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Bishop KW, Erion Barner LA, Han Q, Baraznenok E, Lan L, Poudel C, Gao G, Serafin RB, Chow SSL, Glaser AK, Janowczyk A, Brenes D, Huang H, Miyasato D, True LD, Kang S, Vaughan JC, Liu JTC. An end-to-end workflow for nondestructive 3D pathology. Nat Protoc 2024; 19:1122-1148. [PMID: 38263522 DOI: 10.1038/s41596-023-00934-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/23/2023] [Indexed: 01/25/2024]
Abstract
Recent advances in 3D pathology offer the ability to image orders of magnitude more tissue than conventional pathology methods while also providing a volumetric context that is not achievable with 2D tissue sections, and all without requiring destructive tissue sectioning. Generating high-quality 3D pathology datasets on a consistent basis, however, is not trivial and requires careful attention to a series of details during tissue preparation, imaging and initial data processing, as well as iterative optimization of the entire process. Here, we provide an end-to-end procedure covering all aspects of a 3D pathology workflow (using light-sheet microscopy as an illustrative imaging platform) with sufficient detail to perform well-controlled preclinical and clinical studies. Although 3D pathology is compatible with diverse staining protocols and computationally generated color palettes for visual analysis, this protocol focuses on the use of a fluorescent analog of hematoxylin and eosin, which remains the most common stain used for gold-standard pathological reports. We present our guidelines for a broad range of end users (e.g., biologists, clinical researchers and engineers) in a simple format. The end-to-end workflow requires 3-6 d to complete, bearing in mind that data analysis may take longer.
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Affiliation(s)
- Kevin W Bishop
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | | | - Qinghua Han
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Elena Baraznenok
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Lydia Lan
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Chetan Poudel
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Gan Gao
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Robert B Serafin
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Sarah S L Chow
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Adam K Glaser
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | - Andrew Janowczyk
- Department of Biomedical Engineering, Emory University, Atlanta, GA, USA
- Department of Oncology, Division of Precision Oncology, University Hospital of Geneva, Geneva, Switzerland
- Department of Diagnostics, Division of Clinical Pathology, University Hospital of Geneva, Geneva, Switzerland
| | - David Brenes
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Hongyi Huang
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Dominie Miyasato
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Lawrence D True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Soyoung Kang
- Department of Mechanical Engineering, 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
| | - Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
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2
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Bishop KW, Barner LAE, Han Q, Baraznenok E, Lan L, Poudel C, Gao G, Serafin RB, Chow SS, Glaser AK, Janowczyk A, Brenes D, Huang H, Miyasato D, True LD, Kang S, Vaughan JC, Liu JT. An end-to-end workflow for non-destructive 3D pathology. bioRxiv 2023:2023.08.03.551845. [PMID: 37577615 PMCID: PMC10418226 DOI: 10.1101/2023.08.03.551845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Recent advances in 3D pathology offer the ability to image orders-of-magnitude more tissue than conventional pathology while providing a volumetric context that is lacking with 2D tissue sections, all without requiring destructive tissue sectioning. Generating high-quality 3D pathology datasets on a consistent basis is non-trivial, requiring careful attention to many details regarding tissue preparation, imaging, and data/image processing in an iterative process. Here we provide an end-to-end protocol covering all aspects of a 3D pathology workflow (using light-sheet microscopy as an illustrative imaging platform) with sufficient detail to perform well-controlled preclinical and clinical studies. While 3D pathology is compatible with diverse staining protocols and computationally generated color palettes for visual analysis, this protocol will focus on a fluorescent analog of hematoxylin and eosin (H&E), which remains the most common stain for gold-standard diagnostic determinations. We present our guidelines for a broad range of end-users (e.g., biologists, clinical researchers, and engineers) in a simple tutorial format.
