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Mu X, Ma C, Mei X, Liao J, Bojar R, Kuang S, Rong Q, Yao J, Zhang YS. On-demand expansion fluorescence and photoacoustic microscopy (ExFLPAM). PHOTOACOUSTICS 2024; 38:100610. [PMID: 38726025 PMCID: PMC11079527 DOI: 10.1016/j.pacs.2024.100610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 03/04/2024] [Accepted: 04/21/2024] [Indexed: 05/12/2024]
Abstract
Expansion microscopy (ExM) is a promising technology that enables nanoscale imaging on conventional optical microscopes by physically magnifying the specimens. Here, we report the development of a strategy that enables i) on-demand labeling of subcellular organelles in live cells for ExM through transfection of fluorescent proteins that are well-retained during the expansion procedure; and ii) non-fluorescent chromogenic color-development towards efficient bright-field and photoacoustic imaging in both planar and volumetric formats, which is applicable to both cultured cells and biological tissues. Compared to the conventional ExM methods, our strategy provides an expanded toolkit, which we term as expansion fluorescence and photoacoustic microscopy (ExFLPAM), by allowing on-demand fluorescent protein labeling of cultured cells, as well as non-fluorescent absorption contrast-imaging of biological samples.
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Affiliation(s)
- Xuan Mu
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
| | - Chenshuo Ma
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Xuan Mei
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
| | - Junlong Liao
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
| | - Rebecca Bojar
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
- Barnard College, Columbia University, New York, NY 10027, USA
| | - Sizhe Kuang
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Qiangzhou Rong
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Junjie Yao
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
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2
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Langner E, Puapatanakul P, Pudlowski R, Alsabbagh DY, Miner JH, Horani A, Dutcher SK, Brody SL, Wang JT, Suleiman HY, Mahjoub MR. Ultrastructure expansion microscopy (U-ExM) of mouse and human kidneys for analysis of subcellular structures. Cytoskeleton (Hoboken) 2024. [PMID: 38715433 DOI: 10.1002/cm.21870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/21/2024]
Abstract
Ultrastructure expansion microscopy (U-ExM) involves the physical magnification of specimens embedded in hydrogels, which allows for super-resolution imaging of subcellular structures using a conventional diffraction-limited microscope. Methods for expansion microscopy exist for several organisms, organs, and cell types, and used to analyze cellular organelles and substructures in nanoscale resolution. Here, we describe a simple step-by-step U-ExM protocol for the expansion, immunostaining, imaging, and analysis of cytoskeletal and organellar structures in kidney tissue. We detail the critical modified steps to optimize isotropic kidney tissue expansion, and preservation of the renal cell structures of interest. We demonstrate the utility of the approach using several markers of renal cell types, centrioles, cilia, the extracellular matrix, and other cytoskeletal elements. Finally, we show that the approach works well on mouse and human kidney samples that were preserved using different fixation and embedding conditions. Overall, this protocol provides a simple and cost-effective approach to analyze both preclinical and clinical renal samples in high detail, using conventional lab supplies and standard widefield or confocal microscopy.
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Affiliation(s)
- Ewa Langner
- Department of Medicine, Washington University, St. Louis, Missouri, USA
| | - Pongpratch Puapatanakul
- Department of Medicine, Washington University, St. Louis, Missouri, USA
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Rachel Pudlowski
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | | | - Jeffrey H Miner
- Department of Medicine, Washington University, St. Louis, Missouri, USA
| | - Amjad Horani
- Department of Pediatrics, Washington University, St. Louis, Missouri, USA
| | - Susan K Dutcher
- Department of Genetics, Washington University, St. Louis, Missouri, USA
| | - Steven L Brody
- Department of Medicine, Washington University, St. Louis, Missouri, USA
| | - Jennifer T Wang
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Hani Y Suleiman
- Department of Medicine, Washington University, St. Louis, Missouri, USA
| | - Moe R Mahjoub
- Department of Medicine, Washington University, St. Louis, Missouri, USA
- Department of Cell Biology and Physiology, Washington University, St. Louis, Missouri, USA
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3
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Langner E, Puapatanakul P, Pudlowski R, Alsabbagh DY, Miner JH, Horani A, Dutcher SK, Brody SL, Wang JT, Suleiman HY, Mahjoub MR. Ultrastructure expansion microscopy (U-ExM) of mouse and human kidneys for analysis of subcellular structures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580708. [PMID: 38405695 PMCID: PMC10889020 DOI: 10.1101/2024.02.16.580708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Ultrastructure expansion microscopy (U-ExM) involves the physical magnification of specimens embedded in hydrogels, which allows for super-resolution imaging of subcellular structures using a conventional diffraction-limited microscope. Methods for expansion microscopy exist for several organisms, organs, and cell types, and used to analyze cellular organelles and substructures in nanoscale resolution. Here, we describe a simple step-by-step U-ExM protocol for the expansion, immunostaining, imaging, and analysis of cytoskeletal and organellar structures in kidney tissue. We detail the critical modified steps to optimize isotropic kidney tissue expansion, and preservation of the renal cell structures of interest. We demonstrate the utility of the approach using several markers of renal cell types, centrioles, cilia, the extracellular matrix, and other cytoskeletal elements. Finally, we show that the approach works well on mouse and human kidney samples that were preserved using different fixation and storage conditions. Overall, this protocol provides a simple and cost-effective approach to analyze both pre-clinical and clinical renal samples in high detail, using conventional lab supplies and standard widefield or confocal microscopy.
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4
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Smerkous D, Mauer M, Tøndel C, Svarstad E, Gubler MC, Nelson RG, Oliveira JP, Sargolzaeiaval F, Najafian B. Development of an automated estimation of foot process width using deep learning in kidney biopsies from patients with Fabry, minimal change, and diabetic kidney diseases. Kidney Int 2024; 105:165-176. [PMID: 37774924 PMCID: PMC10842003 DOI: 10.1016/j.kint.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/06/2023] [Accepted: 09/15/2023] [Indexed: 10/01/2023]
Abstract
Podocyte injury plays a key role in pathogenesis of many kidney diseases with increased podocyte foot process width (FPW), an important measure of podocyte injury. Unfortunately, there is no consensus on the best way to estimate FPW and unbiased stereology, the current gold standard, is time consuming and not widely available. To address this, we developed an automated FPW estimation technique using deep learning. A U-Net architecture variant model was trained to semantically segment the podocyte-glomerular basement membrane interface and filtration slits. Additionally, we employed a post-processing computer vision approach to accurately estimate FPW. A custom segmentation utility was also created to manually classify these structures on digital electron microscopy (EM) images and to prepare a training dataset. The model was applied to EM images of kidney biopsies from 56 patients with Fabry disease, 15 with type 2 diabetes, 10 with minimal change disease, and 17 normal individuals. The results were compared with unbiased stereology measurements performed by expert technicians unaware of the clinical information. FPW measured by deep learning and by the expert technicians were highly correlated and not statistically different in any of the studied groups. A Bland-Altman plot confirmed interchangeability of the methods. FPW measurement time per biopsy was substantially reduced by deep learning. Thus, we have developed a novel validated deep learning model for FPW measurement on EM images. The model is accessible through a cloud-based application making calculation of this important biomarker more widely accessible for research and clinical applications.
