DOCSLIB.ORG

Expansion Microscopy: Scalable and Multiplexed Nanoscale Imaging

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Expansion Microscopy: Scalable and Multiplexed Nanoscale Imaging Expansion Microscopy: Scalable and Multiplexed Nanoscale Imaging by Fei Chen B.S. Electrical Engineering California Institute of Technology, 2011 Submitted to the Department of Biological Engineering in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biological Engineering at the Massachusetts Institute of Technology February 2017 2017 Massachusetts Institute of Technology. All rights reserved. Signature of author Signature redacted Department of Biological Engineering 2017 Certified bj Sr rd February, 22, Signature redacted_____ - Edward S. Boyden Professor of Biological Engineering, Brain and Cognitive Sciences, Media Arts and Sciences Thesis Supervisor AcceptedbySig ature redacted Mark Bathe MASSACHUSETTS INSTITUTE Professor of Biological Engineering OF TECHNOLOGY (/ Chair, Graduate Program Committee LU MAY 0 9 2017 LIBRARIES Thesis Committee Members Peter T. C. So, Ph.D. Professor of Biological Engineering and Mechanical Engineering Thesis Committee Chair Scott R. Manalis, Ph.D. Professor of Biological Engineering and Mechanical Engineering Thesis Committee Member Edward S. Boyden, Ph.D. Professor of Biological Engineering, Brain and Cognitive Sciences, Media Arts and Sciences Thesis Supervisor Table of Contents A B S T R A C T ................................................................................ ------ .... ......----------. .. .. - I ACKNOWLEDGEMENTS..................................................................................................... 2 CHAPTER ONE: INTRODUCTION.......................................... 4 SUPER-RESOLUTION M ICROSCOPY............................................................ ....- --- ---........................................................... 4 EXPANSION M ICROSCOPY........................................................................---------............................................................5 CITATIONS TO PUBLISHED WORK AND ACKNOWLEDGEMENTS TO CO-A UTHORS ....................................................................... 8 CHAPTER TWO: EXPANSION MICROSCOPY, A SCALABLE SUPER-RESOLUTION MICROSCOPY PLATFORM ........................................................................................... 9 RESULTS.............. .............................................................................-- - -......------- DISCUSSION.................................................................................... ------------............................................................ 12 FIGURES............ ................................................................................ - -- - - - - - - ... 14 Figure 1-1: Expansion microscopy (ExM) concept. ......................................... 14 Figure 1-2: Expansion microscopy physically magnifies with nanoscale isotropy, enabling super-resolution imaging on diffraction-limited microscopes..............................................15 Figure 1-3: Super-resolution imaging of synapses and neurons in intact mammalian brain tissue using ExM. 17 Figure 1-4: Scalable 3D super-resolution microscopy of mouse brain tissue. ....................... 19 SUPPLEM ENTARY INFORM ATIO N ...................................................-- ........... .... -------------------------------------- 20 M ETHODS ............................................ .. .. .. ... ...- ..---- ----...- -------..--- --.-- ----............................................................28 Labels for ExM :......................................................................................................... ---. -....--. ------.................... 28 Cultured cell preparation and staining:.................................................-28 Brain tissue preparation and staining:.............................................. -- 29 In situ polym er synthesis: ..............................................................................---- ..... --.----.................... 29 D igestion and expansion:..................................................................................... ...... ----.-. ----.-.-.-.................. 30 Optical clearing m easurements: .........................................................................................---.-.. ...- ---.-.......... 31 CHAPTER THREE: PROTEIN RETENTION EXPANSION MICROSCOPY......................... 34 INTRODUCTION........................................................................ ....- - - -- - - -- - --............................................................34 RESULTS............................................................................................................................... 34 DISCUSSION ................................................................... .....--.. -.-.-.--.-------.-----........................................................... 38 FIGURES ................................................................................................................................. 40 Figure 3-1. Post-expansion antibody delivery, after epitope-preserving homogenization..... .......... 40 Figure 3-2. Retention offluorescent protein (FP) and antibody fluorescence signals in proExM and pro ExM of FP fusions. ............................................................................-- .......... ..---. -...............................42 Figure 3-3. Validation of proExM in different marnmalian tissue types...........................44 Figure 3-4. proExM of mammalian brain circuitry. ....................................... .46 Figure 3-5. Workflows for expansion microscopy with protein retention. ................................................ 