1
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Tripathi R, Aggarwal T, Lindberg FA, Klemm AH, Fredriksson R. SLC38A10 Regulate Glutamate Homeostasis and Modulate the AKT/TSC2/mTOR Pathway in Mouse Primary Cortex Cells. Front Cell Dev Biol 2022; 10:854397. [PMID: 35450293 PMCID: PMC9017388 DOI: 10.3389/fcell.2022.854397] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/15/2022] [Indexed: 12/13/2022] Open
Abstract
Glutamate acts as a critical regulator of neurotransmitter balance, recycling, synaptic function and homeostasis in the brain and glutamate transporters control glutamate levels in the brain. SLC38A10 is a member of the SLC38 family and regulates protein synthesis and cellular stress responses. Here, we uncover the role of SLC38A10 as a transceptor involved in glutamate-sensing signaling pathways that control both the glutamate homeostasis and mTOR-signaling. The culture of primary cortex cells from SLC38A10 knockout mice had increased intracellular glutamate. In addition, under nutrient starvation, KO cells had an impaired response in amino acid-dependent mTORC1 signaling. Combined studies from transcriptomics, protein arrays and metabolomics established that SLC38A10 is involved in mTOR signaling and that SLC38A10 deficient primary cortex cells have increased protein synthesis. Metabolomic data showed decreased cholesterol levels, changed fatty acid synthesis, and altered levels of fumaric acid, citrate, 2-oxoglutarate and succinate in the TCA cycle. These data suggests that SLC38A10 may act as a modulator of glutamate homeostasis, and mTOR-sensing and loss of this transceptor result in lower cholesterol, which could have implications in neurodegenerative diseases.
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Affiliation(s)
- Rekha Tripathi
- Department of Pharmaceutical Bioscience, Unit of Molecular Neuropharmacology, Uppsala University, Uppsala, Sweden
- *Correspondence: Rekha Tripathi,
| | - Tanya Aggarwal
- Department of Pharmaceutical Bioscience, Unit of Molecular Neuropharmacology, Uppsala University, Uppsala, Sweden
| | - Frida A. Lindberg
- Department of Pharmaceutical Bioscience, Unit of Molecular Neuropharmacology, Uppsala University, Uppsala, Sweden
| | - Anna H. Klemm
- BioImage Informatics Facility, SciLifeLab, Division of Visual Information and Interaction, Department of Information Technology, Uppsala, Sweden
| | - Robert Fredriksson
- Department of Pharmaceutical Bioscience, Unit of Molecular Neuropharmacology, Uppsala University, Uppsala, Sweden
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2
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Solorzano L, Wik L, Olsson Bontell T, Wang Y, Klemm AH, Öfverstedt J, Jakola AS, Östman A, Wählby C. Machine learning for cell classification and neighborhood analysis in glioma tissue. Cytometry A 2021; 99:1176-1186. [PMID: 34089228 DOI: 10.1002/cyto.a.24467] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/28/2021] [Accepted: 05/25/2021] [Indexed: 12/21/2022]
Abstract
Multiplexed and spatially resolved single-cell analyses that intend to study tissue heterogeneity and cell organization invariably face as a first step the challenge of cell classification. Accuracy and reproducibility are important for the downstream process of counting cells, quantifying cell-cell interactions, and extracting information on disease-specific localized cell niches. Novel staining techniques make it possible to visualize and quantify large numbers of cell-specific molecular markers in parallel. However, due to variations in sample handling and artifacts from staining and scanning, cells of the same type may present different marker profiles both within and across samples. We address multiplexed immunofluorescence data from tissue microarrays of low-grade gliomas and present a methodology using two different machine learning architectures and features insensitive to illumination to perform cell classification. The fully automated cell classification provides a measure of confidence for the decision and requires a comparably small annotated data set for training, which can be created using freely available tools. Using the proposed method, we reached an accuracy of 83.1% on cell classification without the need for standardization of samples. Using our confidence measure, cells with low-confidence classifications could be excluded, pushing the classification accuracy to 94.5%. Next, we used the cell classification results to search for cell niches with an unsupervised learning approach based on graph neural networks. We show that the approach can re-detect specialized tissue niches in previously published data, and that our proposed cell classification leads to niche definitions that may be relevant for sub-groups of glioma, if applied to larger data sets.
