanden Berghe T, Cappe B, Ladik M, Riquet FB, Heyndrickx L, Bridelance J, Vuylsteke M, Vandecasteele K, Vandenabeele P. Ionizing radiation results in a mixture of cellular outcomes including mitotic catastrophe, senescence, methuosis, and iron-dependent cell death. Cell Death Dis 2020; 11:1003. [PMID: 33230108 PMCID: PMC7684309 DOI: 10.1038/s41419-020-03209-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [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: 02/17/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022]
Abstract
Radiotherapy is commonly used as a cytotoxic treatment of a wide variety of tumors. Interestingly, few case reports underlined its potential to induce immune-mediated abscopal effects, resulting in regression of metastases, distant from the irradiated site. These observations are rare, and apparently depend on the dose used, suggesting that dose-related cellular responses may be involved in the distant immunogenic responses. Ionizing radiation (IR) has been reported to elicit immunogenic apoptosis, necroptosis, mitotic catastrophe, and senescence. In order to link a cellular outcome with a particular dose of irradiation, we performed a systematic study in a panel of cell lines on the cellular responses at different doses of X-rays. Remarkably, we observed that all cell lines tested responded in a similar fashion to IR with characteristics of mitotic catastrophe, senescence, lipid peroxidation, and caspase activity. Iron chelators (but not Ferrostatin-1 or vitamin E) could prevent the formation of lipid peroxides and cell death induced by IR, suggesting a crucial role of iron-dependent cell death during high-dose irradiation. We also show that in K-Ras-mutated cells, IR can induce morphological features reminiscent of methuosis, a cell death modality that has been recently described following H-Ras or K-Ras mutation overexpression.
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Affiliation(s)
- Sandy Adjemian
- Unit of Molecular Signaling and Cell Death, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Teodora Oltean
- Unit of Molecular Signaling and Cell Death, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Sofie Martens
- Unit of Molecular Signaling and Cell Death, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Bartosz Wiernicki
- Unit of Molecular Signaling and Cell Death, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Vera Goossens
- VIB Screening Core & UGhent Expertise Centre for Bioassay Development and Screening (C-BIOS), VIB, UGhent, Ghent, Belgium
| | - Tom Vanden Berghe
- Unit of Molecular Signaling and Cell Death, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.,Laboratory of Pathophysiology, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Benjamin Cappe
- Unit of Molecular Signaling and Cell Death, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Maria Ladik
- Unit of Molecular Signaling and Cell Death, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Franck B Riquet
- Unit of Molecular Signaling and Cell Death, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.,Université de Lille, Lille, France
| | - Liesbeth Heyndrickx
- Unit of Molecular Signaling and Cell Death, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Jolien Bridelance
- Unit of Molecular Signaling and Cell Death, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | | | - Katrien Vandecasteele
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium.,Radiation Oncology, Ghent University Hospital, Ghent, Belgium
| | - Peter Vandenabeele
- Unit of Molecular Signaling and Cell Death, VIB Center for Inflammation Research, Ghent, Belgium. .,Department of Biomedical Molecular Biology, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium. .,Cancer Research Institute Ghent (CRIG), Ghent, Belgium. .,Methusalem program, Ghent University, Ghent, Belgium.
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12
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Declercq J, Bosteels C, Van Damme K, De Leeuw E, Maes B, Vandecauter A, Vermeersch S, Delporte A, Demeyere B, Vuylsteke M, Lalla M, Smart T, Detalle L, Bouw R, Streffer J, Degeeter T, Vergotte M, Guisez T, Van Braeckel E, Van Der Straeten C, Lambrecht BN. Zilucoplan in patients with acute hypoxic respiratory failure due to COVID-19 (ZILU-COV): A structured summary of a study protocol for a randomised controlled trial. Trials 2020; 21:934. [PMID: 33213529 PMCID: PMC7675383 DOI: 10.1186/s13063-020-04884-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 11/04/2020] [Accepted: 11/10/2020] [Indexed: 11/10/2022] Open
Abstract
Objectives Zilucoplan (complement C5 inhibitor) has profound effects on inhibiting acute lung injury post COVID-19, and can promote lung repair mechanisms that lead to improvement in lung oxygenation parameters. The purpose of this study is to investigate the efficacy and safety of Zilucoplan in improving oxygenation and short- and long-term outcome of COVID-19 patients with acute hypoxic respiratory failure. Trial design This is a phase 2 academic, prospective, 2:1 randomized, open-label, multi-center interventional study. Participants Adult patients (≥18y old) will be recruited at specialized COVID-19 units and ICUs at 9 Belgian hospitals. The main eligibility criteria are as follows: 1) Inclusion criteria: a. Recent (≥6 days and ≤16 days) SARS-CoV-2 infection. b. Chest CT scan showing bilateral infiltrates within the last 2 days prior to randomisation. c. Acute hypoxia (defined as PaO2/FiO2 below 350 mmHg or SpO2 below 93% on minimal 2 L/min supplemental oxygen). d. Signs of cytokine release syndrome characterized by either high serum ferritin, or high D-dimers, or high LDH or deep lymphopenia or a combination of those. 2) Exclusion criteria: e. Mechanical ventilation for more than 24 hours prior to randomisation. f. Active bacterial or fungal infection. g. History of meningococcal disease (due to the known high predisposition to invasive, often recurrent meningococcal infections of individuals deficient in components of the alternative and terminal complement pathways). Intervention and comparator Patients in the experimental arm will receive daily 32,4 mg Zilucoplan subcutaneously and a daily IV infusion of 2g of the antibiotic ceftriaxone for 14 days (or until hospital discharge, whichever comes first) in addition to standard of care. These patients will receive additional prophylactic antibiotics until 14 days after the last Zilucoplan dose: hospitalized patients will receive a daily IV infusion of 2g of ceftriaxone, discharged patients will switch to daily 500 mg of oral ciprofloxacin. The control group will receive standard of care and a daily IV infusion of 2g of ceftriaxone for 1 week (or until hospital discharge, whichever comes first), to control for the effects of antibiotics on the clinical course of COVID-19. Main outcomes The primary endpoint is the improvement of oxygenation as measured by mean and/or median change from pre-treatment (day 1) to post-treatment (day 6 and 15 or at discharge, whichever comes first) in PaO2/FiO2 ratio, P(A-a)O2 gradient and a/A PO2 ratio. (PAO2= Partial alveolar pressure of oxygen, PaO2=partial arterial pressure of oxygen, FiO2=Fraction of inspired oxygen). Randomisation Patients will be randomized in a 2:1 ratio (Zilucoplan: control). Randomization will be done using an Interactive Web Response System (REDCap). Blinding (masking) In this open-label trial neither participants, caregivers, nor those assessing the outcomes will be blinded to group assignment. Numbers to be randomised (sample size) A total of 81 patients will be enrolled: 54 patients will be randomized to the experimental arm and 27 patients to the control arm. Trial Status ZILU-COV protocol Version 4.0 (June 10 2020). Participant recruitment started on June 23 2020 and is ongoing. Given the uncertainty of the pandemic, it is difficult to predict the anticipated end date. Trial registration The trial was registered on Clinical Trials.gov on May 11th, 2020 (ClinicalTrials.gov Identifier: NCT04382755) and on EudraCT (Identifier: 2020-002130-33). Full protocol The full protocol is attached as an additional file, accessible from the Trials website (Additional file 1). In the interest in expediting dissemination of this material, the familiar formatting has been eliminated; this Letter serves as a summary of the key elements of the full protocol. Supplementary Information The online version contains supplementary material available at 10.1186/s13063-020-04884-0.
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Affiliation(s)
- Jozefien Declercq
- VIB Center for Inflammation Research, Ghent, Belgium and Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Cedric Bosteels
- VIB Center for Inflammation Research, Ghent, Belgium and Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Karel Van Damme
- VIB Center for Inflammation Research, Ghent, Belgium and Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Elisabeth De Leeuw
- VIB Center for Inflammation Research, Ghent, Belgium and Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Bastiaan Maes
- VIB Center for Inflammation Research, Ghent, Belgium and Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | | | | | | | | | | | | | | | | | - René Bouw
- UCB Biopharma SRL, Braine-l'Alleud, Belgium
| | | | | | | | | | | | | | - Bart N Lambrecht
- VIB Center for Inflammation Research, Ghent, Belgium and Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.
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13
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Van Gorp H, Huang L, Saavedra P, Vuylsteke M, Asaoka T, Prencipe G, Insalaco A, Ogunjimi B, Jeyaratnam J, Cataldo I, Jacques P, Vermaelen K, Dullaers M, Joos R, Sabato V, Stella A, Frenkel J, De Benedetti F, Dehoorne J, Haerynck F, Calamita G, Portincasa P, Lamkanfi M. Blood-based test for diagnosis and functional subtyping of familial Mediterranean fever. Ann Rheum Dis 2020; 79:960-968. [PMID: 32312770 PMCID: PMC7307214 DOI: 10.1136/annrheumdis-2019-216701] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 11/25/2019] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND AND OBJECTIVE Familial Mediterranean fever (FMF) is the most common monogenic autoinflammatory disease (AID) worldwide. The disease is caused by mutations in the MEFV gene encoding the inflammasome sensor Pyrin. Clinical diagnosis of FMF is complicated by overlap in symptoms with other diseases, and interpretation of genetic testing is confounded by the lack of a clear genotype-phenotype association for most of the 340 reported MEFV variants. In this study, the authors designed a functional assay and evaluated its potential in supporting FMF diagnosis. METHODS Peripheral blood mononuclear cells (PBMCs) were obtained from patients with Pyrin-associated autoinflammation with an FMF phenotype (n=43) or with autoinflammatory features not compatible with FMF (n=8), 10 asymptomatic carriers and 48 healthy donors. Sera were obtained from patients with distinct AIDs (n=10), and whole blood from a subset of patients and controls. The clinical, demographic, molecular genetic factors and other characteristics of the patient population were assessed for their impact on the diagnostic test read-out. Interleukin (IL)-1β and IL-18 levels were measured by Luminex assay. RESULTS The ex vivo colchicine assay may be performed on whole blood or PBMC. The functional assay robustly segregated patients with FMF from healthy controls and patients with related clinical disorders. The diagnostic test distinguished patients with classical FMF mutations (M694V, M694I, M680I, R761H) from patients with other MEFV mutations and variants (K695R, P369S, R202Q, E148Q) that are considered benign or of uncertain clinical significance. CONCLUSION The ex vivo colchicine assay may support diagnosis of FMF and functional subtyping of Pyrin-associated autoinflammation.