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Affiliation(s)
- David Smerkous
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington, USA
| | - Michael Mauer
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Camilla Tøndel
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway; Institute of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Einar Svarstad
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Marie-Claire Gubler
- INSERM U1163, Imagine Institute, Necker-Enfants Malades Hospital, Paris, France
| | - Robert G Nelson
- Chronic Kidney Disease Section, Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona, USA
| | - João-Paulo Oliveira
- Service of Medical Genetics, São João University Hospital; Department of Medical Genetics, Faculty of Medicine and i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Forough Sargolzaeiaval
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Behzad Najafian
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA.
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Klimas A, Gallagher BR, Wijesekara P, Fekir S, DiBernardo EF, Cheng Z, Stolz DB, Cambi F, Watkins SC, Brody SL, Horani A, Barth AL, Moore CI, Ren X, Zhao Y. Magnify is a universal molecular anchoring strategy for expansion microscopy. Nat Biotechnol 2023; 41:858-869. [PMID: 36593399 PMCID: PMC10264239 DOI: 10.1038/s41587-022-01546-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/05/2022] [Indexed: 01/03/2023]
Abstract
Expansion microscopy enables nanoimaging with conventional microscopes by physically and isotropically magnifying preserved biological specimens embedded in a crosslinked water-swellable hydrogel. Current expansion microscopy protocols require prior treatment with reactive anchoring chemicals to link specific labels and biomolecule classes to the gel. We describe a strategy called Magnify, which uses a mechanically sturdy gel that retains nucleic acids, proteins and lipids without the need for a separate anchoring step. Magnify expands biological specimens up to 11 times and facilitates imaging of cells and tissues with effectively around 25-nm resolution using a diffraction-limited objective lens of about 280 nm on conventional optical microscopes or with around 15 nm effective resolution if combined with super-resolution optical fluctuation imaging. We demonstrate Magnify on a broad range of biological specimens, providing insight into nanoscopic subcellular structures, including synaptic proteins from mouse brain, podocyte foot processes in formalin-fixed paraffin-embedded human kidney and defects in cilia and basal bodies in drug-treated human lung organoids.
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Affiliation(s)
- Aleksandra Klimas
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Brendan R Gallagher
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Piyumi Wijesekara
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Sinda Fekir
- Department of Neuroscience, Brown University, Providence, RI, USA
- Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - Emma F DiBernardo
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Zhangyu Cheng
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Donna B Stolz
- Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, USA
| | - Franca Cambi
- Veterans Administration Pittsburgh, Pittsburgh, PA, USA
- Department of Neurology/PIND, University of Pittsburgh, Pittsburgh, PA, USA
| | - Simon C Watkins
- Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, USA
| | - Steven L Brody
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Amjad Horani
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Alison L Barth
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Christopher I Moore
- Department of Neuroscience, Brown University, Providence, RI, USA
- Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - Xi Ren
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yongxin Zhao
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
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6
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Hawkins TJ, Robson JL, Cole B, Bush SJ. Expansion Microscopy of Plant Cells (PlantExM). Methods Mol Biol 2023; 2604:127-142. [PMID: 36773230 DOI: 10.1007/978-1-0716-2867-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Expansion microscopy (ExM) achieves super-resolution imaging without the need for sophisticated super-resolution microscopy hardware through a combination of physical and optical magnification. Samples are fixed, stained, and embedded in a swellable gel. Following cross-linking of fluorophores to the gel matrix, the components of the sample are digested away and the gel expanded in water. Labeled objects which are too close to be resolved by diffraction-limited microscopy are moved far enough apart that these can now be resolved as individual objects on a standard confocal. Originally developed for animal cells and tissues, ExM for plants requires the additional consideration of cell wall digestion. Super-resolution can be limited in plants due to the size of cells, light scattering of tissues, and variations in refractive index. By removing the components which cause these limitations, ExM opens up the possibility of super-resolution at depth within plant tissues for the first time. Here we describe our method for PlantExM which is optimized for cytoskeleton resolution, which, when also coupled with compatible optical super-resolution technologies, can produce images of the plant cytoskeleton in unprecedented detail.
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Affiliation(s)
| | | | - Bethany Cole
- Department of Biosciences, Durham University, Durham, UK
| | - Simon J Bush
- Department of Biosciences, Durham University, Durham, UK
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7
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Valentino M, Bianco V, Miccio L, Memmolo P, Brancato V, Libretti P, Gambacorta M, Salvatore M, Ferraro P. Beyond conventional microscopy: Observing kidney tissues by means of fourier ptychography. Front Physiol 2023; 14:1120099. [PMID: 36860516 PMCID: PMC9968938 DOI: 10.3389/fphys.2023.1120099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/01/2023] [Indexed: 02/17/2023] Open
Abstract
Kidney microscopy is a mainstay in studying the morphological structure, physiology and pathology of kidney tissues, as histology provides important results for a reliable diagnosis. A microscopy modality providing at same time high-resolution images and a wide field of view could be very useful for analyzing the whole architecture and the functioning of the renal tissue. Recently, Fourier Ptychography (FP) has been proofed to yield images of biology samples such as tissues and in vitro cells while providing high resolution and large field of view, thus making it a unique and attractive opportunity for histopathology. Moreover, FP offers tissue imaging with high contrast assuring visualization of small desirable features, although with a stain-free mode that avoids any chemical process in histopathology. Here we report an experimental measuring campaign for creating the first comprehensive and extensive collection of images of kidney tissues captured by this FP microscope. We show that FP microscopy unlocks a new opportunity for the physicians to observe and judge renal tissue slides through the novel FP quantitative phase-contrast microscopy. Phase-contrast images of kidney tissue are analyzed by comparing them with the corresponding renal images taken under a conventional bright-field microscope both for stained and unstained tissue samples of different thicknesses. In depth discussion on the advantages and limitations of this new stain-free microscopy modality is reported, showing its usefulness over the classical light microscopy and opening a potential route for using FP in clinical practice for histopathology of kidney.