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Affiliation(s)
- Leslie Solorzano
- Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Lina Wik
- Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Thomas Olsson Bontell
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Physiology, Institute of Neuroscience and Physiology, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
| | - Yuyu Wang
- Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Anna H Klemm
- Department of Information Technology, Uppsala University, Uppsala, Sweden.,BioImage Informatics Facility, Science for Life Laboratory, SciLifeLab, Sweden
| | - Johan Öfverstedt
- Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Asgeir S Jakola
- Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden.,Institute of Neuroscience and Physiology, Department of Clinical Neuroscience, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
| | - Arne Östman
- Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Carolina Wählby
- Department of Information Technology, Uppsala University, Uppsala, Sweden.,BioImage Informatics Facility, Science for Life Laboratory, SciLifeLab, Sweden
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3
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Dobson ETA, Cimini B, Klemm AH, Wählby C, Carpenter AE, Eliceiri KW. ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis. Curr Protoc 2021; 1:e89. [PMID: 34038030 DOI: 10.1002/cpz1.89] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
ImageJ and CellProfiler have long been leading open-source platforms in the field of bioimage analysis. ImageJ's traditional strength is in single-image processing and investigation, while CellProfiler is designed for building large-scale, modular analysis pipelines. Although many image analysis problems can be well solved with one or the other, using these two platforms together in a single workflow can be powerful. Here, we share two pipelines demonstrating mechanisms for productively and conveniently integrating ImageJ and CellProfiler for (1) studying cell morphology and migration via tracking, and (2) advanced stitching techniques for handling large, tiled image sets to improve segmentation. No single platform can provide all the key and most efficient functionality needed for all studies. While both programs can be and are often used separately, these pipelines demonstrate the benefits of using them together for image analysis workflows. ImageJ and CellProfiler are both committed to interoperability between their platforms, with ongoing development to improve how both are leveraged from the other. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Studying cell morphology and cell migration in time-lapse datasets using TrackMate (Fiji) and CellProfiler Basic Protocol 2: Creating whole plate montages to easily assess adaptability of segmentation parameters.
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Affiliation(s)
- Ellen T A Dobson
- Laboratory for Optical and Computational Instrumentation (LOCI), Center for Quantitative Cell Imaging, University of Wisconsin at Madison, Madison, Wisconsin
| | - Beth Cimini
- Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Anna H Klemm
- Science for Life Laboratory BioImage Informatics Facility and Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Carolina Wählby
- Science for Life Laboratory BioImage Informatics Facility and Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Kevin W Eliceiri
- Laboratory for Optical and Computational Instrumentation (LOCI), Center for Quantitative Cell Imaging, University of Wisconsin at Madison, Madison, Wisconsin.,Department of Medical Physics, University of Wisconsin at Madison, Madison, Wisconsin.,Morgridge Institute for Research, Madison, Wisconsin
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4
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Martins GG, Cordelières FP, Colombelli J, D'Antuono R, Golani O, Guiet R, Haase R, Klemm AH, Louveaux M, Paul-Gilloteaux P, Tinevez JY, Miura K. Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists. F1000Res 2021; 10:334. [PMID: 34164115 PMCID: PMC8215561 DOI: 10.12688/f1000research.25485.1] [Citation(s) in RCA: 6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/15/2021] [Indexed: 11/20/2022] Open
Abstract
NEUBIAS, the European Network of Bioimage Analysts, was created in 2016 with the goal of improving the communication and the knowledge transfer among the various stakeholders involved in the acquisition, processing and analysis of biological image data, and to promote the establishment and recognition of the profession of Bioimage Analyst. One of the most successful initiatives of the NEUBIAS programme was its series of 15 training schools, which trained over 400 new Bioimage Analysts, coming from over 40 countries. Here we outline the rationale behind the innovative three-level program of the schools, the curriculum, the trainer recruitment and turnover strategy, the outcomes for the community and the career path of analysts, including some success stories. We discuss the future of the materials created during this programme and some of the new initiatives emanating from the community of NEUBIAS-trained analysts, such as the NEUBIAS Academy. Overall, we elaborate on how this training programme played a key role in collectively leveraging Bioimaging and Life Science research by bringing the latest innovations into structured, frequent and intensive training activities, and on why we believe this should become a model to further develop in Life Sciences.