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Affiliation(s)
- Hanne Van Gorp
- VIB Center for Inflammation Research, Zwijnaarde, Belgium
- Department of Internal Medicine and Paediatrics, Ghent University, Gent, Belgium
| | - Linyan Huang
- VIB Center for Inflammation Research, Zwijnaarde, Belgium
- Department of Internal Medicine and Paediatrics, Ghent University, Gent, Belgium
- School of Medical Technology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Pedro Saavedra
- VIB Center for Inflammation Research, Zwijnaarde, Belgium
- Department of Internal Medicine and Paediatrics, Ghent University, Gent, Belgium
| | | | - Tomoko Asaoka
- VIB Center for Inflammation Research, Zwijnaarde, Belgium
- Department of Internal Medicine and Paediatrics, Ghent University, Gent, Belgium
| | - Giusi Prencipe
- Rheumatology Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | | | - Benson Ogunjimi
- Department of Paediatrics, Antwerp University Hospital, Edegem, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
- Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
- Department of Paediatric Rheumatology, Antwerp Hospital Network, Berchem, Belgium
- Department of Paediatrics, University Hospital Brussel, Jette, Belgium
- Antwerp centre for paediatric rheumatology and auto-inflammatory diseases, Antwerp Hospital Network and Antwerp University Hospital, Antwerp, Belgium
| | - Jerold Jeyaratnam
- Department of Pediatric Rheumatology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Ilaria Cataldo
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Peggy Jacques
- VIB Center for Inflammation Research, Zwijnaarde, Belgium
- Department of Paediatric Rheumatology, Ghent University, Gent, Belgium
| | - Karim Vermaelen
- Department of Internal Medicine and Paediatrics, Ghent University, Gent, Belgium
- Tumor Immunology Laboratory, Department of Pulmonary Medicine, Ghent University Hospital, Gent, Belgium
| | - Melissa Dullaers
- VIB Center for Inflammation Research, Zwijnaarde, Belgium
- Clinical Immunology Research Lab, Centre for Primary Immunodeficiency Ghent, Ghent University Hospital, Gent, Belgium
| | - Rik Joos
- Antwerp centre for paediatric rheumatology and auto-inflammatory diseases, Antwerp Hospital Network and Antwerp University Hospital, Antwerp, Belgium
- Department of Pediatric Rheumatology, Ghent University Hospital, Gent, Belgium
| | - Vito Sabato
- Antwerp centre for paediatric rheumatology and auto-inflammatory diseases, Antwerp Hospital Network and Antwerp University Hospital, Antwerp, Belgium
- Immunology-Allergology-Rheumatology, University of Antwerp and Antwerp University Hospital, Edegem, Belgium
| | - Alessandro Stella
- Division of Medical Genetics, Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - Joost Frenkel
- Department of Pediatric Rheumatology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Joke Dehoorne
- VIB Center for Inflammation Research, Zwijnaarde, Belgium
- Department of Paediatric Rheumatology, Ghent University, Gent, Belgium
| | - Filomeen Haerynck
- Clinical Immunology Research Lab, Centre for Primary Immunodeficiency Ghent, Ghent University Hospital, Gent, Belgium
- Department of Paediatric Immunology and Pulmonology, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Gent, Belgium
| | - Giuseppe Calamita
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Piero Portincasa
- Division of Internal Medicine, Department of Biomedical Sciences and Human Oncology, Clinica Medica "A Murri", University of Bari "Aldo Moro", Bari, Italy
| | - Mohamed Lamkanfi
- VIB Center for Inflammation Research, Zwijnaarde, Belgium
- Department of Internal Medicine and Paediatrics, Ghent University, Gent, Belgium
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14
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Bosteels C, Maes B, Van Damme K, De Leeuw E, Declercq J, Delporte A, Demeyere B, Vermeersch S, Vuylsteke M, Willaert J, Bollé L, Vanbiervliet Y, Decuypere J, Libeer F, Vandecasteele S, Peene I, Lambrecht BN. Correction to: Sargramostim to treat patients with acute hypoxic respiratory failure due to COVID-19 (SARPAC): A structured summary of a study protocol for a randomised controlled trial. Trials 2020; 21:554. [PMID: 32571428 PMCID: PMC7306655 DOI: 10.1186/s13063-020-04520-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via the original article.
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Affiliation(s)
- Cedric Bosteels
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Bastiaan Maes
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium.
| | - Karel Van Damme
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | | | - Jozefien Declercq
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Anja Delporte
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | | | | | - Marnik Vuylsteke
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Joren Willaert
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Laura Bollé
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Yuri Vanbiervliet
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Jana Decuypere
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Frederick Libeer
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | | | - Isabelle Peene
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Bart N Lambrecht
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
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15
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Maes B, Bosteels C, De Leeuw E, Declercq J, Van Damme K, Delporte A, Demeyere B, Vermeersch S, Vuylsteke M, Willaert J, Bollé L, Vanbiervliet Y, Decuypere J, Libeer F, Vandecasteele S, Peene I, Lambrecht BN. Correction to: Treatment of severely ill COVID-19 patients with anti-interleukin drugs (COV-AID): A structured summary of a study protocol for a randomised controlled trial. Trials 2020; 21:556. [PMID: 32571394 PMCID: PMC7306650 DOI: 10.1186/s13063-020-04519-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Bastiaan Maes
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium.
| | - Cedric Bosteels
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | | | - Jozefien Declercq
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Karel Van Damme
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Anja Delporte
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | | | | | - Marnik Vuylsteke
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Joren Willaert
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Laura Bollé
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Yuri Vanbiervliet
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Jana Decuypere
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Frederick Libeer
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | | | - Isabelle Peene
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Bart N Lambrecht
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
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Bosteels C, Maes B, Van Damme K, De Leeuw E, Declercq J, Delporte A, Demeyere B, Vermeersch S, Vuylsteke M, Willaert J, Bollé L, Vanbiervliet Y, Decuypere J, Libeer F, Vandecasteele S, Peene I, Lambrecht B. Sargramostim to treat patients with acute hypoxic respiratory failure due to COVID-19 (SARPAC): A structured summary of a study protocol for a randomised controlled trial. Trials 2020; 21:491. [PMID: 32503663 PMCID: PMC7273817 DOI: 10.1186/s13063-020-04451-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 05/24/2020] [Accepted: 05/24/2020] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES The hypothesis of the proposed intervention is that Granulocyte-macrophage colony-stimulating factor (GM-CSF) has profound effects on antiviral immunity, and can provide the stimulus to restore immune homeostasis in the lung with acute lung injury post COVID-19, and can promote lung repair mechanisms, that lead to a 25% improvement in lung oxygenation parameters. Sargramostim is a man-made form of the naturally-occurring protein GM-CSF. TRIAL DESIGN A phase 4 academic, prospective, 2 arm (1:1 ratio), randomized, open-label, controlled trial. PARTICIPANTS Patients aged 18-80 years admitted to specialized COVID-19 wards in 5 Belgian hospitals with recent (< 2 weeks prior to randomization) confirmed COVID-19 infection and acute respiratory failure defined as a PaO2/FiO2 below 350 mmHg or SpO2 below 93% on minimal 2 L/min supplemental oxygen. Patients were excluded from the trial in case of (1) known serious allergic reactions to yeast-derived products, (2) lithium carbonate therapy, (3) mechanical ventilation prior to randomization, (4) peripheral white blood cell count above 25.000/μL and/or active myeloid malignancy, (5) high dose systemic steroid therapy (> 20 mg methylprednisolone or equivalent), (6) enrolment in another investigational study, (7) pregnant or breastfeeding or (8) ferritin levels > 2000 μg/mL. INTERVENTION AND COMPARATOR Inhaled sargramostim 125 μg twice daily for 5 days in addition to standard care. Upon progression of disease requiring mechanical ventilation or to acute respiratory distress syndrome (ARDS) and initiation of mechanical ventilator support within the 5 day period, inhaled sargramostim will be replaced by intravenous sargramostim 125 μg/m2 body surface area once daily until the 5 day period is reached. From day 6 onwards, progressive patients in the active group will have the option to receive an additional 5 days of IV sargramostim, based on the treating physician's assessment. Intervention will be compared to standard of care. Subjects progressing to ARDS and requiring invasive mechanical ventilatory support, from day 6 onwards in the standard of care group will have the option (clinician's decision) to initiate IV sargramostim 125m μg/m2 body surface area once daily for 5 days. MAIN OUTCOMES The primary endpoint of this intervention is measuring oxygenation after 5 days of inhaled (and intravenous) treatment through assessment of a change in pretreatment and post-treatment ratio of PaO2/FiO2 and through measurement of the P(A-a)O2 gradient (PAO2= Partial alveolar pressure of oxygen, PaO2=Partial arterial pressure of oxygen; FiO2= Fraction of inspired oxygen). RANDOMISATION Patients will be randomized in a 1:1 ratio. Randomization will be done using REDCap (electronic IWRS system). BLINDING (MASKING) In this open-label trial neither participants, caregivers, nor those assessing the outcomes will be blinded to group assignment. NUMBERS TO BE RANDOMISED (SAMPLE SIZE) A total of 80 patients with confirmed COVID-19 and acute hypoxic respiratory failure will be enrolled, 40 in the active and 40 in the control group. TRIAL STATUS SARPAC protocol Version 2.0 (April 15 2020). Participant recruitment is ongoing in 5 Belgian Hospitals (i.e. University Hospital Ghent, AZ Sint-Jan Bruges, AZ Delta Roeselare, University Hospital Brussels and ZNA Middelheim Antwerp). Participant recruitment started on March 26th 2020. Given the current decline of the COVID-19 pandemic in Belgium, it is difficult to anticipate the rate of participant recruitment. TRIAL REGISTRATION The trial was registered on Clinical Trials.gov on March 30th, 2020 (ClinicalTrials.gov Identifier: NCT04326920) - retrospectively registered; https://clinicaltrials.gov/ct2/show/NCT04326920?term=sarpac&recrs=ab&draw=2&rank=1 and on EudraCT on March 24th, 2020 (Identifier: 2020-001254-22). FULL PROTOCOL The full protocol is attached as an additional file, accessible from the Trials website (Additional file 1). In the interest in expediting dissemination of this material, the familiar formatting has been eliminated; this Letter serves as a summary of the key elements of the full protocol.
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Affiliation(s)
- Cedric Bosteels
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Bastiaan Maes
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium.
