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Pascual-García M, Unkel M, Slotman JA, Bolleboom A, Bouwen B, Houtsmuller AB, Dirven C, Gao Z, Hijazi S, Kushner SA. Morphological correlates of pyramidal cell axonal myelination in mouse and human neocortex. Cereb Cortex 2024; 34:bhae147. [PMID: 38610088 PMCID: PMC11014882 DOI: 10.1093/cercor/bhae147] [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: 12/11/2023] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 04/14/2024] Open
Abstract
The axons of neocortical pyramidal neurons are frequently myelinated. Heterogeneity in the topography of axonal myelination in the cerebral cortex has been attributed to a combination of electrophysiological activity, axonal morphology, and neuronal-glial interactions. Previously, we showed that axonal segment length and caliber are critical local determinants of fast-spiking interneuron myelination. However, the factors that determine the myelination of individual axonal segments along neocortical pyramidal neurons remain largely unexplored. Here, we used structured illumination microscopy to examine the extent to which axonal morphology is predictive of the topography of myelination along neocortical pyramidal neurons. We identified critical thresholds for axonal caliber and interbranch distance that are necessary, but not sufficient, for myelination of pyramidal cell axons in mouse primary somatosensory cortex (S1). Specifically, we found that pyramidal neuron axonal segments with a caliber < 0.24 μm or interbranch distance < 18.10 μm are rarely myelinated. Moreover, we further confirmed that these findings in mice are similar for human neocortical pyramidal cell myelination (caliber < 0.25 μm, interbranch distance < 19.00 μm), suggesting that this mechanism is evolutionarily conserved. Taken together, our findings suggest that axonal morphology is a critical correlate of the topography and cell-type specificity of neocortical myelination.
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Affiliation(s)
- Maria Pascual-García
- Department of Psychiatry, Erasmus MC, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
| | - Maurits Unkel
- Department of Psychiatry, Erasmus MC, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
| | - Johan A Slotman
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
| | - Anne Bolleboom
- Department of Neuroscience, Erasmus MC, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
- Department of Neurosurgery, Erasmus MC, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
| | - Bibi Bouwen
- Department of Neuroscience, Erasmus MC, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
- Department of Neurosurgery, Erasmus MC, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
| | - Clemens Dirven
- Department of Neurosurgery, Erasmus MC, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
| | - Zhenyu Gao
- Department of Neuroscience, Erasmus MC, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
| | - Sara Hijazi
- Department of Psychiatry, Erasmus MC, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, United Kingdom
| | - Steven A Kushner
- Department of Psychiatry, Erasmus MC, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
- Department of Psychiatry, Columbia University, 1051 Riverside Drive, New York, NY 10032, United States
- SNF Center for Precision Psychiatry & Mental Health, Columbia University, 630 West 168th Street, New York, NY 10032, United States
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2
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Koornneef L, Paul MW, Houtsmuller AB, Baarends WM, Slotman JA. Three-color dSTORM Imaging and Analysis of Recombination Foci in Mouse Spread Meiotic Nuclei. Bio Protoc 2023; 13:e4780. [PMID: 37497444 PMCID: PMC10367009 DOI: 10.21769/bioprotoc.4780] [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] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/04/2023] [Accepted: 06/13/2023] [Indexed: 07/28/2023] Open
Abstract
During the first meiotic prophase in mouse, repair of SPO11-induced DNA double-strand breaks (DSBs), facilitating homologous chromosome synapsis, is essential to successfully complete the first meiotic cell division. Recombinases RAD51 and DMC1 play an important role in homology search, but their mechanistic contribution to this process is not fully understood. Super-resolution, single-molecule imaging of RAD51 and DMC1 provides detailed information on recombinase accumulation on DSBs during meiotic prophase. Here, we present a detailed protocol of recombination foci analysis of three-color direct stochastic optical reconstruction microscopy (dSTORM) imaging of SYCP3, RAD51, and DMC1, fluorescently labeled by antibody staining in mouse spermatocytes. This protocol consists of sample preparation, data acquisition, pre-processing, and data analysis. The sample preparation procedure includes an updated version of the nuclear spreading of mouse testicular cells, followed by immunocytochemistry and the preparation steps for dSTORM imaging. Data acquisition consists of three-color dSTORM imaging, which is extensively described. The pre-processing that converts fluorescent signals to localization data also includes channel alignment and image reconstruction, after which regions of interest (ROIs) are identified based on RAD51 and/or DMC1 localization patterns. The data analysis steps then require processing of the fluorescent signal localization within these ROIs into discrete nanofoci, which can be further analyzed. This multistep approach enables the systematic investigation of spatial distributions of proteins associated with individual DSB sites and can be easily adapted for analyses of other foci-forming proteins. All computational scripts and software are freely accessible, making them available to a broad audience. Key features Preparation of spread nuclei, resulting in a flattened preparation with easy antibody-accessible chromatin-associated proteins on dSTORM-compatible coverslips. dSTORM analysis of immunofluorescent repair foci in meiotic prophase nuclei. Detailed descriptions of data acquisition, (pre-)processing, and nanofoci feature analysis applicable to all proteins that assemble in immunodetection as discrete foci. Graphical overview.
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Affiliation(s)
- Lieke Koornneef
- Department of Developmental Biology, Erasmus MC, Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Maarten W. Paul
- Oncode Institute, Erasmus MC, Rotterdam, The Netherlands
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | | | - Willy M. Baarends
- Department of Developmental Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Johan A. Slotman
- Erasmus Optical Imaging Center, Erasmus MC, Rotterdam, The Netherlands
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3
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Legerstee K, Sueters J, Abraham TE, Slotman JA, Kremers GJ, Hoogenboom JP, Houtsmuller AB. Correlative light and electron microscopy reveals fork-shaped structures at actin entry sites of focal adhesions. Biol Open 2022; 11:283176. [PMID: 36409550 PMCID: PMC9836080 DOI: 10.1242/bio.059417] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 10/21/2022] [Indexed: 11/23/2022] Open
Abstract
Focal adhesions (FAs) are the main cellular structures to link the intracellular cytoskeleton to the extracellular matrix. FAs mediate cell adhesion, are important for cell migration and are involved in many (patho)-physiological processes. Here we examined FAs and their associated actin fibres using correlative fluorescence and scanning electron microscopy (SEM). We used fluorescence images of cells expressing paxillin-GFP to define the boundaries of FA complexes in SEM images, without using SEM contrast enhancing stains. We observed that SEM contrast was increased around the actin fibre entry site in 98% of FAs, indicating increases in protein density and possibly also phosphorylation levels in this area. In nearly three quarters of the FAs, these nanostructures had a fork shape, with the actin forming the stem and the high-contrast FA areas the fork. In conclusion, the combination of fluorescent and electron microscopy allowed accurate localisation of a highly abundant, novel fork structure at the FA-actin interface.
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Affiliation(s)
- Karin Legerstee
- Erasmus Medical Centre Rotterdam, Department of Pathology, Optical Imaging Centre, 3000 CA, Rotterdam, The Netherlands
| | - Jason Sueters
- Delft University of Technology, Department of Imaging Physics, 2628 CD, Delft, The Netherlands
| | - Tsion E. Abraham
- Erasmus Medical Centre Rotterdam, Department of Pathology, Optical Imaging Centre, 3000 CA, Rotterdam, The Netherlands
| | - Johan A. Slotman
- Erasmus Medical Centre Rotterdam, Department of Pathology, Optical Imaging Centre, 3000 CA, Rotterdam, The Netherlands
| | - Gert-Jan Kremers
- Erasmus Medical Centre Rotterdam, Department of Pathology, Optical Imaging Centre, 3000 CA, Rotterdam, The Netherlands
| | - Jacob P. Hoogenboom
- Delft University of Technology, Department of Imaging Physics, 2628 CD, Delft, The Netherlands
| | - Adriaan B. Houtsmuller
- Erasmus Medical Centre Rotterdam, Department of Pathology, Optical Imaging Centre, 3000 CA, Rotterdam, The Netherlands,Author for correspondence ()
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4
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Steurer B, Janssens RC, Geijer ME, Aprile-Garcia F, Geverts B, Theil AF, Hummel B, van Royen ME, Evers B, Bernards R, Houtsmuller AB, Sawarkar R, Marteijn J. DNA damage-induced transcription stress triggers the genome-wide degradation of promoter-bound Pol II. Nat Commun 2022; 13:3624. [PMID: 35750669 PMCID: PMC9232492 DOI: 10.1038/s41467-022-31329-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 12/04/2020] [Accepted: 06/10/2022] [Indexed: 01/22/2023] Open
Abstract
The precise regulation of RNA Polymerase II (Pol II) transcription after genotoxic stress is crucial for proper execution of the DNA damage-induced stress response. While stalling of Pol II on transcription-blocking lesions (TBLs) blocks transcript elongation and initiates DNA repair in cis, TBLs additionally elicit a response in trans that regulates transcription genome-wide. Here we uncover that, after an initial elongation block in cis, TBLs trigger the genome-wide VCP-mediated proteasomal degradation of promoter-bound, P-Ser5-modified Pol II in trans. This degradation is mechanistically distinct from processing of TBL-stalled Pol II, is signaled via GSK3, and contributes to the TBL-induced transcription block, even in transcription-coupled repair-deficient cells. Thus, our data reveal the targeted degradation of promoter-bound Pol II as a critical pathway that allows cells to cope with DNA damage-induced transcription stress and enables the genome-wide adaptation of transcription to genotoxic stress.
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Affiliation(s)
- Barbara Steurer
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Roel C Janssens
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marit E Geijer
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Bart Geverts
- Department of Pathology, Optical Imaging Centre, Erasmus MC, Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Barbara Hummel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Martin E van Royen
- Department of Pathology, Optical Imaging Centre, Erasmus MC, Rotterdam, The Netherlands
| | - Bastiaan Evers
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - René Bernards
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Adriaan B Houtsmuller
- Department of Pathology, Optical Imaging Centre, Erasmus MC, Rotterdam, The Netherlands
| | - Ritwick Sawarkar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- MRC, University of Cambridge, Cambridge, UK
| | - Jurgen Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
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5
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Snaterse G, Mies R, van Weerden WM, French PJ, Jonker JW, Houtsmuller AB, van Royen ME, Visser JA, Hofland J. Androgen receptor mutations modulate activation by 11-oxygenated androgens and glucocorticoids. Prostate Cancer Prostatic Dis 2022:10.1038/s41391-022-00491-z. [PMID: 35046557 DOI: 10.1038/s41391-022-00491-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/15/2021] [Accepted: 01/07/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Androgen receptor (AR) ligand-binding domain (LBD) mutations occur in ~20% of all castration-resistant prostate cancer (CRPC) patients. These mutations confer ligand promiscuity, but the affinity for many steroid hormone pathway intermediates is unknown. In this study, we investigated the stimulation of clinically relevant AR-LBD mutants by endogenous and exogenous steroid hormones present in CRPC patients to unravel their potential contribution to AR pathway reactivation. METHODS A meta-analysis of studies reporting untargeted analysis of AR mutants was performed to identify clinically relevant AR-LBD mutations. Using luciferase reporter and quantitative fluorescent microscopy, these AR mutants were screened for sensitivity for various endogenous steroids and synthetic glucocorticoids used in the treatment of CRPC. RESULTS The meta-analysis revealed that ARL702H (3.4%), ARH875Y (4.9%), and ART878A (4.4%) were the most prevalent AR-LBD mutations across 1614 CRPC patients from 21 unique studies. Testosterone (EC50: 0.22 nmol/L) and 11-ketotestosterone (11KT, EC50: 0.74 nmol/L) displayed subnanomolar affinity for ARWT. The p.H875Y mutation selectively increased sensitivity of the AR for 11KT (EC50: 0.15 nmol/L, p < 0.05 vs ARWT), whereas p.L702H decreased sensitivity for 11KT by almost 50-fold. While cortisol and prednisolone both stimulate ARL702H, dexamethasone importantly does not. CONCLUSION Both testosterone and 11KT effectively contribute to ARWT activation, while selective sensitization positions 11KT as a more prominent activator of ARH875Y. Dexamethasone may be a suitable alternative to prednisolone and should be explored in patients bearing the ARL702H.
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Affiliation(s)
- Gido Snaterse
- Department of Internal Medicine, Section of Endocrinology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Rosinda Mies
- Department of Internal Medicine, Section of Endocrinology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Wytske M van Weerden
- Department of Urology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Pim J French
- Cancer Treatment Screening Facility, Department of Neurology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Johan W Jonker
- Section of Molecular Metabolism and Nutrition, Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Adriaan B Houtsmuller
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Martin E van Royen
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jenny A Visser
- Department of Internal Medicine, Section of Endocrinology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Johannes Hofland
- Department of Internal Medicine, Section of Endocrinology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
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6
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Legerstee K, Houtsmuller AB. A Layered View on Focal Adhesions. Biology (Basel) 2021; 10:biology10111189. [PMID: 34827182 PMCID: PMC8614905 DOI: 10.3390/biology10111189] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 12/31/2022]
Abstract
Simple Summary The cytoskeleton is a network of protein fibres within cells that provide structure and support intracellular transport. Focal adhesions are protein complexes associated with the outer cell membrane that are found at the ends of specialised actin fibres of this cytoskeleton. They mediate cell adhesion by connecting the cytoskeleton to the extracellular matrix, a protein and sugar network that surrounds cells in tissues. Focal adhesions also translate forces on actin fibres into forces contributing to cell migration. Cell adhesion and migration are crucial to diverse biological processes such as embryonic development, proper functioning of the immune system or the metastasis of cancer cells. Advances in fluorescence microscopy and data analysis methods provided a more detailed understanding of the dynamic ways in which proteins bind and dissociate from focal adhesions and how they are organised within these protein complexes. In this review, we provide an overview of the advances in the current scientific understanding of focal adhesions and summarize relevant imaging techniques. One of the key insights is that focal adhesion proteins are organised into three layers parallel to the cell membrane. We discuss the relevance of this layered nature for the functioning of focal adhesion. Abstract The cytoskeleton provides structure to cells and supports intracellular transport. Actin fibres are crucial to both functions. Focal Adhesions (FAs) are large macromolecular multiprotein assemblies at the ends of specialised actin fibres linking these to the extracellular matrix. FAs translate forces on actin fibres into forces contributing to cell migration. This review will discuss recent insights into FA protein dynamics and their organisation within FAs, made possible by advances in fluorescence imaging techniques and data analysis methods. Over the last decade, evidence has accumulated that FAs are composed of three layers parallel to the plasma membrane. We focus on some of the most frequently investigated proteins, two from each layer, paxillin and FAK (bottom, integrin signalling layer), vinculin and talin (middle, force transduction layer) and zyxin and VASP (top, actin regulatory layer). Finally, we discuss the potential impact of this layered nature on different aspects of FA behaviour.