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Affiliation(s)
| | - Fabrice P Cordelières
- Bordeaux Imaging Center (BIC), Université de Bordeaux - US4 INSERM, Bordeaux, France
| | - Julien Colombelli
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Rocco D'Antuono
- Crick Advanced Light Microscopy STP (CALM), The Francis Crick Institute, London, UK
| | - Ofra Golani
- The department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Romain Guiet
- BioImaging and Optics Platform (BIOP), Faculty of Life Sciences (SV), École Polytechnique Fédérale (EPFL), Lausanne, Switzerland
| | - Robert Haase
- DFG Cluster of Excellence "Physics of Life", University of Technology TU, Dresden, Germany
| | - Anna H Klemm
- Science for Life Laboratory BioImage Informatics Facility and Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Marion Louveaux
- BioImage Analysis Unit, Institut Pasteur, Paris, France.,Image Analysis Hub, C2RT Institut Pasteur, Paris, France
| | - Perrine Paul-Gilloteaux
- Université de Nantes, CNRS, INSERM, Nantes, France.,Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Sante, Inserm UMS 016, CNRS UMS3556, Nantes, France
| | | | - Kota Miura
- Nikon Imaging Center, University of Heidelberg, Heidelberg, Germany.,Bioimage Analysis & Research, Heidelberg, Germany
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5
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Partel G, Hilscher MM, Milli G, Solorzano L, Klemm AH, Nilsson M, Wählby C. Automated identification of the mouse brain's spatial compartments from in situ sequencing data. BMC Biol 2020; 18:144. [PMID: 33076915 PMCID: PMC7574211 DOI: 10.1186/s12915-020-00874-5] [Citation(s) in RCA: 8] [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: 02/28/2020] [Accepted: 09/18/2020] [Indexed: 01/03/2023] Open
Abstract
Background Neuroanatomical compartments of the mouse brain are identified and outlined mainly based on manual annotations of samples using features related to tissue and cellular morphology, taking advantage of publicly available reference atlases. However, this task is challenging since sliced tissue sections are rarely perfectly parallel or angled with respect to sections in the reference atlas and organs from different individuals may vary in size and shape and requires manual annotation. With the advent of in situ sequencing technologies and automated approaches, it is now possible to profile the gene expression of targeted genes inside preserved tissue samples and thus spatially map biological processes across anatomical compartments. Results Here, we show how in situ sequencing data combined with dimensionality reduction and clustering can be used to identify spatial compartments that correspond to known anatomical compartments of the brain. We also visualize gradients in gene expression and sharp as well as smooth transitions between different compartments. We apply our method on mouse brain sections and show that a fully unsupervised approach can computationally define anatomical compartments, which are highly reproducible across individuals, using as few as 18 gene markers. We also show that morphological variation does not always follow gene expression, and different spatial compartments can be defined by various cell types with common morphological features but distinct gene expression profiles. Conclusion We show that spatial gene expression data can be used for unsupervised and unbiased annotations of mouse brain spatial compartments based only on molecular markers, without the need of subjective manual annotations based on tissue and cell morphology or matching reference atlases.
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Affiliation(s)
- Gabriele Partel
- Centre for Image Analysis, Department of Information Technology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Markus M Hilscher
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Giorgia Milli
- Centre for Image Analysis, Department of Information Technology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Leslie Solorzano
- Centre for Image Analysis, Department of Information Technology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna H Klemm
- Centre for Image Analysis, Department of Information Technology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,BioImage Informatics Facility of SciLifeLab, Uppsala, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Carolina Wählby
- Centre for Image Analysis, Department of Information Technology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden. .,BioImage Informatics Facility of SciLifeLab, Uppsala, Sweden.