| | - Karel Van Damme
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | | | - Jozefien Declercq
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Anja Delporte
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | | | | | - Marnik Vuylsteke
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Joren Willaert
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Laura Bollé
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Yuri Vanbiervliet
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Jana Decuypere
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Frederick Libeer
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | | | - Isabelle Peene
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Bart Lambrecht
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
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Maes B, Bosteels C, De Leeuw E, Declercq J, Van Damme K, Delporte A, Demeyere B, Vermeersch S, Vuylsteke M, Willaert J, Bollé L, Vanbiervliet Y, Decuypere J, Libeer F, Vandecasteele S, Peene I, Lambrecht B. Treatment of severely ill COVID-19 patients with anti-interleukin drugs (COV-AID): A structured summary of a study protocol for a randomised controlled trial. Trials 2020; 21:468. [PMID: 32493441 PMCID: PMC7267751 DOI: 10.1186/s13063-020-04453-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [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: 05/24/2020] [Accepted: 05/24/2020] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES The purpose of this study is to test the safety and effectiveness of individually or simultaneously blocking IL-6, IL-6 receptor and IL-1 versus standard of care on blood oxygenation and systemic cytokine release syndrome in patients with COVID-19 coronavirus infection and acute hypoxic respiratory failure and systemic cytokine release syndrome. TRIAL DESIGN A phase 3 prospective, multi-center, interventional, open label, 6-arm 2x2 factorial design study. PARTICIPANTS Subjects will be recruited at the specialized COVID-19 wards and/or ICUs at 16 Belgian participating hospitals. Only adult (≥18y old) patients will be recruited with recent (≤16 days) COVID-19 infection and acute hypoxia (defined as PaO2/FiO2 below 350mmHg or PaO2/FiO2 below 280 on supplemental oxygen and immediately requiring high flow oxygen device or mechanical ventilation) and signs of systemic cytokine release syndrome characterized by high serum ferritin, or high D-dimers, or high LDH or deep lymphopenia or a combination of those, who have not been on mechanical ventilation for more than 24 hours before randomisation. Patients should have had a chest X-ray and/or CT scan showing bilateral infiltrates within the last 2 days before randomisation. Patients with active bacterial or fungal infection will be excluded. INTERVENTION AND COMPARATOR Patients will be randomized to 1 of 5 experimental arms versus usual care. The experimental arms consist of Anakinra alone (anti-IL-1 binding the IL-1 receptor), Siltuximab alone (anti-IL-6 chimeric antibody), a combination of Siltuximab and Anakinra, Tocilizumab alone (humanised anti-IL-6 receptor antibody) or a combination of Anakinra with Tocilizumab in addition to standard care. Patients treated with Anakinra will receive a daily subcutaneous injection of 100mg for a maximum of 28 days or until hospital discharge, whichever comes first. Siltuximab (11mg/kg) or Tocilizumab (8mg/kg, with a maximum dose of 800mg) are administered as a single intravenous injection immediately after randomization. MAIN OUTCOMES The primary end point is the time to clinical improvement defined as the time from randomization to either an improvement of two points on a six-category ordinal scale measured daily till day 28 or discharge from the hospital or death. This ordinal scale is composed of (1) Death; (2) Hospitalized, on invasive mechanical ventilation or ECMO; (3) Hospitalized, on non-invasive ventilation or high flow oxygen devices; (4) Hospitalized, requiring supplemental oxygen; (5) Hospitalized, not requiring supplemental oxygen; (6) Not hospitalized. RANDOMISATION Patients will be randomized using an Interactive Web Response System (REDCap). A 2x2 factorial design was selected with a 2:1 randomization regarding the IL-1 blockade (Anakinra) and a 1:2 randomization regarding the IL-6 blockade (Siltuximab and Tocilizumab). BLINDING (MASKING) In this open-label trial neither participants, caregivers, nor those assessing the outcomes are blinded to group assignment. NUMBERS TO BE RANDOMISED (SAMPLE SIZE) A total of 342 participants will be enrolled: 76 patients will receive usual care, 76 patients will receive Siltuximab alone, 76 patients will receive Tocilizumab alone, 38 will receive Anakinra alone, 38 patients will receive Anakinra and Siltuximab and 38 patients will receive Anakinra and Tocilizumab. TRIAL STATUS COV-AID protocol version 3.0 (15 Apr 2020). Participant recruitment is ongoing and started on April 4th 2020. Given the current decline of the COVID-19 pandemic in Belgium, it is difficult to anticipate the rate of participant recruitment. TRIAL REGISTRATION The trial was registered on Clinical Trials.gov on April 1st, 2020 (ClinicalTrials.gov Identifier: NCT04330638) and on EudraCT on April 3rd 2020 (Identifier: 2020-001500-41). FULL PROTOCOL The full protocol is attached as an additional file, accessible from the Trials website (Additional file 1). In the interest in expediting dissemination of this material, the familiar formatting has been eliminated; this Letter serves as a summary of the key elements of the full protocol.
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Affiliation(s)
- Bastiaan Maes
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium.
| | - Cedric Bosteels
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | | | - Jozefien Declercq
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Karel Van Damme
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Anja Delporte
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | | | | | - Marnik Vuylsteke
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Joren Willaert
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Laura Bollé
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Yuri Vanbiervliet
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Jana Decuypere
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Frederick Libeer
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | | | - Isabelle Peene
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
| | - Bart Lambrecht
- VIB-UGent Inflammatie-researchcentrum, Oost-Vlaanderen, Ghent, Belgium
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Bolli E, D'Huyvetter M, Murgaski A, Berus D, Stangé G, Clappaert EJ, Arnouk S, Pombo Antunes AR, Krasniqi A, Lahoutte T, Gonçalves A, Vuylsteke M, Raes G, Devoogdt N, Movahedi K, Van Ginderachter JA. Stromal-targeting radioimmunotherapy mitigates the progression of therapy-resistant tumors. J Control Release 2019; 314:1-11. [PMID: 31626860 DOI: 10.1016/j.jconrel.2019.10.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 01/04/2019] [Revised: 09/17/2019] [Accepted: 10/12/2019] [Indexed: 12/12/2022]
Abstract
Radioimmunotherapy (RIT) aims to deliver a high radiation dose to cancer cells, while minimizing the exposure of normal cells. Typically, monoclonal antibodies are used to target the radionuclides to cancer cell surface antigens. However, antibodies face limitations due to their poor tumor penetration and suboptimal pharmacokinetics, while the expression of their target on the cancer cell surface may be gradually lost. In addition, most antigens are expressed in a limited number of tumor types. To circumvent these problems, we developed a Nanobody (Nb)-based RIT against a prominent stromal cell (stromal-targeting radioimmunotherapy or STRIT) present in nearly all tumors, the tumor-associated macrophage (TAM). Macrophage Mannose Receptor (MMR) functions as a stable molecular target on TAM residing in hypoxic areas, further allowing the delivery of a high radiation dose to the more radioresistant hypoxic tumor regions. Since MMR expression is not restricted to TAM, we first optimized a strategy to block extra-tumoral MMR to prevent therapy-induced toxicity. A 100-fold molar excess of unlabeled bivalent Nb largely blocks extra-tumoral binding of 177Lu-labeled anti-MMR Nb and prevents toxicity, while still allowing the intra-tumoral binding of the monovalent Nb. Interestingly, three doses of 177Lu-labeled anti-MMR Nb resulted in a significantly retarded tumor growth, thereby outcompeting the effects of anti-PD1, anti-VEGFR2, doxorubicin and paclitaxel in the TS/A mammary carcinoma model. Together, these data propose anti-MMR STRIT as a valid new approach for cancer treatment.
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Affiliation(s)
- Evangelia Bolli
- Laboratory of Myeloid Cell Immunology, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Matthias D'Huyvetter
- In vivo Cellular and Molecular Immunology Laboratory, Vrije Universiteit Brussel, Brussels, Belgium
| | - Aleksandar Murgaski
- Laboratory of Myeloid Cell Immunology, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Danielle Berus
- Department of Radiation Protection, Vrije Universiteit Brussel, UZ Brussel, Brussels, Belgium
| | - Geert Stangé
- Diabetes Research Center, Vrije Universiteit Brussel, Brussels, Belgium
| | - Emile J Clappaert
- Laboratory of Myeloid Cell Immunology, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sana Arnouk
- Laboratory of Myeloid Cell Immunology, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ana Rita Pombo Antunes
- Laboratory of Myeloid Cell Immunology, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ahmet Krasniqi
- In vivo Cellular and Molecular Immunology Laboratory, Vrije Universiteit Brussel, Brussels, Belgium
| | - Tony Lahoutte
- In vivo Cellular and Molecular Immunology Laboratory, Vrije Universiteit Brussel, Brussels, Belgium
| | - Amanda Gonçalves
- VIB Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; VIB Bio Imaging Core Gent, Ghent, Belgium
| | | | - Geert Raes
- Laboratory of Myeloid Cell Immunology, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Nick Devoogdt
- In vivo Cellular and Molecular Immunology Laboratory, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kiavash Movahedi
- Laboratory of Myeloid Cell Immunology, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jo A Van Ginderachter
- Laboratory of Myeloid Cell Immunology, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium.
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Detry S, Składanowska K, Vuylsteke M, Savvides SN, Bloch Y. Revisiting the combinatorial potential of cytokine subunits in the IL-12 family. Biochem Pharmacol 2019; 165:240-248. [PMID: 30885765 DOI: 10.1016/j.bcp.2019.03.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 02/25/2019] [Accepted: 03/14/2019] [Indexed: 12/15/2022]
Abstract
The four core members of the Interleukin-12 (IL-12) family of cytokines, IL-12, IL-23, IL-27 and IL-35 are heterodimers which share α- and β-cytokine subunits. All four cytokines are immune modulators and have been proposed to play divergent roles in inflammatory arthritis. In recent years additional combinations of α- and β-cytokine subunits belonging to the IL-12 family have been proposed to form novel cytokines such as IL-39. However, the actual extent of the combinatorial potential of the cytokine subunits in the human IL-12 family is not known. Here, we identify several combinations of subunits that form secreted heterodimeric assemblies based on a systematic orthogonal approach. The heterodimers are detected in the conditioned media harvested from mammalian cell cultures transfected with unfused pairs of cytokine subunits. While certain previously reported subunit combinations could not be recapitulated, our approach showed robustly that all four of the canonical members could be secreted. Furthermore, we provide evidence for the interaction between Cytokine Receptor Like Factor 1 (CRLF1) and Interleukin-12 subunit alpha (p35). Similar to IL-27 and IL-35 this novel heterodimer is not abundantly secreted rendering isolation from the conditioned medium very challenging, unlike IL-12 and IL-23. Our findings set the stage for fine-tuning approaches towards the biochemical reconstitution of IL-12 family cytokines for biochemical, cellular, and structural studies.
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Affiliation(s)
- Sammy Detry
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium; Unit for Structural Biology, VIB Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Katarzyna Składanowska
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium; Unit for Structural Biology, VIB Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | | | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium; Unit for Structural Biology, VIB Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium.
| | - Yehudi Bloch
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium; Unit for Structural Biology, VIB Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium.
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20
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Bauwens M, Garanto A, Sangermano R, Naessens S, Weisschuh N, De Zaeytijd J, Khan M, Sadler F, Balikova I, Van Cauwenbergh C, Rosseel T, Bauwens J, De Leeneer K, De Jaegere S, Van Laethem T, De Vries M, Carss K, Arno G, Fakin A, Webster AR, de Ravel de l'Argentière TJL, Sznajer Y, Vuylsteke M, Kohl S, Wissinger B, Cherry T, Collin RWJ, Cremers FPM, Leroy BP, De Baere E. ABCA4-associated disease as a model for missing heritability in autosomal recessive disorders: novel noncoding splice, cis-regulatory, structural, and recurrent hypomorphic variants. Genet Med 2019; 21:1761-1771. [PMID: 30670881 PMCID: PMC6752479 DOI: 10.1038/s41436-018-0420-y] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 12/17/2018] [Indexed: 12/30/2022] Open
Abstract
Purpose ABCA4-associated disease, a recessive retinal dystrophy, is hallmarked by a large proportion of patients with only one pathogenic ABCA4 variant, suggestive for missing heritability. Methods By locus-specific analysis of ABCA4, combined with extensive functional studies, we aimed to unravel the missing alleles in a cohort of 67 patients (p), with one (p = 64) or no (p = 3) identified coding pathogenic variants of ABCA4. Results We identified eight pathogenic (deep-)intronic ABCA4 splice variants, of which five are novel and six structural variants, four of which are novel, including two duplications. Together, these variants account for the missing alleles in 40.3% of patients. Furthermore, two novel variants with a putative cis-regulatory effect were identified. The common hypomorphic variant c.5603A>T p.(Asn1868Ile) was found as a candidate second allele in 43.3% of patients. Overall, we have elucidated the missing heritability in 83.6% of our cohort. In addition, we successfully rescued three deep-intronic variants using antisense oligonucleotide (AON)-mediated treatment in HEK 293-T cells and in patient-derived fibroblast cells. Conclusion Noncoding pathogenic variants, novel structural variants, and a common hypomorphic allele of the ABCA4 gene explain the majority of unsolved cases with ABCA4-associated disease, rendering this retinopathy a model for missing heritability in autosomal recessive disorders.