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Affiliation(s)
- Marika Valentino
- National Research Council (CNR) of Italy, Institute of Applied Sciences and Intelligent Systems (ISASI), Pozzuoli, Italy,Department of Electric and Information Technologies Engineering, University of Naples “Federico II”, Naples, Italy
| | - Vittorio Bianco
- National Research Council (CNR) of Italy, Institute of Applied Sciences and Intelligent Systems (ISASI), Pozzuoli, Italy,*Correspondence: Vittorio Bianco, ; Marcello Gambacorta,
| | - Lisa Miccio
- National Research Council (CNR) of Italy, Institute of Applied Sciences and Intelligent Systems (ISASI), Pozzuoli, Italy
| | - Pasquale Memmolo
- National Research Council (CNR) of Italy, Institute of Applied Sciences and Intelligent Systems (ISASI), Pozzuoli, Italy
| | | | | | - Marcello Gambacorta
- IRCCS SYNLAB SDN, Naples, Italy,*Correspondence: Vittorio Bianco, ; Marcello Gambacorta,
| | | | - Pietro Ferraro
- National Research Council (CNR) of Italy, Institute of Applied Sciences and Intelligent Systems (ISASI), Pozzuoli, Italy
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8
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Siegerist F, Drenic V, Koppe TM, Telli N, Endlich N. Super-Resolution Microscopy: A Technique to Revolutionize Research and Diagnosis of Glomerulopathies. GLOMERULAR DISEASES 2022; 3:19-28. [PMID: 36816428 PMCID: PMC9936760 DOI: 10.1159/000528713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Background For decades, knowledge about glomerular (patho)physiology has been tightly linked with advances in microscopic imaging technology. For example, the invention of electron microscopy was required to hypothesize about the mode of glomerular filtration barrier function. Summary Super-resolution techniques, defined as fluorescence microscopy approaches that surpass the optical resolution limit of around 200 nm, have been made available to the scientific community. Several of these different techniques are currently in use in glomerular research. Using three-dimensional structured illumination microscopy, the exact morphology of the podocyte filtration slit can be morphometrically analyzed and quantitatively compared across samples originating from animal models or human biopsies. Key Messages Several quantitative image analysis approaches and their potential influence on glomerular research and diagnostics are discussed. By improving not only optical resolution but also information content and turnaround time, super-resolution microscopy has the potential to expand the diagnosis of glomerular disease. Soon, these approaches could be introduced into glomerular disease diagnosis.
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Affiliation(s)
- Florian Siegerist
- Institute for Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | | | - Thor-Magnus Koppe
- Institute for Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | | | - Nicole Endlich
- Institute for Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany,NIPOKA GmbH, Greifswald, Germany,*Nicole Endlich,
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9
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Sheard TMD, Hurley ME, Smith AJ, Colyer J, White E, Jayasinghe I. Three-dimensional visualization of the cardiac ryanodine receptor clusters and the molecular-scale fraying of dyads. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210316. [PMID: 36189802 PMCID: PMC9527906 DOI: 10.1098/rstb.2021.0316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Clusters of ryanodine receptor calcium channels (RyRs) form the primary molecular machinery of intracellular calcium signalling in cardiomyocytes. While a range of optical super-resolution microscopy techniques have revealed the nanoscale structure of these clusters, the three-dimensional (3D) nanoscale topologies of the clusters have remained mostly unresolved. In this paper, we demonstrate the exploitation of molecular-scale resolution in enhanced expansion microscopy (EExM) along with various 2D and 3D visualization strategies to observe the topological complexities, geometries and molecular sub-domains within the RyR clusters. Notably, we observed sub-domains containing RyR-binding protein junctophilin-2 (JPH2) occupying the central regions of RyR clusters in the deeper interior of the myocytes (including dyads), while the poles were typically devoid of JPH2, lending to a looser RyR arrangement. By contrast, peripheral RyR clusters exhibited variable co-clustering patterns and ratios between RyR and JPH2. EExM images of dyadic RyR clusters in right ventricular (RV) myocytes isolated from rats with monocrotaline-induced RV failure revealed hallmarks of RyR cluster fragmentation accompanied by breaches in the JPH2 sub-domains. Frayed RyR patterns observed adjacent to these constitute new evidence that the destabilization of the RyR arrays inside the JPH2 sub-domains may seed the primordial foci of dyad remodelling observed in heart failure. This article is part of the theme issue 'The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease'.
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Affiliation(s)
- Thomas M D Sheard
- School of Biosciences, Faculty of Science, University of Sheffield, Sheffield S10 2TN, UK.,School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Miriam E Hurley
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Andrew J Smith
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - John Colyer
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Ed White
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Izzy Jayasinghe
- School of Biosciences, Faculty of Science, University of Sheffield, Sheffield S10 2TN, UK.,School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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10
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Lee MY, Mao C, Glaser AK, Woodworth MA, Halpern AR, Ali A, Liu JTC, Vaughan JC. Fluorescent labeling of abundant reactive entities (FLARE) for cleared-tissue and super-resolution microscopy. Nat Protoc 2022; 17:819-846. [PMID: 35110740 DOI: 10.1038/s41596-021-00667-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 09/21/2021] [Indexed: 11/08/2022]
Abstract
Fluorescence microscopy is a vital tool in biomedical research but faces considerable challenges in achieving uniform or bright labeling. For instance, fluorescent proteins are limited to model organisms, and antibody conjugates can be inconsistent and difficult to use with thick specimens. To partly address these challenges, we developed a labeling protocol that can rapidly visualize many well-contrasted key features and landmarks on biological specimens in both thin and thick tissues or cultured cells. This approach uses established reactive fluorophores to label a variety of biological specimens for cleared-tissue microscopy or expansion super-resolution microscopy and is termed FLARE (fluorescent labeling of abundant reactive entities). These fluorophores target chemical groups and reveal their distribution on the specimens; amine-reactive fluorophores such as hydroxysuccinimidyl esters target accessible amines on proteins, while hydrazide fluorophores target oxidized carbohydrates. The resulting stains provide signals analogous to traditional general histology stains such as H&E or periodic acid-Schiff but use fluorescent probes that are compatible with volumetric imaging. In general, the stains for FLARE are performed in the order of carbohydrates, amine and DNA, and the incubation time for the stains varies from 1 h to 1 d depending on the combination of stains and the type and thickness of the biological specimens. FLARE is powerful, robust and easy to implement in laboratories that already routinely do fluorescence microscopy.
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Affiliation(s)
- Min Yen Lee
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Chenyi Mao
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Adam K Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | | | - Aaron R Halpern
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Adilijiang Ali
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, WA, USA.
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA.