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6
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Klemm AH, Thomae AW, Wachal K, Dietzel S. Tracking Microscope Performance: A Workflow to Compare Point Spread Function Evaluations Over Time. Microsc Microanal 2019; 25:699-704. [PMID: 30722807 DOI: 10.1017/s1431927619000060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Routine system checks are essential for supervising the performance of an advanced light microscope. Recording and evaluating the point spread function (PSF) of a given system provides information about the resolution and imaging. We compared the performance of fluorescent and gold beads for PSF recordings. We then combined the open-source evaluation software PSFj with a newly developed KNIME pipeline named PSFtracker to create a standardized workflow to track a system's performance over several measurements and thus over long time periods. PSFtracker produces example images of recorded PSFs, plots full-width-half-maximum (FWHM) measurements over time and creates an html file which embeds the images and plots, together with a table of results. Changes of the PSF over time are thus easily spotted, either in FWHM plots or in the time series of bead images which allows recognition of aberrations in the shape of the PSF. The html file, viewed in a local browser or uploaded on the web, therefore provides intuitive visualization of the state of the PSF over time. In addition, uploading of the html file on the web allows other microscopists to compare such data with their own.
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Affiliation(s)
- Anna H Klemm
- Core Facility Bioimaging at the Biomedical Center and Walter-Brendel-Zentrum für Experimentelle Medizin, Ludwig-Maximilians-Univeristät München,Großhaderner Straße 9, 82152 Planegg-Martinsried,Germany
| | - Andreas W Thomae
- Core Facility Bioimaging at the Biomedical Center and Walter-Brendel-Zentrum für Experimentelle Medizin, Ludwig-Maximilians-Univeristät München,Großhaderner Straße 9, 82152 Planegg-Martinsried,Germany
| | - Katarina Wachal
- Core Facility Bioimaging at the Biomedical Center and Walter-Brendel-Zentrum für Experimentelle Medizin, Ludwig-Maximilians-Univeristät München,Großhaderner Straße 9, 82152 Planegg-Martinsried,Germany
| | - Steffen Dietzel
- Core Facility Bioimaging at the Biomedical Center and Walter-Brendel-Zentrum für Experimentelle Medizin, Ludwig-Maximilians-Univeristät München,Großhaderner Straße 9, 82152 Planegg-Martinsried,Germany
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7
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Gupta A, Harrison PJ, Wieslander H, Pielawski N, Kartasalo K, Partel G, Solorzano L, Suveer A, Klemm AH, Spjuth O, Sintorn I, Wählby C. Deep Learning in Image Cytometry: A Review. Cytometry A 2019; 95:366-380. [PMID: 30565841 PMCID: PMC6590257 DOI: 10.1002/cyto.a.23701] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [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: 10/05/2018] [Revised: 11/07/2018] [Accepted: 11/29/2018] [Indexed: 12/18/2022]
Abstract
Artificial intelligence, deep convolutional neural networks, and deep learning are all niche terms that are increasingly appearing in scientific presentations as well as in the general media. In this review, we focus on deep learning and how it is applied to microscopy image data of cells and tissue samples. Starting with an analogy to neuroscience, we aim to give the reader an overview of the key concepts of neural networks, and an understanding of how deep learning differs from more classical approaches for extracting information from image data. We aim to increase the understanding of these methods, while highlighting considerations regarding input data requirements, computational resources, challenges, and limitations. We do not provide a full manual for applying these methods to your own data, but rather review previously published articles on deep learning in image cytometry, and guide the readers toward further reading on specific networks and methods, including new methods not yet applied to cytometry data. © 2018 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Anindya Gupta
- Centre for Image AnalysisUppsala UniversityUppsala75124Sweden