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Affiliation(s)
- Miriam Bauwens
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Riccardo Sangermano
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sarah Naessens
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Nicole Weisschuh
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Françoise Sadler
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Irina Balikova
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Caroline Van Cauwenbergh
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Toon Rosseel
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Jim Bauwens
- Department of Computer Science, Free University of Brussels, Brussels, Belgium
| | - Kim De Leeneer
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Sarah De Jaegere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Thalia Van Laethem
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Meindert De Vries
- Department of Ophthalmology, Hôpital des Enfants Reine Fabiola, Brussels, Belgium
| | - Keren Carss
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Cambridge, UK.,UK NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, London, UK
| | - Ana Fakin
- UCL Institute of Ophthalmology, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Andrew R Webster
- UCL Institute of Ophthalmology, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | | | - Yves Sznajer
- Centre de Génétique Humaine, Cliniques Universitaires St. Luc, Université Catholique de Louvain, Brussels, Belgium
| | | | - Susanne Kohl
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Timothy Cherry
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bart P Leroy
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Division of Ophthalmology and Center for Cellular & Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
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21
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Souffriau J, Eggermont M, Van Ryckeghem S, Van Looveren K, Van Wyngene L, Van Hamme E, Vuylsteke M, Beyaert R, De Bosscher K, Libert C. A screening assay for Selective Dimerizing Glucocorticoid Receptor Agonists and Modulators (SEDIGRAM) that are effective against acute inflammation. Sci Rep 2018; 8:12894. [PMID: 30150712 PMCID: PMC6110732 DOI: 10.1038/s41598-018-31150-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 04/12/2018] [Accepted: 08/13/2018] [Indexed: 02/07/2023] Open
Abstract
It has been suggested that glucocorticoid receptor (GR) agonists that promote GR homodimerization more than standard glucocorticoids such as Dexamethasone could be more effective anti-inflammatory molecules against acute and life-threatening inflammatory conditions. To test this hypothesis, we set up a screening pipeline aimed at discovering such Selective Dimerizing GR Agonists and Modulators (SEDIGRAM). The pipeline consists of a reporter gene assay based on a palindromic glucocorticoid responsive element (GRE). This assay represents GR dimerization in human A549 lung epithelial cells. In the pipeline, this is followed by analysis of endogenous GRE-driven gene expression, a FRET assay confirming dimerization, and monitoring of in vitro and in vivo anti-inflammatory activity. In a proof of principle experiment, starting from seven candidate compounds, we identified two potentially interesting compounds (Cortivazol and AZD2906) that confer strong protection in a mouse model of aggressive TNF-induced lethal inflammation. A screening pipeline for SEDIGRAM may assist the search for compounds that promote GR dimerization and limit overwhelming acute inflammatory responses.
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Affiliation(s)
- Jolien Souffriau
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Melanie Eggermont
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Sara Van Ryckeghem
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Kelly Van Looveren
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Lise Van Wyngene
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Evelien Van Hamme
- Bio Imaging Core, Center for Inflammation Research, VIB, Ghent, Belgium
| | | | - Rudi Beyaert
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Karolien De Bosscher
- Receptor Research Laboratories, Nuclear Receptor Lab, Center for Medical Biotechnology Center, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Claude Libert
- Center for Inflammation Research, VIB, Ghent, Belgium. .,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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22
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Martens S, Goossens V, Devisscher L, Hofmans S, Claeys P, Vuylsteke M, Takahashi N, Augustyns K, Vandenabeele P. RIPK1-dependent cell death: a novel target of the Aurora kinase inhibitor Tozasertib (VX-680). Cell Death Dis 2018; 9:211. [PMID: 29434255 PMCID: PMC5833749 DOI: 10.1038/s41419-017-0245-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [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: 08/18/2017] [Revised: 11/24/2017] [Accepted: 12/14/2017] [Indexed: 12/17/2022]
Abstract
The Aurora kinase family (Aurora A, B and C) are crucial regulators of several mitotic events, including cytokinesis. Increased expression of these kinases is associated with tumorigenesis and several compounds targeting Aurora kinase are under evaluation in clinical trials (a.o. AT9283, AZD1152, Danusertib, MLN8054). Here, we demonstrate that the pan-Aurora kinase inhibitor Tozasertib (VX-680 and MK-0457) not only causes cytokinesis defects through Aurora kinase inhibition, but is also a potent inhibitor of necroptosis, a cell death process regulated and executed by the RIPK1, RIPK3 and MLKL signalling axis. Tozasertib’s potency to inhibit RIPK1-dependent necroptosis and to block cytokinesis in cells is in the same concentration range, with an IC50 of 1.06 µM and 0.554 µM, respectively. A structure activity relationship (SAR) analysis of 67 Tozasertib analogues, modified at 4 different positions, allowed the identification of analogues that showed increased specificity for either cytokinesis inhibition or for necroptosis inhibition, reflecting more specific inhibition of Aurora kinase or RIPK1, respectively. These results also suggested that RIPK1 and Aurora kinases are functionally non-interacting targets of Tozasertib and its analogues. Indeed, more specific Aurora kinase inhibitors did not show any effect in necroptosis and Necrostatin-1s treatment did not result in cytokinesis defects, demonstrating that both cellular processes are not interrelated. Finally, Tozasertib inhibited recombinant human RIPK1, human Aurora A and human Aurora B kinase activity, but not RIPK3. The potency ranking of the newly derived Tozasertib analogues and their specificity profile, as observed in cellular assays, coincide with ADP-Glo recombinant kinase activity assays. Overall, we show that Tozasertib not only targets Aurora kinases but also RIPK1 independently, and that we could generate analogues with increased selectivity to RIPK1 or Aurora kinases, respectively.
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Affiliation(s)
- Sofie Martens
- Inflammation Research Center (IRC), VIB, Ghent, 9052, Belgium.,Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, 9052, Belgium
| | - Vera Goossens
- Inflammation Research Center (IRC), VIB, Ghent, 9052, Belgium.,Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, 9052, Belgium
| | - Lars Devisscher
- Laboratory of Medicinal Chemistry, University of Antwerp, Antwerp, 2610, Belgium
| | - Sam Hofmans
- Laboratory of Medicinal Chemistry, University of Antwerp, Antwerp, 2610, Belgium
| | - Polien Claeys
- Inflammation Research Center (IRC), VIB, Ghent, 9052, Belgium.,Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, 9052, Belgium
| | - Marnik Vuylsteke
- Inflammation Research Center (IRC), VIB, Ghent, 9052, Belgium.,Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, 9052, Belgium.,Gnomixx, Melle, 9090, Belgium
| | - Nozomi Takahashi
- Inflammation Research Center (IRC), VIB, Ghent, 9052, Belgium.,Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, 9052, Belgium
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, University of Antwerp, Antwerp, 2610, Belgium
| | - Peter Vandenabeele
- Inflammation Research Center (IRC), VIB, Ghent, 9052, Belgium. .,Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, 9052, Belgium.
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23
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Nelissen H, Sun X, Rymen B, Jikumaru Y, Kojima M, Takebayashi Y, Abbeloos R, Demuynck K, Storme V, Vuylsteke M, De Block J, Herman D, Coppens F, Maere S, Kamiya Y, Sakakibara H, Beemster GT, Inzé D. The reduction in maize leaf growth under mild drought affects the transition between cell division and cell expansion and cannot be restored by elevated gibberellic acid levels. Plant Biotechnol J 2018; 16:615-627. [PMID: 28730636 PMCID: PMC5787831 DOI: 10.1111/pbi.12801] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/07/2017] [Accepted: 07/12/2017] [Indexed: 05/05/2023]
Abstract
Growth is characterized by the interplay between cell division and cell expansion, two processes that occur separated along the growth zone at the maize leaf. To gain further insight into the transition between cell division and cell expansion, conditions were investigated in which the position of this transition zone was positively or negatively affected. High levels of gibberellic acid (GA) in plants overexpressing the GA biosynthesis gene GA20-OXIDASE (GA20OX-1OE ) shifted the transition zone more distally, whereas mild drought, which is associated with lowered GA biosynthesis, resulted in a more basal positioning. However, the increased levels of GA in the GA20OX-1OE line were insufficient to convey tolerance to the mild drought treatment, indicating that another mechanism in addition to lowered GA levels is restricting growth during drought. Transcriptome analysis with high spatial resolution indicated that mild drought specifically induces a reprogramming of transcriptional regulation in the division zone. 'Leaf Growth Viewer' was developed as an online searchable tool containing the high-resolution data.
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Affiliation(s)
- Hilde Nelissen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Xiao‐Huan Sun
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Bart Rymen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Yusuke Jikumaru
- Growth Regulation Research GroupPlant Science CenterRIKENYokohamaJapan
| | - Mikko Kojima
- Plant Productivity Systems Research GroupPlant Science CenterRIKENYokohamaJapan
| | - Yumiko Takebayashi
- Plant Productivity Systems Research GroupPlant Science CenterRIKENYokohamaJapan
| | - Rafael Abbeloos
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Kirin Demuynck
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Veronique Storme
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Marnik Vuylsteke
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Jolien De Block
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Dorota Herman
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Frederik Coppens
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Steven Maere
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Yuji Kamiya
- Growth Regulation Research GroupPlant Science CenterRIKENYokohamaJapan
| | - Hitoshi Sakakibara
- Plant Productivity Systems Research GroupPlant Science CenterRIKENYokohamaJapan
| | - Gerrit T.S. Beemster
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
- Department of BiologyUniversity of AntwerpAntwerpBelgium
| | - Dirk Inzé
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
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24
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Deckers J, Bougarne N, Mylka V, Desmet S, Luypaert A, Devos M, Tanghe G, Van Moorleghem J, Vanheerswynghels M, De Cauwer L, Thommis J, Vuylsteke M, Tavernier J, Lambrecht BN, Hammad H, De Bosscher K. Co-Activation of Glucocorticoid Receptor and Peroxisome Proliferator-Activated Receptor-γ in Murine Skin Prevents Worsening of Atopic March. J Invest Dermatol 2017; 138:1360-1370. [PMID: 29288652 DOI: 10.1016/j.jid.2017.12.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 12/06/2017] [Accepted: 12/11/2017] [Indexed: 12/18/2022]
Abstract
Children with atopic dermatitis show an increased risk to develop asthma later in life, a phenomenon referred to as "atopic march," which emphasizes the need for secondary prevention therapies. This study aimed to investigate whether relief of skin inflammation by glucocorticoids and peroxisome proliferator-activated receptor agonists might influence the subsequent development of asthma in a murine model for the atopic march in which mice were repeatedly exposed to house dust mite via the skin, followed by exposure to house dust mite in lungs. To abrogate atopic dermatitis, mice received topical treatment with glucocorticoid receptor/peroxisome proliferator-activated receptor-γ agonists. Nuclear receptor ligand effects were assessed on primary keratinocytes and dendritic cells, as central players in skin inflammation. Prior house dust mite-induced skin inflammation aggravates allergic airway inflammation and induces a mixed T helper type 2/T helper type 17 response in the lungs. Cutaneous combined activation of glucocorticoid receptor/peroxisome proliferator-activated receptor-γ reduced skin inflammation to a higher extent compared to single activation. Additive anti-inflammatory effects were more prominent in dendritic cells, as compared to keratinocytes. Alleviation of allergic skin inflammation by activation of glucocorticoid receptor/peroxisome proliferator-activated receptor-γ appeared insufficient to avoid the allergic immune response in the lungs, but efficiently reduced asthma severity by counteracting the Th17 response. Glucocorticoid receptor/peroxisome proliferator-activated receptor-γ co-activation represents a potent remedy against allergic skin inflammation and worsening of atopic march.