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11
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Möller-Kerutt A, Rodriguez-Gatica JE, Wacker K, Bhatia R, Siebrasse JP, Boon N, Van Marck V, Boor P, Kubitscheck U, Wijnholds J, Pavenstädt H, Weide T. Crumbs2 Is an Essential Slit Diaphragm Protein of the Renal Filtration Barrier. J Am Soc Nephrol 2021; 32:1053-1070. [PMID: 33687977 PMCID: PMC8259666 DOI: 10.1681/asn.2020040501] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 12/28/2020] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Crumbs2 is expressed at embryonic stages as well as in the retina, brain, and glomerular podocytes. Recent studies identified CRB2 mutations as a novel cause of steroid-resistant nephrotic syndrome (SRNS). METHODS To study the function of Crb2 at the renal filtration barrier, mice lacking Crb2 exclusively in podocytes were generated. Gene expression and histologic studies as well as transmission and scanning electron microscopy were used to analyze these Crb2podKO knockout mice and their littermate controls. Furthermore, high-resolution expansion microscopy was used to investigate Crb2 distribution in murine glomeruli. For pull-down experiments, live cell imaging, and transcriptome analyses, cell lines were applied that inducibly express fluorescent protein-tagged CRB2 wild type and mutants. RESULTS Crb2podKO mice developed proteinuria directly after birth that preceded a prominent development of disordered and effaced foot processes, upregulation of renal injury and inflammatory markers, and glomerulosclerosis. Pull-down assays revealed an interaction of CRB2 with Nephrin, mediated by their extracellular domains. Expansion microscopy showed that in mice glomeruli, Crb2 and Nephrin are organized in adjacent clusters. SRNS-associated CRB2 protein variants and a mutant that lacks a putative conserved O-glycosylation site were not transported to the cell surface. Instead, mutants accumulated in the ER, showed altered glycosylation pattern, and triggered an ER stress response. CONCLUSIONS Crb2 is an essential component of the podocyte's slit diaphragm, interacting with Nephrin. Loss of slit diaphragm targeting and increasing ER stress are pivotal factors for onset and progression of CRB2-related SRNS.
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Affiliation(s)
- Annika Möller-Kerutt
- Internal Medicine D, Department of Molecular Nephrology, University Hospital of Muenster, Muenster, Germany
| | - Juan E. Rodriguez-Gatica
- Institute of Physical and Theoretical Chemistry, Department of Biophysical Chemistry, Rheinische Friedrich Wilhelms University Bonn, Bonn, Germany
| | - Karin Wacker
- Internal Medicine D, Department of Molecular Nephrology, University Hospital of Muenster, Muenster, Germany
| | - Rohan Bhatia
- Institute of Physical and Theoretical Chemistry, Department of Biophysical Chemistry, Rheinische Friedrich Wilhelms University Bonn, Bonn, Germany
| | - Jan-Peter Siebrasse
- Institute of Physical and Theoretical Chemistry, Department of Biophysical Chemistry, Rheinische Friedrich Wilhelms University Bonn, Bonn, Germany
| | - Nanda Boon
- Leiden University Medical Center, Department of Ophthalmology, Leiden, The Netherlands
| | - Veerle Van Marck
- Gerhard-Domagk Institute of Pathology, University Hospital of Muenster, Muenster, Germany
| | - Peter Boor
- Institute of Pathology, Department of Nephrology and Immunology, RWTH Aachen University Hospital, Aachen, Germany,The Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, Department of Biophysical Chemistry, Rheinische Friedrich Wilhelms University Bonn, Bonn, Germany
| | - Jan Wijnholds
- Leiden University Medical Center, Department of Ophthalmology, Leiden, The Netherlands
| | - Hermann Pavenstädt
- Internal Medicine D, Department of Molecular Nephrology, University Hospital of Muenster, Muenster, Germany
| | - Thomas Weide
- Internal Medicine D, Department of Molecular Nephrology, University Hospital of Muenster, Muenster, Germany
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12
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Matsumoto A, Matsui I, Katsuma Y, Yasuda S, Shimada K, Namba-Hamano T, Sakaguchi Y, Kaimori JY, Takabatake Y, Inoue K, Isaka Y. Quantitative Analyses of Foot Processes, Mitochondria, and Basement Membranes by Structured Illumination Microscopy Using Elastica-Masson- and Periodic-Acid-Schiff-Stained Kidney Sections. Kidney Int Rep 2021; 6:1923-1938. [PMID: 34307987 PMCID: PMC8258503 DOI: 10.1016/j.ekir.2021.04.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 04/16/2021] [Indexed: 11/28/2022] Open
Abstract
Introduction Foot process effacement and mitochondrial fission associate with kidney disease pathogenesis. Electron microscopy is the gold-standard method for their visualization, but the observable area of electron microscopy is smaller than light microscopy. It is important to develop alternative ways to quantitatively evaluate these microstructural changes because the lesion site of renal diseases can be focal. Methods We analyzed elastica-Masson trichrome (EMT) and periodic acid-Schiff (PAS) stained kidney sections using structured illumination microscopy (SIM). Results EMT staining revealed three-dimensional (3D) structures of foot process, whereas ponceau xylidine acid fuchsin azophloxine solution induced fluorescence. Conversion of foot process images into their constituent frequencies by Fourier transform showed that the concentric square of (1/4)2-(1/16)2 in the power spectra (PS) included information for normal periodic structures of foot processes. Foot process integrity, assessed by PS, negatively correlated with proteinuria. EMT-stained sections revealed fragmented mitochondria in mice with mitochondrial injuries and patients with tubulointerstitial nephritis; Fourier transform quantified associated mitochondrial injury. Quantified mitochondrial damage in patients with immunoglobulin A (IgA) nephropathy predicted a decline in estimated glomerular filtration rate (eGFR) after kidney biopsy but did not correlate with eGFR at biopsy. PAS-stained sections, excited by a 640 nm laser, combined with the coefficient of variation values, quantified subtle changes in the basement membranes of patients with membranous nephropathy stage I. Conclusions Kidney microstructures are quantified from sections prepared in clinical practice using SIM.
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Affiliation(s)
- Ayumi Matsumoto
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Isao Matsui
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yusuke Katsuma
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Seiichi Yasuda
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Karin Shimada
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Tomoko Namba-Hamano
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yusuke Sakaguchi
- Department of Inter-Organ Communication Research in Kidney Disease, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Jun-Ya Kaimori
- Department of Inter-Organ Communication Research in Kidney Disease, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoshitsugu Takabatake
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kazunori Inoue
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoshitaka Isaka
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
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13
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Angelotti ML, Antonelli G, Conte C, Romagnani P. Imaging the kidney: from light to super-resolution microscopy. Nephrol Dial Transplant 2021; 36:19-28. [PMID: 31325314 PMCID: PMC7771978 DOI: 10.1093/ndt/gfz136] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Indexed: 12/13/2022] Open
Abstract
The important achievements in kidney physiological and pathophysiological mechanisms can largely be ascribed to progress in the technology of microscopy. Much of what we know about the architecture of the kidney is based on the fundamental descriptions of anatomic microscopists using light microscopy and later by ultrastructural analysis provided by electron microscopy. These two techniques were used for the first classification systems of kidney diseases and for their constant updates. More recently, a series of novel imaging techniques added the analysis in further dimensions of time and space. Confocal microscopy allowed us to sequentially visualize optical sections along the z-axis and the availability of specific analysis software provided a three-dimensional rendering of thicker tissue specimens. Multiphoton microscopy permitted us to simultaneously investigate kidney function and structure in real time. Fluorescence-lifetime imaging microscopy allowed to study the spatial distribution of metabolites. Super-resolution microscopy increased sensitivity and resolution up to nanoscale levels. With cryo-electron microscopy, researchers could visualize the individual biomolecules at atomic levels directly in the tissues and understand their interaction at subcellular levels. Finally, matrix-assisted laser desorption/ionization imaging mass spectrometry permitted the measuring of hundreds of different molecules at the same time on tissue sections at high resolution. This review provides an overview of available kidney imaging strategies, with a focus on the possible impact of the most recent technical improvements.