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7
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Zhang S, Übelmesser N, Josipovic N, Forte G, Slotman JA, Chiang M, Gothe HJ, Gusmao EG, Becker C, Altmüller J, Houtsmuller AB, Roukos V, Wendt KS, Marenduzzo D, Papantonis A. RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis. Sci Adv 2021; 7:eabg8205. [PMID: 34678064 PMCID: PMC8535795 DOI: 10.1126/sciadv.abg8205] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Mammalian chromosomes are three-dimensional entities shaped by converging and opposing forces. Mitotic cell division induces marked chromosome condensation, but following reentry into the G1 phase of the cell cycle, chromosomes reestablish their interphase organization. Here, we tested the role of RNA polymerase II (RNAPII) in this transition using a cell line that allows its auxin-mediated degradation. In situ Hi-C showed that RNAPII is required for both compartment and loop establishment following mitosis. RNAPs often counteract loop extrusion, and in their absence, longer and more prominent loops arose. Evidence from chromatin binding, super-resolution imaging, and in silico modeling allude to these effects being a result of RNAPII-mediated cohesin loading upon G1 reentry. Our findings reconcile the role of RNAPII in gene expression with that in chromatin architecture.
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Affiliation(s)
- Shu Zhang
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Nadine Übelmesser
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Natasa Josipovic
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Giada Forte
- School of Physics and Astronomy, University of Edinburgh, EH9 3FD Edinburgh, UK
| | - Johan A. Slotman
- Optical Imaging Centre, Erasmus Medical Center, 3015 GD Rotterdam, Netherlands
| | - Michael Chiang
- School of Physics and Astronomy, University of Edinburgh, EH9 3FD Edinburgh, UK
| | | | - Eduardo Gade Gusmao
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Christian Becker
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | | | | | - Kerstin S. Wendt
- Department of Cell Biology, Erasmus Medical Center, 3015 GD Rotterdam, Netherlands
| | - Davide Marenduzzo
- School of Physics and Astronomy, University of Edinburgh, EH9 3FD Edinburgh, UK
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Corresponding author.
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8
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El Kharraz S, Dubois V, van Royen ME, Houtsmuller AB, Pavlova E, Atanassova N, Nguyen T, Voet A, Eerlings R, Handle F, Prekovic S, Smeets E, Moris L, Devlies W, Ohlsson C, Poutanen M, Verstrepen KJ, Carmeliet G, Launonen KM, Helminen L, Palvimo JJ, Libert C, Vanderschueren D, Helsen C, Claessens F. The androgen receptor depends on ligand-binding domain dimerization for transcriptional activation. EMBO Rep 2021; 22:e52764. [PMID: 34661369 DOI: 10.15252/embr.202152764] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 01/28/2023] Open
Abstract
Whereas dimerization of the DNA-binding domain of the androgen receptor (AR) plays an evident role in recognizing bipartite response elements, the contribution of the dimerization of the ligand-binding domain (LBD) to the correct functioning of the AR remains unclear. Here, we describe a mouse model with disrupted dimerization of the AR LBD (ARLmon/Y ). The disruptive effect of the mutation is demonstrated by the feminized phenotype, absence of male accessory sex glands, and strongly affected spermatogenesis, despite high circulating levels of testosterone. Testosterone replacement studies in orchidectomized mice demonstrate that androgen-regulated transcriptomes in ARLmon/Y mice are completely lost. The mutated AR still translocates to the nucleus and binds chromatin, but does not bind to specific AR binding sites. In vitro studies reveal that the mutation in the LBD dimer interface also affects other AR functions such as DNA binding, ligand binding, and co-regulator binding. In conclusion, LBD dimerization is crucial for the development of AR-dependent tissues through its role in transcriptional regulation in vivo. Our findings identify AR LBD dimerization as a possible target for AR inhibition.
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Affiliation(s)
- Sarah El Kharraz
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Vanessa Dubois
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | | | | | - Ekatarina Pavlova
- Institute of Experimental Morphology Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Nina Atanassova
- Institute of Experimental Morphology Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Tien Nguyen
- Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Arnout Voet
- Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Roy Eerlings
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Florian Handle
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Stefan Prekovic
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.,Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Elien Smeets
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Lisa Moris
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Wout Devlies
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Claes Ohlsson
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden
| | - Matti Poutanen
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden.,Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology and KU Leuven Laboratory for Genetics and Genomics, VIB - KU Leuven Center for Microbiology, Leuven, Belgium
| | - Geert Carmeliet
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | | | - Laura Helminen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Jorma J Palvimo
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Claude Libert
- VIB Center for Inflammation Research, VIB, Ghent, Belgium.,Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | | | - Christine Helsen
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frank Claessens
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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9
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Swinkels M, Atiq F, Bürgisser PE, Slotman JA, Houtsmuller AB, de Heus C, Klumperman J, Leebeek FWG, Voorberg J, Jansen AJG, Bierings R. Quantitative 3D microscopy highlights altered von Willebrand factor α-granule storage in patients with von Willebrand disease with distinct pathogenic mechanisms. Res Pract Thromb Haemost 2021; 5:e12595. [PMID: 34532631 PMCID: PMC8440947 DOI: 10.1002/rth2.12595] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 02/22/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Platelets play a key role in hemostasis through plug formation and secretion of their granule contents at sites of endothelial injury. Defects in von Willebrand factor (VWF), a platelet α-granule protein, are implicated in von Willebrand disease (VWD), and may lead to defective platelet adhesion and/or aggregation. Studying VWF quantity and subcellular localization may help us better understand the pathophysiology of VWD. OBJECTIVE Quantitative analysis of the platelet α-granule compartment and VWF storage in healthy individuals and VWD patients. PATIENTS/METHODS Structured illumination microscopy (SIM) was used to study VWF content and organization in platelets of healthy individuals and patients with VWD in combination with established techniques. RESULTS SIM capably quantified clear morphological and granular changes in platelets stimulated with proteinase-activated receptor 1 (PAR-1) activating peptide and revealed a large intra- and interdonor variability in VWF-positive object numbers within healthy resting platelets, similar to variation in secreted protein acidic and rich in cysteine (SPARC). We subsequently characterized VWD platelets to identify changes in the α-granule compartment of patients with different VWF defects, and were able to stratify two patients with type 3 VWD rising from different pathological mechanisms. We further analyzed VWF storage in α-granules of a patient with homozygous p.C1190R using electron microscopy and found discrepant VWF levels and different degrees of multimerization in platelets of patients with heterozygous p.C1190 in comparison to VWF in plasma. CONCLUSIONS Our findings highlight the utility of quantitative imaging approaches in assessing platelet granule content, which may help to better understand VWF storage in α-granules and to gain new insights in the etiology of VWD.
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Affiliation(s)
- Maurice Swinkels
- Department of HematologyErasmus MCUniversity Medical Center RotterdamRotterdamThe Netherlands
| | - Ferdows Atiq
- Department of HematologyErasmus MCUniversity Medical Center RotterdamRotterdamThe Netherlands
| | - Petra E. Bürgisser
- Department of HematologyErasmus MCUniversity Medical Center RotterdamRotterdamThe Netherlands
| | - Johan A. Slotman
- Department of PathologyOptical Imaging CenterErasmus MCUniversity Medical Center RotterdamRotterdamThe Netherlands
| | - Adriaan B. Houtsmuller
- Department of PathologyOptical Imaging CenterErasmus MCUniversity Medical Center RotterdamRotterdamThe Netherlands
| | - Cilia de Heus
- Department of Cell BiologyUniversity Medical CenterUtrechtThe Netherlands
| | - Judith Klumperman
- Department of Cell BiologyUniversity Medical CenterUtrechtThe Netherlands
| | - Frank W. G. Leebeek
- Department of HematologyErasmus MCUniversity Medical Center RotterdamRotterdamThe Netherlands
| | - Jan Voorberg
- Molecular and Cellular HemostasisSanquin Research and Landsteiner LaboratoryAmsterdam University Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
- Experimental Vascular MedicineAmsterdam University Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Arend Jan Gerard Jansen
- Department of HematologyErasmus MCUniversity Medical Center RotterdamRotterdamThe Netherlands
| | - Ruben Bierings
- Department of HematologyErasmus MCUniversity Medical Center RotterdamRotterdamThe Netherlands
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10
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Özgün F, Kaya Z, Morova T, Geverts B, Abraham TE, Houtsmuller AB, van Royen ME, Lack NA. DNA binding alters ARv7 dimer interactions. J Cell Sci 2021; 134:jcs258332. [PMID: 34318896 DOI: 10.1242/jcs.258332] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/02/2021] [Indexed: 11/20/2022] Open
Abstract
Androgen receptor (AR) splice variants are proposed to be a potential driver of lethal castration-resistant prostate cancer. AR splice variant 7 (ARv7) is the most commonly observed isoform and strongly correlates with resistance to second-generation anti-androgens. Despite this clinical evidence, the interplay between ARv7 and the highly expressed full-length AR (ARfl) remains unclear. In this work, we show that ARfl/ARv7 heterodimers readily form in the nucleus via an intermolecular N/C interaction that brings the four termini of the proteins in close proximity. Combining fluorescence resonance energy transfer and fluorescence recovery after photobleaching, we demonstrate that these heterodimers undergo conformational changes following DNA binding, indicating dynamic nuclear receptor interaction. Although transcriptionally active, ARv7 can only form short-term interactions with DNA at highly accessible high-occupancy ARfl binding sites. Dimerization with ARfl does not affect ARv7 binding dynamics, suggesting that DNA binding occupancy is determined by the individual protein monomers and not the homodimer or heterodimer complex. Overall, these biophysical studies reveal detailed properties of ARv7 dynamics as both a homodimer or heterodimer with ARfl.
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Affiliation(s)
- Fatma Özgün
- School of Medicine, Koç University, Istanbul 34450, Turkey
| | - Zeynep Kaya
- School of Medicine, Koç University, Istanbul 34450, Turkey
| | - Tunç Morova
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
| | - Bart Geverts
- Erasmus Optical Imaging Centre, Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Tsion E Abraham
- Erasmus Optical Imaging Centre, Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Centre, Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
- Department of Pathology, Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Martin E van Royen
- Erasmus Optical Imaging Centre, Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
- Department of Pathology, Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Nathan A Lack
- School of Medicine, Koç University, Istanbul 34450, Turkey
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul 34450, Turkey
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11
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Lin Z, Wu B, Paul MW, Li KW, Yao Y, Smal I, Proietti Onori M, Hasanbegovic H, Bezstarosti K, Demmers J, Houtsmuller AB, Meijering E, Hoebeek FE, Schonewille M, Smit AB, Gao Z, De Zeeuw CI. Protein Phosphatase 2B Dual Function Facilitates Synaptic Integrity and Motor Learning. J Neurosci 2021; 41:5579-5594. [PMID: 34021041 PMCID: PMC8244972 DOI: 10.1523/jneurosci.1741-20.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 04/01/2021] [Accepted: 04/23/2021] [Indexed: 11/21/2022] Open
Abstract
Protein phosphatase 2B (PP2B) is critical for synaptic plasticity and learning, but the molecular mechanisms involved remain unclear. Here we identified different types of proteins that interact with PP2B, including various structural proteins of the postsynaptic densities (PSDs) of Purkinje cells (PCs) in mice. Deleting PP2B reduced expression of PSD proteins and the relative thickness of PSD at the parallel fiber to PC synapses, whereas reexpression of inactive PP2B partly restored the impaired distribution of nanoclusters of PSD proteins, together indicating a structural role of PP2B. In contrast, lateral mobility of surface glutamate receptors solely depended on PP2B phosphatase activity. Finally, the level of motor learning covaried with both the enzymatic and nonenzymatic functions of PP2B. Thus, PP2B controls synaptic function and learning both through its action as a phosphatase and as a structural protein that facilitates synapse integrity.SIGNIFICANCE STATEMENT Phosphatases are generally considered to serve their critical role in learning and memory through their enzymatic operations. Here, we show that protein phosphatase 2B (PP2B) interacts with structural proteins at the synapses of cerebellar Purkinje cells. Differentially manipulating the enzymatic and structural domains of PP2B leads to different phenotypes in cerebellar learning. We propose that PP2B is crucial for cerebellar learning via two complementary actions, an enzymatic and a structural operation.