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Affiliation(s)
- Julie Deckers
- Nuclear Receptor Lab, Ghent University, Ghent, Belgium; Receptor Research Laboratories, VIB Center for Medical Biotechnology, Department of Biochemistry, Ghent University, Ghent, Belgium; Laboratory of Immunoregulation, VIB Center for Inflammation Research, Department of Internal Medicine, Ghent University, Ghent, Belgium
| | - Nadia Bougarne
- Nuclear Receptor Lab, Ghent University, Ghent, Belgium; Receptor Research Laboratories, VIB Center for Medical Biotechnology, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Viacheslav Mylka
- Nuclear Receptor Lab, Ghent University, Ghent, Belgium; Receptor Research Laboratories, VIB Center for Medical Biotechnology, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Sofie Desmet
- Nuclear Receptor Lab, Ghent University, Ghent, Belgium; Receptor Research Laboratories, VIB Center for Medical Biotechnology, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Astrid Luypaert
- Nuclear Receptor Lab, Ghent University, Ghent, Belgium; Receptor Research Laboratories, VIB Center for Medical Biotechnology, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Michael Devos
- Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Giel Tanghe
- Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Justine Van Moorleghem
- Laboratory of Immunoregulation, VIB Center for Inflammation Research, Department of Internal Medicine, Ghent University, Ghent, Belgium
| | - Manon Vanheerswynghels
- Laboratory of Immunoregulation, VIB Center for Inflammation Research, Department of Internal Medicine, Ghent University, Ghent, Belgium
| | - Lode De Cauwer
- Nuclear Receptor Lab, Ghent University, Ghent, Belgium; Receptor Research Laboratories, VIB Center for Medical Biotechnology, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Jonathan Thommis
- Nuclear Receptor Lab, Ghent University, Ghent, Belgium; Receptor Research Laboratories, VIB Center for Medical Biotechnology, Department of Biochemistry, Ghent University, Ghent, Belgium
| | | | - Jan Tavernier
- Receptor Research Laboratories, VIB Center for Medical Biotechnology, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Bart N Lambrecht
- Laboratory of Immunoregulation, VIB Center for Inflammation Research, Department of Internal Medicine, Ghent University, Ghent, Belgium
| | - Hamida Hammad
- Laboratory of Immunoregulation, VIB Center for Inflammation Research, Department of Internal Medicine, Ghent University, Ghent, Belgium
| | - Karolien De Bosscher
- Nuclear Receptor Lab, Ghent University, Ghent, Belgium; Receptor Research Laboratories, VIB Center for Medical Biotechnology, Department of Biochemistry, Ghent University, Ghent, Belgium.
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25
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Ye HL, Li DR, Yang JS, Chen DF, De Vos S, Vuylsteke M, Sorgeloos P, Van Stappen G, Bossier P, Nagasawa H, Yang WJ. Molecular characterization and functional analyses of a diapause hormone receptor-like gene in parthenogenetic Artemia. Peptides 2017; 90:100-110. [PMID: 28174072 DOI: 10.1016/j.peptides.2017.01.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 01/19/2017] [Accepted: 01/23/2017] [Indexed: 01/03/2023]
Abstract
In arthropods, mature females under certain conditions produce and release encysted gastrula embryos that enter diapause, a state of obligate dormancy. The process is presumably regulated by diapause hormone (DH) and diapause hormone receptor (DHR) that were identified in the silkworm, Bombyx mori and other insects. However, the molecular structure and function of DHR in crustaceans remains unknown. Here, a DHR-like gene from parthenogenetic Artemia (Ar-DHR) was isolated and sequenced. The cDNA sequence consists of 1410bp with a 1260-bp open reading frame encoding a protein consisting of 420 amino acid residues. The results of real-time PCR (qRT-PCR) and Western blot analysis showed that the mRNA and protein of Ar-DHR were mainly expressed at the diapause stage. Furthermore, we found that Ar-DHR was located on the cell membrane of the pre-diapause cyst but in the cytoplasm of the diapause cyst by analysis of immunofluorescence. In vivo knockdown of Ar-DHR by RNA interference (RNAi) and antiserum neutralization consistently inhibited diapause cysts formation. The results indicated that Ar-DHR plays an important role in the induction and maintenance of embryonic diapause in Artemia. Thus, our findings provide an insight into the regulation of diapause formation in Artemia and the function of Ar-DHR.
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Affiliation(s)
- Hui-Li Ye
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Dong-Rui Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Jin-Shu Yang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Dian-Fu Chen
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Stephanie De Vos
- Laboratory of Aquaculture & Artemia Reference Center, Ghent University, Belgium
| | - Marnik Vuylsteke
- Laboratory of Aquaculture & Artemia Reference Center, Ghent University, Belgium
| | - Patrick Sorgeloos
- Laboratory of Aquaculture & Artemia Reference Center, Ghent University, Belgium
| | - Gilbert Van Stappen
- Laboratory of Aquaculture & Artemia Reference Center, Ghent University, Belgium
| | - Peter Bossier
- Laboratory of Aquaculture & Artemia Reference Center, Ghent University, Belgium
| | - Hiromichi Nagasawa
- Department of Applied Biological Chemistry, The University of Tokyo, Yayoi, Bunkyo, Tokyo 113-8657, Japan.
| | - Wei-Jun Yang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China.
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26
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Li DR, Ye HL, Yang JS, Yang F, Wang MR, De Vos S, Vuylsteke M, Sorgeloos P, Van Stappen G, Bossier P, Yang WJ. Identification and characterization of a Masculinizer (Masc) gene involved in sex differentiation in Artemia. Gene 2017; 614:56-64. [PMID: 28300613 DOI: 10.1016/j.gene.2017.03.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 12/01/2016] [Revised: 02/17/2017] [Accepted: 03/10/2017] [Indexed: 11/15/2022]
Abstract
The sex of relatively primitive animals such as invertebrates is mostly determined by environmental factors and chromosome ploidy. Heteromorphic chromosomes may also play an important role, as in the ZW system in lepidopterans. However, the mechanisms of these various sex determination systems are still largely undefined. In the present study, a Masculinizer gene (Ar-Masc) was identified in the crustacean Artemia franciscana Kellogg 1906. Sequence analysis revealed that the 1140-bp full-length open reading frame of Ar-Masc encodes a 380-aa protein containing two CCCH-type zinc finger domains having a high degree of shared identities with the MASC protein characterized in the silkworm Bombyx mori, which has been determined to participate in the production of male-specific splice variants. Furthermore, although Ar-Masc could be detected in almost all stages in both sexual and parthenogenetic Artemia, there were significant variations in expression between these two reproductive modes. Firstly, qRT-PCR and Western blot analysis showed that levels of both Ar-Masc mRNA and protein in sexual nauplii were much higher than in parthenogenetic nauplii throughout the hatching process. Secondly, both sexual and parthenogenetic Artemia had decreased levels of Ar-Masc along with the embryonic developmental stages, while the sexual ones had a relatively higher and more stable expression than those of parthenogenetic ones. Thirdly, immunofluorescence analysis determined that sexual individuals had higher levels of Ar-MASC protein than parthenogenetic individuals during embryonic development. Lastly, RNA interference with dsRNA showed that gene silencing of Ar-Masc in sexual A. franciscana caused the female-male ratio of progeny to be 2.19:1. These data suggest that Ar-Masc participates in the process of sex determination in A. franciscana, and provide insight into the evolution of sex determination in sexual organisms.
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Affiliation(s)
- Dong-Rui Li
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Hui-Li Ye
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Jin-Shu Yang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Fan Yang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Mo-Ran Wang
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Department of Fisheries Science, Tianjin Agricultural University, People's Republic of China
| | - Stephanie De Vos
- Laboratory of Aquaculture &Artemia Reference center, Ghent University, Belgium
| | - Marnik Vuylsteke
- Laboratory of Aquaculture &Artemia Reference center, Ghent University, Belgium
| | - Patrick Sorgeloos
- Laboratory of Aquaculture &Artemia Reference center, Ghent University, Belgium
| | - Gilbert Van Stappen
- Laboratory of Aquaculture &Artemia Reference center, Ghent University, Belgium
| | - Peter Bossier
- Laboratory of Aquaculture &Artemia Reference center, Ghent University, Belgium
| | - Wei-Jun Yang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China.
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27
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Devos M, Gilbert B, Denecker G, Leurs K, Mc Guire C, Lemeire K, Hochepied T, Vuylsteke M, Lambert J, Van Den Broecke C, Libbrecht L, Haigh J, Berx G, Lippens S, Vandenabeele P, Declercq W. Elevated ΔNp63α Levels Facilitate Epidermal and Biliary Oncogenic Transformation. J Invest Dermatol 2016; 137:494-505. [PMID: 27725202 DOI: 10.1016/j.jid.2016.09.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 09/05/2016] [Accepted: 09/20/2016] [Indexed: 12/23/2022]
Abstract
Unlike its family member p53, TP63 is rarely mutated in human cancer. However, ΔNp63α protein levels are often elevated in tumors of epithelial origin, such as squamous cell carcinoma and cholangiocarcinoma. To study the oncogenic properties of ΔNp63α in vivo, we generated transgenic mice overexpressing ΔNp63α from the Rosa26 locus promoter controlled by keratin 5-Cre. We found that these mice spontaneously develop epidermal cysts and ectopic ΔNp63α expression in the bile duct epithelium that leads to dilatation of the intrahepatic biliary ducts, to hepatic cyst formation and bile duct adenoma. Moreover, when subjected to models of 7,12-dimethylbenz[a]anthracene-based carcinogenesis, tumor initiation was increased in ΔNp63α transgenic mice in a gene dosage-dependent manner although ΔNp63α overexpression did not alter the sensitivity to 7,12-dimethylbenz[a]anthracene-induced cytotoxicity in vivo. However, keratinocytes isolated from ΔNp63α transgenic mice displayed increased survival and delayed cellular senescence compared with wild-type keratinocytes, marked by decreased p16Ink4a and p19Arf expression. Taken together, we show that increased ΔNp63α protein levels facilitate oncogenic transformation in the epidermis as well as in the bile duct.