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Affiliation(s)
- Kevin W. Bishop
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | | | - Qinghua Han
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Elena Baraznenok
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Lydia Lan
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Chetan Poudel
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Gan Gao
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Robert B. Serafin
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Sarah S.L. Chow
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Adam K. Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Andrew Janowczyk
- Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
- Department of Oncology, Division of Precision Oncology, University Hospital of Geneva, Geneva, Switzerland
- Department of Clinical Pathology, Division of Clinical Pathology, University Hospital of Geneva, Geneva, Switzerland
| | - David Brenes
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Hongyi Huang
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Dominie Miyasato
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Lawrence D. True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Soyoung Kang
- Department of Mechanical Engineering, 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
| | - Jonathan T.C. Liu
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
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3
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Kaverina N, Schweickart RA, Chan GC, Maggiore JC, Eng DG, Zeng Y, McKinzie SR, Perry HS, Ali A, O’Connor C, Pereira BMV, Theberge AB, Vaughan JC, Loretz CJ, Chang A, Hukriede NA, Bitzer M, Pippin JW, Wessely O, Shankland SJ. Inhibiting NLRP3 signaling in aging podocytes improves their life- and health-span. Aging (Albany NY) 2023; 15:6658-6689. [PMID: 37487005 PMCID: PMC10415579 DOI: 10.18632/aging.204897] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023]
Abstract
The decrease in the podocyte's lifespan and health-span that typify healthy kidney aging cause a decrease in their normal structure, physiology and function. The ability to halt and even reverse these changes becomes clinically relevant when disease is superimposed on an aged kidney. RNA-sequencing of podocytes from middle-aged mice showed an inflammatory phenotype with increases in the NLRP3 inflammasome, signaling for IL2/Stat5, IL6 and TNF, interferon gamma response, allograft rejection and complement, consistent with inflammaging. Furthermore, injury-induced NLRP3 signaling in podocytes was further augmented in aged mice compared to young ones. The NLRP3 inflammasome (NLRP3, Caspase-1, IL1β IL-18) was also increased in podocytes of middle-aged humans. Higher transcript expression for NLRP3 in human glomeruli was accompanied by reduced podocyte density and increased global glomerulosclerosis and glomerular volume. Pharmacological inhibition of NLRP3 with MCC950, or gene deletion, reduced podocyte senescence and the genes typifying aging in middle-aged mice, which was accompanied by an improved podocyte lifespan and health-span. Moreover, modeling the injury-dependent increase in NLRP3 signaling in human kidney organoids confirmed the anti-senescence effect of MC9950. Finally, NLRP3 also impacted liver aging. Together, these results suggest a critical role for the NLRP3 inflammasome in podocyte and liver aging.
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Affiliation(s)
- Natalya Kaverina
- Division of Nephrology, University of Washington, Seattle, WA 98109, USA
| | - R. Allen Schweickart
- Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44106, USA
| | - Gek Cher Chan
- Department of Medicine, Division of Nephrology, National University Hospital, Singapore
| | - Joseph C. Maggiore
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Diana G. Eng
- Division of Nephrology, University of Washington, Seattle, WA 98109, USA
| | - Yuting Zeng
- Department of Chemistry, University of Washington, Seattle, WA 98109, USA
| | - Sierra R. McKinzie
- Division of Nephrology, University of Washington, Seattle, WA 98109, USA
| | - Hannah S. Perry
- Department of Chemistry, University of Washington, Seattle, WA 98109, USA
| | - Adilijiang Ali
- Department of Chemistry, University of Washington, Seattle, WA 98109, USA
| | | | | | | | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, WA 98109, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98109, USA
| | - Carol J. Loretz
- Division of Nephrology, University of Washington, Seattle, WA 98109, USA
| | - Anthony Chang
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Neil A. Hukriede
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Markus Bitzer
- Division of Nephrology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeffrey W. Pippin
- Division of Nephrology, University of Washington, Seattle, WA 98109, USA
| | - Oliver Wessely
- Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44106, USA
| | - Stuart J. Shankland
- Division of Nephrology, University of Washington, Seattle, WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
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4
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Liu JTC, Glaser AK, Poudel C, Vaughan JC. Nondestructive 3D Pathology with Light-Sheet Fluorescence Microscopy for Translational Research and Clinical Assays. Annu Rev Anal Chem (Palo Alto Calif) 2023; 16:231-252. [PMID: 36854208 DOI: 10.1146/annurev-anchem-091222-092734] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In recent years, there has been a revived appreciation for the importance of spatial context and morphological phenotypes for both understanding disease progression and guiding treatment decisions. Compared with conventional 2D histopathology, which is the current gold standard of medical diagnostics, nondestructive 3D pathology offers researchers and clinicians the ability to visualize orders of magnitude more tissue within their natural volumetric context. This has been enabled by rapid advances in tissue-preparation methods, high-throughput 3D microscopy instrumentation, and computational tools for processing these massive feature-rich data sets. Here, we provide a brief overview of many of these technical advances along with remaining challenges to be overcome. We also speculate on the future of 3D pathology as applied in translational investigations, preclinical drug development, and clinical decision-support assays.
