8 results on '"M. Filip Sluzewski"'
Search Results
2. Integrated intracellular organization and its variations in human iPS cells
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Matheus P. Viana, Jianxu Chen, Theo A. Knijnenburg, Ritvik Vasan, Calysta Yan, Joy E. Arakaki, Matte Bailey, Ben Berry, Antoine Borensztejn, Eva M. Brown, Sara Carlson, Julie A. Cass, Basudev Chaudhuri, Kimberly R. Cordes Metzler, Mackenzie E. Coston, Zach J. Crabtree, Steve Davidson, Colette M. DeLizo, Shailja Dhaka, Stephanie Q. Dinh, Thao P. Do, Justin Domingus, Rory M. Donovan-Maiye, Alexandra J. Ferrante, Tyler J. Foster, Christopher L. Frick, Griffin Fujioka, Margaret A. Fuqua, Jamie L. Gehring, Kaytlyn A. Gerbin, Tanya Grancharova, Benjamin W. Gregor, Lisa J. Harrylock, Amanda Haupt, Melissa C. Hendershott, Caroline Hookway, Alan R. Horwitz, H. Christopher Hughes, Eric J. Isaac, Gregory R. Johnson, Brian Kim, Andrew N. Leonard, Winnie W. Leung, Jordan J. Lucas, Susan A. Ludmann, Blair M. Lyons, Haseeb Malik, Ryan McGregor, Gabe E. Medrash, Sean L. Meharry, Kevin Mitcham, Irina A. Mueller, Timothy L. Murphy-Stevens, Aditya Nath, Angelique M. Nelson, Sandra A. Oluoch, Luana Paleologu, T. Alexander Popiel, Megan M. Riel-Mehan, Brock Roberts, Lisa M. Schaefbauer, Magdalena Schwarzl, Jamie Sherman, Sylvain Slaton, M. Filip Sluzewski, Jacqueline E. Smith, Youngmee Sul, Madison J. Swain-Bowden, W. Joyce Tang, Derek J. Thirstrup, Daniel M. Toloudis, Andrew P. Tucker, Veronica Valencia, Winfried Wiegraebe, Thushara Wijeratna, Ruian Yang, Rebecca J. Zaunbrecher, Ramon Lorenzo D. Labitigan, Adrian L. Sanborn, Graham T. Johnson, Ruwanthi N. Gunawardane, Nathalie Gaudreault, Julie A. Theriot, and Susanne M. Rafelski
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Multidisciplinary - Abstract
Understanding how a subset of expressed genes dictates cellular phenotype is a considerable challenge owing to the large numbers of molecules involved, their combinatorics and the plethora of cellular behaviours that they determine1,2. Here we reduced this complexity by focusing on cellular organization—a key readout and driver of cell behaviour3,4—at the level of major cellular structures that represent distinct organelles and functional machines, and generated the WTC-11 hiPSC Single-Cell Image Dataset v1, which contains more than 200,000 live cells in 3D, spanning 25 key cellular structures. The scale and quality of this dataset permitted the creation of a generalizable analysis framework to convert raw image data of cells and their structures into dimensionally reduced, quantitative measurements that can be interpreted by humans, and to facilitate data exploration. This framework embraces the vast cell-to-cell variability that is observed within a normal population, facilitates the integration of cell-by-cell structural data and allows quantitative analyses of distinct, separable aspects of organization within and across different cell populations. We found that the integrated intracellular organization of interphase cells was robust to the wide range of variation in cell shape in the population; that the average locations of some structures became polarized in cells at the edges of colonies while maintaining the ‘wiring’ of their interactions with other structures; and that, by contrast, changes in the location of structures during early mitotic reorganization were accompanied by changes in their wiring.