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Affiliation(s)
- Michael Devos
- Molecular Signaling and Cell Death Unit, Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Barbara Gilbert
- Molecular Signaling and Cell Death Unit, Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Geertrui Denecker
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Molecular and Cellular Oncology Unit, Inflammation Research Center, VIB, Ghent, Belgium
| | - Kirsten Leurs
- Molecular Signaling and Cell Death Unit, Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Conor Mc Guire
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Molecular Signal Transduction in Inflammation Unit, Inflammation Research Center, VIB, Ghent, Belgium
| | - Kelly Lemeire
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Inflammation Research Center, VIB, Ghent, Belgium
| | - Tino Hochepied
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Transgenic mice core facility, VIB, Ghent, Belgium
| | | | - Jo Lambert
- Department of Dermatology, Ghent University Hospital, Ghent, Belgium
| | | | - Louis Libbrecht
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Jody Haigh
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Vascular Cell Biology Unit, Department for Molecular Biomedical Research, VIB, Ghent, Belgium
| | - Geert Berx
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Molecular and Cellular Oncology Unit, Inflammation Research Center, VIB, Ghent, Belgium
| | - Saskia Lippens
- Molecular Signaling and Cell Death Unit, Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Peter Vandenabeele
- Molecular Signaling and Cell Death Unit, Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Wim Declercq
- Molecular Signaling and Cell Death Unit, Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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28
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Grootjans S, Hassannia B, Delrue I, Goossens V, Wiernicki B, Dondelinger Y, Bertrand MJM, Krysko DV, Vuylsteke M, Vandenabeele P, Vanden Berghe T. A real-time fluorometric method for the simultaneous detection of cell death type and rate. Nat Protoc 2016; 11:1444-54. [PMID: 27414760 DOI: 10.1038/nprot.2016.085] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Several cell death assays have been developed based on a single biochemical parameter such as caspase activation or plasma membrane permeabilization. Our fluorescent apoptosis/necrosis (FAN) assay directly measures cell death and distinguishes between caspase-dependent apoptosis and caspase-independent necrosis of cells grown in any multiwell plate. Cell death is monitored in standard growth medium as an increase in fluorescence intensity of a cell-impermeable dye (SYTOX Green) after plasma membrane disintegration, whereas apoptosis is detected through caspase-mediated release of a fluorophore from its quencher (DEVD-amc). The assay determines the normalized percentage of dead cells and caspase activation per condition as an end-point measurement or in real time (automated). The protocol can be applied to screen drugs, proteins or siRNAs for interference with cell death while simultaneously detecting cell death modality switching between apoptosis and necrosis. Initial preparation may take up to 5 d, but the typical hands-on time is ∼2 h.
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Affiliation(s)
- Sasker Grootjans
- Molecular Signaling and Cell Death Unit, VIB Inflammation Research Center, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Behrouz Hassannia
- Molecular Signaling and Cell Death Unit, VIB Inflammation Research Center, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Iris Delrue
- Molecular Signaling and Cell Death Unit, VIB Inflammation Research Center, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Vera Goossens
- Molecular Signaling and Cell Death Unit, VIB Inflammation Research Center, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Bartosz Wiernicki
- Molecular Signaling and Cell Death Unit, VIB Inflammation Research Center, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Yves Dondelinger
- Molecular Signaling and Cell Death Unit, VIB Inflammation Research Center, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Mathieu J M Bertrand
- Molecular Signaling and Cell Death Unit, VIB Inflammation Research Center, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Dmitri V Krysko
- Molecular Signaling and Cell Death Unit, VIB Inflammation Research Center, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | | | - Peter Vandenabeele
- Molecular Signaling and Cell Death Unit, VIB Inflammation Research Center, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Methusalem Program, Ghent University, Ghent, Belgium
| | - Tom Vanden Berghe
- Molecular Signaling and Cell Death Unit, VIB Inflammation Research Center, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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29
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Abstract
Objective: The aim of this study was to compare the minimally invasive endovenous laser technique for treatment of primary varicose veins with the conventional stripping operation in terms of short-term recovery and cost for economically active patients. Methods: One hundred and sixty four patients with varicose veins caused by great saphenous vein insufficiency were assigned to the endovenous laser obliteration procedure ( n = 80, 118 legs) or stripping operation ( n = 84, 124 legs). Postoperative morbidity, the need for analgesics and the duration of sick leave were recorded. The comparison of costs included both direct medical costs and costs resulting from lost productivity of the patients. Results: Overall there were less postoperative complications in the laser group. Sick leave was significantly shorter in the endovenous obliteration group ( P<0.001). Although the variable costs of the conventional stripping operation were lower than those of the endovenous laser procedure, the total costs at public expense were higher because of the difference in lost productivity of the patients. Conclusions: Endovenous laser obliteration may offer advantages over the stripping operation in terms of reduced postoperative pain, shorter sick leave and faster return to usual occupational activities, and it appears to be cost-saving for society.
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Affiliation(s)
- M Vuylsteke
- Department of Vascular Surgery, St-Andries Hospital, Tielt, Belgium
| | | | - E A Audenaert
- Department of Vascular Surgery, St-Andries Hospital, Tielt, Belgium
| | - P Lissens
- Department of Vascular Surgery, St-Andries Hospital, Tielt, Belgium
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30
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Walton A, Stes E, Goeminne G, Braem L, Vuylsteke M, Matthys C, De Cuyper C, Staes A, Vandenbussche J, Boyer FD, Vanholme R, Fromentin J, Boerjan W, Gevaert K, Goormachtig S. The Response of the Root Proteome to the Synthetic Strigolactone GR24 in Arabidopsis. Mol Cell Proteomics 2016; 15:2744-55. [PMID: 27317401 DOI: 10.1074/mcp.m115.050062] [Citation(s) in RCA: 28] [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] [Received: 03/30/2015] [Indexed: 11/06/2022] Open
Abstract
Strigolactones are plant metabolites that act as phytohormones and rhizosphere signals. Whereas most research on unraveling the action mechanisms of strigolactones is focused on plant shoots, we investigated proteome adaptation during strigolactone signaling in the roots of Arabidopsis thaliana. Through large-scale, time-resolved, and quantitative proteomics, the impact of the strigolactone analog rac-GR24 was elucidated on the root proteome of the wild type and the signaling mutant more axillary growth 2 (max2). Our study revealed a clear MAX2-dependent rac-GR24 response: an increase in abundance of enzymes involved in flavonol biosynthesis, which was reduced in the max2-1 mutant. Mass spectrometry-driven metabolite profiling and thin-layer chromatography experiments demonstrated that these changes in protein expression lead to the accumulation of specific flavonols. Moreover, quantitative RT-PCR revealed that the flavonol-related protein expression profile was caused by rac-GR24-induced changes in transcript levels of the corresponding genes. This induction of flavonol production was shown to be activated by the two pure enantiomers that together make up rac-GR24. Finally, our data provide much needed clues concerning the multiple roles played by MAX2 in the roots and a comprehensive view of the rac-GR24-induced response in the root proteome.
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Affiliation(s)
- Alan Walton
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; ¶Medical Biotechnology Center, VIB, 9000 Ghent, Belgium; ‖Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Elisabeth Stes
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; ¶Medical Biotechnology Center, VIB, 9000 Ghent, Belgium; ‖Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Geert Goeminne
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Lukas Braem
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | | | - Cedrick Matthys
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Carolien De Cuyper
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - An Staes
- ¶Medical Biotechnology Center, VIB, 9000 Ghent, Belgium; ‖Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Jonathan Vandenbussche
- ¶Medical Biotechnology Center, VIB, 9000 Ghent, Belgium; ‖Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - François-Didier Boyer
- ‡‡Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, 78026 Versailles, France; §§AgroParisTech, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, 78026 Versailles, France; ¶¶Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, Unité Propre de Recherche 2301, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, France
| | - Ruben Vanholme
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Justine Fromentin
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; ‖‖Laboratoire des Interactions Plantes-Microorganismes, Unité Mixte de Recherche 441, Institut National de la Recherche Agronomique, 31326 Castanet-Tolosan, France; and Laboratoire des Interactions Plantes-Microorganismes, Unité Mixte de Recherche 2594, Centre National de la Recherche Scientifique, 31326 Castanet-Tolosan, France
| | - Wout Boerjan
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Kris Gevaert
- ¶Medical Biotechnology Center, VIB, 9000 Ghent, Belgium; ‖Department of Biochemistry, Ghent University, 9000 Ghent, Belgium;
| | - Sofie Goormachtig
- From the ‡Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; §Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
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31
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Betti C, Vanhoutte I, Coutuer S, De Rycke R, Mishev K, Vuylsteke M, Aesaert S, Rombaut D, Gallardo R, De Smet F, Xu J, Van Lijsebettens M, Van Breusegem F, Inzé D, Rousseau F, Schymkowitz J, Russinova E. Sequence-Specific Protein Aggregation Generates Defined Protein Knockdowns in Plants. Plant Physiol 2016; 171:773-87. [PMID: 27208282 PMCID: PMC4902617 DOI: 10.1104/pp.16.00335] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 04/29/2016] [Indexed: 05/04/2023]
Abstract
Protein aggregation is determined by short (5-15 amino acids) aggregation-prone regions (APRs) of the polypeptide sequence that self-associate in a specific manner to form β-structured inclusions. Here, we demonstrate that the sequence specificity of APRs can be exploited to selectively knock down proteins with different localization and function in plants. Synthetic aggregation-prone peptides derived from the APRs of either the negative regulators of the brassinosteroid (BR) signaling, the glycogen synthase kinase 3/Arabidopsis SHAGGY-like kinases (GSK3/ASKs), or the starch-degrading enzyme α-glucan water dikinase were designed. Stable expression of the APRs in Arabidopsis (Arabidopsis thaliana) and maize (Zea mays) induced aggregation of the target proteins, giving rise to plants displaying constitutive BR responses and increased starch content, respectively. Overall, we show that the sequence specificity of APRs can be harnessed to generate aggregation-associated phenotypes in a targeted manner in different subcellular compartments. This study points toward the potential application of induced targeted aggregation as a useful tool to knock down protein functions in plants and, especially, to generate beneficial traits in crops.
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Affiliation(s)
- Camilla Betti
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.)
| | - Isabelle Vanhoutte
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.)
| | - Silvie Coutuer
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.)
| | - Riet De Rycke
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.)
| | - Kiril Mishev
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.)
| | - Marnik Vuylsteke
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.)
| | - Stijn Aesaert
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.)
| | - Debbie Rombaut
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.)
| | - Rodrigo Gallardo
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.)
| | - Frederik De Smet
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.)
| | - Jie Xu
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.)
| | - Mieke Van Lijsebettens
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.)
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.)
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.)
| | - Frederic Rousseau
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.)
| | - Joost Schymkowitz
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.)
| | - Eugenia Russinova
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.)
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32
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Thoonen R, Cauwels A, Decaluwe K, Geschka S, Tainsh RE, Delanghe J, Hochepied T, De Cauwer L, Rogge E, Voet S, Sips P, Karas RH, Bloch KD, Vuylsteke M, Stasch JP, Van de Voorde J, Buys ES, Brouckaert P. Cardiovascular and pharmacological implications of haem-deficient NO-unresponsive soluble guanylate cyclase knock-in mice. Nat Commun 2015; 6:8482. [PMID: 26442659 PMCID: PMC4699393 DOI: 10.1038/ncomms9482] [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: 02/27/2015] [Accepted: 08/27/2015] [Indexed: 12/15/2022] Open
Abstract
Oxidative stress, a central mediator of cardiovascular disease, results in loss of the prosthetic haem group of soluble guanylate cyclase (sGC), preventing its activation by nitric oxide (NO). Here we introduce Apo-sGC mice expressing haem-free sGC. Apo-sGC mice are viable and develop hypertension. The haemodynamic effects of NO are abolished, but those of the sGC activator cinaciguat are enhanced in apo-sGC mice, suggesting that the effects of NO on smooth muscle relaxation, blood pressure regulation and inhibition of platelet aggregation require sGC activation by NO. Tumour necrosis factor (TNF)-induced hypotension and mortality are preserved in apo-sGC mice, indicating that pathways other than sGC signalling mediate the cardiovascular collapse in shock. Apo-sGC mice allow for differentiation between sGC-dependent and -independent NO effects and between haem-dependent and -independent sGC effects. Apo-sGC mice represent a unique experimental platform to study the in vivo consequences of sGC oxidation and the therapeutic potential of sGC activators. Haem-free, NO-insensitive soluble guanylate cyclase (apo-sGC) generated during oxidative stress contributes to cardiovascular pathology. By generating and characterizing apo-sGC knock-in mice, Thoonen et al. provide a scientific ground for the therapeutic concept of sGC activators, and dissect the relevance of the NO-sGC axis.