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Affiliation(s)
- Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA;
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Adam K Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA;
- Allen Institute for Neural Dynamics, Seattle, Washington, USA
| | - Chetan Poudel
- 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
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Jung SR, Kim J, Vojtech L, Vaughan JC, Chiu DT. Error-Correction Method for High-Throughput Sizing of Nanoscale Vesicles with Single-Molecule Localization Microscopy. J Phys Chem B 2023; 127:2701-2707. [PMID: 36944080 PMCID: PMC10224584 DOI: 10.1021/acs.jpcb.2c09053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Single-molecule localization microscopy (SMLM) allows super-resolution imaging, mapping, counting, and sizing of biological nanostructures such as cell organelles and extracellular vesicles (EVs), but sizing structures smaller than ∼100 nm can be inaccurate due to single-molecule localization error caused by distortion of the point spread function and limited photon number. Here we demonstrate a method to correct localization error when sizing vesicles and other spherical nanoparticles with SMLM and compare sizing results using two vesicle labeling schemes. We use mean approximation theory to derive a simple equation using full width at half-maximum (FWHM) for correcting particle sizes measured by two-dimensional SMLM, validate the method by sizing streptavidin-coated polystyrene nanobeads with the SMLM technique dSTORM with and without error correction, using transmission electron microscopy (TEM) for comparison, and then apply the method to sizing small seminal EVs. Nanobead sizes measured by dSTORM became increasingly less accurate (larger than TEM values) for beads smaller than 50 nm. The error-correction method reduced the size difference versus TEM from 15% without error correction to 7% with error correction for 40 nm beads, from 44% to 9% for 30 nm beads, and from 66% to 15% for 20 nm beads. Seminal EVs were labeled with a lipophilic membrane dye (MemBright 700) and with an Alexa Fluor 488-anti-CD63 antibody conjugate, and were sized separately using both dyes by dSTORM. Error-corrected exosome diameters were smaller than uncorrected values: 72 nm vs 79 nm mean diameter with membrane dyes; 84 nm vs 97 nm with the antibody-conjugated dyes. The mean error-corrected diameter was 12 nm smaller when using the membrane dye than when using the antibody-conjugated dye likely due to the large size of the antibody. Thus, both the error-correction method and the compact membrane labeling scheme reduce overestimation of vesicle size by SMLM. This error-correction method has a low computational cost as it does not require correction of individual blinking events, and it is compatible with all SMLM techniques (e.g., PALM, STORM, and DNA-PAINT).
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Affiliation(s)
- Seung-Ryoung Jung
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - James Kim
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Lucia Vojtech
- Departments of Obstetrics and Gynecology,University of Washington, Seattle, WA 98195, USA
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
- Departments of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Daniel T. Chiu
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
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6
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Pippin JW, Kaverina N, Wang Y, Eng DG, Zeng Y, Tran U, Loretz CJ, Chang A, Akilesh S, Poudel C, Perry HS, O’Connor C, Vaughan JC, Bitzer M, Wessely O, Shankland SJ. Upregulated PD-1 signaling antagonizes glomerular health in aged kidneys and disease. J Clin Invest 2022; 132:156250. [PMID: 35968783 PMCID: PMC9374384 DOI: 10.1172/jci156250] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 06/24/2022] [Indexed: 01/21/2023] Open
Abstract
With an aging population, kidney health becomes an important medical and socioeconomic factor. Kidney aging mechanisms are not well understood. We previously showed that podocytes isolated from aged mice exhibit increased expression of programmed cell death protein 1 (PD-1) surface receptor and its 2 ligands (PD-L1 and PD-L2). PDCD1 transcript increased with age in microdissected human glomeruli, which correlated with lower estimated glomerular filtration rate and higher segmental glomerulosclerosis and vascular arterial intima-to-lumen ratio. In vitro studies in podocytes demonstrated a critical role for PD-1 signaling in cell survival and in the induction of a senescence-associated secretory phenotype. To prove PD-1 signaling was critical to podocyte aging, aged mice were injected with anti-PD-1 antibody. Treatment significantly improved the aging phenotype in both kidney and liver. In the glomerulus, it increased the life span of podocytes, but not that of parietal epithelial, mesangial, or endothelial cells. Transcriptomic and immunohistochemistry studies demonstrated that anti-PD-1 antibody treatment improved the health span of podocytes. Administering the same anti-PD-1 antibody to young mice with experimental focal segmental glomerulosclerosis (FSGS) lowered proteinuria and improved podocyte number. These results suggest a critical contribution of increased PD-1 signaling toward both kidney and liver aging and in FSGS.