| | - Philip J. Harrison
- Department of Pharmaceutical BiosciencesUppsala UniversityUppsala75124Sweden
| | | | | | - Kimmo Kartasalo
- Faculty of Medicine and Life SciencesUniversity of TampereTampere33014Finland
- Faculty of Biomedical Sciences and EngineeringTampere University of TechnologyTampere33720Finland
| | - Gabriele Partel
- Centre for Image AnalysisUppsala UniversityUppsala75124Sweden
| | | | - Amit Suveer
- Centre for Image AnalysisUppsala UniversityUppsala75124Sweden
| | - Anna H. Klemm
- Centre for Image AnalysisUppsala UniversityUppsala75124Sweden
- BioImage Informatics Facility of SciLifeLabUppsala75124Sweden
| | - Ola Spjuth
- Department of Pharmaceutical BiosciencesUppsala UniversityUppsala75124Sweden
| | | | - Carolina Wählby
- Centre for Image AnalysisUppsala UniversityUppsala75124Sweden
- BioImage Informatics Facility of SciLifeLabUppsala75124Sweden
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8
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Lasch M, Nekolla K, Klemm AH, Buchheim JI, Pohl U, Dietzel S, Deindl E. Estimating hemodynamic shear stress in murine peripheral collateral arteries by two-photon line scanning. Mol Cell Biochem 2018; 453:41-51. [PMID: 30128948 DOI: 10.1007/s11010-018-3430-9] [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: 03/20/2018] [Accepted: 08/16/2018] [Indexed: 12/20/2022]
Abstract
Changes in wall shear stress of blood vessels are assumed to be an important component of many physiological and pathophysiological processes. However, due to technical limitations experimental in vivo data are rarely available. Here, we investigated two-photon excitation fluorescence microscopy as an option to measure vessel diameter as well as blood flow velocities in a murine hindlimb model of arteriogenesis (collateral artery growth). Using line scanning at high frequencies, we measured the movement of blood cells along the vessel axis. We found that peak systolic blood flow velocity averaged 9 mm/s and vessel diameter 42 µm in resting collaterals. Induction of arteriogenesis by femoral artery ligation resulted in a significant increase in centerline peak systolic velocity after 1 day with an average of 51 mm/s, whereas the averaged luminal diameter of collaterals (52 µm) changed much less. Thereof calculations revealed a significant fourfold increase in hemodynamic wall shear rate. Our results indicate that two-photon line scanning is a suitable tool to estimate wall shear stress e.g., in experimental animal models, such as of arteriogenesis, which may not only help to understand the relevance of mechanical forces in vivo, but also to adjust wall shear stress in ex vivo investigations on isolated vessels as well as cell culture experiments.
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Affiliation(s)
- Manuel Lasch
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, Marchioninistr.15, 81377, Munich, Germany.,Department of Otorhinolaryngology, Head & Neck Surgery, Klinikum der Universität München, Ludwig- Maximilians-Universität München, Munich, Germany
| | - Katharina Nekolla
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, Marchioninistr.15, 81377, Munich, Germany
| | - Anna H Klemm
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, Marchioninistr.15, 81377, Munich, Germany.,Core Facility Bioimaging at the Biomedical Center, LMU Munich, Planegg-Martinsried, Germany
| | - Judith-Irina Buchheim
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, Marchioninistr.15, 81377, Munich, Germany.,Department of Anesthesiology, Laboratory for Stress and Immunity, Hospital of the University of the LMU Munich, Munich, Germany
| | - Ulrich Pohl
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, Marchioninistr.15, 81377, Munich, Germany.,Core Facility Bioimaging at the Biomedical Center, LMU Munich, Planegg-Martinsried, Germany.,German Center for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
| | - Steffen Dietzel
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, Marchioninistr.15, 81377, Munich, Germany.,Core Facility Bioimaging at the Biomedical Center, LMU Munich, Planegg-Martinsried, Germany
| | - Elisabeth Deindl
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, Marchioninistr.15, 81377, Munich, Germany.