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Affiliation(s)
- Zhanmin Lin
- Department of Neuroscience, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
| | - Bin Wu
- Department of Neuroscience, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
- Department of Neurology and Institute of Neurology, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Maarten W Paul
- Optical Imaging Center, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam Neuroscience, 1081 HV, Amsterdam, The Netherlands
| | - Yao Yao
- Department of Medical informatics, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
| | - Ihor Smal
- Department of Medical informatics, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
| | | | - Hana Hasanbegovic
- Department of Neuroscience, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
| | - Karel Bezstarosti
- Center for Proteomics, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
| | - Jeroen Demmers
- Center for Proteomics, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
| | | | - Erik Meijering
- School of Computer Science and Engineering & Graduate School of Biomedical Engineering, University of New South Wales, Sydney, 2052, New South Wales, Australia
| | - Freek E Hoebeek
- Department of Neuroscience, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
- Department for Developmental Origins of Disease, Wilhelmina Children's Hospital and Brain Center, Utrecht Medical Center, 3584 EA, Utrecht, The Netherlands
| | | | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam Neuroscience, 1081 HV, Amsterdam, The Netherlands
| | - Zhenyu Gao
- Department of Neuroscience, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
| | - Chris I De Zeeuw
- Department of Neuroscience, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
- Netherlands Institute for Neuroscience, KNAW, 1105 BA, Amsterdam, The Netherlands
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12
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Geijer ME, Zhou D, Selvam K, Steurer B, Mukherjee C, Evers B, Cugusi S, van Toorn M, van der Woude M, Janssens RC, Kok YP, Gong W, Raams A, Lo CSY, Lebbink JHG, Geverts B, Plummer DA, Bezstarosti K, Theil AF, Mitter R, Houtsmuller AB, Vermeulen W, Demmers JAA, Li S, van Vugt MATM, Lans H, Bernards R, Svejstrup JQ, Ray Chaudhuri A, Wyrick JJ, Marteijn JA. Publisher Correction: Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability. Nat Cell Biol 2021; 23:809. [PMID: 34163038 DOI: 10.1038/s41556-021-00720-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marit E Geijer
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Di Zhou
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kathiresan Selvam
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Barbara Steurer
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Chirantani Mukherjee
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bastiaan Evers
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Simona Cugusi
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK
| | - Marvin van Toorn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Melanie van der Woude
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Roel C Janssens
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yannick P Kok
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Wenzhi Gong
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Anja Raams
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Calvin S Y Lo
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bart Geverts
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Dalton A Plummer
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Karel Bezstarosti
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Shisheng Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - René Bernards
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK
| | - Arnab Ray Chaudhuri
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
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13
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Geijer ME, Zhou D, Selvam K, Steurer B, Mukherjee C, Evers B, Cugusi S, van Toorn M, van der Woude M, Janssens RC, Kok YP, Gong W, Raams A, Lo CSY, Lebbink JHG, Geverts B, Plummer DA, Bezstarosti K, Theil AF, Mitter R, Houtsmuller AB, Vermeulen W, Demmers JAA, Li S, van Vugt MATM, Lans H, Bernards R, Svejstrup JQ, Ray Chaudhuri A, Wyrick JJ, Marteijn JA. Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability. Nat Cell Biol 2021; 23:608-619. [PMID: 34108662 PMCID: PMC7611218 DOI: 10.1038/s41556-021-00692-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 04/29/2021] [Indexed: 02/05/2023]
Abstract
Correct transcription is crucial for life. However, DNA damage severely impedes elongating RNA polymerase II, causing transcription inhibition and transcription-replication conflicts. Cells are equipped with intricate mechanisms to counteract the severe consequence of these transcription-blocking lesions. However, the exact mechanism and factors involved remain largely unknown. Here, using a genome-wide CRISPR-Cas9 screen, we identified the elongation factor ELOF1 as an important factor in the transcription stress response following DNA damage. We show that ELOF1 has an evolutionarily conserved role in transcription-coupled nucleotide excision repair (TC-NER), where it promotes recruitment of the TC-NER factors UVSSA and TFIIH to efficiently repair transcription-blocking lesions and resume transcription. Additionally, ELOF1 modulates transcription to protect cells against transcription-mediated replication stress, thereby preserving genome stability. Thus, ELOF1 protects the transcription machinery from DNA damage via two distinct mechanisms.
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Affiliation(s)
- Marit E Geijer
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Di Zhou
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kathiresan Selvam
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Barbara Steurer
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Chirantani Mukherjee
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bastiaan Evers
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Simona Cugusi
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK
| | - Marvin van Toorn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Melanie van der Woude
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Roel C Janssens
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yannick P Kok
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Wenzhi Gong
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Anja Raams
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Calvin S Y Lo
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bart Geverts
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Dalton A Plummer
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Karel Bezstarosti
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Shisheng Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - René Bernards
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK
| | - Arnab Ray Chaudhuri
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
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14
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Mhaskar AN, Koornneef L, Zelensky AN, Houtsmuller AB, Baarends WM. High Resolution View on the Regulation of Recombinase Accumulation in Mammalian Meiosis. Front Cell Dev Biol 2021; 9:672191. [PMID: 34109178 PMCID: PMC8181746 DOI: 10.3389/fcell.2021.672191] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/19/2021] [Indexed: 11/19/2022] Open
Abstract
A distinguishing feature of meiotic DNA double-strand breaks (DSBs), compared to DSBs in somatic cells, is the fact that they are induced in a programmed and specifically orchestrated manner, which includes chromatin remodeling prior to DSB induction. In addition, the meiotic homologous recombination (HR) repair process that follows, is different from HR repair of accidental DSBs in somatic cells. For instance, meiotic HR involves preferred use of the homolog instead of the sister chromatid as a repair template and subsequent formation of crossovers and non-crossovers in a tightly regulated manner. An important outcome of this distinct repair pathway is the pairing of homologous chromosomes. Central to the initial steps in homology recognition during meiotic HR is the cooperation between the strand exchange proteins (recombinases) RAD51 and its meiosis-specific paralog DMC1. Despite our understanding of their enzymatic activity, details on the regulation of their assembly and subsequent molecular organization at meiotic DSBs in mammals have remained largely enigmatic. In this review, we summarize recent mouse data on recombinase regulation via meiosis-specific factors. Also, we reflect on bulk “omics” studies of initial meiotic DSB processing, compare these with studies using super-resolution microscopy in single cells, at single DSB sites, and explore the implications of these findings for our understanding of the molecular mechanisms underlying meiotic HR regulation.
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Affiliation(s)
- Aditya N Mhaskar
- Department of Developmental Biology, Erasmus MC, Rotterdam, Netherlands
| | - Lieke Koornneef
- Department of Developmental Biology, Erasmus MC, Rotterdam, Netherlands.,Oncode Institute, Utrecht, Netherlands
| | - Alex N Zelensky
- Department of Molecular Genetics, Erasmus MC, Rotterdam, Netherlands
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC, Rotterdam, Netherlands.,Department of Pathology, Erasmus MC, Rotterdam, Netherlands
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, Rotterdam, Netherlands
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15
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Peter S, Urbanus BHA, Klaassen RV, Wu B, Boele HJ, Azizi S, Slotman JA, Houtsmuller AB, Schonewille M, Hoebeek FE, Spijker S, Smit AB, De Zeeuw CI. AMPAR Auxiliary Protein SHISA6 Facilitates Purkinje Cell Synaptic Excitability and Procedural Memory Formation. Cell Rep 2021; 31:107515. [PMID: 32294428 PMCID: PMC7175376 DOI: 10.1016/j.celrep.2020.03.079] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 01/31/2020] [Accepted: 03/23/2020] [Indexed: 12/15/2022] Open
Abstract
The majority of excitatory postsynaptic currents in the brain are gated through AMPA-type glutamate receptors, the kinetics and trafficking of which can be modulated by auxiliary proteins. It remains to be elucidated whether and how auxiliary proteins can modulate synaptic function to contribute to procedural memory formation. In this study, we report that the AMPA-type glutamate receptor (AMPAR) auxiliary protein SHISA6 (CKAMP52) is expressed in cerebellar Purkinje cells, where it co-localizes with GluA2-containing AMPARs. The absence of SHISA6 in Purkinje cells results in severe impairments in the adaptation of the vestibulo-ocular reflex and eyeblink conditioning. The physiological abnormalities include decreased presence of AMPARs in synaptosomes, impaired excitatory transmission, increased deactivation of AMPA receptors, and reduced induction of long-term potentiation at Purkinje cell synapses. Our data indicate that Purkinje cells require SHISA6-dependent modification of AMPAR function in order to facilitate cerebellar, procedural memory formation. SHISA6 is prominently expressed in Purkinje cells in close association with AMPARs SHISA6 absence in Purkinje cells results in impaired procedural memory formation Purkinje cell synaptic baseline excitatory transmission is facilitated by SHISA6 Purkinje cell AMPAR kinetics are modulated by SHISA6
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Affiliation(s)
- Saša Peter
- Department of Neuroscience, Erasmus MC, 3000 DR Rotterdam, the Netherlands
| | | | - Remco V Klaassen
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Bin Wu
- Department of Neuroscience, Erasmus MC, 3000 DR Rotterdam, the Netherlands; Department of Neurology, Huashan Hospital, Fudan University, 200040 Shanghai, China
| | - Henk-Jan Boele
- Department of Neuroscience, Erasmus MC, 3000 DR Rotterdam, the Netherlands
| | - Sameha Azizi
- Department of Neuroscience, Erasmus MC, 3000 DR Rotterdam, the Netherlands
| | - Johan A Slotman
- Optical Imaging Centre, Department of Pathology, Erasmus MC, 3000 DR Rotterdam, the Netherlands
| | - Adriaan B Houtsmuller
- Optical Imaging Centre, Department of Pathology, Erasmus MC, 3000 DR Rotterdam, the Netherlands
| | | | - Freek E Hoebeek
- Department of Neuroscience, Erasmus MC, 3000 DR Rotterdam, the Netherlands; Department for Developmental Origins of Disease, Wilhelmina Children's Hospital, Brain Center, UMC Utrecht, 3584 EA Utrecht, the Netherlands
| | - Sabine Spijker
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, 1081 HV Amsterdam, the Netherlands.
| | - Chris I De Zeeuw
- Department of Neuroscience, Erasmus MC, 3000 DR Rotterdam, the Netherlands; Netherlands Institute for Neuroscience, 1105 CA Amsterdam, the Netherlands.
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16
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Lu T, Haemmerich D, Liu H, Seynhaeve AL, van Rhoon GC, Houtsmuller AB, ten Hagen TL. Externally triggered smart drug delivery system encapsulating idarubicin shows superior kinetics and enhances tumoral drug uptake and response. Am J Cancer Res 2021; 11:5700-5712. [PMID: 33897876 PMCID: PMC8058728 DOI: 10.7150/thno.55163] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/09/2021] [Indexed: 12/20/2022] Open
Abstract
Rationale: Increasing the bioavailable drug level in a tumor is the key to enhance efficacy of chemotherapy. Thermosensitive smart drug delivery systems (SDDS) in combination with local hyperthermia facilitate high local drug levels, thus improving uptake in the tumor. However, inability to rapidly and efficiently absorb the locally released drug results in reduced efficacy, as well as undesired redistribution of the drug away from the tumor to the system. Methods: Based on this paradigm we propose a novel approach in which we replaced doxorubicin (DXR), one of the classic drugs for nanocarrier-based delivery, with idarubicin (IDA), a hydrophobic anthracycline used solely in the free form for treatment hematologic cancers. We established a series of in vitro and in vivo experiments to in depth study the kinetics of SDDS-based delivery, drug release, intratumor biodistribution and subsequent cell uptake. Results: We demonstrate that IDA is taken up over 10 times more rapidly by cancer cells than DXR in vitro. Similar trend is observed in in vivo online imaging and less drug redistribution is shown for IDA, together resulting in 4-times higher whole tumor drug uptake for IDA vs. DXR. Together his yielded an improved intratumoral drug distribution for IDA-SDDS, translating into superior tumor response compared to DXR-SDDS treatment at the same dose. Thus, IDA - a drug that is not used for treatment of solid cancers - shows superior therapeutic index and better outcome when administered in externally triggered SDDS. Conclusions: We show that a shift in selection of chemotherapeutics is urgently needed, away from the classic drugs towards selection based on properties of a chemotherapeutic in context of the nanoparticle and delivery mode, to maximize the therapeutic efficacy.
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17
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Legerstee K, Abraham TE, van Cappellen WA, Nigg AL, Slotman JA, Houtsmuller AB. Growth factor dependent changes in nanoscale architecture of focal adhesions. Sci Rep 2021; 11:2315. [PMID: 33504939 PMCID: PMC7841166 DOI: 10.1038/s41598-021-81898-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 06/23/2020] [Accepted: 01/12/2021] [Indexed: 01/21/2023] Open
Abstract
Focal adhesions (FAs) are flat elongated structures that mediate cell migration and link the cytoskeleton to the extracellular matrix. Along the vertical axis FAs were shown to be composed of three layers. We used structured illumination microscopy to examine the longitudinal distribution of four hallmark FA proteins, which we also used as markers for these layers. At the FA ends pointing towards the adherent membrane edge (heads), bottom layer protein paxillin protruded, while at the opposite ends (tails) intermediate layer protein vinculin and top layer proteins zyxin and VASP extended further. At the tail tips, only intermediate layer protein vinculin protruded. Importantly, head and tail compositions were altered during HGF-induced scattering with paxillin heads being shorter and zyxin tails longer. Additionally, FAs at protruding or retracting membrane edges had longer paxillin heads than FAs at static edges. These data suggest that redistribution of FA-proteins with respect to each other along FAs is involved in cell movement.
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Affiliation(s)
- Karin Legerstee
- Department of Pathology, Erasmus Medical Center Rotterdam, Rotterdam, 3015 GE, the Netherlands
| | - Tsion E Abraham
- Optical Imaging Centre, Erasmus Medical Center Rotterdam, Rotterdam, 3015 GE, the Netherlands
| | - Wiggert A van Cappellen
- Optical Imaging Centre, Erasmus Medical Center Rotterdam, Rotterdam, 3015 GE, the Netherlands
| | - Alex L Nigg
- Department of Pathology, Erasmus Medical Center Rotterdam, Rotterdam, 3015 GE, the Netherlands.,Optical Imaging Centre, Erasmus Medical Center Rotterdam, Rotterdam, 3015 GE, the Netherlands
| | - Johan A Slotman
- Optical Imaging Centre, Erasmus Medical Center Rotterdam, Rotterdam, 3015 GE, the Netherlands
| | - Adriaan B Houtsmuller
- Department of Pathology, Erasmus Medical Center Rotterdam, Rotterdam, 3015 GE, the Netherlands. .,Optical Imaging Centre, Erasmus Medical Center Rotterdam, Rotterdam, 3015 GE, the Netherlands.