48 SUPPLEMENTARY INFORMATION ..................................................... .... ........ ............................................................ 49 M ETHODS...........................................- ................ ..-.----...... .- ..- - --............................................................ 64 CHAPTER FOUR: NANOSCALE IMAGING OF RNA WITH EXPANSION MICROSCOPY ....................................................................................................... 71 INT RO D U CT IO N ............................................................................................................................................................ 7 1 R ESU LTS ..................................................................................................................................................................... 71 D ISC U SSIO N ................................................................................................................................................................ 75 F IG U RES ..................................................................................................................................................................... 77 Figure 4-1. Design and validation of ExFISH chemistry. ..................................................................................... 77 Figure 4-2. Serially hybridized and m ultiplexed ExFISH ...................................................................................... 78 Figure 4-3. Nanoscale imaging of RNA in mammalian brain. ............................................................................ 79 SUPPLEMENTARY INFORMATION ..................................................................................................................................... 80 M ET H O D S .................................................................................................................................................................. 9 2 R EFER EN C ES ............................................................................................................................. 99 Abstract Microscopy has facilitated the discovery of many biological insights by optically magnifying small structures in cells and tissues. However, the resolution of optical microscopy is limited by the diffraction of light to ~200-300 nm, comparable or larger to the size of many subcellular structures. In this thesis, we describe a suite of tools based on a novel super-resolution microscopy approach called Expansion microscopy. Expansion microscopy (ExM) physically expands tissues so that the resolution of ordinary microscopes is increased -5 times by leveraging the swelling properties of polyelectrolyte hydrogels. Ordinary microscopes used with ExM are more accessible and faster than the specialized optical systems designed to image beyond the diffraction limit (e.g., STORM/PALM, STED, SIM), while yielding similar performance. Expanded tissues are also optically clear, allowing for unprecedented super-resolution imaging in thick tissues and facile reagent diffusion into the sample. We have since developed a variant of ExM, called protein retention ExM, in which proteins are directly anchored to the swellable gel using a commercially available cross-linking molecule. This strategy enables ExM of genetically encoded fluorescent proteins and commercial fluorescently labeled secondary antibodies. With these advancements, ExM can be carried out with purely commercial reagents and represents a simple extension of standard histological methods used to prepare samples for imaging. Furthermore, we have developed a variant of the ExM technology that enables RNA molecules to be directly linked to the ExM gel network via a small molecule linker and isotropic expansion. This technology, termed ExFISH, enables visualization of RNAs with nanoscale precision and single molecule resolution. We have demonstrated
Load more

Recommended publications
  • Imaging Beyond the Super-Resolution Limits Using Ultrastructure Expansion
    bioRxiv preprint first posted online Apr. 25, 2018; doi: http://dx.doi.org/10.1101/308270. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Imaging beyond the super-resolution limits using ultrastructure expansion microscopy (UltraExM) D. Gambarotto1†, F. U. Zwettler2†, M. Cernohorska1, D. Fortun3‡, S. Borgers1, J. Heine4, J. G. Schloetel4, M. Reuss4, M. Unser5, E. S. Boyden6, M. Sauer2*, V. Hamel1* and P. Guichard1* Affiliations: 1University of Geneva, Department of Cell Biology, Sciences III, Geneva. 2University of Würzburg, Department of Biotechnology and Biophysics, Biocenter, Am Hubland, 97074 Würzburg, Germany. 3Signal Processing core of Center for Biomedical Imaging (CIBM-SP), EPFL, Lausanne 4Abberior Instruments GmbH, 37077 Göttingen, Germany. 5 Ecole Polytechnique Fédérale de Lausanne (EPFL), Biomedical Imaging Group, Lausanne 6Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA. ‡Present address: ICube, CNRS, University of Strasbourg, Illkirch, France *Correspondence to: [email protected], [email protected] and [email protected] † equal contribution 1 bioRxiv preprint first posted online Apr. 25, 2018; doi: http://dx.doi.org/10.1101/308270. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. ABSTRACT For decades, electron microscopy (EM) was the only method able to reveal the ultrastructure of cellular organelles and molecular complexes because of the diffraction limit of optical microscopy.