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- 2023
3. Microglial Calcium Waves During the Hyperacute Phase of Ischemic Stroke
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M. Yashar S. Kalani, Elizabeth W.J. Carlson, Petr Tvrdik, M. Filip Sluzewski, Scott T. Acton, Min S. Park, Sauson Soldozy, Khadijeh A Sharifi, Ilyas M. Eli, Kenneth A. Stauderman, Kathryn N. Kearns, Lei Liu, and Kyle W. Scott
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Lipopolysaccharides ,Pathology ,medicine.medical_specialty ,Lipopolysaccharide ,MEDLINE ,chemistry.chemical_element ,Calcium ,Article ,Potassium Chloride ,Cellular and Molecular Neuroscience ,03 medical and health sciences ,chemistry.chemical_compound ,Mice ,0302 clinical medicine ,Internal medicine ,medicine ,Image Processing, Computer-Assisted ,Animals ,Calcium Waves ,Myeloid Cells ,Calcium Signaling ,Stroke ,Microinjection ,Pathological ,030304 developmental biology ,Ischemic Stroke ,Advanced and Specialized Nursing ,0303 health sciences ,Microglia ,business.industry ,Infarction, Middle Cerebral Artery ,Somatosensory Cortex ,medicine.disease ,Calcium Channel Blockers ,medicine.anatomical_structure ,Microscopy, Fluorescence, Multiphoton ,chemistry ,Cerebral cortex ,Ischemic stroke ,Acute Disease ,Cardiology ,Encephalitis ,Neurology (clinical) ,Cardiology and Cardiovascular Medicine ,business ,030217 neurology & neurosurgery - Abstract
Background and Purpose: Ischemic injury triggers multiple pathological responses in the brain tissue, including spreading depolarizations across the cerebral cortex (cortical spreading depolarizations [CSD]). Microglia have been recently shown to play a significant role in the propagation of CSD. However, the intracellular responses of myeloid cells during ischemic stroke have not been investigated. Methods: We have studied intracellular calcium activity in cortical microglia in the stroke model of the middle cerebral artery occlusion, using the murine Polr2a-based and Cre-dependent GCaMP5 and tdTomato reporter (PC::G5-tdT). High-speed 2-photon microscopy through cranial windows was employed to record signals from genetically encoded indicators of calcium. Inflammatory stimuli and pharmacological inhibition were used to modulate microglial calcium responses in the somatosensory cortex. Results: In vivo imaging revealed periodical calcium activity in microglia during the hyperacute phase of ischemic stroke. This activity was more frequent during the first 6 hours after occlusion, but the amplitudes of calcium transients became larger at later time points. Consistent with CSD nature of these events, we reproducibly triggered comparable calcium transients with microinjections of potassium chloride (KCl) into adjacent cortical areas. Furthermore, lipopolysaccharide-induced peripheral inflammation, mimicking sterile inflammation during ischemic stroke, produced significantly greater microglial calcium transients during CSD. Finally, in vivo pharmacological analysis with CRAC (calcium release-activated channel) inhibitor CM-EX-137 demonstrated that CSD-associated microglial calcium transients after KCl microinjections are mediated at least in part by the CRAC mechanism. Conclusions: Our findings demonstrate that microglia participate in ischemic brain injury via previously undetected mechanisms, which may provide new avenues for therapeutic interventions.