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18
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van der Burght SN, Rademakers S, Johnson JL, Li C, Kremers GJ, Houtsmuller AB, Leroux MR, Jansen G. Ciliary Tip Signaling Compartment Is Formed and Maintained by Intraflagellar Transport. Curr Biol 2020; 30:4299-4306.e5. [DOI: 10.1016/j.cub.2020.08.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 07/13/2020] [Accepted: 08/07/2020] [Indexed: 02/07/2023]
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19
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Sierksma MC, Slotman JA, Houtsmuller AB, Borst JGG. Structure-function relation of the developing calyx of Held synapse in vivo. J Physiol 2020; 598:4603-4619. [PMID: 33439501 PMCID: PMC7689866 DOI: 10.1113/jp279976] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/07/2020] [Indexed: 12/18/2022] Open
Abstract
KEY POINTS During development the giant, auditory calyx of Held forms a one-to-one connection with a principal neuron of the medial nucleus of the trapezoid body. While anatomical studies described that most of the target cells are temporarily contacted by multiple calyces, multi-calyceal innervation was only sporadically observed in in vivo recordings, suggesting a structure-function discrepancy. We correlated synaptic strength of inputs, identified in in vivo recordings, with post hoc labelling of the recorded neuron and synaptic terminals containing vesicular glutamate transporters (VGluT). During development only one input increased to the level of the calyx of Held synapse, and its strength correlated with the large VGluT cluster contacting the postsynaptic soma. As neither competing strong inputs nor multiple large VGluT clusters on a single cell were observed, our findings did not indicate a structure-function discrepancy. ABSTRACT In adult rodents, a principal neuron in the medial nucleus of the trapezoid (MNTB) is generally contacted by a single, giant axosomatic terminal called the calyx of Held. How this one-on-one relation is established is still unknown, but anatomical evidence suggests that during development principal neurons are innervated by multiple calyces, which may indicate calyceal competition. However, in vivo electrophysiological recordings from principal neurons indicated that only a single strong synaptic connection forms per cell. To test whether a mismatch exists between synaptic strength and terminal size, we compared the strength of synaptic inputs with the morphology of the synaptic terminals. In vivo whole-cell recordings of the MNTB neurons from newborn Wistar rats of either sex were made while stimulating their afferent axons, allowing us to identify multiple inputs. The strength of the strongest input increased to calyceal levels in a few days across cells, while the strength of the second strongest input was stable. The recorded cells were subsequently immunolabelled for vesicular glutamate transporters (VGluT) to reveal axosomatic terminals with structured-illumination microscopy. Synaptic strength of the strongest input was correlated with the contact area of the largest VGluT cluster at the soma (r = 0.8), and no indication of a mismatch between structure and strength was observed. Together, our data agree with a developmental scheme in which one input strengthens and becomes the calyx of Held, but not with multi-calyceal competition.
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Affiliation(s)
- Martijn C Sierksma
- Department of Neuroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, 3000 CA, The Netherlands.,Sorbonne Université, Inserm, CNRS, Institut de la Vision, 17 Rue Moreau, Paris, F-75012, France
| | - Johan A Slotman
- Department of Pathology-Optical Imaging Centre, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, 3000 CA, The Netherlands
| | - Adriaan B Houtsmuller
- Department of Pathology-Optical Imaging Centre, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, 3000 CA, The Netherlands
| | - J Gerard G Borst
- Department of Neuroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, 3000 CA, The Netherlands
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20
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Slotman JA, Paul MW, Carofiglio F, de Gruiter HM, Vergroesen T, Koornneef L, van Cappellen WA, Houtsmuller AB, Baarends WM. Super-resolution imaging of RAD51 and DMC1 in DNA repair foci reveals dynamic distribution patterns in meiotic prophase. PLoS Genet 2020; 16:e1008595. [PMID: 32502153 PMCID: PMC7310863 DOI: 10.1371/journal.pgen.1008595] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 06/23/2020] [Accepted: 05/05/2020] [Indexed: 11/19/2022] Open
Abstract
The recombinase RAD51, and its meiosis-specific paralog DMC1 localize at DNA double-strand break (DSB) sites in meiotic prophase. While both proteins are required during meiotic prophase, their spatial organization during meiotic DSB repair is not fully understood. Using super-resolution microscopy on mouse spermatocyte nuclei, we aimed to define their relative position at DSB foci, and how these vary in time. We show that a large fraction of meiotic DSB repair foci (38%) consisted of a single RAD51 nanofocus and a single DMC1 nanofocus (D1R1 configuration) that were partially overlapping with each other (average center-center distance around 70 nm). The vast majority of the rest of the foci had a similar large RAD51 and DMC1 nanofocus, but in combination with additional smaller nanofoci (D2R1, D1R2, D2R2, or DxRy configuration) at an average distance of around 250 nm. As prophase progressed, less D1R1 and more D2R1 foci were observed, where the large RAD51 nanofocus in the D2R1 foci elongated and gradually oriented towards the distant small DMC1 nanofocus. D1R2 foci frequency was relatively constant, and the single DMC1 nanofocus did not elongate, but was frequently observed between the two RAD51 nanofoci in early stages. D2R2 foci were rare (<10%) and nearest neighbour analyses also did not reveal cofoci formation between D1R1 foci. However, overall, foci localized nonrandomly along the SC, and the frequency of the distance distributions peaked at 800 nm, indicating interference and/or a preferred distance between two ends of a DSB. DMC1 nanofoci where somewhat further away from the axial or lateral elements of the synaptonemal complex (SC, connecting the chromosomal axes of homologs) compared to RAD51 nanofoci. In the absence of the transverse filament of the SC, early configurations were more prominent, and RAD51 nanofocus elongation occurred only transiently. This in-depth analysis of single cell landscapes of RAD51 and DMC1 accumulation patterns at DSB repair sites at super-resolution revealed the variability of foci composition, and defined functional consensus configurations that change over time.
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Affiliation(s)
- Johan A. Slotman
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
- Department of Pathology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
| | - Maarten W. Paul
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
| | - Fabrizia Carofiglio
- Department of Developmental Biology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
| | - H. Martijn de Gruiter
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
| | - Tessa Vergroesen
- Department of Developmental Biology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
| | - Lieke Koornneef
- Department of Developmental Biology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
| | - Wiggert A. van Cappellen
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
| | - Adriaan B. Houtsmuller
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
- Department of Pathology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
| | - Willy M. Baarends
- Department of Developmental Biology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
- * E-mail:
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21
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Casa V, Moronta Gines M, Gade Gusmao E, Slotman JA, Zirkel A, Josipovic N, Oole E, van IJcken WFJ, Houtsmuller AB, Papantonis A, Wendt KS. Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control. Genome Res 2020; 30:515-527. [PMID: 32253279 PMCID: PMC7197483 DOI: 10.1101/gr.253211.119] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 04/01/2020] [Indexed: 12/28/2022]
Abstract
Cohesin is a ring-shaped multiprotein complex that is crucial for 3D genome organization and transcriptional regulation during differentiation and development. It also confers sister chromatid cohesion and facilitates DNA damage repair. Besides its core subunits SMC3, SMC1A, and RAD21, cohesin in somatic cells contains one of two orthologous STAG subunits, STAG1 or STAG2. How these variable subunits affect the function of the cohesin complex is still unclear. STAG1- and STAG2-cohesin were initially proposed to organize cohesion at telomeres and centromeres, respectively. Here, we uncover redundant and specific roles of STAG1 and STAG2 in gene regulation and chromatin looping using HCT116 cells with an auxin-inducible degron (AID) tag fused to either STAG1 or STAG2. Following rapid depletion of either subunit, we perform high-resolution Hi-C, gene expression, and sequential ChIP studies to show that STAG1 and STAG2 do not co-occupy individual binding sites and have distinct ways by which they affect looping and gene expression. These findings are further supported by single-molecule localizations via direct stochastic optical reconstruction microscopy (dSTORM) super-resolution imaging. Since somatic and congenital mutations of the STAG subunits are associated with cancer (STAG2) and intellectual disability syndromes with congenital abnormalities (STAG1 and STAG2), we verified STAG1-/STAG2-dependencies using human neural stem cells, hence highlighting their importance in particular disease contexts.
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Affiliation(s)
- Valentina Casa
- Department of Cell Biology, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | | | - Eduardo Gade Gusmao
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Institute of Pathology, University Medical Center, Georg-August University of Göttingen, 37075 Göttingen, Germany
| | - Johan A Slotman
- Optical Imaging Centre, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Anne Zirkel
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Natasa Josipovic
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Institute of Pathology, University Medical Center, Georg-August University of Göttingen, 37075 Göttingen, Germany
| | - Edwin Oole
- Center for Biomics, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Wilfred F J van IJcken
- Department of Cell Biology, Erasmus MC, 3015 GD Rotterdam, The Netherlands
- Center for Biomics, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | | | - Argyris Papantonis
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Institute of Pathology, University Medical Center, Georg-August University of Göttingen, 37075 Göttingen, Germany
| | - Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, 3015 GD Rotterdam, The Netherlands
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22
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Roobol SJ, Hartjes TA, Slotman JA, de Kruijff RM, Torrelo G, Abraham TE, Bruchertseifer F, Morgenstern A, Kanaar R, van Gent DC, Houtsmuller AB, Denkova AG, van Royen ME, Essers J. Uptake and subcellular distribution of radiolabeled polymersomes for radiotherapy. Nanotheranostics 2020; 4:14-25. [PMID: 31911891 PMCID: PMC6940201 DOI: 10.7150/ntno.37080] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 11/06/2019] [Indexed: 12/17/2022] Open
Abstract
Polymersomes have the potential to be applied in targeted alpha radionuclide therapy, while in addition preventing release of recoiling daughter isotopes. In this study, we investigated the cellular uptake, post uptake processing and intracellular localization of polymersomes. Methods: High-content microscopy was used to validate polymersome uptake kinetics. Confocal (live cell) microscopy was used to elucidate the uptake mechanism and DNA damage induction. Intracellular distribution of polymersomes in 3-D was determined using super-resolution microscopy. Results: We found that altering polymersome size and concentration affects the initial uptake and overall uptake capacity; uptake efficiency and eventual plateau levels varied between cell lines; and mitotic cells show increased uptake. Intracellular polymersomes were transported along microtubules in a fast and dynamic manner. Endocytic uptake of polymersomes was evidenced through co-localization with endocytic pathway components. Finally, we show the intracellular distribution of polymersomes in 3-D and DNA damage inducing capabilities of 213Bi labeled polymersomes. Conclusion: Polymersome size and concentration affect the uptake efficiency, which also varies for different cell types. In addition, we present advanced assays to investigate uptake characteristics in detail, a necessity for optimization of nano-carriers. Moreover, by elucidating the uptake mechanism, as well as uptake extent and geometrical distribution of radiolabeled polymersomes we provide insight on how to improve polymersome design.
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Affiliation(s)
- Stefan J. Roobol
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
- Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Radiology & Nuclear Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Thomas A. Hartjes
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Optical Imaging Centre (OIC), Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Johan A. Slotman
- Optical Imaging Centre (OIC), Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robin M. de Kruijff
- Department of Radiation Science and Technology, Delft University of Technology, Delft, The Netherlands
| | - Guzman Torrelo
- Department of Radiation Science and Technology, Delft University of Technology, Delft, The Netherlands
| | - Tsion E. Abraham
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Optical Imaging Centre (OIC), Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Frank Bruchertseifer
- European Commission, Joint Research Centre, Directorate for Nuclear Safety and Security, Karlsruhe, Germany
| | - Alfred Morgenstern
- European Commission, Joint Research Centre, Directorate for Nuclear Safety and Security, Karlsruhe, Germany
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
- Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Dik C. van Gent
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
- Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Adriaan B. Houtsmuller
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Optical Imaging Centre (OIC), Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Antonia G. Denkova
- Department of Radiation Science and Technology, Delft University of Technology, Delft, The Netherlands
| | - Martin E. van Royen
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Optical Imaging Centre (OIC), Erasmus University Medical Center, Rotterdam, The Netherlands
- Cancer Treatment Screening Facility (CTSF), Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen Essers
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Vascular Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands
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23
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Stedehouder J, Brizee D, Slotman JA, Pascual-Garcia M, Leyrer ML, Bouwen BL, Dirven CM, Gao Z, Berson DM, Houtsmuller AB, Kushner SA. Local axonal morphology guides the topography of interneuron myelination in mouse and human neocortex. eLife 2019; 8:48615. [PMID: 31742557 PMCID: PMC6927753 DOI: 10.7554/elife.48615] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 11/18/2019] [Indexed: 12/30/2022] Open
Abstract
GABAergic fast-spiking parvalbumin-positive (PV) interneurons are frequently myelinated in the cerebral cortex. However, the factors governing the topography of cortical interneuron myelination remain incompletely understood. Here, we report that segmental myelination along neocortical interneuron axons is strongly predicted by the joint combination of interbranch distance and local axon caliber. Enlargement of PV+ interneurons increased axonal myelination, while reduced cell size led to decreased myelination. Next, we considered regular-spiking SOM+ cells, which normally have relatively shorter interbranch distances and thinner axon diameters than PV+ cells, and are rarely myelinated. Consistent with the importance of axonal morphology for guiding interneuron myelination, enlargement of SOM+ cell size dramatically increased the frequency of myelinated axonal segments. Lastly, we confirm that these findings also extend to human neocortex by quantifying interneuron axonal myelination from ex vivo surgical tissue. Together, these findings establish a predictive model of neocortical GABAergic interneuron myelination determined by local axonal morphology.
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Affiliation(s)
- Jeffrey Stedehouder
- Department of Psychiatry, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Demi Brizee
- Department of Psychiatry, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Johan A Slotman
- Erasmus Optical Imaging Center, Department of Pathology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Maria Pascual-Garcia
- Department of Psychiatry, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Megan L Leyrer
- Department of Neuroscience, Brown University, Providence, United States
| | - Bibi Lj Bouwen
- Department of Neuroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands.,Department of Neurosurgery, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Clemens Mf Dirven
- Department of Neurosurgery, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Zhenyu Gao
- Department of Neuroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - David M Berson
- Department of Neuroscience, Brown University, Providence, United States
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Center, Department of Pathology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Steven A Kushner
- Department of Psychiatry, Erasmus MC University Medical Center, Rotterdam, Netherlands
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24
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van den Dries K, Nahidiazar L, Slotman JA, Meddens MBM, Pandzic E, Joosten B, Ansems M, Schouwstra J, Meijer A, Steen R, Wijers M, Fransen J, Houtsmuller AB, Wiseman PW, Jalink K, Cambi A. Modular actin nano-architecture enables podosome protrusion and mechanosensing. Nat Commun 2019; 10:5171. [PMID: 31729386 PMCID: PMC6858452 DOI: 10.1038/s41467-019-13123-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [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: 04/25/2018] [Accepted: 10/11/2019] [Indexed: 01/03/2023] Open
Abstract
Basement membrane transmigration during embryonal development, tissue homeostasis and tumor invasion relies on invadosomes, a collective term for invadopodia and podosomes. An adequate structural framework for this process is still missing. Here, we reveal the modular actin nano-architecture that enables podosome protrusion and mechanosensing. The podosome protrusive core contains a central branched actin module encased by a linear actin module, each harboring specific actin interactors and actin isoforms. From the core, two actin modules radiate: ventral filaments bound by vinculin and connected to the plasma membrane and dorsal interpodosomal filaments crosslinked by myosin IIA. On stiff substrates, the actin modules mediate long-range substrate exploration, associated with degradative behavior. On compliant substrates, the vinculin-bound ventral actin filaments shorten, resulting in short-range connectivity and a focally protrusive, non-degradative state. Our findings redefine podosome nanoscale architecture and reveal a paradigm for how actin modularity drives invadosome mechanosensing in cells that breach tissue boundaries.