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Affiliation(s)
| | | | - Yuliang Wang
- Paul G. Allen School of Computer Science and Engineering, and
| | | | - Yuting Zeng
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Uyen Tran
- Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | | | - Anthony Chang
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
| | - Shreeram Akilesh
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Chetan Poudel
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Hannah S. Perry
- 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 and
| | - Markus Bitzer
- Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Oliver Wessely
- Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Stuart J. Shankland
- Division of Nephrology,,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA
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Hardin WR, Alas GCM, Taparia N, Thomas EB, Steele-Ogus MC, Hvorecny KL, Halpern AR, Tůmová P, Kollman JM, Vaughan JC, Sniadecki NJ, Paredez AR. The Giardia ventrolateral flange is a lamellar membrane protrusion that supports attachment. PLoS Pathog 2022; 18:e1010496. [PMID: 35482847 PMCID: PMC9089883 DOI: 10.1371/journal.ppat.1010496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/10/2022] [Accepted: 04/04/2022] [Indexed: 12/01/2022] Open
Abstract
Attachment to the intestinal epithelium is critical to the lifestyle of the ubiquitous parasite Giardia lamblia. The ventrolateral flange is a sheet-like membrane protrusion at the interface between parasites and attached surfaces. This structure has been implicated in attachment, but its role has been poorly defined. Here, we identified a novel actin associated protein with putative WH2-like actin binding domains we named Flangin. Flangin complexes with Giardia actin (GlActin) and is enriched in the ventrolateral flange making it a valuable marker for studying the flanges' role in Giardia biology. Live imaging revealed that the flange grows to around 1 μm in width after cytokinesis, then remains uniform in size during interphase, grows in mitosis, and is resorbed during cytokinesis. A flangin truncation mutant stabilizes the flange and blocks cytokinesis, indicating that flange disassembly is necessary for rapid myosin-independent cytokinesis in Giardia. Rho family GTPases are important regulators of membrane protrusions and GlRac, the sole Rho family GTPase in Giardia, was localized to the flange. Knockdown of Flangin, GlActin, and GlRac result in flange formation defects. This indicates a conserved role for GlRac and GlActin in forming membrane protrusions, despite the absence of canonical actin binding proteins that link Rho GTPase signaling to lamellipodia formation. Flangin-depleted parasites had reduced surface contact and when challenged with fluid shear force in flow chambers they had a reduced ability to remain attached, confirming a role for the flange in attachment. This secondary attachment mechanism complements the microtubule based adhesive ventral disc, a feature that may be particularly important during mitosis when the parental ventral disc disassembles in preparation for cytokinesis. This work supports the emerging view that Giardia's unconventional actin cytoskeleton has an important role in supporting parasite attachment.
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Affiliation(s)
- William R. Hardin
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Germain C. M. Alas
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Nikita Taparia
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Elizabeth B. Thomas
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Melissa C. Steele-Ogus
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Kelli L. Hvorecny
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Aaron R. Halpern
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Pavla Tůmová
- Institute of Immunology and Microbiology, 1 Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Justin M. Kollman
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, United States of America
| | - Nathan J. Sniadecki
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
- Bioengineering, University of Washington, Seattle, Washington, United States of America
- Lab Medicine & Pathology, University of Washington, Seattle, Washington, United States of America
- Center for Cardiovascular Biology, University of Washington, Seattle, Washington, United States of America
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Alexander R. Paredez
- Department of Biology, University of Washington, Seattle, Washington, United States of America
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8
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Barner LA, Glaser AK, Mao C, Susaki EA, Vaughan JC, Dintzis SM, Liu JTC. Multiresolution nondestructive 3D pathology of whole lymph nodes for breast cancer staging. J Biomed Opt 2022; 27:036501. [PMID: 35315258 PMCID: PMC8936940 DOI: 10.1117/1.jbo.27.3.036501] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
SIGNIFICANCE For breast cancer patients, the extent of regional lymph node (LN) metastasis influences the decision to remove all axillary LNs. Metastases are currently identified and classified with visual analysis of a few thin tissue sections with conventional histology that may underrepresent the extent of metastases. AIM We sought to enable nondestructive three-dimensional (3D) pathology of human axillary LNs and to develop a practical workflow for LN staging with our method. We also sought to evaluate whether 3D pathology improves staging accuracy in comparison to two-dimensional (2D) histology. APPROACH We developed a method to fluorescently stain and optically clear LN specimens for comprehensive imaging with multiresolution open-top light-sheet microscopy. We present an efficient imaging and data-processing workflow for rapid evaluation of H&E-like datasets in 3D, with low-resolution screening to identify potential metastases followed by high-resolution localized imaging to confirm malignancy. RESULTS We simulate LN staging with 3D and 2D pathology datasets from 10 metastatic nodes, showing that 2D pathology consistently underestimates metastasis size, including instances in which 3D pathology would lead to upstaging of the metastasis with important implications on clinical treatment. CONCLUSIONS Our 3D pathology method may improve clinical management for breast cancer patients by improving staging accuracy of LN metastases.