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Affiliation(s)
- Maria Lucia Angelotti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy.,Excellence Centre for Research, Transfer and High Education for the development of DE NOVO Therapies (DENOTHE), Florence, Italy
| | - Giulia Antonelli
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy.,Excellence Centre for Research, Transfer and High Education for the development of DE NOVO Therapies (DENOTHE), Florence, Italy
| | - Carolina Conte
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy.,Excellence Centre for Research, Transfer and High Education for the development of DE NOVO Therapies (DENOTHE), Florence, Italy
| | - Paola Romagnani
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy.,Excellence Centre for Research, Transfer and High Education for the development of DE NOVO Therapies (DENOTHE), Florence, Italy
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14
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Heiden S, Siwek R, Lotz ML, Borkowsky S, Schröter R, Nedvetsky P, Rohlmann A, Missler M, Krahn MP. Apical-basal polarity regulators are essential for slit diaphragm assembly and endocytosis in Drosophila nephrocytes. Cell Mol Life Sci 2021; 78:3657-3672. [PMID: 33651172 PMCID: PMC8038974 DOI: 10.1007/s00018-021-03769-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 01/11/2021] [Accepted: 01/16/2021] [Indexed: 12/02/2022]
Abstract
Apical-basal polarity is a key feature of most epithelial cells and it is regulated by highly conserved protein complexes. In mammalian podocytes, which emerge from columnar epithelial cells, this polarity is preserved and the tight junctions are converted to the slit diaphragms, establishing the filtration barrier. In Drosophila, nephrocytes show several structural and functional similarities with mammalian podocytes and proximal tubular cells. However, in contrast to podocytes, little is known about the role of apical-basal polarity regulators in these cells. In this study, we used expansion microscopy and found the apical polarity determinants of the PAR/aPKC and Crb-complexes to be predominantly targeted to the cell cortex in proximity to the nephrocyte diaphragm, whereas basolateral regulators also accumulate intracellularly. Knockdown of PAR-complex proteins results in severe endocytosis and nephrocyte diaphragm defects, which is due to impaired aPKC recruitment to the plasma membrane. Similar, downregulation of most basolateral polarity regulators disrupts Nephrin localization but had surprisingly divergent effects on endocytosis. Our findings suggest that morphology and slit diaphragm assembly/maintenance of nephrocytes is regulated by classical apical-basal polarity regulators, which have distinct functions in endocytosis.
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Affiliation(s)
- Stefanie Heiden
- Medical Cell Biology, Medical Clinic D, University Hospital of Münster, Albert-Schweitzer Campus 1-A14, 48149, Münster, Germany
| | - Rebecca Siwek
- Medical Cell Biology, Medical Clinic D, University Hospital of Münster, Albert-Schweitzer Campus 1-A14, 48149, Münster, Germany
| | - Marie-Luise Lotz
- Medical Cell Biology, Medical Clinic D, University Hospital of Münster, Albert-Schweitzer Campus 1-A14, 48149, Münster, Germany
| | - Sarah Borkowsky
- Medical Cell Biology, Medical Clinic D, University Hospital of Münster, Albert-Schweitzer Campus 1-A14, 48149, Münster, Germany
| | - Rita Schröter
- Medical Cell Biology, Medical Clinic D, University Hospital of Münster, Albert-Schweitzer Campus 1-A14, 48149, Münster, Germany
| | - Pavel Nedvetsky
- Medical Cell Biology, Medical Clinic D, University Hospital of Münster, Albert-Schweitzer Campus 1-A14, 48149, Münster, Germany
| | - Astrid Rohlmann
- Institute of Anatomy and Molecular Neurobiology, University of Münster, Vesaliusweg 2-4, 48149, Münster, Germany
| | - Markus Missler
- Institute of Anatomy and Molecular Neurobiology, University of Münster, Vesaliusweg 2-4, 48149, Münster, Germany
| | - Michael P Krahn
- Medical Cell Biology, Medical Clinic D, University Hospital of Münster, Albert-Schweitzer Campus 1-A14, 48149, Münster, Germany.
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15
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Wunderlich LCS, Ströhl F, Ströhl S, Vanderpoorten O, Mascheroni L, Kaminski CF. Superresolving the kidney-a practical comparison of fluorescence nanoscopy of the glomerular filtration barrier. Anal Bioanal Chem 2021; 413:1203-1214. [PMID: 33277998 PMCID: PMC7813708 DOI: 10.1007/s00216-020-03084-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/31/2020] [Accepted: 11/19/2020] [Indexed: 01/19/2023]
Abstract
Immunofluorescence microscopy is routinely used in the diagnosis of and research on renal impairments. However, this highly specific technique is restricted in its maximum resolution to about 250 nm in the lateral and 700 nm in the axial directions and thus not sufficient to investigate the fine subcellular structure of the kidney's glomerular filtration barrier. In contrast, electron microscopy offers high resolution, but this comes at the cost of poor preservation of immunogenic epitopes and antibody penetration alongside a low throughput. Many of these drawbacks were overcome with the advent of super-resolution microscopy methods. So far, four different super-resolution approaches have been used to study the kidney: single-molecule localization microscopy (SMLM), stimulated emission depletion (STED) microscopy, structured illumination microscopy (SIM), and expansion microscopy (ExM), however, using different preservation methods and widely varying labelling strategies. In this work, all four methods were applied and critically compared on kidney slices obtained from samples treated with the most commonly used preservation technique: fixation by formalin and embedding in paraffin (FFPE). Strengths and weaknesses, as well as the practicalities of each method, are discussed to enable users of super-resolution microscopy in renal research make an informed decision on the best choice of technique. The methods discussed enable the efficient investigation of biopsies stored in kidney banks around the world. Graphical abstract.
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Affiliation(s)
- Lucia C S Wunderlich
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Florian Ströhl
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
- Department of Physics and Technology, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Stefan Ströhl
- Department of Nephrology, University Hospital Regensburg, 93053, Regensburg, Germany
| | - Oliver Vanderpoorten
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
- Department of Physics and Technology, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Luca Mascheroni
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK.