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9
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Klemm AH, Bosilj A, Gluncˇic M, Pavin N, Tolic IM. Metaphase kinetochore movements are regulated by kinesin-8 motors and microtubule dynamic instability. Mol Biol Cell 2018; 29:1332-1345. [PMID: 29851559 PMCID: PMC5994901 DOI: 10.1091/mbc.e17-11-0667] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
During metaphase, sister chromatids are connected to microtubules extending from the opposite spindle poles via kinetochores to protein complexes on the chromosome. Kinetochores congress to the equatorial plane of the spindle and oscillate around it, with kinesin-8 motors restricting these movements. Yet, the physical mechanism underlying kinetochore movements is unclear. We show that kinetochore movements in the fission yeast Schizosaccharomyces pombe are regulated by kinesin-8-promoted microtubule catastrophe, force-induced rescue, and microtubule dynamic instability. A candidate screen showed that among the selected motors only kinesin-8 motors Klp5/Klp6 are required for kinetochore centering. Kinesin-8 accumulates at the end of microtubules, where it promotes catastrophe. Laser ablation of the spindle resulted in kinetochore movement toward the intact spindle pole in wild-type and klp5Δ cells, suggesting that kinetochore movement is driven by pulling forces. Our theoretical model with Langevin description of microtubule dynamic instability shows that kinesin-8 motors are required for kinetochore centering, whereas sensitivity of rescue to force is necessary for the generation of oscillations. We found that irregular kinetochore movements occur for a broader range of parameters than regular oscillations. Thus, our work provides an explanation for how regulation of microtubule dynamic instability contributes to kinetochore congression and the accompanying movements around the spindle center.
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Affiliation(s)
- Anna H Klemm
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Agneza Bosilj
- Department of Physics, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Matko Gluncˇic
- Department of Physics, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Nenad Pavin
- Department of Physics, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Iva M Tolic
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Division of Molecular Biology, Rud¯er Boškovic´ Institute, 10000 Zagreb, Croatia
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10
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Follwaczny P, Schieweck R, Riedemann T, Demleitner A, Straub T, Klemm AH, Bilban M, Sutor B, Popper B, Kiebler MA. Pumilio2-deficient mice show a predisposition for epilepsy. Dis Model Mech 2017; 10:1333-1342. [PMID: 29046322 PMCID: PMC5719250 DOI: 10.1242/dmm.029678] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [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: 02/23/2017] [Accepted: 09/06/2017] [Indexed: 01/18/2023] Open
Abstract
Epilepsy is a neurological disease that is caused by abnormal hypersynchronous activities of neuronal ensembles leading to recurrent and spontaneous seizures in human patients. Enhanced neuronal excitability and a high level of synchrony between neurons seem to trigger these spontaneous seizures. The molecular mechanisms, however, regarding the development of neuronal hyperexcitability and maintenance of epilepsy are still poorly understood. Here, we show that pumilio RNA-binding family member 2 (Pumilio2; Pum2) plays a role in the regulation of excitability in hippocampal neurons of weaned and 5-month-old male mice. Almost complete deficiency of Pum2 in adult Pum2 gene-trap mice (Pum2 GT) causes misregulation of genes involved in neuronal excitability control. Interestingly, this finding is accompanied by the development of spontaneous epileptic seizures in Pum2 GT mice. Furthermore, we detect an age-dependent increase in Scn1a (Nav1.1) and Scn8a (Nav1.6) mRNA levels together with a decrease in Scn2a (Nav1.2) transcript levels in weaned Pum2 GT that is absent in older mice. Moreover, field recordings of CA1 pyramidal neurons show a tendency towards a reduced paired-pulse inhibition after stimulation of the Schaffer-collateral-commissural pathway in Pum2 GT mice, indicating a predisposition to the development of spontaneous seizures at later stages. With the onset of spontaneous seizures at the age of 5 months, we detect increased protein levels of Nav1.1 and Nav1.2 as well as decreased protein levels of Nav1.6 in those mice. In addition, GABA receptor subunit alpha-2 (Gabra2) mRNA levels are increased in weaned and adult mice. Furthermore, we observe an enhanced GABRA2 protein level in the dendritic field of the CA1 subregion in the Pum2 GT hippocampus. We conclude that altered expression levels of known epileptic risk factors such as Nav1.1, Nav1.2, Nav1.6 and GABRA2 result in enhanced seizure susceptibility and manifestation of epilepsy in the hippocampus. Thus, our results argue for a role of Pum2 in epileptogenesis and the maintenance of epilepsy. Summary: Epileptogenic risk factors are misregulated in Pumilio2-deficient mice, determining a predisposition to develop seizures. This article has an associated First Person interview with the first author of the paper as part of the supplementary information.