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Affiliation(s)
- Lindsey A. Barner
- University of Washington, Department of Mechanical Engineering, Seattle, Washington, United States
| | - Adam K. Glaser
- University of Washington, Department of Mechanical Engineering, Seattle, Washington, United States
| | - Chenyi Mao
- University of Washington, Department of Chemistry, Seattle, Washington, United States
| | - Etsuo A. Susaki
- Juntendo University Graduate School of Medicine, Department of Biochemistry and Systems Biomedicine, Tokyo, Japan
- RIKEN Center for Biosystems Dynamics Research, Laboratory for Synthetic Biology, Osaka, Japan
| | - Joshua C. Vaughan
- University of Washington, Department of Chemistry, Seattle, Washington, United States
- University of Washington, Department of Physiology and Biophysics, Seattle, Washington, United States
| | - Suzanne M. Dintzis
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, Washington, United States
| | - Jonathan T. C. Liu
- University of Washington, Department of Mechanical Engineering, Seattle, Washington, United States
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, Washington, United States
- University of Washington, Department of Bioengineering, Seattle, Washington, United States
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Halpern AR, Lee MY, Howard MD, Woodworth MA, Nicovich PR, Vaughan JC. Versatile, do-it-yourself, low-cost spinning disk confocal microscope. Biomed Opt Express 2022; 13:1102-1120. [PMID: 35284165 PMCID: PMC8884209 DOI: 10.1364/boe.442087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/20/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Confocal microscopy is an invaluable tool for 3D imaging of biological specimens, however, accessibility is often limited to core facilities due to the high cost of the hardware. We describe an inexpensive do-it-yourself (DIY) spinning disk confocal microscope (SDCM) module based on a commercially fabricated chromium photomask that can be added on to a laser-illuminated epifluorescence microscope. The SDCM achieves strong performance across a wide wavelength range (∼400-800 nm) as demonstrated through a series of biological imaging applications that include conventional microscopy (immunofluorescence, small-molecule stains, and fluorescence in situ hybridization) and super-resolution microscopy (single-molecule localization microscopy and expansion microscopy). This low-cost and simple DIY SDCM is well-documented and should help increase accessibility to confocal microscopy for researchers.
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Affiliation(s)
- Aaron R Halpern
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA
| | - Min Yen Lee
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA
| | - Marco D Howard
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA
| | - Marcus A Woodworth
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA
| | | | - Joshua C Vaughan
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA
- University of Washington, Department of Physiology and Biophysics, Seattle, WA 98195, USA
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11
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Xie W, Reder NP, Koyuncu C, Leo P, Hawley S, Huang H, Mao C, Postupna N, Kang S, Serafin R, Gao G, Han Q, Bishop KW, Barner LA, Fu P, Wright JL, Keene CD, Vaughan JC, Janowczyk A, Glaser AK, Madabhushi A, True LD, Liu JTC. Prostate Cancer Risk Stratification via Nondestructive 3D Pathology with Deep Learning-Assisted Gland Analysis. Cancer Res 2022; 82:334-345. [PMID: 34853071 PMCID: PMC8803395 DOI: 10.1158/0008-5472.can-21-2843] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/19/2021] [Accepted: 11/24/2021] [Indexed: 01/07/2023]
Abstract
Prostate cancer treatment planning is largely dependent upon examination of core-needle biopsies. The microscopic architecture of the prostate glands forms the basis for prognostic grading by pathologists. Interpretation of these convoluted three-dimensional (3D) glandular structures via visual inspection of a limited number of two-dimensional (2D) histology sections is often unreliable, which contributes to the under- and overtreatment of patients. To improve risk assessment and treatment decisions, we have developed a workflow for nondestructive 3D pathology and computational analysis of whole prostate biopsies labeled with a rapid and inexpensive fluorescent analogue of standard hematoxylin and eosin (H&E) staining. This analysis is based on interpretable glandular features and is facilitated by the development of image translation-assisted segmentation in 3D (ITAS3D). ITAS3D is a generalizable deep learning-based strategy that enables tissue microstructures to be volumetrically segmented in an annotation-free and objective (biomarker-based) manner without requiring immunolabeling. As a preliminary demonstration of the translational value of a computational 3D versus a computational 2D pathology approach, we imaged 300 ex vivo biopsies extracted from 50 archived radical prostatectomy specimens, of which, 118 biopsies contained cancer. The 3D glandular features in cancer biopsies were superior to corresponding 2D features for risk stratification of patients with low- to intermediate-risk prostate cancer based on their clinical biochemical recurrence outcomes. The results of this study support the use of computational 3D pathology for guiding the clinical management of prostate cancer. SIGNIFICANCE: An end-to-end pipeline for deep learning-assisted computational 3D histology analysis of whole prostate biopsies shows that nondestructive 3D pathology has the potential to enable superior prognostic stratification of patients with prostate cancer.