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16
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Unnersjö-Jess D, Butt L, Höhne M, Witasp A, Kühne L, Hoyer PF, Patrakka J, Brinkkötter PT, Wernerson A, Schermer B, Benzing T, Scott L, Brismar H, Blom H. A fast and simple clearing and swelling protocol for 3D in-situ imaging of the kidney across scales. Kidney Int 2020; 99:1010-1020. [PMID: 33285146 DOI: 10.1016/j.kint.2020.10.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/02/2020] [Accepted: 10/15/2020] [Indexed: 11/29/2022]
Abstract
In recent years, many light-microscopy protocols have been published for visualization of nanoscale structures in the kidney. These protocols present researchers with new tools to evaluate both foot process anatomy and effacement, as well as protein distributions in foot processes, the slit diaphragm and in the glomerular basement membrane. However, these protocols either involve the application of different complicated super resolution microscopes or lengthy sample preparation protocols. Here, we present a fast and simple, five-hour long procedure for three-dimensional visualization of kidney morphology on all length scales. The protocol combines optical clearing and tissue expansion concepts to produce a mild swelling, sufficient for resolving nanoscale structures using a conventional confocal microscope. We show that the protocol can be applied to visualize a wide variety of pathologic features in both mouse and human kidneys. Thus, our fast and simple protocol can be beneficial for conventional microscopic evaluation of kidney tissue integrity both in research and possibly in future clinical routines.
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Affiliation(s)
- David Unnersjö-Jess
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Solna, Sweden; Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany.
| | - Linus Butt
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Anna Witasp
- Division of Renal Medicine, Department of Clinical Sciences, Intervention, and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Lucas Kühne
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Peter F Hoyer
- Pediatric Nephrology, Pediatrics II, University of Duisburg-Essen, Essen, Germany
| | - Jaakko Patrakka
- KI/AZ Integrated CardioMetabolic Center, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Paul T Brinkkötter
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Annika Wernerson
- Division of Renal Medicine, Department of Clinical Sciences, Intervention, and Technology, Karolinska Institutet, Stockholm, Sweden; Clinical Pathology and Cytology, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Lena Scott
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
| | - Hjalmar Brismar
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Solna, Sweden; Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
| | - Hans Blom
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Solna, Sweden
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17
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Wang Y, Eng DG, Kaverina NV, Loretz CJ, Koirala A, Akilesh S, Pippin JW, Shankland SJ. Global transcriptomic changes occur in aged mouse podocytes. Kidney Int 2020; 98:1160-1173. [PMID: 32592814 PMCID: PMC7606654 DOI: 10.1016/j.kint.2020.05.052] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/17/2020] [Accepted: 05/28/2020] [Indexed: 01/15/2023]
Abstract
Glomerular podocytes undergo structural and functional changes with advanced age, that increase susceptibility of aging kidneys to worse outcomes following superimposed glomerular diseases. To delineate transcriptional changes in podocytes in aged mice, RNA-seq was performed on isolated populations of reporter-labeled (tdTomato) podocytes from multiple young (two to three months) and advanced aged mice (22 to 24 months, equivalent to 70 plus year old humans). Of the 2,494 differentially expressed genes, 1,219 were higher and 1,275 were lower in aged podocytes. Pathway enrichment showed that major biological processes increased in aged podocytes included immune responses, non-coding RNA metabolism, gene silencing and MAP kinase signaling. Conversely, aged podocytes showed downregulation of developmental, morphogenesis and metabolic processes. Canonical podocyte marker gene expression decreased in aged podocytes, with increases in apoptotic and senescence genes providing a mechanism for the progressive loss of podocytes seen with aging. In addition, we revealed aberrations in the podocyte autocrine signaling network, identified the top transcription factors perturbed in aged podocytes, and uncovered candidate gene modulations that might promote healthy aging in podocytes. The transcriptional signature of aging is distinct from other kidney diseases. Thus, our study provides insights into biomarker discovery and molecular targeting of the aging process itself within podocytes.
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Affiliation(s)
- Yuliang Wang
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington, USA; Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington, USA
| | - Diana G Eng
- Division of Nephrology, University of Washington, Seattle, Washington, USA
| | - Natalya V Kaverina
- Division of Nephrology, University of Washington, Seattle, Washington, USA
| | - Carol J Loretz
- Division of Nephrology, University of Washington, Seattle, Washington, USA
| | - Abbal Koirala
- Division of Nephrology, University of Washington, Seattle, Washington, USA
| | - Shreeram Akilesh
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Jeffrey W Pippin
- Division of Nephrology, University of Washington, Seattle, Washington, USA
| | - Stuart J Shankland
- Division of Nephrology, University of Washington, Seattle, Washington, USA.
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18
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Ranjit S, Lanzanò L, Libby AE, Gratton E, Levi M. Advances in fluorescence microscopy techniques to study kidney function. Nat Rev Nephrol 2020; 17:128-144. [PMID: 32948857 DOI: 10.1038/s41581-020-00337-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2020] [Indexed: 02/07/2023]
Abstract
Fluorescence microscopy, in particular immunofluorescence microscopy, has been used extensively for the assessment of kidney function and pathology for both research and diagnostic purposes. The development of confocal microscopy in the 1950s enabled imaging of live cells and intravital imaging of the kidney; however, confocal microscopy is limited by its maximal spatial resolution and depth. More recent advances in fluorescence microscopy techniques have enabled increasingly detailed assessment of kidney structure and provided extraordinary insights into kidney function. For example, nanoscale precise imaging by rapid beam oscillation (nSPIRO) is a super-resolution microscopy technique that was originally developed for functional imaging of kidney microvilli and enables detection of dynamic physiological events in the kidney. A variety of techniques such as fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS) and Förster resonance energy transfer (FRET) enable assessment of interaction between proteins. The emergence of other super-resolution techniques, including super-resolution stimulated emission depletion (STED), photoactivated localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM) and structured illumination microscopy (SIM), has enabled functional imaging of cellular and subcellular organelles at ≤50 nm resolution. The deep imaging via emission recovery (DIVER) detector allows deep, label-free and high-sensitivity imaging of second harmonics, enabling assessment of processes such as fibrosis, whereas fluorescence lifetime imaging microscopy (FLIM) enables assessment of metabolic processes.
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Affiliation(s)
- Suman Ranjit
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA. .,Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, USA.
| | - Luca Lanzanò
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy.,Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy
| | - Andrew E Libby
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, USA.
| | - Moshe Levi
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA.