    [Show full text]
  • Feasibility of 3D Reconstruction of Neural Morphology Using Expansion Microscopy and Barcode-Guided Agglomeration
    Feasibility of 3D Reconstruction of Neural Morphology Using Expansion Microscopy and Barcode-Guided Agglomeration The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Yoon, Young-Gyu et al. “Feasibility of 3D Reconstruction of Neural Morphology Using Expansion Microscopy and Barcode-Guided Agglomeration.” Frontiers in Computational Neuroscience 11 (October 2017): 97 © 2017 Yoon et al. As Published http://dx.doi.org/10.3389/FNCOM.2017.00097 Publisher Frontiers Research Foundation Version Final published version Citable link http://hdl.handle.net/1721.1/115370 Terms of Use Attribution 4.0 International (CC BY 4.0) Detailed Terms https://creativecommons.org/licenses/by/4.0/ HYPOTHESIS AND THEORY published: 24 October 2017 doi: 10.3389/fncom.2017.00097 Feasibility of 3D Reconstruction of Neural Morphology Using Expansion Microscopy and Barcode-Guided Agglomeration Young-Gyu Yoon 1, 2, Peilun Dai 2, 3, Jeremy Wohlwend 1, 2, Jae-Byum Chang 2, 4, Adam H. Marblestone 2* and Edward S. Boyden 2, 3, 5, 6* 1 Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, United States, 2 MIT Media Lab, MIT, Cambridge, MA, United States, 3 Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, United States, 4 Department of Biomedical Engineering, Sungkyunkwan University, Seoul, South Korea, 5 Department of Biological Engineering, MIT, Cambridge, MA, United States, 6 McGovern Institute, MIT, Cambridge, MA, United States We here introduce and study the properties, via computer simulation, of a candidate automated approach to algorithmic reconstruction of dense neural morphology, based on simulated data of the kind that would be obtained via two emerging molecular technologies—expansion microscopy (ExM) and in-situ molecular barcoding.
    [Show full text]
  • Nanoscale Imaging of RNA with Expansion Microscopy
    ARTICLES Nanoscale imaging of RNA with expansion microscopy Fei Chen1–3,10, Asmamaw T Wassie1–3,10, Allison J Cote4, Anubhav Sinha5, Shahar Alon2,3, Shoh Asano2,3, Evan R Daugharthy6,7, Jae-Byum Chang2,3, Adam Marblestone2,3, George M Church6,8, Arjun Raj4 & Edward S Boyden1–3,9 The ability to image RNA identity and location with Here, we have developed a small-molecule linker that enables nanoscale precision in intact tissues is of great interest RNA to be covalently attached to the ExM gel. We show that this for defining cell types and states in normal and pathological procedure, which we call ExFISH, enables RNA FISH, which biological settings. Here, we present a strategy for enables identification of transcripts in situ with single-molecule expansion microscopy of RNA. We developed a small-molecule precision. In RNA FISH, a set of fluorescent probes complemen- linker that enables RNA to be covalently attached to a tary to a target strand of mRNA is delivered2,3. Single-molecule swellable polyelectrolyte gel synthesized throughout FISH (smFISH) can be performed with multiple fluorophores a biological specimen. Then, postexpansion, fluorescent delivered to a single mRNA via oligonucleotide probes4. In intact in situ hybridization (FISH) imaging of RNA can be performed tissues, amplification strategies, such as hybridization chain reac- with high yield and specificity as well as single-molecule tion (HCR)5,6 and branched DNA amplification7,8, can allow precision in both cultured cells and intact brain tissue. a large number of fluorophores to be targeted to a single mRNA. Expansion FISH (ExFISH) separates RNAs and supports We show that ExFISH can support smFISH in cell culture and amplification of single-molecule signals (i.e., via hybridization HCR-amplified FISH in intact mouse brain tissues.