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Affiliation(s)
- Weisi Xie
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | - Nicholas P Reder
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington
| | - Can Koyuncu
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Patrick Leo
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio
| | | | - Hongyi Huang
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | - Chenyi Mao
- Department of Chemistry, University of Washington, Seattle, Washington
| | - Nadia Postupna
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington
| | - Soyoung Kang
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | - Robert Serafin
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | - Gan Gao
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | - Qinghua Han
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Kevin W Bishop
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Lindsey A Barner
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | - Pingfu Fu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Jonathan L Wright
- Department of Urology, University of Washington, Seattle, Washington
| | - C Dirk Keene
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington
- Department of Physiology & Biophysics, Seattle, Washington
| | - Andrew Janowczyk
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio
- Department of Oncology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Adam K Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio
- Louis Stokes Cleveland Veterans Administration Medical Center, Cleveland, Ohio
| | - Lawrence D True
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington
- Department of Urology, University of Washington, Seattle, Washington
| | - Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, Washington.
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington
- Department of Bioengineering, University of Washington, Seattle, Washington
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12
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Shankland SJ, Wang Y, Shaw AS, Vaughan JC, Pippin JW, Wessely O. Podocyte Aging: Why and How Getting Old Matters. J Am Soc Nephrol 2021; 32:2697-2713. [PMID: 34716239 PMCID: PMC8806106 DOI: 10.1681/asn.2021050614] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/26/2021] [Indexed: 02/04/2023] Open
Abstract
The effects of healthy aging on the kidney, and how these effects intersect with superimposed diseases, are highly relevant in the context of the population's increasing longevity. Age-associated changes to podocytes, which are terminally differentiated glomerular epithelial cells, adversely affect kidney health. This review discusses the molecular and cellular mechanisms underlying podocyte aging, how these mechanisms might be augmented by disease in the aged kidney, and approaches to mitigate progressive damage to podocytes. Furthermore, we address how biologic pathways such as those associated with cellular growth confound aging in humans and rodents.
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Affiliation(s)
- Stuart J. Shankland
- Division of Nephrology, University of Washington, Seattle, Washington
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington
| | - Yuliang Wang
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington
| | - Andrey S. Shaw
- Department of Research Biology, Genentech, South San Francisco, California
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington
| | - Jeffrey W. Pippin
- Division of Nephrology, University of Washington, Seattle, Washington
| | - Oliver Wessely
- Lerner Research Institute, Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic Foundation, Cleveland, Ohio
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13
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Woodworth MA, Ng KKH, Halpern AR, Pease NA, Nguyen PHB, Kueh HY, Vaughan JC. Multiplexed single-cell profiling of chromatin states at genomic loci by expansion microscopy. Nucleic Acids Res 2021; 49:e82. [PMID: 34048564 PMCID: PMC8373070 DOI: 10.1093/nar/gkab423] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 04/09/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Proper regulation of genome architecture and activity is essential for the development and function of multicellular organisms. Histone modifications, acting in combination, specify these activity states at individual genomic loci. However, the methods used to study these modifications often require either a large number of cells or are limited to targeting one histone mark at a time. Here, we developed a new method called Single Cell Evaluation of Post-TRanslational Epigenetic Encoding (SCEPTRE) that uses Expansion Microscopy (ExM) to visualize and quantify multiple histone modifications at non-repetitive genomic regions in single cells at a spatial resolution of ∼75 nm. Using SCEPTRE, we distinguished multiple histone modifications at a single housekeeping gene, quantified histone modification levels at multiple developmentally-regulated genes in individual cells, and evaluated the relationship between histone modifications and RNA polymerase II loading at individual loci. We find extensive variability in epigenetic states between individual gene loci hidden from current population-averaged measurements. These findings establish SCEPTRE as a new technique for multiplexed detection of combinatorial chromatin states at single genomic loci in single cells.