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19
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Kaverina NV, Eng DG, Miner JH, Pippin JW, Shankland SJ. Parietal epithelial cell differentiation to a podocyte fate in the aged mouse kidney. Aging (Albany NY) 2020; 12:17601-17624. [PMID: 32858527 PMCID: PMC7521511 DOI: 10.18632/aging.103788] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/29/2020] [Indexed: 01/24/2023]
Abstract
Healthy aging is typified by a progressive and absolute loss of podocytes over the lifespan of animals and humans. To test the hypothesis that a subset of glomerular parietal epithelial cell (PEC) progenitors transition to a podocyte fate with aging, dual reporter PEC-rtTA|LC1|tdTomato|Nphs1-FLPo|FRT-EGFP mice were generated. PECs were inducibly labeled with a tdTomato reporter, and podocytes were constitutively labeled with an EGFP reporter. With advancing age (14 and 24 months) glomeruli in the juxta-medullary cortex (JMC) were more severely injured than those in the outer cortex (OC). In aged mice (24m), injured glomeruli with lower podocyte number (41% decrease), showed more PEC migration and differentiation to a podocyte fate than mildly injured or healthy glomeruli. PECs differentiated to a podocyte fate had ultrastructural features of podocytes and co-expressed the podocyte markers podocin, nephrin, p57 and VEGF164, but not markers of mesangial (Perlecan) or endothelial (ERG) cells. PECs differentiated to a podocyte fate did not express CD44, a marker of PEC activation. Taken together, we demonstrate that a subpopulation of PECs differentiate to a podocyte fate predominantly in injured glomeruli in mice of advanced age.
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Affiliation(s)
| | - Diana G. Eng
- Division of Nephrology, University of Washington, Seattle, WA 98195, USA
| | - Jeffrey H. Miner
- Division of Nephrology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Jeffrey W. Pippin
- Division of Nephrology, University of Washington, Seattle, WA 98195, USA
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20
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Abstract
The glomerular basement membrane (GBM) is a key component of the glomerular capillary wall and is essential for kidney filtration. The major components of the GBM include laminins, type IV collagen, nidogens and heparan sulfate proteoglycans. In addition, the GBM harbours a number of other structural and regulatory components and provides a reservoir for growth factors. New technologies have improved our ability to study the composition and assembly of basement membranes. We now know that the GBM is a complex macromolecular structure that undergoes key transitions during glomerular development. Defects in GBM components are associated with a range of hereditary human diseases such as Alport syndrome, which is caused by defects in the genes COL4A3, COL4A4 and COL4A5, and Pierson syndrome, which is caused by variants in LAMB2. In addition, the GBM is affected by acquired autoimmune disorders and metabolic diseases such as diabetes mellitus. Current treatments for diseases associated with GBM involvement aim to reduce intraglomerular pressure and to treat the underlying cause where possible. As our understanding about the maintenance and turnover of the GBM improves, therapies to replace GBM components or to stimulate GBM repair could translate into new therapies for patients with GBM-associated disease.
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21
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Klimas A, Zhao Y. Expansion Microscopy: Toward Nanoscale Imaging of a Diverse Range of Biomolecules. ACS NANO 2020; 14:7689-7695. [PMID: 32628828 PMCID: PMC7456618 DOI: 10.1021/acsnano.0c04374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Expansion microscopy (ExM) has become a powerful imaging tool for visualizing the nanoscale organization of protein and nucleic acid targets in cells and tissues using only a conventional microscope. Until recently, current ExM approaches have had limited applicability to imaging other biomolecules, such as lipids and small molecules. With the new TRITON probes reported by Wen et al. in this issue of ACS Nano, ExM can now be used to perform nanoscale imaging of the cytoskeleton and lipid membranes. In this Perspective, we offer a brief overview of recent developments in ExM, with a focus on biomolecule anchoring and labeling strategies that target a wide range of biomolecules to the water-swellable polymer formed in situ, a key step that ensures biomolecules or labels of interest are separated in space and can be resolved on a conventional microscope. In addition to these new advancements, we discuss challenges and future directions in this exciting field.
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Affiliation(s)
- Aleksandra Klimas
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yongxin Zhao
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
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22
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Tillberg P. Protein-retention expansion microscopy: Improved sub-cellular imaging resolution through physical specimen expansion. Methods Cell Biol 2020; 161:1-14. [PMID: 33478684 DOI: 10.1016/bs.mcb.2020.04.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Super-resolution microscopy methods circumvent the classical diffraction limit of optical microscopy using combinations of specially engineered excitation light, fluorescent dyes, highly sensitive detectors, and reconstruction algorithms. Protein-retention expansion microscopy (ExM) is a method to physically expand biological specimens, enabling effectively sub-diffraction limited imaging on standard microscopes with standard staining reagents. Specimen expansion is driven by a swellable gel material that can be synthesized in situ using off-the-shelf chemicals and materials. The expansion material and process are robust and amenable to further development, which has enabled the emergence of numerous ExM variants with extended capabilities from multiple independent labs. The method presented here is useful for routine expansion of tissue slices and adherent or floating cultured cells, and also forms the basis for these variant methods.
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Affiliation(s)
- Paul Tillberg
- Janelia Research Campus, HHMI, Ashburn, VA, United States.
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23
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Tillberg PW, Chen F. Expansion Microscopy: Scalable and Convenient Super-Resolution Microscopy. Annu Rev Cell Dev Biol 2019; 35:683-701. [DOI: 10.1146/annurev-cellbio-100818-125320] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Expansion microscopy (ExM) is a physical form of magnification that increases the effective resolving power of any microscope. Here, we describe the fundamental principles of ExM, as well as how recently developed ExM variants build upon and apply those principles. We examine applications of ExM in cell and developmental biology for the study of nanoscale structures as well as ExM's potential for scalable mapping of nanoscale structures across large sample volumes. Finally, we explore how the unique anchoring and hydrogel embedding properties enable postexpansion molecular interrogation in a purified chemical environment. ExM promises to play an important role complementary to emerging live-cell imaging techniques, because of its relative ease of adoption and modification and its compatibility with tissue specimens up to at least 200 μm thick.