    [Show full text]
  • Mechanical Expansion Microscopy
    ARTICLE IN PRESS Mechanical expansion microscopy Yuhang Fana,†, Youngbin Lima,†, Livia S. Wyssb, Seongjin Parkc, Cancan Xue, Huikang Fue, Jingyi Feic,d, Yi Honge, Bo Wanga,f,* aDepartment of Bioengineering, Stanford University, Stanford, CA, United States bDepartment of Biology, Stanford University, Stanford, CA, United States cDepartment of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States dInstitute for Biophysical Dynamics, University of Chicago, Chicago, IL, United States eDepartment of Bioengineering, University of Texas at Arlington, Arlington, TX, United States fDepartment of Developmental Biology, Stanford University School of Medicine, Stanford, CA, United States *Corresponding author: e-mail address: [email protected] Chapter outline 1 Introduction..........................................................................................................2 1.1 Mechanically resolved expansion microscopy.............................................2 1.2 Mechanically locked expansion microscopy...............................................6 2 Mechanically resolved expansion microscopy of bacteria.......................................11 2.1 Rationale............................................................................................11 2.2 Materials, equipment, reagents..............................................................11 2.3 Protocols.............................................................................................13 3 Mechanically locked expansion microscopy for
    [Show full text]
  • Expansion Microscopy: Development and Neuroscience Applications
    Available online at www.sciencedirect.com ScienceDirect Expansion microscopy: development and neuroscience applications 1 1,2,3,4 Emmanouil D Karagiannis and Edward S Boyden Many neuroscience questions center around understanding organized to yield complex emergent functions. Under- how the molecules and wiring in neural circuits mechanistically standing the nature of brain disorders, and pointing the yield behavioral functions, or go awry in disease states. way to new therapeutics, is also increasingly demanding a However, mapping the molecules and wiring of neurons across knowledge of how brain cells, molecular cascades, and the large scales of neural circuits has posed a great challenge. connections change in disease states. Ideally one would We recently developed expansion microscopy (ExM), a be able to map biomolecules such as neurotransmitters, process in which we physically magnify biological specimens receptors, and ion channels, across the spatial extents of such as brain circuits. We synthesize throughout preserved neurons and neural circuits. Traditional microscopes are brain specimens a dense, even mesh of a swellable polymer limited by diffraction, and thus specialized technologies such as sodium polyacrylate, anchoring key biomolecules such have been required to perform imaging with nanoscale as proteins and nucleic acids to the polymer. After mechanical precision. Electron microscopy is capable of nanoscale homogenization of the specimen-polymer composite, we add resolution, and has yielded many insights into the wiring water, and the polymer swells, pulling biomolecules apart. Due diagrams of neural circuits [1,2], but typically yields little to the larger separation between molecules, ordinary molecular information about the molecules in those cir- microscopes can then perform nanoscale resolution imaging.
    [Show full text]
  • Whole-Exm: Expansion Microscopy Imaging of All Anatomical Structures
    bioRxiv preprint doi: https://doi.org/10.1101/2021.05.18.443629; this version posted May 18, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Whole-ExM: Expansion microscopy imaging of all 2 anatomical structures of whole larval zebrafish 3 4 Jueun Sim1,18, Chan E Park1,18, In Cho1,18, Kyeongbae Min2, Jeong-Soo Lee3,4,5, Yosep Chong6, Jeewon 5 Kim7, Jeong Seuk Kang8, Kiryl D. Piatkevich9,10,11, Erica E. Jung12, Seok-Kyu Kwon13,14, Young-Gyu Yoon7, 6 Edward S. Boyden15,16,17, and Jae-Byum Chang1* 7 8 1Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, 9 Daejeon, Republic of Korea 10 2Department of Biomedical Engineering, Sungkyunkwan University, Suwon, Republic of Korea 11 3Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, 12 Daejeon, Republic of Korea 13 4KRIBB School, University of Science and Technology, Daejeon, Republic of Korea 14 5Convergence Research Center for Dementia, Korea Institute of Science and Technology, Seoul, Republic 15 of Korea 16 6Department of Hospital Pathology, Uijeongbu St. Mary's Hospital, College of Medicine, The Catholic 17 University of Korea, Uijeongbu, Republic of Korea 18 7School of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic 19 of Korea 20 8John A. Paulson School of Engineering and Applied Sciences Harvard University, Cambridge, MA, USA 21
    [Show full text]
  • Expansion Microscopy Protocol on Neuronal Cells
    An investigation of performing the protein- retention expansion microscopy protocol on neuronal cells ELIZA LINDQVIST Department of Applied Physics KTH Royal Institute of Technology Supervisor: Hans Blom Examiner: Erik Lindahl Master’s Thesis Stockholm, Sweden 2018 TRITA-SCI-GRU 2018:317 Department of Applied Physics School of Engineering Sciences Royal Institute of Technology Stockholm SWEDEN Examensarbete som med tillstånd av Kungliga Tekniska Högskolan främlägges till offentlig granskning för avläggande av Civilingenjörsexamen i Teknisk Fysik 4 augusti 2018 i Seminarierum Becquerel på SciLifeLab, Tomtebodavägen 23, Solna. © Eliza Lindqvist, 4 augusti 2018 Abstract Expansion microscopy (ExM) enables imaging of preserved cellular or tissue specimens with nanoscale resolution on diffraction-limited instead of super-resolution microscopes. On broad terms ExM works by physically enlarging the specimen, after having labeled it with fluorescent probes anchored to a swellable gel. In this Master Thesis work I present an investigation of the protein retention Expansion Microscopy (proExM) protocol for expansion of cultured neuronal cells. The expansion of neurological networks enables for example the ability to pinpoint small topological protein changes inside the brain, which could take affect during the development of diseases like Alzheimer’s, epilepsy and Parkinson’s disease. To evaluate the protein retention protocol I stained neuronal cells with different antibodies and I compared images of samples imaged with confocal, STED and Expansion Microscopy. I quantified the expansion factor in neurons by measuring of the distance between fixed architectural Spectrin rings. To evaluate retained protein content I varied the digestion times and anchoring treatments to study how different treatments affected the imaged intensity. Here, I show that samples anchored with Acryloyl X – SE lose a significant amount of protein with increased enzymatic digestion times.