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Affiliation(s)
- Koen van den Dries
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Leila Nahidiazar
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, Netherlands
- van Leeuwenhoek Centre of Advanced Microscopy, Amsterdam, Netherlands
| | - Johan A Slotman
- Department of Pathology, Optical imaging center Erasmus MC, Rotterdam, Netherlands
| | - Marjolein B M Meddens
- Department of Physics and Astronomy and Department of Pathology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Elvis Pandzic
- Biomedical Imaging Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Ben Joosten
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marleen Ansems
- Radiotherapy & OncoImmunology Laboratory, Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Joost Schouwstra
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Anke Meijer
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Raymond Steen
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Mietske Wijers
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jack Fransen
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Paul W Wiseman
- Departments of Physics and Chemistry, McGill University Otto Maass (OM), Chemistry Building, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Kees Jalink
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, Netherlands
- van Leeuwenhoek Centre of Advanced Microscopy, Amsterdam, Netherlands
| | - Alessandra Cambi
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands.
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25
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Verhoef EI, van Cappellen WA, Slotman JA, Kremers GJ, Ewing-Graham PC, Houtsmuller AB, van Royen ME, van Leenders GJLH. Three-dimensional architecture of common benign and precancerous prostate epithelial lesions. Histopathology 2019; 74:1036-1044. [PMID: 30815904 PMCID: PMC6849837 DOI: 10.1111/his.13848] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 02/25/2019] [Indexed: 12/12/2022]
Abstract
Aims Many glandular lesions can mimic prostate cancer microscopically, including atrophic glands, adenosis and prostatic intraepithelial neoplasia. While the characteristic histopathological and immunohistochemical features of these lesions have been well established, little is known about their three‐dimensional architecture. Our objective was to evaluate the three‐dimensional organisation of common prostate epithelial lesions. Methods and results 500 μm‐thick punches (n = 42) were taken from radical prostatectomy specimens, and stained with antibodies targeting keratin 8–18 and keratin 5 for identification of luminal and basal cells, respectively. Tissue samples were optically cleared in benzyl alcohol:benzyl benzoate and imaged using a confocal laser scanning microscope. The three‐dimensional architecture of peripheral and transition zone glands was acinar, composed of interconnecting and blind‐ending saccular tubules. In simple atrophy, partial atrophy and post‐atrophic hyperplasia, the acinar structure was attenuated with branching blind‐ending tubules from parental tubular structures. Three‐dimensional imaging revealed a novel variant of prostate atrophy characterised by large Golgi‐like atrophic spaces parallel to the prostate surface, which were represented by thin, elongated tubular structures on haematoxylin and eosin (H&E) slides. Conversely, adenosis lacked acinar organisation, so that it closely mimicked low‐grade prostate cancer. High‐grade prostatic intraepithelial neoplasia displayed prominent papillary intraluminal protrusions but retained an acinar organisation, whereas intraductal carcinoma predominantly consisted of cribriform proliferations with either spheroid, ellipsoid or complex interconnecting lumens. Conclusions While various prostate epithelial lesions might mimic malignancy on H&E slides, their three‐dimensional architecture is acinar and clearly different from the tubular structure of prostate cancer, with adenosis as an exception.
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Affiliation(s)
- Esther I Verhoef
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Wiggert A van Cappellen
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.,Department of Optical Imaging Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Johan A Slotman
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.,Department of Optical Imaging Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Gert-Jan Kremers
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.,Department of Optical Imaging Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Patricia C Ewing-Graham
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Adriaan B Houtsmuller
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.,Department of Optical Imaging Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Martin E van Royen
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.,Department of Optical Imaging Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Geert J L H van Leenders
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
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26
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Roell D, Rösler TW, Hessenkemper W, Kraft F, Hauschild M, Bartsch S, Abraham TE, Houtsmuller AB, Matusch R, van Royen ME, Baniahmad A. Halogen-substituted anthranilic acid derivatives provide a novel chemical platform for androgen receptor antagonists. J Steroid Biochem Mol Biol 2019; 188:59-70. [PMID: 30615932 DOI: 10.1016/j.jsbmb.2018.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 09/14/2018] [Revised: 12/04/2018] [Accepted: 12/07/2018] [Indexed: 10/27/2022]
Abstract
Androgen receptor (AR) antagonists are used for hormone therapy of prostate cancer (PCa). However resistance to the treatment occurs eventually. One possible reason is the occurrence of AR mutations that prevent inhibition of AR-mediated transactivation by antagonists. To offer in future more options to inhibit AR signaling, novel chemical lead structures for new AR antagonists would be beneficial. Here we analyzed structure-activity relationships of a battery of 36 non-steroidal structural variants of methyl anthranilate including 23 synthesized compounds. We identified structural requirements that lead to more potent AR antagonists. Specific compounds inhibit the transactivation of wild-type AR as well as AR mutants that render treatment resistance to hydroxyflutamide, bicalutamide and the second-generation AR antagonist enzalutamide. This suggests a distinct mode of inhibiting the AR compared to the clinically used compounds. Competition assays suggest binding of these compounds to the AR ligand binding domain and inhibit PCa cell proliferation. Moreover, active compounds induce cellular senescence despite inhibition of AR-mediated transactivation indicating a transactivation-independent AR-pathway. In line with this, fluorescence resonance after photobleaching (FRAP) - assays reveal higher mobility of the AR in the cell nuclei. Mechanistically, fluorescence resonance energy transfer (FRET) - assays indicate that the amino-carboxy (N/C)-interaction of the AR is not affected, which is in contrast to known AR-antagonists. This suggests a mechanistically novel mode of AR-antagonism. Together, these findings indicate the identification of a novel chemical platform as a new lead structure that extends the diversity of known AR antagonists and possesses a distinct mode of antagonizing AR-function.
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Affiliation(s)
- Daniela Roell
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Thomas W Rösler
- Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany
| | | | - Florian Kraft
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Monique Hauschild
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Sophie Bartsch
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Tsion E Abraham
- Department of Pathology and Erasmus Optical Imaging Center OIC, Erasmus MC, Rotterdam, the Netherlands
| | - Adriaan B Houtsmuller
- Department of Pathology and Erasmus Optical Imaging Center OIC, Erasmus MC, Rotterdam, the Netherlands
| | - Rudolf Matusch
- Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany
| | - Martin E van Royen
- Department of Pathology and Erasmus Optical Imaging Center OIC, Erasmus MC, Rotterdam, the Netherlands
| | - Aria Baniahmad
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
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27
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Cato L, de Tribolet-Hardy J, Lee I, Rottenberg JT, Coleman I, Melchers D, Houtman R, Xiao T, Li W, Uo T, Sun S, Kuznik NC, Göppert B, Ozgun F, van Royen ME, Houtsmuller AB, Vadhi R, Rao PK, Li L, Balk SP, Den RB, Trock BJ, Karnes RJ, Jenkins RB, Klein EA, Davicioni E, Gruhl FJ, Long HW, Liu XS, Cato ACB, Lack NA, Nelson PS, Plymate SR, Groner AC, Brown M. ARv7 Represses Tumor-Suppressor Genes in Castration-Resistant Prostate Cancer. Cancer Cell 2019; 35:401-413.e6. [PMID: 30773341 PMCID: PMC7246081 DOI: 10.1016/j.ccell.2019.01.008] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 08/23/2018] [Accepted: 01/14/2019] [Indexed: 12/19/2022]
Abstract
Androgen deprivation therapy for prostate cancer (PCa) benefits patients with early disease, but becomes ineffective as PCa progresses to a castration-resistant state (CRPC). Initially CRPC remains dependent on androgen receptor (AR) signaling, often through increased expression of full-length AR (ARfl) or expression of dominantly active splice variants such as ARv7. We show in ARv7-dependent CRPC models that ARv7 binds together with ARfl to repress transcription of a set of growth-suppressive genes. Expression of the ARv7-repressed targets and ARv7 protein expression are negatively correlated and predicts for outcome in PCa patients. Our results provide insights into the role of ARv7 in CRPC and define a set of potential biomarkers for tumors dependent on ARv7.
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Affiliation(s)
- Laura Cato
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jonas de Tribolet-Hardy
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Irene Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jaice T Rottenberg
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ilsa Coleman
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Diana Melchers
- PamGene International B.V., 5211 HH Den Bosch, the Netherlands
| | - René Houtman
- PamGene International B.V., 5211 HH Den Bosch, the Netherlands
| | - Tengfei Xiao
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard TH Chan School of Public Health, Boston, MA 02215, USA
| | - Wei Li
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard TH Chan School of Public Health, Boston, MA 02215, USA
| | - Takuma Uo
- Department of Medicine, University of Washington School of Medicine and GRECC-VAPSHCS, Seattle, WA 98104, USA
| | - Shihua Sun
- Department of Medicine, University of Washington School of Medicine and GRECC-VAPSHCS, Seattle, WA 98104, USA
| | - Nane C Kuznik
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Bettina Göppert
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Fatma Ozgun
- School of Medicine, Koç University, 34450 Istanbul, Turkey
| | - Martin E van Royen
- Department of Pathology, Erasmus Optical Imaging Centre, Erasmus MC, 3015 GE Rotterdam, the Netherlands
| | - Adriaan B Houtsmuller
- Department of Pathology, Erasmus Optical Imaging Centre, Erasmus MC, 3015 GE Rotterdam, the Netherlands
| | - Raga Vadhi
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Prakash K Rao
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Lewyn Li
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Steven P Balk
- Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Robert B Den
- Department of Radiation Oncology, Sidney Kimmel Cancer Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Bruce J Trock
- Department of Urology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - Friederike J Gruhl
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - X Shirley Liu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard TH Chan School of Public Health, Boston, MA 02215, USA
| | - Andrew C B Cato
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Nathan A Lack
- School of Medicine, Koç University, 34450 Istanbul, Turkey; Vancouver Prostate Center, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
| | - Peter S Nelson
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Stephen R Plymate
- Department of Medicine, University of Washington School of Medicine and GRECC-VAPSHCS, Seattle, WA 98104, USA.
| | - Anna C Groner
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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28
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Seibert M, Krüger M, Watson NA, Sen O, Daum JR, Slotman JA, Braun T, Houtsmuller AB, Gorbsky GJ, Jacob R, Kracht M, Higgins JMG, Schmitz ML. CDK1-mediated phosphorylation at H2B serine 6 is required for mitotic chromosome segregation. J Cell Biol 2019; 218:1164-1181. [PMID: 30765437 PMCID: PMC6446833 DOI: 10.1083/jcb.201806057] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 06/08/2018] [Revised: 10/17/2018] [Accepted: 01/17/2019] [Indexed: 12/11/2022] Open
Abstract
Faithful mitotic chromosome segregation is required for the maintenance of genomic stability. We discovered the phosphorylation of histone H2B at serine 6 (H2B S6ph) as a new chromatin modification site and found that this modification occurs during the early mitotic phases at inner centromeres and pericentromeric heterochromatin. This modification is directly mediated by cyclin B1-associated CDK1, and indirectly by Aurora B, and is antagonized by PP1-mediated dephosphorylation. H2B S6ph impairs chromatin binding of the histone chaperone SET (I2PP2A), which is important for mitotic fidelity. Injection of phosphorylation-specific H2B S6 antibodies in mitotic cells caused anaphase defects with impaired chromosome segregation and incomplete cytokinesis. As H2B S6ph is important for faithful chromosome separation, this modification may contribute to the prevention chromosomal instability and aneuploidy which frequently occur in cancer cells.