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- 2020
4. Cell states beyond transcriptomics: integrating structural organization and gene expression in hiPSC-derived cardiomyocytes
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Ruwanthi N. Gunawardane, Kimberly R. Cordes Metzler, Angelique M. Nelson, Georg Seelig, M. Filip Sluzewski, Jamie L. Gehring, Melissa C. Hendershott, Theo A. Knijnenburg, Sean P. Palecek, Charles M. Roco, Kaytlyn A. Gerbin, Stephanie Q. Dinh, Jackson M. Brown, Aditya Nath, Gregory R. Johnson, Julie A. Theriot, Matthew Hirano, Vilas Menon, Tanya Grancharova, Susanne M. Rafelski, Nathalie Gaudreault, Alexander B. Rosenberg, Rebecca J. Zaunbrecher, Calysta Yan, Rory Donovan-Maiye, and Matheus P. Viana
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Transcriptome ,medicine.anatomical_structure ,Structural organization ,Cell ,Gene expression ,medicine ,RNA ,Computational biology ,Sarcomere organization ,Biology ,Induced pluripotent stem cell ,Gene - Abstract
SummaryWe present a quantitative co-analysis of RNA abundance and sarcomere organization in single cells and an integrated framework to predict subcellular organization states from gene expression. We used human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes expressing mEGFP-tagged alpha-actinin-2 to develop quantitative image analysis tools for systematic and automated classification of subcellular organization. This captured a wide range of sarcomeric organization states within cell populations that were previously difficult to quantify. We performed RNA FISH targeting genes identified by single cell RNA sequencing to simultaneously assess the relationship between transcript abundance and structural states in single cells. Co-analysis of gene expression and sarcomeric patterns in the same cells revealed biologically meaningful correlations that could be used to predict organizational states. This study establishes a framework for multi-dimensional analysis of single cells to study the relationships between gene expression and subcellular organization and to develop a more nuanced description of cell states.Graphical AbstractTranscriptional profiling and structural classification was performed on human induced pluripotent stem cell-derived cardiomyocytes to characterize the relationship between transcript abundance and subcellular organization.
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- 2020
5. Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes
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Tanya Grancharova, Nathalie Gaudreault, Rebecca J. Zaunbrecher, M. Filip Sluzewski, Ruwanthi N. Gunawardane, Melissa C. Hendershott, Matheus P. Viana, HyeonWoo Lee, Jamie L. Gehring, Calysta Yan, Jianxu Chen, Rory Donovan-Maiye, Gregory R. Johnson, Jackson M. Brown, Kaytlyn A. Gerbin, Aditya Nath, Kimberly R. Cordes Metzler, Angelique M. Nelson, Susanne M. Rafelski, Julie A. Theriot, Stephanie Q. Dinh, Helen G. Anderson, and Theo A. Knijnenburg
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0303 health sciences ,Cell type ,Histology ,Induced Pluripotent Stem Cells ,Cell Differentiation ,Cell Biology ,Computational biology ,Biology ,Pathology and Forensic Medicine ,Transcriptome ,03 medical and health sciences ,0302 clinical medicine ,Gene expression ,Humans ,Myocytes, Cardiac ,Sarcomere organization ,Stem cell ,Induced pluripotent stem cell ,Gene ,030217 neurology & neurosurgery ,Function (biology) ,030304 developmental biology - Abstract
Although some cell types may be defined anatomically or by physiological function, a rigorous definition of cell state remains elusive. Here, we develop a quantitative, imaging-based platform for the systematic and automated classification of subcellular organization in single cells. We use this platform to quantify subcellular organization and gene expression in >30,000 individual human induced pluripotent stem cell-derived cardiomyocytes, producing a publicly available dataset that describes the population distributions of local and global sarcomere organization, mRNA abundance, and correlations between these traits. While the mRNA abundance of some phenotypically important genes correlates with subcellular organization (e.g., the beta-myosin heavy chain, MYH7), these two cellular metrics are heterogeneous and often uncorrelated, which suggests that gene expression alone is not sufficient to classify cell states. Instead, we posit that cell state should be defined by observing full distributions of quantitative, multidimensional traits in single cells that also account for space, time, and function.