    [Show full text]
  • Imaging Renal Ultrastructure Using a Fast and Simple Optical Clearing
    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.10.196733; this version posted July 12, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Imaging Renal Ultrastructure using a Fast and Simple Optical Clearing and Swelling Protocol David Unnersjö-Jess1,2,3* PhD, Linus Butt2 MD, Martin Höhne2,3 PhD, Anna Witasp4 PhD, Lucas Kühne2,3 MD, Peter F. Hoyer5 MD, Jaakko Patrakka6 MD, Paul T. Brinkkötter2,3 MD, Annika Wernerson4 MD, Bernhard Schermer2,3 MD, Thomas Benzing2,3 MD, Lena Scott7 PhD, Hjalmar Brismar1,7 PhD, Hans Blom1 PhD. 1Science for Life Laboratory, Dept. of Applied Physics, Royal Institute of Technology, Solna, Sweden 2 Department II of Internal Medicine and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany 3 Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany 4Division of Renal Medicine, Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden and Clinical Pathology and Cytology, Karolinska Universiy Hospital Huddinge, Stockholm Sweden 5Pediatric Nephrology, Pediatrics II, University of Duisburg-Essen, Essen, Germany 6KI/AZ Integrated CardioMetabolic Center, Department of Laboratory Medicine. Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden 7Science for Life Laboratory, Dept. of Women´s and Children´s Health, Karolinska Institutet, Solna, Sweden Running title: Fast Imaging of Renal Ultrastructure Corresponding author: David Unnersjö-Jess Uniklinik Köln Kerpener Strasse 62 509 37 Köln Germany Tel#: +46-73-5104395 Email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.10.196733; this version posted July 12, 2020.
    [Show full text]
  • Novel Microscopic Techniques for Podocyte Research
    REVIEW published: 11 July 2018 doi: 10.3389/fendo.2018.00379 Novel Microscopic Techniques for Podocyte Research Florian Siegerist †, Karlhans Endlich † and Nicole Endlich* Institute for Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany Together with endothelial cells and the glomerular basement membrane, podocytes form the size-specific filtration barrier of the glomerulus with their interdigitating foot processes. Since glomerulopathies are associated with so-called foot process effacement—a severe change of well-formed foot processes into flat and broadened processes—visualization of the three-dimensional podocyte morphology is a crucial part for diagnosis of nephrotic diseases. However, interdigitating podocyte foot processes are too narrow to be resolved by classic light microscopy due to Ernst Abbe’s law making electron microscopy necessary. Although three dimensional electron microscopy approaches like Edited by: Barbara Lewko, serial block face and focused ion beam scanning electron microscopy and electron Gdansk Medical University, Poland tomography allow volumetric reconstruction of podocytes, these techniques are very Reviewed by: time-consuming and too specialized for routine use or screening purposes. During the Giuseppe Remuzzi, Istituto Di Ricerche Farmacologiche last few years, different super-resolution microscopic techniques were developed to Mario Negri, Italy overcome the optical resolution limit enabling new insights into podocyte morphology. Chris Robert Neal, Super-resolution microscopy approaches like three dimensional structured illumination University of Bristol, United Kingdom microscopy (3D-SIM), stimulated emission depletion microscopy (STED) and localization *Correspondence: Nicole Endlich microscopy [stochastic optical reconstruction microscopy (STORM), photoactivated [email protected] localization microscopy (PALM)] reach resolutions down to 80–20 nm and can be used †Florian Siegerist, to image and further quantify podocyte foot process morphology.