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Affiliation(s)
- Markus Seibert
- Institute of Biochemistry, Justus-Liebig-University, Member of the German Center for Lung Research, Giessen, Germany
| | - Marcus Krüger
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany.,Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Nikolaus A Watson
- Cell Division Biology Research Group, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, England, UK
| | - Onur Sen
- Cell Division Biology Research Group, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, England, UK
| | - John R Daum
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, and Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Johan A Slotman
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Rotterdam, Netherlands
| | - Thomas Braun
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Adriaan B Houtsmuller
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Rotterdam, Netherlands
| | - Gary J Gorbsky
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, and Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Ralf Jacob
- Department of Cell Biology and Cell Pathology, Philipps University of Marburg, Marburg, Germany
| | - Michael Kracht
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University, Member of the German Center for Lung Research, Giessen, Germany
| | - Jonathan M G Higgins
- Cell Division Biology Research Group, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, England, UK
| | - M Lienhard Schmitz
- Institute of Biochemistry, Justus-Liebig-University, Member of the German Center for Lung Research, Giessen, Germany
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29
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Paul MW, de Gruiter HM, Lin Z, Baarends WM, van Cappellen WA, Houtsmuller AB, Slotman JA. SMoLR: visualization and analysis of single-molecule localization microscopy data in R. BMC Bioinformatics 2019; 20:30. [PMID: 30646838 PMCID: PMC6334411 DOI: 10.1186/s12859-018-2578-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/11/2018] [Indexed: 02/05/2023] Open
Abstract
Background Single-molecule localization microscopy is a super-resolution microscopy technique that allows for nanoscale determination of the localization and organization of proteins in biological samples. For biological interpretation of the data it is essential to extract quantitative information from the super-resolution data sets. Due to the complexity and size of these data sets flexible and user-friendly software is required. Results We developed SMoLR (Single Molecule Localization in R): a flexible framework that enables exploration and analysis of single-molecule localization data within the R programming environment. SMoLR is a package aimed at extracting, visualizing and analyzing quantitative information from localization data obtained by single-molecule microscopy. SMoLR is a platform not only to visualize nanoscale subcellular structures but additionally provides means to obtain statistical information about the distribution and localization of molecules within them. This can be done for individual images or SMoLR can be used to analyze a large set of super-resolution images at once. Additionally, we describe a method using SMoLR for image feature-based particle averaging, resulting in identification of common features among nanoscale structures. Conclusions Embedded in the extensive R programming environment, SMoLR allows scientists to study the nanoscale organization of biomolecules in cells by extracting and visualizing quantitative information and hence provides insight in a wide-variety of different biological processes at the single-molecule level. Electronic supplementary material The online version of this article (10.1186/s12859-018-2578-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maarten W Paul
- Erasmus Optical Imaging Centre, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - H Martijn de Gruiter
- Erasmus Optical Imaging Centre, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Zhanmin Lin
- Department of Neuroscience, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Wiggert A van Cappellen
- Erasmus Optical Imaging Centre, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Centre, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands. .,Department of Pathology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
| | - Johan A Slotman
- Erasmus Optical Imaging Centre, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
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30
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Verhoef EI, van Cappellen WA, Slotman JA, Kremers GJ, Ewing-Graham PC, Houtsmuller AB, van Royen ME, van Leenders GJLH. Three-dimensional analysis reveals two major architectural subgroups of prostate cancer growth patterns. Mod Pathol 2019; 32:1032-1041. [PMID: 30737469 PMCID: PMC6760644 DOI: 10.1038/s41379-019-0221-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/16/2019] [Accepted: 01/17/2019] [Indexed: 12/15/2022]
Abstract
The Gleason score is one of the most important parameters for therapeutic decision-making in prostate cancer patients. Gleason growth patterns are defined by their histological features on 4- to 5-µm cross sections, and little is known about their three-dimensional architecture. Our objective was to characterize the three-dimensional architecture of prostate cancer growth patterns. Intact tissue punches (n = 46) of representative Gleason growth patterns from radical prostatectomy specimens were fluorescently stained with antibodies targeting Keratin 8/18 and Keratin 5 for the detection of luminal and basal epithelial cells, respectively. Punches were optically cleared in benzyl alcohol-benzyl benzoate and imaged using a confocal laser scanning microscope up to a depth of 500 µm. Gleason pattern 3, poorly formed pattern 4, and cords pattern 5 all formed a continuum of interconnecting tubules in which the diameter of the structures and the lumen size decreased with higher grades. In fused pattern 4, the interconnections between the tubules were markedly closer together. In these patterns, all tumor cells were in direct contact with the surrounding stroma. In contrast, cribriform Gleason pattern 4 and solid pattern 5 demonstrated a three-dimensional continuum of contiguous tumor cells, in which the vast majority of cells had no contact with the surrounding stroma. Transitions between cribriform pattern 4 and solid pattern 5 were seen. There was a decrease in the number and size of intercellular lumens from cribriform to solid growth pattern. Glomeruloid pattern 4 formed an intermediate structure consisting of a tubular network with intraluminal epithelial protrusions close to the tubule splitting points. In conclusion, three-dimensional microscopy revealed two major architectural subgroups of prostate cancer growth patterns: (1) a tubular interconnecting network including Gleason pattern 3, poorly formed and fused Gleason pattern 4, and cords Gleason pattern 5, and (2) serpentine contiguous epithelial proliferations including cribriform Gleason pattern 4 and solid Gleason pattern 5.
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Affiliation(s)
- Esther I. Verhoef
- 000000040459992Xgrid.5645.2Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Wiggert A. van Cappellen
- 000000040459992Xgrid.5645.2Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands ,000000040459992Xgrid.5645.2Department of Optical Imaging Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Johan A. Slotman
- 000000040459992Xgrid.5645.2Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands ,000000040459992Xgrid.5645.2Department of Optical Imaging Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Gert-Jan Kremers
- 000000040459992Xgrid.5645.2Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands ,000000040459992Xgrid.5645.2Department of Optical Imaging Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Patricia C. Ewing-Graham
- 000000040459992Xgrid.5645.2Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Adriaan B. Houtsmuller
- 000000040459992Xgrid.5645.2Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands ,000000040459992Xgrid.5645.2Department of Optical Imaging Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Martin E. van Royen
- 000000040459992Xgrid.5645.2Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands ,000000040459992Xgrid.5645.2Department of Optical Imaging Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Geert J. L. H. van Leenders
- 000000040459992Xgrid.5645.2Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands
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31
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Keizer VIP, Coppola S, Houtsmuller AB, Geverts B, van Royen ME, Schmidt T, Schaaf MJM. Repetitive switching between DNA binding modes enables target finding by the glucocorticoid receptor. J Cell Sci 2019; 132:jcs.217455. [DOI: 10.1242/jcs.217455] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 01/16/2019] [Indexed: 12/21/2022] Open
Abstract
Transcription factor mobility is a determining factor in the regulation of gene expression. Here, we have studied the intranuclear dynamics of the glucocorticoid receptor (GR) using fluorescence recovery after photobleaching and single-molecule microscopy. First we have described the dynamic states in which the GR occurs. Subsequently we have analyzed the transitions between these states using a continuous time Markov chain model, and functionally investigated these states by making specific mutations in the DNA-binding domain. This analysis revealed that the GR diffuses freely through the nucleus, and once it leaves this free diffusion state it most often enters a repetitive switching mode. In this mode it alternates between slow diffusion as a result of brief nonspecific DNA binding events, and a state of stable binding to specific DNA target sites. This repetitive switching mechanism results in a compact searching strategy which facilitates finding DNA target sites by the GR.
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Affiliation(s)
| | - Stefano Coppola
- Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Adriaan B. Houtsmuller
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
- Erasmus Optical Imaging Center, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bart Geverts
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
- Erasmus Optical Imaging Center, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Martin E. van Royen
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
- Erasmus Optical Imaging Center, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Thomas Schmidt
- Institute of Physics, Leiden University, Leiden, The Netherlands
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32
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Prekovic S, van den Broeck T, Linder S, van Royen ME, Houtsmuller AB, Handle F, Joniau S, Zwart W, Claessens F. Molecular underpinnings of enzalutamide resistance. Endocr Relat Cancer 2018; 25:R545–R557. [PMID: 30306781 DOI: 10.1530/erc-17-0136] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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] [Indexed: 12/23/2022]
Abstract
Prostate cancer (PCa) is among the most common adult malignancies, and the second leading cause of cancer-related death in men. As PCa is hormone dependent, blockade of the androgen receptor (AR) signaling is an effective therapeutic strategy for men with advanced metastatic disease. The discovery of enzalutamide, a compound that effectively blocks the AR axis and its clinical application has led to a significant improvement in survival time. However, the effect of enzalutamide is not permanent, and resistance to treatment ultimately leads to development of lethal disease, for which there currently is no cure. This review will focus on the molecular underpinnings of enzalutamide resistance, bridging the gap between the preclinical and clinical research on novel therapeutic strategies for combating this lethal stage of prostate cancer.
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Affiliation(s)
- S Prekovic
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - T van den Broeck
- Laboratory of Molecular Endocrinology, KU Leuven, Leuven, Belgium
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - S Linder
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - M E van Royen
- Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
- Erasmus Optical Imaging Centre, Erasmus MC, Rotterdam, The Netherlands
| | - A B Houtsmuller
- Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
- Erasmus Optical Imaging Centre, Erasmus MC, Rotterdam, The Netherlands
| | - F Handle
- Laboratory of Molecular Endocrinology, KU Leuven, Leuven, Belgium
| | - S Joniau
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - W Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Biomedical Engineering, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - F Claessens
- Laboratory of Molecular Endocrinology, KU Leuven, Leuven, Belgium
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33
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Stedehouder J, Couey JJ, Brizee D, Hosseini B, Slotman JA, Dirven CMF, Shpak G, Houtsmuller AB, Kushner SA. Fast-spiking Parvalbumin Interneurons are Frequently Myelinated in the Cerebral Cortex of Mice and Humans. Cereb Cortex 2018; 27:5001-5013. [PMID: 28922832 DOI: 10.1093/cercor/bhx203] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Indexed: 12/29/2022] Open
Abstract
Myelination, the insulating ensheathment of axons by oligodendrocytes, is thought to both optimize signal propagation and provide metabolic support. Despite the well-established physiological importance of myelination to neuronal function, relatively little is known about the myelination of GABAergic interneurons in the cerebral cortex. Here, we report that a large fraction of myelin in mouse cerebral cortex ensheaths GABAergic interneurons, reaching up to 80% in hippocampal subregions. Moreover, we find that a very high proportion of neocortical and hippocampal parvalbumin (PV) interneurons exhibit axonal myelination. Using a combination of intracellular recordings and biocytin labeling of ex vivo human neocortex, we also confirm that axons of fast-spiking PV interneurons are extensively myelinated in the human brain. PV interneuron myelination in both mice and humans exhibits a stereotyped topography with a bias towards proximal axonal segments and relatively short internodes (~27 μm) interspersed with branch points. Interestingly, myelin-deficient Shiverer mice exhibit an increased density and more proximal location of en passant boutons, suggesting that myelination might function in part to regulate synapse formation along PV interneuron axons. Taken together, fast-spiking interneuron myelination is likely to have broad implications for cerebral cortex function in health and disease.
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Affiliation(s)
- J Stedehouder
- Department of Psychiatry, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - J J Couey
- Department of Psychiatry, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - D Brizee
- Department of Psychiatry, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - B Hosseini
- Department of Psychiatry, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - J A Slotman
- Erasmus Optical Imaging Centre, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - C M F Dirven
- Department of Neurosurgery, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - G Shpak
- Department of Psychiatry, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - A B Houtsmuller
- Erasmus Optical Imaging Centre, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - S A Kushner
- Department of Psychiatry, Erasmus MC, 3000 CA Rotterdam, The Netherlands
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34
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Hoppenbrouwers T, Sultan AR, Abraham TE, Lemmens-den Toom NA, Hansenová Maňásková S, van Cappellen WA, Houtsmuller AB, van Wamel WJB, de Maat MPM, van Neck JW. Staphylococcal Protein A Is a Key Factor in Neutrophil Extracellular Traps Formation. Front Immunol 2018; 9:165. [PMID: 29459871 PMCID: PMC5807341 DOI: 10.3389/fimmu.2018.00165] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/18/2018] [Indexed: 01/05/2023] Open
Abstract
Staphylococcus aureus are strong inducers of neutrophil extracellular traps (NETs), a defense mechanism of neutrophils against pathogens. Our aim was to explore the role of Protein A in S. aureus-induced NETosis. We determined the Protein A production of four different S. aureus strains and found a direct relationship between the degree of NETosis induction and Protein A production: strains producing higher concentrations of Protein A evoke significantly more NETs. A S. aureus strain in which Protein A as well as a second binding protein for immunoglobulins (Sbi) have been knocked-out (ΔSpA ΔSbi) induced significantly less NETosis than the wild-type strain. NETosis induction by this knockout strain can be rescued by the addition of purified Protein A. Dead S. aureus did not induce NETosis. In conclusion, Protein A is a determinant for NETosis induction by S. aureus.
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Affiliation(s)
- Tamara Hoppenbrouwers
- Department of Plastic and Reconstructive Surgery, Erasmus MC, Rotterdam, Netherlands.,Department of Hematology, Erasmus MC, Rotterdam, Netherlands
| | - Andi R Sultan
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, Netherlands
| | - Tsion E Abraham
- Erasmus Optical Imaging Center, Department of Pathology, Erasmus MC, Rotterdam, Netherlands
| | | | | | | | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Center, Department of Pathology, Erasmus MC, Rotterdam, Netherlands
| | - Willem J B van Wamel
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, Netherlands
| | | | - Johan W van Neck
- Department of Plastic and Reconstructive Surgery, Erasmus MC, Rotterdam, Netherlands
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35
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Kouwenberg JJM, Kremers GJ, Slotman JA, Wolterbeek HT, Houtsmuller AB, Denkova AG, Bos AJJ. Alpha particle spectroscopy using FNTD and SIM super-resolution microscopy. J Microsc 2018; 270:326-334. [PMID: 29393521 DOI: 10.1111/jmi.12686] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 09/11/2017] [Revised: 12/22/2017] [Accepted: 01/12/2018] [Indexed: 11/26/2022]
Abstract
Structured illumination microscopy (SIM) for the imaging of alpha particle tracks in fluorescent nuclear track detectors (FNTD) was evaluated and compared to confocal laser scanning microscopy (CLSM). FNTDs were irradiated with an external alpha source and imaged using both methodologies. SIM imaging resulted in improved resolution, without increase in scan time. Alpha particle energy estimation based on the track length, direction and intensity produced results in good agreement with the expected alpha particle energy distribution. A pronounced difference was seen in the spatial scattering of alpha particles in the detectors, where SIM showed an almost 50% reduction compared to CLSM. The improved resolution of SIM allows for more detailed studies of the tracks induced by ionising particles. The combination of SIM and FNTDs for alpha radiation paves the way for affordable and fast alpha spectroscopy and dosimetry.
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Affiliation(s)
- J J M Kouwenberg
- Radiation, Science & Technology, Technische Universiteit Delft Faculteit Technische Natuurwetenschappen, Mekelweg 15, Delft, the Netherlands
| | - G J Kremers
- Erasmus Optical Imaging Centre, Erasmus MC, 's-Gravendijkwal 230, Rotterdam, the Netherlands
| | - J A Slotman
- Erasmus Optical Imaging Centre, Erasmus MC, 's-Gravendijkwal 230, Rotterdam, the Netherlands
| | - H T Wolterbeek
- Radiation, Science & Technology, Technische Universiteit Delft Faculteit Technische Natuurwetenschappen, Mekelweg 15, Delft, the Netherlands
| | - A B Houtsmuller
- Erasmus Optical Imaging Centre, Erasmus MC, 's-Gravendijkwal 230, Rotterdam, the Netherlands
| | - A G Denkova
- Radiation, Science & Technology, Technische Universiteit Delft Faculteit Technische Natuurwetenschappen, Mekelweg 15, Delft, the Netherlands
| | - A J J Bos
- Radiation, Science & Technology, Technische Universiteit Delft Faculteit Technische Natuurwetenschappen, Mekelweg 15, Delft, the Netherlands
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36
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Pandya NJ, Koopmans F, Slotman JA, Paliukhovich I, Houtsmuller AB, Smit AB, Li KW. Correlation profiling of brain sub-cellular proteomes reveals co-assembly of synaptic proteins and subcellular distribution. Sci Rep 2017; 7:12107. [PMID: 28935861 PMCID: PMC5608747 DOI: 10.1038/s41598-017-11690-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [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: 03/20/2017] [Accepted: 08/21/2017] [Indexed: 12/13/2022] Open
Abstract
Protein correlation profiling might assist in defining co-assembled proteins and subcellular distribution. Here, we quantified the proteomes of five biochemically isolated mouse brain cellular sub-fractions, with emphasis on synaptic compartments, from three brain regions, hippocampus, cortex and cerebellum. We demonstrated the expected co-fractionation of canonical synaptic proteins belonging to the same functional groups. The enrichment profiles also suggested the presence of many novel pre- and post-synaptic proteins. Using super-resolution microscopy on primary neuronal culture we confirmed the postsynaptic localization of PLEKHA5 and ADGRA1. We further detected profound brain region specific differences in the extent of enrichment for some functionally associated proteins. This is exemplified by different AMPA receptor subunits and substantial differences in sub-fraction distribution of their potential interactors, which implicated the differences of AMPA receptor complex compositions. This resource aids the identification of proteins partners and subcellular distribution of synaptic proteins.