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Affiliation(s)
- Marcus A Woodworth
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Kenneth K H Ng
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Aaron R Halpern
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Nicholas A Pease
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Phuc H B Nguyen
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Hao Yuan Kueh
- Department of Bioengineering, University of Washington, Seattle, WA 98195, 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
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14
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Pease NA, Nguyen PHB, Woodworth MA, Ng KKH, Irwin B, Vaughan JC, Kueh HY. Tunable, division-independent control of gene activation timing by a polycomb switch. Cell Rep 2021; 34:108888. [PMID: 33761349 PMCID: PMC8024876 DOI: 10.1016/j.celrep.2021.108888] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/17/2020] [Accepted: 03/01/2021] [Indexed: 01/09/2023] Open
Abstract
During development, progenitors often differentiate many cell generations after receiving signals. These delays must be robust yet tunable for precise population size control. Polycomb repressive mechanisms, involving histone H3 lysine-27 trimethylation (H3K27me3), restrain the expression of lineage-specifying genes in progenitors and may delay their activation and ensuing differentiation. Here, we elucidate an epigenetic switch controlling the T cell commitment gene Bcl11b that holds its locus in a heritable inactive state for multiple cell generations before activation. Integrating experiments and modeling, we identify a mechanism where H3K27me3 levels at Bcl11b, regulated by methyltransferase and demethylase activities, set the time delay at which the locus switches from a compacted, silent state to an extended, active state. This activation delay robustly spans many cell generations, is tunable by chromatin modifiers and transcription factors, and is independent of cell division. With their regulatory flexibility, such timed epigenetic switches may broadly control timing in development.
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Affiliation(s)
- Nicholas A Pease
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Phuc H B Nguyen
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98195, USA
| | - Marcus A Woodworth
- Biological Physics, Structure and Design Program, University of Washington, Seattle, WA 98195, USA; Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Kenneth K H Ng
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Blythe Irwin
- Department of Bioengineering, University of Washington, Seattle, WA 98195, 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
| | - Hao Yuan Kueh
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, USA.
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15
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Mao C, Lee MY, Jhan JR, Halpern AR, Woodworth MA, Glaser AK, Chozinski TJ, Shin L, Pippin JW, Shankland SJ, Liu JT, Vaughan JC. Feature-rich covalent stains for super-resolution and cleared tissue fluorescence microscopy. Sci Adv 2020; 6:eaba4542. [PMID: 32518827 PMCID: PMC7253160 DOI: 10.1126/sciadv.aba4542] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/11/2020] [Indexed: 05/02/2023]
Abstract
Fluorescence microscopy is a workhorse tool in biomedical imaging but often poses substantial challenges to practitioners in achieving bright or uniform labeling. In addition, while antibodies are effective specific labels, their reproducibility is often inconsistent, and they are difficult to use when staining thick specimens. We report the use of conventional, commercially available fluorescent dyes for rapid and intense covalent labeling of proteins and carbohydrates in super-resolution (expansion) microscopy and cleared tissue microscopy. This approach, which we refer to as Fluorescent Labeling of Abundant Reactive Entities (FLARE), produces simple and robust stains that are modern equivalents of classic small-molecule histology stains. It efficiently reveals a wealth of key landmarks in cells and tissues under different fixation or sample processing conditions and is compatible with immunolabeling of proteins and in situ hybridization labeling of nucleic acids.
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Affiliation(s)
- Chenyi Mao
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Min Yen Lee
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Jing-Ru Jhan
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Aaron R. Halpern
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | | | - Adam K. Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | | | - Leonard Shin
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Jeffrey W. Pippin
- Department of Medicine, Division of Nephrology, University of Washington, Seattle, Washington, USA
| | - Stuart J. Shankland
- Department of Medicine, Division of Nephrology, University of Washington, Seattle, Washington, USA
| | - Jonathan T.C. Liu
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Pathology, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, 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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16
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Yan C, Wang F, Peng Y, Williams CR, Jenkins B, Wildonger J, Kim HJ, Perr JB, Vaughan JC, Kern ME, Falvo MR, O'Brien ET, Superfine R, Tuthill JC, Xiang Y, Rogers SL, Parrish JZ. Microtubule Acetylation Is Required for Mechanosensation in Drosophila. Cell Rep 2019; 25:1051-1065.e6. [PMID: 30355484 DOI: 10.1016/j.celrep.2018.09.075] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 08/04/2018] [Accepted: 09/24/2018] [Indexed: 01/13/2023] Open
Abstract
At the cellular level, α-tubulin acetylation alters the structure of microtubules to render them mechanically resistant to compressive forces. How this biochemical property of microtubule acetylation relates to mechanosensation remains unknown, although prior studies have shown that microtubule acetylation influences touch perception. Here, we identify the major Drosophila α-tubulin acetylase (dTAT) and show that it plays key roles in several forms of mechanosensation. dTAT is highly expressed in the larval peripheral nervous system (PNS), but it is largely dispensable for neuronal morphogenesis. Mutation of the acetylase gene or the K40 acetylation site in α-tubulin impairs mechanical sensitivity in sensory neurons and behavioral responses to gentle touch, harsh touch, gravity, and vibration stimuli, but not noxious thermal stimulus. Finally, we show that dTAT is required for mechanically induced activation of NOMPC, a microtubule-associated transient receptor potential channel, and functions to maintain integrity of the microtubule cytoskeleton in response to mechanical stimulation.