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Affiliation(s)
- Philipp Follwaczny
- Biomedical Center (BMC), Department for Cell Biology, Faculty of Medicine, LMU, Munich, 82152 Planegg-Martinsried, Germany
| | - Rico Schieweck
- Biomedical Center (BMC), Department for Cell Biology, Faculty of Medicine, LMU, Munich, 82152 Planegg-Martinsried, Germany
| | - Therese Riedemann
- Biomedical Center (BMC), Department of Physiological Genomics, Ludwig-Maximilians-University, Munich, 82152 Planegg-Martinsried, Germany
| | - Antonia Demleitner
- Biomedical Center (BMC), Department for Cell Biology, Faculty of Medicine, LMU, Munich, 82152 Planegg-Martinsried, Germany
| | - Tobias Straub
- Biomedical Center (BMC), Core Facility Bioinformatics, Ludwig-Maximilians-University, Munich, 82152 Planegg-Martinsried, Germany
| | - Anna H Klemm
- Biomedical Center (BMC), Core Facility Bioimaging, Ludwig-Maximilians-University, Munich, 82152 Planegg-Martinsried, Germany.,Walter Brendel Centre of Experimental Medicine, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Martin Bilban
- Department of Laboratory Medicine and Core Facility Genomics, Medical University of Vienna, 1090 Vienna, Austria
| | - Bernd Sutor
- Biomedical Center (BMC), Department of Physiological Genomics, Ludwig-Maximilians-University, Munich, 82152 Planegg-Martinsried, Germany
| | - Bastian Popper
- Biomedical Center (BMC), Department for Cell Biology, Faculty of Medicine, LMU, Munich, 82152 Planegg-Martinsried, Germany .,Biomedical Center (BMC), Core Facility Animal Models, Ludwig-Maximilians-University, Munich, 82152 Planegg-Martinsried, Germany
| | - Michael A Kiebler
- Biomedical Center (BMC), Department for Cell Biology, Faculty of Medicine, LMU, Munich, 82152 Planegg-Martinsried, Germany
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Fabry B, Klemm AH, Kienle S, Schäffer TE, Goldmann WH. Focal adhesion kinase stabilizes the cytoskeleton. Biophys J 2011; 101:2131-8. [PMID: 22067150 DOI: 10.1016/j.bpj.2011.09.043] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 09/21/2011] [Accepted: 09/23/2011] [Indexed: 01/13/2023] Open
Abstract
Focal adhesion kinase (FAK) is a central focal adhesion protein that promotes focal adhesion turnover, but the role of FAK for cell mechanical stability is unknown. We measured the mechanical properties of wild-type (FAKwt), FAK-deficient (FAK-/-), FAK-silenced (siFAK), and siControl mouse embryonic fibroblasts by magnetic tweezer, atomic force microscopy, traction microscopy, and nanoscale particle tracking microrheology. FAK-deficient cells showed lower cell stiffness, reduced adhesion strength, and increased cytoskeletal dynamics compared to wild-type cells. These observations imply a reduced stability of the cytoskeleton in FAK-deficient cells. We attribute the reduced cytoskeletal stability to rho-kinase activation in FAK-deficient cells that suppresses the formation of ordered stress fiber bundles, enhances cortical actin distribution, and reduces cell spreading. In agreement with this interpretation is that cell stiffness and cytoskeletal stability in FAK-/- cells is partially restored to wild-type level after rho-kinase inhibition with Y27632.
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Affiliation(s)
- Ben Fabry
- Department of Physics, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
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Klemm AH, Kienle S, Rheinlaender J, Schäffer TE, Goldmann WH. The influence of Pyk2 on the mechanical properties in fibroblasts. Biochem Biophys Res Commun 2010; 393:694-7. [PMID: 20170630 DOI: 10.1016/j.bbrc.2010.02.059] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 02/10/2010] [Indexed: 10/25/2022]
Abstract
The cell surface receptor integrin is involved in signaling mechanical stresses via the focal adhesion complex (FAC) into the cell. Within FAC, the focal adhesion kinase (FAK) and Pyk2 are believed to act as important scaffolding proteins. Based on the knowledge that many signal transducing molecules are transiently immobilized within FAC connecting the cytoskeleton with integrins, we applied magnetic tweezer and atomic force microscopic measurements to determine the influence of FAK and Pyk2 in cells mechanically. Using mouse embryonic fibroblasts (MEF; FAK(+/+), FAK(-/-), and siRNA-Pyk2 treated FAK(-/-) cells) provided a unique opportunity to describe the function of FAK and Pyk2 in more detail and to define their influence on FAC and actin distribution.