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Affiliation(s)
- Nikhil J Pandya
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank Koopmans
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Johan A Slotman
- Optical Imaging Center, Department of Pathology, Erasmus Medical Center, 3015 GE, Rotterdam, Netherlands
| | - Iryna Paliukhovich
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Adriaan B Houtsmuller
- Optical Imaging Center, Department of Pathology, Erasmus Medical Center, 3015 GE, Rotterdam, Netherlands
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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37
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Sánchez H, Paul MW, Grosbart M, van Rossum-Fikkert SE, Lebbink JHG, Kanaar R, Houtsmuller AB, Wyman C. Architectural plasticity of human BRCA2-RAD51 complexes in DNA break repair. Nucleic Acids Res 2017; 45:4507-4518. [PMID: 28168276 PMCID: PMC5416905 DOI: 10.1093/nar/gkx084] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/03/2017] [Indexed: 12/05/2022] Open
Abstract
The tumor suppressor BRCA2 is a large multifunctional protein mutated in 50–60% of familial breast cancers. BRCA2 interacts with many partners and includes multiple regions with potentially disordered structure. In homology directed DNA repair BRCA2 delivers RAD51 to DNA resulting in removal of RPA and assembly of a RAD51 nucleoprotein filament. Dynamic rearrangements of BRCA2 likely drive this molecular hand-off initiating DNA strand exchange. We show human BRCA2 forms oligomers which can have an extended shape. Scanning force microscopy and quantitative single molecule fluorescence define the variety of BRCA2 complexes, reveal dramatic rearrangements upon RAD51 binding and the loading of RAD51 patches on single strand DNA. At sites of repair in cell nuclei, super-resolution microscopy shows BRCA2 and RAD51 arranged in largely separate locations. We identified dynamic structural transitions in BRCA2 complexes suggested to facilitate loading of RAD51 onto RPA coated single strand DNA and subsequent release of BRCA2.
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Affiliation(s)
- Humberto Sánchez
- Department of Molecular Genetics, Cancer Genomics Center Netherlands, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Maarten W Paul
- Erasmus Optical Imaging Centre, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands.,Department of Pathology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Malgorzata Grosbart
- Department of Molecular Genetics, Cancer Genomics Center Netherlands, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Sarah E van Rossum-Fikkert
- Department of Molecular Genetics, Cancer Genomics Center Netherlands, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands.,Department of Radiation Oncology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Cancer Genomics Center Netherlands, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands.,Department of Radiation Oncology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Cancer Genomics Center Netherlands, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands.,Department of Radiation Oncology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Centre, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands.,Department of Pathology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Claire Wyman
- Department of Molecular Genetics, Cancer Genomics Center Netherlands, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands.,Department of Radiation Oncology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
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38
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Baar MP, Brandt RMC, Putavet DA, Klein JDD, Derks KWJ, Bourgeois BRM, Stryeck S, Rijksen Y, van Willigenburg H, Feijtel DA, van der Pluijm I, Essers J, van Cappellen WA, van IJcken WF, Houtsmuller AB, Pothof J, de Bruin RWF, Madl T, Hoeijmakers JHJ, Campisi J, de Keizer PLJ. Targeted Apoptosis of Senescent Cells Restores Tissue Homeostasis in Response to Chemotoxicity and Aging. Cell 2017; 169:132-147.e16. [PMID: 28340339 DOI: 10.1016/j.cell.2017.02.031] [Citation(s) in RCA: 837] [Impact Index Per Article: 119.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 12/29/2016] [Accepted: 02/22/2017] [Indexed: 02/06/2023]
Abstract
The accumulation of irreparable cellular damage restricts healthspan after acute stress or natural aging. Senescent cells are thought to impair tissue function, and their genetic clearance can delay features of aging. Identifying how senescent cells avoid apoptosis allows for the prospective design of anti-senescence compounds to address whether homeostasis can also be restored. Here, we identify FOXO4 as a pivot in senescent cell viability. We designed a FOXO4 peptide that perturbs the FOXO4 interaction with p53. In senescent cells, this selectively causes p53 nuclear exclusion and cell-intrinsic apoptosis. Under conditions where it was well tolerated in vivo, this FOXO4 peptide neutralized doxorubicin-induced chemotoxicity. Moreover, it restored fitness, fur density, and renal function in both fast aging XpdTTD/TTD and naturally aged mice. Thus, therapeutic targeting of senescent cells is feasible under conditions where loss of health has already occurred, and in doing so tissue homeostasis can effectively be restored.
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Affiliation(s)
- Marjolein P Baar
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Renata M C Brandt
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Diana A Putavet
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Julian D D Klein
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Kasper W J Derks
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Benjamin R M Bourgeois
- Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Sarah Stryeck
- Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Yvonne Rijksen
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Hester van Willigenburg
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Danny A Feijtel
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Ingrid van der Pluijm
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands; Department of Vascular Surgery, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Jeroen Essers
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands; Department of Vascular Surgery, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands; Department of Radiation Oncology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Wiggert A van Cappellen
- Erasmus Optical Imaging Center and Department of Pathology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Wilfred F van IJcken
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Center and Department of Pathology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Joris Pothof
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Ron W F de Bruin
- Department of Surgery, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Tobias Madl
- Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands
| | - Judith Campisi
- The Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; Lawrence Berkeley National Laboratories, Berkeley, CA 94720, USA
| | - Peter L J de Keizer
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN, Rotterdam, the Netherlands; The Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA.
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39
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Hoppenbrouwers T, Autar ASA, Sultan AR, Abraham TE, van Cappellen WA, Houtsmuller AB, van Wamel WJB, van Beusekom HMM, van Neck JW, de Maat MPM. In vitro induction of NETosis: Comprehensive live imaging comparison and systematic review. PLoS One 2017; 12:e0176472. [PMID: 28486563 PMCID: PMC5423591 DOI: 10.1371/journal.pone.0176472] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 04/11/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Multiple inducers of in vitro Neutrophil Extracellular Trap (NET) formation (NETosis) have been described. Since there is much variation in study design and results, our aim was to create a systematic review of NETosis inducers and perform a standardized in vitro study of NETosis inducers important in (cardiac) wound healing. METHODS In vitro NETosis was studied by incubating neutrophils with PMA, living and dead bacteria (S. aureus and E. coli), LPS, (activated) platelets (supernatant), glucose and calcium ionophore Ionomycin using 3-hour periods of time-lapse confocal imaging. RESULTS PMA is a consistent and potent inducer of NETosis. Ionomycin also consistently resulted in extrusion of DNA, albeit with a process that differs from the NETosis process induced by PMA. In our standardized experiments, living bacteria were also potent inducers of NETosis, but dead bacteria, LPS, (activated) platelets (supernatant) and glucose did not induce NETosis. CONCLUSION Our systematic review confirms that there is much variation in study design and results of NETosis induction. Our experimental results confirm that under standardized conditions, PMA, living bacteria and Ionomycin all strongly induce NETosis, but real-time confocal imaging reveal different courses of events.
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Affiliation(s)
- Tamara Hoppenbrouwers
- Department of Plastic and Reconstructive Surgery, Erasmus MC, Rotterdam, The Netherlands
- Department of Hematology, Erasmus MC, Rotterdam, The Netherlands
| | - Anouchska S. A. Autar
- Department of Hematology, Erasmus MC, Rotterdam, The Netherlands
- Department of Cardiology, Erasmus MC, Rotterdam, The Netherlands
| | - Andi R. Sultan
- Department of Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands
| | - Tsion E. Abraham
- Optical Imaging Center, Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | | | | | - Willem J. B. van Wamel
- Department of Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands
| | | | - Johan W. van Neck
- Department of Plastic and Reconstructive Surgery, Erasmus MC, Rotterdam, The Netherlands
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Meddens MBM, Pandzic E, Slotman JA, Guillet D, Joosten B, Mennens S, Paardekooper LM, Houtsmuller AB, van den Dries K, Wiseman PW, Cambi A. Actomyosin-dependent dynamic spatial patterns of cytoskeletal components drive mesoscale podosome organization. Nat Commun 2016; 7:13127. [PMID: 27721497 PMCID: PMC5062568 DOI: 10.1038/ncomms13127] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [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: 04/04/2016] [Accepted: 09/05/2016] [Indexed: 12/28/2022] Open
Abstract
Podosomes are cytoskeletal structures crucial for cell protrusion and matrix remodelling in osteoclasts, activated endothelial cells, macrophages and dendritic cells. In these cells, hundreds of podosomes are spatially organized in diversely shaped clusters. Although we and others established individual podosomes as micron-sized mechanosensing protrusive units, the exact scope and spatiotemporal organization of podosome clustering remain elusive. By integrating a newly developed extension of Spatiotemporal Image Correlation Spectroscopy with novel image analysis, we demonstrate that F-actin, vinculin and talin exhibit directional and correlated flow patterns throughout podosome clusters. Pattern formation and magnitude depend on the cluster actomyosin machinery. Indeed, nanoscopy reveals myosin IIA-decorated actin filaments interconnecting multiple proximal podosomes. Extending well-beyond podosome nearest neighbours, the actomyosin-dependent dynamic spatial patterns reveal a previously unappreciated mesoscale connectivity throughout the podosome clusters. This directional transport and continuous redistribution of podosome components provides a mechanistic explanation of how podosome clusters function as coordinated mechanosensory area.
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Affiliation(s)
- Marjolein B M Meddens
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands
| | - Elvis Pandzic
- Departments of Physics and Chemistry, McGill University Otto Maass (OM) Chemistry Building, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Johan A Slotman
- Department of Pathology, Josephine Nefkens Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - Dominique Guillet
- Departments of Physics and Chemistry, McGill University Otto Maass (OM) Chemistry Building, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Ben Joosten
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands
| | - Svenja Mennens
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands
| | - Laurent M Paardekooper
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands
| | - Adriaan B Houtsmuller
- Department of Pathology, Josephine Nefkens Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - Koen van den Dries
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands
| | - Paul W Wiseman
- Departments of Physics and Chemistry, McGill University Otto Maass (OM) Chemistry Building, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Alessandra Cambi
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands
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41
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Hansenová Maňásková S, Bikker FJ, Nazmi K, van Zuidam R, Slotman JA, van Cappellen WA, Houtsmuller AB, Veerman ECI, Kaman WE. Incorporation of a Valine-Leucine-Lysine-Containing Substrate in the Bacterial Cell Wall. Bioconjug Chem 2016; 27:2418-2423. [PMID: 27611478 DOI: 10.1021/acs.bioconjchem.6b00381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The emergence of antibiotic-resistant bacteria is a major public health threat, and therefore novel antimicrobial targets and strategies are urgently needed. In this regard, cell-wall-associated proteases are envisaged as interesting antimicrobial targets due to their role in cell wall remodeling. Here, we describe the discovery and characteristics of a protease substrate that is processed by a bacterial cell-wall-associated protease. Stationary-phase grown Gram-positive bacteria were incubated with fluorogenic protease substrates, and their cleavage and covalent incorporation into the cell wall was analyzed. Of all of the substrates used, only one substrate, containing a valine-leucine-lysine (VLK) motif, was covalently incorporated into the bacterial cell wall. Linkage of the VLK-peptide substrate appeared unrelated to sortase A and B activity, as both wild-type and sortase A and B knock out Staphylococcus aureus strains incorporated this substrate into their cell wall with comparable efficiency. Additionally, the VLK-peptide substrate showed significantly higher incorporation in the cell wall of VanA-positive Enterococcus faecium strains than in VanB- and vancomycin-susceptible isolates. In conclusion, the VLK-peptide substrate identified in this study shows promise as a vehicle for targeting antimicrobial compounds and diagnostic contrast agents to the bacterial cell wall.