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Affiliation(s)
- Robrecht Thoonen
- Laboratory for Molecular Pathology and Experimental Therapy, Inflammation Research Center, VIB, B-9052 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Anje Cauwels
- Laboratory for Molecular Pathology and Experimental Therapy, Inflammation Research Center, VIB, B-9052 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Kelly Decaluwe
- Department of Pharmacology, Ghent University, B-9000 Ghent, Belgium
| | - Sandra Geschka
- Cardiovascular Research, Bayer Pharma AG, D-42096 Wuppertal, Germany
| | - Robert E Tainsh
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital Research Institute, Boston, Massachusetts 02114, USA
| | - Joris Delanghe
- Department of Clinical Biology, Ghent University Hospital, B-9000 Ghent, Belgium
| | - Tino Hochepied
- Laboratory for Molecular Pathology and Experimental Therapy, Inflammation Research Center, VIB, B-9052 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Lode De Cauwer
- Laboratory for Molecular Pathology and Experimental Therapy, Inflammation Research Center, VIB, B-9052 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Elke Rogge
- Laboratory for Molecular Pathology and Experimental Therapy, Inflammation Research Center, VIB, B-9052 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Sofie Voet
- Laboratory for Molecular Pathology and Experimental Therapy, Inflammation Research Center, VIB, B-9052 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Patrick Sips
- Laboratory for Molecular Pathology and Experimental Therapy, Inflammation Research Center, VIB, B-9052 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Richard H Karas
- Molecular Cardiology Research Center, Molecular Cardiology Research Institute, Tufts Medical Center, Boston Massachusetts 02111, USA
| | - Kenneth D Bloch
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital Research Institute, Boston, Massachusetts 02114, USA
| | - Marnik Vuylsteke
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium.,Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium
| | - Johannes-Peter Stasch
- Cardiovascular Research, Bayer Pharma AG, D-42096 Wuppertal, Germany.,Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany
| | | | - Emmanuel S Buys
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital Research Institute, Boston, Massachusetts 02114, USA
| | - Peter Brouckaert
- Laboratory for Molecular Pathology and Experimental Therapy, Inflammation Research Center, VIB, B-9052 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
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33
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Vanden Berghe T, Hulpiau P, Martens L, Vandenbroucke RE, Van Wonterghem E, Perry SW, Bruggeman I, Divert T, Choi SM, Vuylsteke M, Shestopalov VI, Libert C, Vandenabeele P. Passenger Mutations Confound Interpretation of All Genetically Modified Congenic Mice. Immunity 2015; 43:200-9. [PMID: 26163370 DOI: 10.1016/j.immuni.2015.06.011] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/09/2015] [Accepted: 06/11/2015] [Indexed: 12/13/2022]
Abstract
Targeted mutagenesis in mice is a powerful tool for functional analysis of genes. However, genetic variation between embryonic stem cells (ESCs) used for targeting (previously almost exclusively 129-derived) and recipient strains (often C57BL/6J) typically results in congenic mice in which the targeted gene is flanked by ESC-derived passenger DNA potentially containing mutations. Comparative genomic analysis of 129 and C57BL/6J mouse strains revealed indels and single nucleotide polymorphisms resulting in alternative or aberrant amino acid sequences in 1,084 genes in the 129-strain genome. Annotating these passenger mutations to the reported genetically modified congenic mice that were generated using 129-strain ESCs revealed that nearly all these mice possess multiple passenger mutations potentially influencing the phenotypic outcome. We illustrated this phenotypic interference of 129-derived passenger mutations with several case studies and developed a Me-PaMuFind-It web tool to estimate the number and possible effect of passenger mutations in transgenic mice of interest.
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Affiliation(s)
- Tom Vanden Berghe
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium.
| | - Paco Hulpiau
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Liesbet Martens
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Roosmarijn E Vandenbroucke
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Elien Van Wonterghem
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Seth W Perry
- Department of Biomedical Engineering, University of Rochester, Rochester NY 14627, USA
| | - Inge Bruggeman
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Tatyana Divert
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Sze Men Choi
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | | | - Valery I Shestopalov
- Department of Ophthalmology, Bascom Palmer Eye Institute, Miami, FL 33136, USA; Department of Cell Biology and Anatomy, University of Miami School of Medicine, Miami, FL 33136, USA; Department of Cell Biology and Anatomy, Vavilov Institute for General Genetics, Moscow 119333, Russia
| | - Claude Libert
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Peter Vandenabeele
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium; Methusalem Program, Ghent University, 9000 Ghent.
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34
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Wittens C, Davies AH, Bækgaard N, Broholm R, Cavezzi A, Chastanet S, de Wolf M, Eggen C, Giannoukas A, Gohel M, Kakkos S, Lawson J, Noppeney T, Onida S, Pittaluga P, Thomis S, Toonder I, Vuylsteke M, Kolh P, de Borst GJ, Chakfé N, Debus S, Hinchliffe R, Koncar I, Lindholt J, de Ceniga MV, Vermassen F, Verzini F, De Maeseneer MG, Blomgren L, Hartung O, Kalodiki E, Korten E, Lugli M, Naylor R, Nicolini P, Rosales A. Editor's Choice - Management of Chronic Venous Disease: Clinical Practice Guidelines of the European Society for Vascular Surgery (ESVS). Eur J Vasc Endovasc Surg 2015; 49:678-737. [PMID: 25920631 DOI: 10.1016/j.ejvs.2015.02.007] [Citation(s) in RCA: 493] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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35
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Robrecht T, Emmanuel B, Cauwels A, Decaluwe K, Geschka S, Tainsh R, Delanghe J, Hochepied T, De Cauwer L, Rogge E, Sips P, Karas R, Bloch K, Van De Voorde J, Stasch JP, Vuylsteke M, Brouckaert P. Heme-deficient NO-unresponsive sGC knock-in mice: Novel aspects of NO–sGC signaling in cardiovascular (patho)physiology. Nitric Oxide 2014. [DOI: 10.1016/j.niox.2014.09.048] [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: 11/17/2022]
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36
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Berghe TV, Demon D, Bogaert P, Vandendriessche B, Goethals A, Depuydt B, Vuylsteke M, Roelandt R, Van Wonterghem E, Vandenbroecke J, Choi SM, Meyer E, Krautwald S, Declercq W, Takahashi N, Cauwels A, Vandenabeele P. Simultaneous targeting of interleukin-1 and interleukin-18 is required for protection against inflammatory and septic shock. Crit Care 2014. [PMCID: PMC4273742 DOI: 10.1186/cc14023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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37
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Berghe TV, Demon D, Bogaert P, Vandendriessche B, Goethals A, Depuydt B, Vuylsteke M, Roelandt R, Van Wonterghem E, Vandenbroecke J, Choi SM, Meyer E, Krautwald S, Declercq W, Takahashi N, Cauwels A, Vandenabeele P. Simultaneous Targeting of IL-1 and IL-18 Is Required for Protection against Inflammatory and Septic Shock. Am J Respir Crit Care Med 2014; 189:282-91. [DOI: 10.1164/rccm.201308-1535oc] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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38
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Bhosale R, Jewell JB, Hollunder J, Koo AJ, Vuylsteke M, Michoel T, Hilson P, Goossens A, Howe GA, Browse J, Maere S. Predicting gene function from uncontrolled expression variation among individual wild-type Arabidopsis plants. Plant Cell 2013; 25:2865-77. [PMID: 23943861 PMCID: PMC3784585 DOI: 10.1105/tpc.113.112268] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 06/16/2013] [Accepted: 07/18/2013] [Indexed: 05/20/2023]
Abstract
Gene expression profiling studies are usually performed on pooled samples grown under tightly controlled experimental conditions to suppress variability among individuals and increase experimental reproducibility. In addition, to mask unwanted residual effects, the samples are often subjected to relatively harsh treatments that are unrealistic in a natural context. Here, we show that expression variations among individual wild-type Arabidopsis thaliana plants grown under the same macroscopic growth conditions contain as much information on the underlying gene network structure as expression profiles of pooled plant samples under controlled experimental perturbations. We advocate the use of subtle uncontrolled variations in gene expression between individuals to uncover functional links between genes and unravel regulatory influences. As a case study, we use this approach to identify ILL6 as a new regulatory component of the jasmonate response pathway.
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Affiliation(s)
- Rahul Bhosale
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Jeremy B. Jewell
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163
| | - Jens Hollunder
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Abraham J.K. Koo
- Department of Energy–Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Marnik Vuylsteke
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Tom Michoel
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Pierre Hilson
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Gregg A. Howe
- Department of Energy–Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - John Browse
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163
| | - Steven Maere
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Address correspondence to
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39
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Pinheiro I, Dejager L, Petta I, Vandevyver S, Puimège L, Mahieu T, Ballegeer M, Van Hauwermeiren F, Riccardi C, Vuylsteke M, Libert C. LPS resistance of SPRET/Ei mice is mediated by Gilz, encoded by the Tsc22d3 gene on the X chromosome. EMBO Mol Med 2013; 5:456-70. [PMID: 23495141 PMCID: PMC3598084 DOI: 10.1002/emmm.201201683] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [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: 06/27/2012] [Revised: 12/07/2012] [Accepted: 12/12/2012] [Indexed: 01/12/2023] Open
Abstract
Natural variation for LPS-induced lethal inflammation in mice is useful for identifying new genes that regulate sepsis, which could form the basis for novel therapies for systemic inflammation in humans. Here we report that LPS resistance of the inbred mouse strain SPRET/Ei, previously reported to depend on the glucocorticoid receptor (GR), maps to the distal region of the X-chromosome. The GR-inducible gene Tsc22d3, encoding the protein Gilz and located in the critical region on the X-chromosome, showed a higher expressed SPRET/Ei allele, regulated in cis. Higher Gilz levels were causally related to reduced inflammation, as shown with knockdown and overexpression studies in macrophages. Transient overexpression of Gilz by hydrodynamic plasmid injection confirmed that Gilz protects mice against endotoxemia Our data strongly suggest that Gilz is responsible for the LPS resistance of SPRET/Ei mice and that it could become a treatment option for sepsis.