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Affiliation(s)
| | - Fei Chen
- Broad Institute of Harvard and MIT, Boston, Massachusetts 02142, USA
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24
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Kaverina NV, Eng DG, Freedman BS, Kutz JN, Chozinski TJ, Vaughan JC, Miner JH, Pippin JW, Shankland SJ. Dual lineage tracing shows that glomerular parietal epithelial cells can transdifferentiate toward the adult podocyte fate. Kidney Int 2019; 96:597-611. [PMID: 31200942 PMCID: PMC7008116 DOI: 10.1016/j.kint.2019.03.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 12/12/2022]
Abstract
Podocytes are differentiated post-mitotic cells that cannot replace themselves after injury. Glomerular parietal epithelial cells are proposed to be podocyte progenitors. To test whether a subset of parietal epithelial cells transdifferentiate to a podocyte fate, dual reporter PEC-rtTA|LC1|tdTomato|Nphs1-FLPo|FRT-EGFP mice, named PEC-PODO, were generated. Doxycycline administration permanently labeled parietal epithelial cells with tdTomato reporter (red), and upon doxycycline removal, the parietal epithelial cells (PECs) cannot label further. Despite the presence or absence of doxycycline, podocytes cannot label with tdTomato, but are constitutively labeled with an enhanced green fluorescent protein (EGFP) reporter (green). Only activation of the Nphs1-FLPo transgene by labeled parietal epithelial cells can generate a yellow color. At day 28 of experimental focal segmental glomerulosclerosis, podocyte density was 20% lower in 20% of glomeruli. At day 56 of experimental focal segmental glomerulosclerosis, podocyte density was 18% lower in 17% of glomeruli. TdTomato+ parietal epithelial cells were restricted to Bowman's capsule in healthy mice. However, by days 28 and 56 of experimental disease, two-thirds of tdTomato+ parietal epithelial cells within glomerular tufts were yellow in color. These cells co-expressed the podocyte markers podocin, nephrin, p57 and VEGF164, but not markers of endothelial (ERG) or mesangial (Perlecan) cells. Expansion microscopy showed primary, secondary and minor processes in tdTomato+EGFP+ cells in glomerular tufts. Thus, our studies provide strong evidence that parietal epithelial cells serve as a source of new podocytes in adult mice.
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Affiliation(s)
- Natalya V Kaverina
- Division of Nephrology, University of Washington, Seattle, Washington, USA
| | - Diana G Eng
- Division of Nephrology, University of Washington, Seattle, Washington, USA
| | | | - J Nathan Kutz
- Department of Applied Mathematics, University of Washington, Seattle, Washington, USA
| | - Tyler J Chozinski
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA; Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA
| | - Jeffrey H Miner
- Division of Nephrology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Jeffrey W Pippin
- Division of Nephrology, University of Washington, Seattle, Washington, USA
| | - Stuart J Shankland
- Division of Nephrology, University of Washington, Seattle, Washington, USA.
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25
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Glaser AK, Reder NP, Chen Y, Yin C, Wei L, Kang S, Barner LA, Xie W, McCarty EF, Mao C, Halpern AR, Stoltzfus CR, Daniels JS, Gerner MY, Nicovich PR, Vaughan JC, True LD, Liu JTC. Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues. Nat Commun 2019; 10:2781. [PMID: 31273194 PMCID: PMC6609674 DOI: 10.1038/s41467-019-10534-0] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/17/2019] [Indexed: 12/22/2022] Open
Abstract
Recent advances in optical clearing and light-sheet microscopy have provided unprecedented access to structural and molecular information from intact tissues. However, current light-sheet microscopes have imposed constraints on the size, shape, number of specimens, and compatibility with various clearing protocols. Here we present a multi-immersion open-top light-sheet microscope that enables simple mounting of multiple specimens processed with a variety of clearing protocols, which will facilitate wide adoption by preclinical researchers and clinical laboratories. In particular, the open-top geometry provides unsurpassed versatility to interface with a wide range of accessory technologies in the future.
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Affiliation(s)
- Adam K Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA.
| | - Nicholas P Reder
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Ye Chen
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Chengbo Yin
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Linpeng Wei
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Soyoung Kang
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Lindsey A Barner
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Weisi Xie
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Erin F McCarty
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Chenyi Mao
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Aaron R Halpern
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Caleb R Stoltzfus
- Department of Immunology, University of Washington, Seattle, WA, 98109, USA
| | | | - Michael Y Gerner
- Department of Immunology, University of Washington, Seattle, WA, 98109, USA
| | | | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, 98195, USA
| | - Lawrence D True
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA.
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA.
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26
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Pullman JM. New Views of the Glomerulus: Advanced Microscopy for Advanced Diagnosis. Front Med (Lausanne) 2019; 6:37. [PMID: 30899761 PMCID: PMC6416220 DOI: 10.3389/fmed.2019.00037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 02/08/2019] [Indexed: 12/11/2022] Open
Abstract
New technologies are ready to revolutionize glomerular imaging and significantly improve or replace immunofluorescence and electron microscopy, which have driven research and diagnosis of glomerular diseases for over 50 years. Advanced forms of transmission and scanning electron microscopy have revealed the detailed spatial relationships of the glomerular basement membrane, podocytes, and endothelial cells. These may be overshadowed by super resolution microscopy (SRM), which combines the advantages of immunofluorescence and electron microscopy, offers high resolution identification of specific molecules, and images large, physiologically relevant volumes of the glomerulus. Rapidity, ease of use and low cost with some types of SRM make them potentially suitable for routine diagnosis. SRM visualizes structures below the classical diffraction limit of conventional light microscopy by adding a time variable to either the illumination of the specimen, or to the fluorescence signal emitted by it. Ensemble techniques vary illumination and include Structured Illumination Microscopy (SIM) and Stimulation Emission Depletion Microscopy (STED). Single molecule localization techniques vary the light emission by fluorescence labels in the specimen, and include Photoactivated Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM). Technologies such as expansion microscopy and genetic labeling can also create effective super resolution imaging by non-optical, specialized preparation techniques. All technologies require dark field fluorescence and some require computer image analysis and reconstruction. Replicating successful application in other areas of biology, SIM, STED, and STORM have visualized normal and nephrotic disease podocytes, and have confirmed their appearances to be similar to those seen by electron microscopy, but with added new information on cell configuration and protein localization. STORM has also localized podocyte cytoskeleton and adhesion proteins, and glomerular basement membrane proteins at a resolution never before possible. These pioneering efforts show the promise of super resolution microscopy, and lay the groundwork for future study and new diagnostic tools for glomerular diseases.
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Affiliation(s)
- James M Pullman
- Division of Anatomic Pathology, Department of Pathology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY, United States
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27
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Wassie AT, Zhao Y, Boyden ES. Expansion microscopy: principles and uses in biological research. Nat Methods 2018; 16:33-41. [PMID: 30573813 DOI: 10.1038/s41592-018-0219-4] [Citation(s) in RCA: 243] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 10/10/2018] [Indexed: 01/08/2023]
Abstract
Many biological investigations require 3D imaging of cells or tissues with nanoscale spatial resolution. We recently discovered that preserved biological specimens can be physically expanded in an isotropic fashion through a chemical process. Expansion microscopy (ExM) allows nanoscale imaging of biological specimens with conventional microscopes, decrowds biomolecules in support of signal amplification and multiplexed readout chemistries, and makes specimens transparent. We review the principles of how ExM works, advances in the technology made by our group and others, and its applications throughout biology and medicine.
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Affiliation(s)
- Asmamaw T Wassie
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.,Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yongxin Zhao
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Edward S Boyden
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Center for Neurobiological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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