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Affiliation(s)
- Anna H Klemm
- Center for Medical Physics and Technology, Biophysics Group, Friedrich-Alexander-University, Erlangen-Nuremberg, Erlangen, Germany
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Mierke CT, Kollmannsberger P, Klemm AH, Zitterbart DP, Koch TM, Marg S, Ziegler WH, Goldmann WH, Fabry B. Vinculin and Fak Facilite Cell Invasion in Dense 3D-Extracellualr Matrix Networks. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.115] [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: 10/19/2022] Open
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Abstract
We investigated the molecular mechanism by which cells recognize and respond to physical forces in their local environment. Using a model system, to study wild type mouse F9 embryonic carcinoma cells, we examined how these cells sense mechanical stresses and translate them into biochemical responses through their cell surface receptor integrin and via the focal adhesion complex (FAC). Based on studies that show that many signal transducing molecules are immobilized on the cytoskeleton at the site of integrin binding within the focal adhesion complex, we found a time-dependent increase of focal adhesion kinase (pp125(FAK)) phosphorylation possibly due to protein kinase C (PKC) activation as well as protein kinase A (PKA) activity increase upon cell adhesion/spreading. These studies provide some insight into intracellular mechano-chemical signaling.
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Affiliation(s)
- Anna H Klemm
- Friedrich-Alexander-University of Erlangen-Nuremberg, Center for Medical Physics and Technology, Biophysics Group, 91052 Erlangen, Germany
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Smith J, Diez G, Klemm AH, Schewkunow V, Goldmann WH. CapZ-lipid membrane interactions: a computer analysis. Theor Biol Med Model 2006; 3:30. [PMID: 16914033 PMCID: PMC1564000 DOI: 10.1186/1742-4682-3-30] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2006] [Accepted: 08/16/2006] [Indexed: 12/03/2022] Open
Abstract
Background CapZ is a calcium-insensitive and lipid-dependent actin filament capping protein, the main function of which is to regulate the assembly of the actin cytoskeleton. CapZ is associated with membranes in cells and it is generally assumed that this interaction is mediated by polyphosphoinositides (PPI) particularly PIP2, which has been characterized in vitro. Results We propose that non-PPI lipids also bind CapZ. Data from computer-aided sequence and structure analyses further suggest that CapZ could become partially buried in the lipid bilayer probably under mildly acidic conditions, in a manner that is not only dependent on the presence of PPIs. We show that lipid binding could involve a number of sites that are spread throughout the CapZ molecule i.e., alpha- and beta-subunits. However, a beta-subunit segment between residues 134–151 is most likely to be involved in interacting with and inserting into lipid membrane due to a slighly higher ratio of positively to negatively charged residues and also due to the presence of a small hydrophobic helix. Conclusion CapZ may therefore play an essential role in providing a stable membrane anchor for actin filaments.
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Affiliation(s)
- James Smith
- Friedrich-Alexander-University of Erlangen-Nuremberg Center for Medical Physics and Technology, Biophysics Group Henkestrasse 91, 91052 Erlangen, Germany
| | - Gerold Diez
- Friedrich-Alexander-University of Erlangen-Nuremberg Center for Medical Physics and Technology, Biophysics Group Henkestrasse 91, 91052 Erlangen, Germany
| | - Anna H Klemm
- Friedrich-Alexander-University of Erlangen-Nuremberg Center for Medical Physics and Technology, Biophysics Group Henkestrasse 91, 91052 Erlangen, Germany
| | - Vitali Schewkunow
- Friedrich-Alexander-University of Erlangen-Nuremberg Center for Medical Physics and Technology, Biophysics Group Henkestrasse 91, 91052 Erlangen, Germany
| | - Wolfgang H Goldmann
- Friedrich-Alexander-University of Erlangen-Nuremberg Center for Medical Physics and Technology, Biophysics Group Henkestrasse 91, 91052 Erlangen, Germany
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