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Affiliation(s)
- Iris Pinheiro
- Department for Molecular Biomedical Research, VIB, Ghent, Belgium
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40
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Vanstechelman I, Sabbe K, Vyverman W, Vanormelingen P, Vuylsteke M. Linkage mapping identifies the sex determining region as a single locus in the Pennate diatom Seminavis robusta. PLoS One 2013; 8:e60132. [PMID: 23527302 PMCID: PMC3603935 DOI: 10.1371/journal.pone.0060132] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [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: 11/23/2012] [Accepted: 02/21/2013] [Indexed: 11/18/2022] Open
Abstract
The pennate diatom Seminavis robusta, characterized by an archetypical diatom life cycle including a heterothallic mating system, is emerging as a model system for studying the molecular regulation of the diatom cell and life cycle. One of its main advantages compared with other diatom model systems is that sexual crosses can be made routinely, offering unprecedented possibilities for forward genetics. To date, nothing is known about the genetic basis of sex determination in diatoms. Here, we report on the construction of mating type-specific linkage maps for S. robusta, and use them to identify a single locus sex determination system in this diatom. We identified 13 mating type plus and 15 mating type minus linkage groups obtained from the analysis of 463 AFLP markers segregating in a full-sib family, covering 963.7 and 972.2 cM, respectively. Five linkage group pairs could be identified as putative homologues. The mating type phenotype mapped as a monogenic trait, disclosing the mating type plus as the heterogametic sex. This study provides the first evidence for a genetic sex determining mechanism in a diatom.
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Affiliation(s)
- Ives Vanstechelman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Gent, Belgium
- VIB Department of Plant Systems Biology, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Koen Sabbe
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Gent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Gent, Belgium
| | - Pieter Vanormelingen
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Gent, Belgium
| | - Marnik Vuylsteke
- VIB Department of Plant Systems Biology, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
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41
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De Vos S, Bossier P, Van Stappen G, Vercauteren I, Sorgeloos P, Vuylsteke M. A first AFLP-based genetic linkage map for brine shrimp Artemia franciscana and its application in mapping the sex locus. PLoS One 2013; 8:e57585. [PMID: 23469207 PMCID: PMC3587612 DOI: 10.1371/journal.pone.0057585] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [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: 10/25/2012] [Accepted: 01/22/2013] [Indexed: 12/26/2022] Open
Abstract
We report on the construction of sex-specific linkage maps, the identification of sex-linked markers and the genome size estimation for the brine shrimp Artemia franciscana. Overall, from the analysis of 433 AFLP markers segregating in a 112 full-sib family we identified 21 male and 22 female linkage groups (2n = 42), covering 1,041 and 1,313 cM respectively. Fifteen putatively homologous linkage groups, including the sex linkage groups, were identified between the female and male linkage map. Eight sex-linked AFLP marker alleles were inherited from the female parent, supporting the hypothesis of a WZ-ZZ sex-determining system. The haploid Artemia genome size was estimated to 0.93 Gb by flow cytometry. The produced Artemia linkage maps provide the basis for further fine mapping and exploring of the sex-determining region and are a possible marker resource for mapping genomic loci underlying phenotypic differences among Artemia species.
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Affiliation(s)
- Stephanie De Vos
- Laboratory of Aquaculture, Artemia Reference Center (ARC), Department of Animal Production, Ghent University, Gent, Belgium
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Peter Bossier
- Laboratory of Aquaculture, Artemia Reference Center (ARC), Department of Animal Production, Ghent University, Gent, Belgium
| | - Gilbert Van Stappen
- Laboratory of Aquaculture, Artemia Reference Center (ARC), Department of Animal Production, Ghent University, Gent, Belgium
| | - Ilse Vercauteren
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Patrick Sorgeloos
- Laboratory of Aquaculture, Artemia Reference Center (ARC), Department of Animal Production, Ghent University, Gent, Belgium
| | - Marnik Vuylsteke
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- * E-mail:
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42
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Gillard J, Frenkel J, Devos V, Sabbe K, Paul C, Rempt M, Inzé D, Pohnert G, Vuylsteke M, Vyverman W. Metabolomik unterstützt die Strukturaufklärung eines Sexualpheromons von Kieselalgen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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43
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Gillard J, Frenkel J, Devos V, Sabbe K, Paul C, Rempt M, Inzé D, Pohnert G, Vuylsteke M, Vyverman W. Rücktitelbild: Metabolomik unterstützt die Strukturaufklärung eines Sexualpheromons von Kieselalgen (Angew. Chem. 3/2013). Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209860] [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: 11/09/2022]
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44
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Gillard J, Frenkel J, Devos V, Sabbe K, Paul C, Rempt M, Inzé D, Pohnert G, Vuylsteke M, Vyverman W. Back Cover: Metabolomics Enables the Structure Elucidation of a Diatom Sex Pheromone (Angew. Chem. Int. Ed. 3/2013). Angew Chem Int Ed Engl 2013. [DOI: 10.1002/anie.201209860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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45
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Gillard J, Frenkel J, Devos V, Sabbe K, Paul C, Rempt M, Inzé D, Pohnert G, Vuylsteke M, Vyverman W. Metabolomics enables the structure elucidation of a diatom sex pheromone. Angew Chem Int Ed Engl 2012; 52:854-7. [PMID: 23315901 DOI: 10.1002/anie.201208175] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Indexed: 11/07/2022]
Affiliation(s)
- Jeroen Gillard
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Gent, Belgium
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46
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Mayzlish-Gati E, De-Cuyper C, Goormachtig S, Beeckman T, Vuylsteke M, Brewer PB, Beveridge CA, Yermiyahu U, Kaplan Y, Enzer Y, Wininger S, Resnick N, Cohen M, Kapulnik Y, Koltai H. Strigolactones are involved in root response to low phosphate conditions in Arabidopsis. Plant Physiol 2012; 160:1329-41. [PMID: 22968830 PMCID: PMC3490576 DOI: 10.1104/pp.112.202358] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 09/10/2012] [Indexed: 05/18/2023]
Abstract
Strigolactones (SLs) are plant hormones that suppress lateral shoot branching, and act to regulate root hair elongation and lateral root formation. Here, we show that SLs are regulators of plant perception of or response to low inorganic phosphate (Pi) conditions. This regulation is mediated by MORE AXILLARY GROWTH2 (MAX2) and correlated with transcriptional induction of the auxin receptor TRANSPORT INHIBITOR RESPONSE1 (TIR1). Mutants of SL signaling (max2-1) or biosynthesis (max4-1) showed reduced response to low Pi conditions relative to the wild type. In max4-1, but not max2-1, the reduction in response to low Pi was compensated by the application of a synthetic strigolactone GR24. Moreover, AbamineSG, which decreases SL levels in plants, reduced the response to low Pi in the wild type, but not in SL-signaling or biosynthesis mutants. In accordance with the reduced response of max2-1 to low Pi relative to the wild type, several phosphate-starvation response and phosphate-transporter genes displayed reduced induction in max2-1, even though Pi content in max2-1 and the wild type were similar. Auxin, but not ethylene, was sufficient to compensate for the reduced max2-1 response to low Pi conditions. Moreover, the expression level of TIR1 was induced under low Pi conditions in the wild type, but not in max2-1. Accordingly, the tir1-1 mutant showed a transient reduction in root hair density in comparison with the wild type under low Pi conditions. Therefore, we suggest that the response of plants to low Pi is regulated by SLs; this regulation is transmitted via the MAX2 component of SL signaling and is correlated with transcriptional induction of the TIR1 auxin receptor.
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47
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Himanen K, Woloszynska M, Boccardi TM, De Groeve S, Nelissen H, Bruno L, Vuylsteke M, Van Lijsebettens M. Histone H2B monoubiquitination is required to reach maximal transcript levels of circadian clock genes in Arabidopsis. Plant J 2012; 72:249-60. [PMID: 22762858 DOI: 10.1111/j.1365-313x.2012.05071.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Previously, we identified HISTONE MONOUBIQUITINATION1 (HUB1) as an unconventional ubiquitin E3 ligase that is not involved in protein degradation but in the histone H2B modification that is implicated in transcriptional activation in plants. HUB1-mediated regulation of gene expression played a role in periodic and inducible processes such as the cell cycle, dormancy, flowering time and defense responses. Here, we determined the effects of the hub1-1 mutation on expression of a set of diurnally induced circadian clock genes identified from a comparative microarray analysis between the hub1-1 mutant and an HUB1 over-expression line. The hub1-1 mutation reduced the amplitudes of a number of induced clock gene expression peaks, as well as the HUB1-mediated histone H2BUb and H3K4Me3 marks associated with the coding regions, suggesting a role for HUB1 in facilitating transcriptional elongation in plants. Furthermore, double mutants between hub1-1 and elongata (elo) showed an embryo-lethal phenotype, indicating a synergistic genetic interaction. The double mutant embryos arrested at the torpedo stage, implying that together histone ubiquitination and acetylation marks are essential to activate expression of target genes in multiple pathways.
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Affiliation(s)
- Kristiina Himanen
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium
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48
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Mortier V, De Wever E, Vuylsteke M, Holsters M, Goormachtig S. Nodule numbers are governed by interaction between CLE peptides and cytokinin signaling. Plant J 2012; 70:367-76. [PMID: 22168914 DOI: 10.1111/j.1365-313x.2011.04881.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
CLE peptides are involved in the balance between cell division and differentiation throughout plant development, including nodulation. Previously, two CLE genes of Medicago truncatula, MtCLE12 and MtCLE13, had been identified whose expression correlated with nodule primordium formation and meristem establishment. Gain-of-function analysis indicated that both MtCLE12 and MtCLE13 interact with the SUPER NUMERIC NODULES (SUNN)-dependent auto-regulation of nodulation to control nodule numbers. Here we demonstrate that cytokinin, which is essential for nodule organ formation, regulates MtCLE13 expression. In addition, simultaneous knockdown of MtCLE12 and MtCLE13 resulted in an increase in nodule number, implying that both genes play a role in controlling nodule number. Additionally, a weak link may exist with the ethylene-dependent mechanism that locally controls nodule number.
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Van Daele I, Gonzalez N, Vercauteren I, de Smet L, Inzé D, Roldán-Ruiz I, Vuylsteke M. A comparative study of seed yield parameters in Arabidopsis thaliana mutants and transgenics. Plant Biotechnol J 2012; 10:488-500. [PMID: 22332878 DOI: 10.1111/j.1467-7652.2012.00687.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Because seed yield is the major factor determining the commercial success of grain crop cultivars, there is a large interest to obtain more understanding of the genetic factors underlying this trait. Despite many studies, mainly in the model plant Arabidopsis thaliana, have reported transgenes and mutants with effects on seed number and/or seed size, knowledge about seed yield parameters remains fragmented. This study investigated the effect of 46 genes, either in gain- and/or loss-of-function situations, with a total of 64 Arabidopsis lines being examined for seed phenotypes such as seed size, seed number per silique, number of inflorescences, number of branches on the main inflorescence and number of siliques. Sixteen of the 46 genes, examined in 14 Arabidopsis lines, were reported earlier to directly affect in seed size and/or seed number or to indirectly affect seed yield by their involvement in biomass production. Other genes involved in vegetative growth, flower or inflorescence development or cell division were hypothesized to potentially affect the final seed size and seed number. Analysis of this comprehensive data set shows that of the 14 lines previously described to be affected in seed size or seed number, only nine showed a comparable effect. Overall, this study provides the community with a useful resource for identifying genes with effects on seed yield and candidate genes underlying seed QTL. In addition, this study highlights the need for more thorough analysis of genes affecting seed yield.
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Nicolaï M, Pisani C, Bouchet JP, Vuylsteke M, Palloix A. Short Communication Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum). Genet Mol Res 2012; 11:2295-300. [DOI: 10.4238/2012.august.13.3] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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