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Affiliation(s)
- Silvie Hansenová Maňásková
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC , Wytemaweg 80, 3015 CE Rotterdam, The Netherlands.,Department of Oral Biochemistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam , Gustav Mahlerlaan 3004, 1081 LA Amsterdam, The Netherlands
| | - Floris J Bikker
- Department of Oral Biochemistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam , Gustav Mahlerlaan 3004, 1081 LA Amsterdam, The Netherlands
| | - Kamran Nazmi
- Department of Oral Biochemistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam , Gustav Mahlerlaan 3004, 1081 LA Amsterdam, The Netherlands
| | - Rianne van Zuidam
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC , Wytemaweg 80, 3015 CE Rotterdam, The Netherlands
| | - Johan A Slotman
- Optical Imaging Center, Department of Pathology, Josephine Nefkens Institute, Erasmus MC , Dr Molewaterplein 50, Rotterdam 3015 GE, The Netherlands
| | - Wiggert A van Cappellen
- Optical Imaging Center, Department of Pathology, Josephine Nefkens Institute, Erasmus MC , Dr Molewaterplein 50, Rotterdam 3015 GE, The Netherlands
| | - Adriaan B Houtsmuller
- Optical Imaging Center, Department of Pathology, Josephine Nefkens Institute, Erasmus MC , Dr Molewaterplein 50, Rotterdam 3015 GE, The Netherlands
| | - Enno C I Veerman
- Department of Oral Biochemistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam , Gustav Mahlerlaan 3004, 1081 LA Amsterdam, The Netherlands
| | - Wendy E Kaman
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC , Wytemaweg 80, 3015 CE Rotterdam, The Netherlands.,Department of Oral Biochemistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam , Gustav Mahlerlaan 3004, 1081 LA Amsterdam, The Netherlands
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42
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van Royen ME, Verhoef EI, Kweldam CF, van Cappellen WA, Kremers GJ, Houtsmuller AB, van Leenders GJLH. Three-dimensional microscopic analysis of clinical prostate specimens. Histopathology 2016; 69:985-992. [DOI: 10.1111/his.13022] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/20/2016] [Accepted: 06/23/2016] [Indexed: 01/15/2023]
Affiliation(s)
- Martin E van Royen
- Department of Pathology; Erasmus Medical Centre; Rotterdam the Netherlands
- Erasmus Optical Imaging Centre; Erasmus Medical Centre; Rotterdam the Netherlands
| | - Esther I Verhoef
- Department of Pathology; Erasmus Medical Centre; Rotterdam the Netherlands
| | | | - Wiggert A van Cappellen
- Department of Pathology; Erasmus Medical Centre; Rotterdam the Netherlands
- Erasmus Optical Imaging Centre; Erasmus Medical Centre; Rotterdam the Netherlands
| | - Gert-Jan Kremers
- Department of Pathology; Erasmus Medical Centre; Rotterdam the Netherlands
- Erasmus Optical Imaging Centre; Erasmus Medical Centre; Rotterdam the Netherlands
| | - Adriaan B Houtsmuller
- Department of Pathology; Erasmus Medical Centre; Rotterdam the Netherlands
- Erasmus Optical Imaging Centre; Erasmus Medical Centre; Rotterdam the Netherlands
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43
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Abstract
Nuclear foci of chromatin binding factors are, in many cases, discussed as sites of long-range chromatin interaction in the three-dimensional nuclear space. Insulator binding proteins have been shown to aggregate into insulator bodies, which are large structures not involved in insulation; however, the more diffusely distributed insulator speckles have not been analysed in this respect. Furthermore, insulator binding proteins have been shown to drive binding sites for Polycomb group proteins into Polycomb bodies. Here we find that insulator speckles, marked by the insulator binding protein dCTCF, and Polycomb bodies show differential association with the insulator protein CP190. They differ in number and three-dimensional location with only 26% of the Polycomb bodies overlapping with CP190. By using fluorescence in situ hybridization (FISH) probes to identify long-range interaction (kissing) of the Hox gene clusters Antennapedia complex (ANT-C) and Bithorax complex (BX-C), we found the frequency of interaction to be very low. However, these rare kissing events were associated with insulator speckles at a significantly shorter distance and an increased speckle number. This suggests that insulator speckles are associated with long-distance interaction.
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Affiliation(s)
- Melanie K Buxa
- Institute for Genetics, Justus-Liebig-University, Heinrich-Buff-Ring 58, Giessen D35392, Germany
| | - Johan A Slotman
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Postbus 2040, Rotterdam 3000 CA, The Netherlands
| | - Martin E van Royen
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Postbus 2040, Rotterdam 3000 CA, The Netherlands
| | - Maarten W Paul
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Postbus 2040, Rotterdam 3000 CA, The Netherlands
| | - Adriaan B Houtsmuller
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Postbus 2040, Rotterdam 3000 CA, The Netherlands
| | - Rainer Renkawitz
- Institute for Genetics, Justus-Liebig-University, Heinrich-Buff-Ring 58, Giessen D35392, Germany
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44
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Prekovic S, van Royen ME, Voet ARD, Geverts B, Houtman R, Melchers D, Zhang KYJ, Van den Broeck T, Smeets E, Spans L, Houtsmuller AB, Joniau S, Claessens F, Helsen C. The Effect of F877L and T878A Mutations on Androgen Receptor Response to Enzalutamide. Mol Cancer Ther 2016; 15:1702-12. [PMID: 27196756 DOI: 10.1158/1535-7163.mct-15-0892] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 04/26/2016] [Indexed: 11/16/2022]
Abstract
Treatment-induced mutations in the ligand-binding domain of the androgen receptor (AR) are known to change antagonists into agonists. Recently, the F877L mutation has been described to convert enzalutamide into an agonist. This mutation was seen to co-occur in the endogenous AR allele of LNCaP cells, next to the T878A mutation. Here, we studied the effects of enzalutamide on the F877L and T878A mutants, as well as the double-mutant AR (F877L/T878A). Molecular modeling revealed favorable structural changes in the double-mutant AR that lead to a decrease in steric clashes for enzalutamide. Ligand-binding assays confirmed that the F877L mutation leads to an increase in relative binding affinity for enzalutamide, but only the combination with the T878A mutation resulted in a strong agonistic activity. This correlated with changes in coregulator recruitment and chromatin interactions. Our data show that enzalutamide is only a very weak partial agonist of the AR F877L, and a strong partial agonist of the double-mutant AR. Mol Cancer Ther; 15(7); 1702-12. ©2016 AACR.
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Affiliation(s)
- Stefan Prekovic
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | | | - Arnout R D Voet
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, Yokohama, Japan. Laboratory for Biomolecular Modeling and Design, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Bart Geverts
- Department of Pathology, Erasmus MC, Rotterdam, the Netherlands
| | | | | | - Kam Y J Zhang
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - Thomas Van den Broeck
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium. Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - Elien Smeets
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Lien Spans
- Laboratory for Genetics of Malignant Disorders, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Adriaan B Houtsmuller
- Department of Pathology, Erasmus MC, Rotterdam, the Netherlands. Erasmus Optical Imaging Center, Erasmus MC, Rotterdam, the Netherlands
| | - Steven Joniau
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
| | - Christine Helsen
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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45
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Broek JAC, Lin Z, de Gruiter HM, van 't Spijker H, Haasdijk ED, Cox D, Ozcan S, van Cappellen GWA, Houtsmuller AB, Willemsen R, de Zeeuw CI, Bahn S. Synaptic vesicle dynamic changes in a model of fragile X. Mol Autism 2016; 7:17. [PMID: 26933487 PMCID: PMC4772588 DOI: 10.1186/s13229-016-0080-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 02/20/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fragile X syndrome (FXS) is a single-gene disorder that is the most common heritable cause of intellectual disability and the most frequent monogenic cause of autism spectrum disorders (ASD). FXS is caused by an expansion of trinucleotide repeats in the promoter region of the fragile X mental retardation gene (Fmr1). This leads to a lack of fragile X mental retardation protein (FMRP), which regulates translation of a wide range of messenger RNAs (mRNAs). The extent of expression level alterations of synaptic proteins affected by FMRP loss and their consequences on synaptic dynamics in FXS has not been fully investigated. METHODS Here, we used an Fmr1 knockout (KO) mouse model to investigate the molecular mechanisms underlying FXS by monitoring protein expression changes using shotgun label-free liquid-chromatography mass spectrometry (LC-MS(E)) in brain tissue and synaptosome fractions. FXS-associated candidate proteins were validated using selected reaction monitoring (SRM) in synaptosome fractions for targeted protein quantification. Furthermore, functional alterations in synaptic release and dynamics were evaluated using live-cell imaging, and interpretation of synaptic dynamics differences was investigated using electron microscopy. RESULTS Key findings relate to altered levels of proteins involved in GABA-signalling, especially in the cerebellum. Further exploration using microscopy studies found reduced synaptic vesicle unloading of hippocampal neurons and increased vesicle unloading in cerebellar neurons, which suggests a general decrease of synaptic transmission. CONCLUSIONS Our findings suggest that FMRP is a regulator of synaptic vesicle dynamics, which supports the role of FMRP in presynaptic functions. Taken together, these studies provide novel insights into the molecular changes associated with FXS.
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Affiliation(s)
- Jantine A C Broek
- Cambridge Centre for Neuropsychiatric Research, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Zhanmin Lin
- Department of Neurosciences, Erasmus MC, Rotterdam, The Netherlands
| | | | - Heleen van 't Spijker
- Cambridge Centre for Neuropsychiatric Research, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Elize D Haasdijk
- Department of Neurosciences, Erasmus MC, Rotterdam, The Netherlands
| | - David Cox
- Cambridge Centre for Neuropsychiatric Research, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Sureyya Ozcan
- Cambridge Centre for Neuropsychiatric Research, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | | | | | - Rob Willemsen
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Chris I de Zeeuw
- Department of Neurosciences, Erasmus MC, Rotterdam, The Netherlands.,Netherlands Institute for Neurosciences, Royal Academy for Arts and Sciences, Amsterdam, The Netherlands
| | - Sabine Bahn
- Cambridge Centre for Neuropsychiatric Research, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK.,Department of Neurosciences, Erasmus MC, Rotterdam, The Netherlands
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46
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van den Dries K, Meddens MB, Pandzic E, Joosten B, Slotman JA, Nahidiazar L, Jalink K, Houtsmuller AB, Wisemann PW, Cambi A. From Nanoscale to Mesoscale: Integrating Advanced Microscopy Techniques to Reveal the Ultrastructure and Coordinated Dynamics of Mechanosensory Podosomes. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.3312] [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: 11/29/2022] Open
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47
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Reuter M, Zelensky A, Smal I, Meijering E, van Cappellen WA, de Gruiter HM, van Belle GJ, van Royen ME, Houtsmuller AB, Essers J, Kanaar R, Wyman C. BRCA2 diffuses as oligomeric clusters with RAD51 and changes mobility after DNA damage in live cells. ACTA ACUST UNITED AC 2015; 208:857. [PMID: 25778924 PMCID: PMC4362460 DOI: 10.1083/jcb.20140501402182015c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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48
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Reuter M, Zelensky A, Smal I, Meijering E, van Cappellen WA, de Gruiter HM, van Belle GJ, van Royen ME, Houtsmuller AB, Essers J, Kanaar R, Wyman C. BRCA2 diffuses as oligomeric clusters with RAD51 and changes mobility after DNA damage in live cells. ACTA ACUST UNITED AC 2015; 207:599-613. [PMID: 25488918 PMCID: PMC4259808 DOI: 10.1083/jcb.201405014] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Nuclear BRCA2 is oligomeric and associated with RAD51, possibly sequestering it until it is delivered to DNA damage sites. Genome maintenance by homologous recombination depends on coordinating many proteins in time and space to assemble at DNA break sites. To understand this process, we followed the mobility of BRCA2, a critical recombination mediator, in live cells at the single-molecule level using both single-particle tracking and fluorescence correlation spectroscopy. BRCA2-GFP and -YFP were compared to distinguish diffusion from fluorophore behavior. Diffusive behavior of fluorescent RAD51 and RAD54 was determined for comparison. All fluorescent proteins were expressed from endogenous loci. We found that nuclear BRCA2 existed in oligomeric clusters, and exhibited heterogeneous mobility. DNA damage increased BRCA2 transient binding, presumably including binding to damaged sites. Despite its very different size, RAD51 displayed mobility similar to BRCA2, which indicates physical interaction between these proteins both before and after induction of DNA damage. We propose that BRCA2-mediated sequestration of nuclear RAD51 serves to prevent inappropriate DNA interactions and that all RAD51 is delivered to DNA damage sites in association with BRCA2.
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Affiliation(s)
- Marcel Reuter
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Alex Zelensky
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Ihor Smal
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Erik Meijering
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Wiggert A van Cappellen
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - H Martijn de Gruiter
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Gijsbert J van Belle
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Martin E van Royen
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Adriaan B Houtsmuller
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Jeroen Essers
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Roland Kanaar
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Claire Wyman
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
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49
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Abstract
We present a Monte Carlo simulation environment for modelling complex biological molecular interaction networks and for the design, validation, and quantitative analysis of FRAP assays to study these. The program is straightforward in its implementation and can be instructed through an intuitive script language. The simulation tool fits very well in a systems biology research setting that aims to maintain an interactive cycle of experiment-driven modelling and model-driven experimentation: the model and the experiment are in the same simulation. The full program can be obtained by request to the authors.
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Affiliation(s)
- Bart Geverts
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Postbus 2040, Rotterdam, 3000 CA, The Netherlands
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50
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Yoo HW, van Royen ME, van Cappellen WA, Houtsmuller AB, Verhaegen M, Schitter G. Automated spherical aberration correction in scanning confocal microscopy. Rev Sci Instrum 2014; 85:123706. [PMID: 25554300 DOI: 10.1063/1.4904370] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Mismatch between the refractive indexes of immersion media and glass coverslips introduces spherical aberrations in microscopes especially for high numerical aperture objectives. This contribution demonstrates an automated adjustment of the coverslip correction collar in scanning confocal microscopy to compensate for spherical aberrations due to coverslip thickness mismatch. With a motorized coverslip correction collar, the adjustment procedure consists of xz image scans, image processing, correction quality evaluation, the mismatch estimation, and eventually the optimal adjustment of the correction collar. For fast correction with less photodamage, coarse-fine Gaussian fitting algorithms are proposed and evaluated with various specimen for their estimation accuracy. The benefits of the proposed automated correction are demonstrated for various coverslips with biological specimens, showing the optimized resolution of the confocal microscope.
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MESH Headings
- Algorithms
- Animals
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Cell Line, Tumor
- Convallaria
- Equipment Design
- Fibroblasts/cytology
- Fibroblasts/metabolism
- Gold/chemistry
- Humans
- Imaging, Three-Dimensional/instrumentation
- Imaging, Three-Dimensional/methods
- Mice
- Microscopy, Confocal/instrumentation
- Microscopy, Confocal/methods
- Microscopy, Fluorescence/instrumentation
- Microscopy, Fluorescence/methods
- Models, Theoretical
- Normal Distribution
- Optical Phenomena
- Pattern Recognition, Automated/methods
- Rhizome/chemistry
- Water/chemistry
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Affiliation(s)
- H W Yoo
- Delft Center for Systems and Control, Delft University of Technology, Mekelweg 2, 2628 CD Delft, The Netherlands
| | - M E van Royen
- Erasmus Optical Imaging Center, Department of Pathology, Josephine Nefkens Institute, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands
| | - W A van Cappellen
- Erasmus Optical Imaging Center, Department of Pathology, Josephine Nefkens Institute, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands
| | - A B Houtsmuller
- Erasmus Optical Imaging Center, Department of Pathology, Josephine Nefkens Institute, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands
| | - M Verhaegen
- Delft Center for Systems and Control, Delft University of Technology, Mekelweg 2, 2628 CD Delft, The Netherlands
| | - G Schitter
- Automation and Control Institute, Vienna University of Technology, Gusshausstr. 27-29, 1040 Vienna, Austria
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