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- 2020
6. Segmentation of Cortical Spreading Depression Wavefronts Through Local Similarity Metric
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Petr Tvrdik, Scott T. Acton, and M. Filip Sluzewski
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Normalization (statistics) ,Similarity (geometry) ,Geodesic ,Computer science ,02 engineering and technology ,Brain tissue ,Similarity measure ,03 medical and health sciences ,0302 clinical medicine ,FOS: Electrical engineering, electronic engineering, information engineering ,0202 electrical engineering, electronic engineering, information engineering ,Segmentation ,Quantitative Biology::Neurons and Cognition ,business.industry ,Image and Video Processing (eess.IV) ,020206 networking & telecommunications ,Pattern recognition ,Image segmentation ,Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science::Computer Vision and Pattern Recognition ,Cortical spreading depression ,Metric (mathematics) ,Artificial intelligence ,Noise (video) ,business ,030217 neurology & neurosurgery - Abstract
In this paper, we present a novel region-based segmentation method for cortical spreading depressions in 2-photon microscopy images. Fluorescent microscopy has become an important tool in neuroscience, but segmentation approaches are challenged by the opaque properties and structures of brain tissue. These challenges are made more extreme when segmenting events such as cortical spreading depressions, where low signal-to-noise ratios and intensity inhomogeneity dominate images. The method we propose uses a local intensity similarity measure that takes advantage of normalized Euclidean and geodesic distance maps of the image. This method provides a smooth segmentation boundary which is robust to the noise and inhomogeneity within cortical spreading depression images. Experimental results yielded a DICE index of 0.9859, an increase of 6% over the current state-of-the-art, and a reduction of root mean square error by 79.9%.
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- 2019
7. Calcium Imaging of Microglial Network Activity in Stroke
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Petr, Tvrdik, Kathryn N, Kearns, Khadijeh A, Sharifi, M Filip, Sluzewski, Scott T, Acton, and M Yashar S, Kalani
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Cerebral Cortex ,Stroke ,Luminescent Proteins ,Mice ,Gene Expression Regulation ,Genes, Reporter ,Calcium-Binding Proteins ,Optical Imaging ,Animals ,Mice, Transgenic ,Microglia ,Crosses, Genetic ,Brain Ischemia - Abstract
Calcium signaling plays a significant role in microglial activation. Genetically encoded calcium indicators (GECI) have been widely used for calcium imaging studies in many brain cell types, including neurons, astrocytes, and oligodendrocytes. However, microglial calcium imaging approaches have been hampered by idiosyncrasies of their gene expression and malleable cell properties. The generation of PC::G5-tdT, a Polr2a locus-based conditional mouse reporter of calcium, facilitated the deployment of GECI in microglia. When crossed with the Iba1(Aif1)-IRES-Cre line, all brain microglia of the progeny are labeled with the calcium indicator variant GCaMP5G and the red fluorescent protein tdTomato. This reporter system has enabled in vivo studies of intracellular calcium in large microglial cell populations in cerebral pathologies such as ischemic stroke. In this chapter, we outline specific guidelines for genetic, surgical, imaging, and data analysis aspects of microglial calcium monitoring of the ischemic cortex following middle cerebral artery occlusion.
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- 2019
8. Calcium Imaging of Microglial Network Activity in Stroke
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Kathryn N. Kearns, M. Yashar S. Kalani, M. Filip Sluzewski, Scott T. Acton, Khadijeh A Sharifi, and Petr Tvrdik
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0301 basic medicine ,Microglia ,Cell ,chemistry.chemical_element ,Calcium ,Biology ,Calcium in biology ,Green fluorescent protein ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,medicine.anatomical_structure ,Calcium imaging ,chemistry ,medicine ,Neuroscience ,030217 neurology & neurosurgery ,Preclinical imaging ,Calcium signaling - Abstract
Calcium signaling plays a significant role in microglial activation. Genetically encoded calcium indicators (GECI) have been widely used for calcium imaging studies in many brain cell types, including neurons, astrocytes, and oligodendrocytes. However, microglial calcium imaging approaches have been hampered by idiosyncrasies of their gene expression and malleable cell properties. The generation of PC::G5-tdT, a Polr2a locus-based conditional mouse reporter of calcium, facilitated the deployment of GECI in microglia. When crossed with the Iba1(Aif1)-IRES-Cre line, all brain microglia of the progeny are labeled with the calcium indicator variant GCaMP5G and the red fluorescent protein tdTomato. This reporter system has enabled in vivo studies of intracellular calcium in large microglial cell populations in cerebral pathologies such as ischemic stroke. In this chapter, we outline specific guidelines for genetic, surgical, imaging, and data analysis aspects of microglial calcium monitoring of the ischemic cortex following middle cerebral artery occlusion.
- Published
- 2019
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