    [Show full text]
  • Expansion Microscopy of Lipid Membranes
    bioRxiv preprint doi: https://doi.org/10.1101/829903; this version posted November 4, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Expansion Microscopy of Lipid Membranes Emmanouil D. Karagiannis1*, Jeong Seuk Kang1*, Tay Won Shin1, Amauche Emenari2, Shoh Asano1†, Leanne Lin4, Emma K. Costa2, IMAXT Grand Challenge Consortium7, Adam H. Marblestone1, Narayanan Kasthuri8,9, Edward S. Boyden1,2,3,4,5,6** 1Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA, 2Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA, 3McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA, 4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA, 5Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA, 6Center for Neurobiological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA, 7CRUK IMAXT Grand Challenge Consortium, 8Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL, USA, 9Department of Neurobiology, University of Chicago, Chicago, IL, USA. †Present address: Internal Medicine Research Unit, Pfizer, Cambridge, MA 02139, USA. *Equal contribution **Corresponding author, email [email protected] bioRxiv preprint doi: https://doi.org/10.1101/829903; this version posted November 4, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.
    [Show full text]
  • NATURE Biotechnology
    ARTICLES Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy Yongxin Zhao1,11, Octavian Bucur2–5,11, Humayun Irshad2,3,5, Fei Chen1,6,7, Astrid Weins8,9, Andreea L Stancu2,5, Eun-Young Oh2, Marcello DiStasio2, Vanda Torous2, Benjamin Glass2, Isaac E Stillman2, Stuart J Schnitt2, Andrew H Beck2,3,5 & Edward S Boyden1,6,7,10 Expansion microscopy (ExM), a method for improving the resolution of light microscopy by physically expanding a specimen, has not been applied to clinical tissue samples. Here we report a clinically optimized form of ExM that supports nanoscale imaging of human tissue specimens that have been fixed with formalin, embedded in paraffin, stained with hematoxylin and eosin, and/or fresh frozen. The method, which we call expansion pathology (ExPath), converts clinical samples into an ExM-compatible state, then applies an ExM protocol with protein anchoring and mechanical homogenization steps optimized for clinical samples. ExPath enables ~70-nm-resolution imaging of diverse biomolecules in intact tissues using conventional diffraction-limited microscopes and standard antibody and fluorescent DNA in situ hybridization reagents. We use ExPath for optical diagnosis of kidney minimal-change disease, a process that previously required electron microscopy, and we demonstrate high-fidelity computational discrimination between early breast neoplastic lesions for which pathologists often disagree in classification. ExPath may enable the routine use of nanoscale imaging in pathology and clinical research. Physicians and researchers have long examined cellular structures and we recently developed protein retention ExM (proExM), a version molecular composition using diffraction-limited microscopy to diag- of ExM that uses a commercially available anchoring molecule to nose or investigate the pathogenesis of a wide variety of predisease tie proteins (such as fluorophore-bearing antibodies) directly to the and disease states.
    [Show full text]
  • Expansion Microscopy for Brain Mapping
    Expansion Microscopy for Brain Mapping The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Kang, Jeong Seuk. 2019. Expansion Microscopy for Brain Mapping. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:42029733 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Expansion Microscopy for Brain Mapping by Jeong Seuk Kang B.S. Electrical Engineering and Computer Sciences/ Materials Science and Engineering University of California, Berkeley (2015) S.M. Applied Physics Harvard University (2017) Submitted to the Harvard John A. Paulson School of Engineering and Applied Sciences in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Applied Physics Harvard University May 2019 © 2019 Jeong Seuk Kang All rights reserved Dissertation Advisor: Professor Edward S. Boyden Jeong Seuk Kang Expansion Microscopy for Brain Mapping Abstract More than one billion people in the world suffer from brain disorders. To address this, more than one trillion US dollars are spent to develop the drugs, but ~92% fail to receive clinical approval. Among many potential reasons why treating brain disorders has been strikingly difficult, one reason could be that the complexity of neural circuitry and molecular composition of the brain have been poorly understood. For this reason, there needs to be new innovations in brain mapping pursuits, and expansion microscopy (ExM) is proposed throughout this thesis as a potential candidate for most effectively meeting the needs of the efforts.
    [Show full text]