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Affiliation(s)
- Connie Yan
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Fei Wang
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Yun Peng
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Claire R Williams
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Brian Jenkins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jill Wildonger
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hyeon-Jin Kim
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Jonathan B Perr
- Department of Chemistry, University of Washington, Seattle, WA 98195, 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
| | - Megan E Kern
- Department of Physics & Astronomy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Michael R Falvo
- Department of Physics & Astronomy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - E Timothy O'Brien
- Department of Physics & Astronomy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Richard Superfine
- Department of Applied and Physical Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - John C Tuthill
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Yang Xiang
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Stephen L Rogers
- Department of Biology, Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.
| | - Jay Z Parrish
- Department of Biology, University of Washington, Seattle, WA 98195, USA.
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17
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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18
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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: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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19
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Jiang N, Rasmussen JP, Clanton JA, Rosenberg MF, Luedke KP, Cronan MR, Parker ED, Kim HJ, Vaughan JC, Sagasti A, Parrish JZ. A conserved morphogenetic mechanism for epidermal ensheathment of nociceptive sensory neurites. eLife 2019; 8:42455. [PMID: 30855229 PMCID: PMC6450671 DOI: 10.7554/elife.42455] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 03/08/2019] [Indexed: 12/13/2022] Open
Abstract
Interactions between epithelial cells and neurons influence a range of sensory modalities including taste, touch, and smell. Vertebrate and invertebrate epidermal cells ensheath peripheral arbors of somatosensory neurons, including nociceptors, yet the developmental origins and functional roles of this ensheathment are largely unknown. Here, we describe an evolutionarily conserved morphogenetic mechanism for epidermal ensheathment of somatosensory neurites. We found that somatosensory neurons in Drosophila and zebrafish induce formation of epidermal sheaths, which wrap neurites of different types of neurons to different extents. Neurites induce formation of plasma membrane phosphatidylinositol 4,5-bisphosphate microdomains at nascent sheaths, followed by a filamentous actin network, and recruitment of junctional proteins that likely form autotypic junctions to seal sheaths. Finally, blocking epidermal sheath formation destabilized dendrite branches and reduced nociceptive sensitivity in Drosophila. Epidermal somatosensory neurite ensheathment is thus a deeply conserved cellular process that contributes to the morphogenesis and function of nociceptive sensory neurons. Humans and other animals perceive and interact with the outside world through their sensory nervous system. Nerve cells, acting as the body’s ‘telegraph wires’, convey signals from sensory organs – like the eyes – to the brain, which then processes this information and tells the body how to respond. There are different kinds of sensory nerve cells that carry different types of information, but they all associate closely with the tissues and organs they connect to the brain. Human skin contains sensory nerve cells, which underpin our senses of touch and pain. There is a highly specialized, complex connection between some of these nerve cells and cells in the skin: the skin cells wrap tightly around the nerve cells’ free ends, forming sheath-like structures. This ‘ensheathment’ process happens in a wide range of animals, including those with a backbone, like fish and humans, and those without, like insects. Ensheathment is thought to be important for the skin’s nerve cells to work properly. Yet it remains unclear how or when these connections first appear. Jiang et al. therefore wanted to determine the developmental origins of ensheathment and to find out if these were also similar in animals with and without backbones. Experiments using fruit fly and zebrafish embryos revealed that nerve cells, not skin cells, were responsible for forming and maintaining the sheaths. In embryos where groups of sensory nerve cells were selectively killed – either using a laser or by making the cells produce a toxin – ensheathment did not occur. Further studies, using a variety of microscopy techniques, revealed that the molecular machinery required to stabilize the sheaths was similar in both fish and flies, and therefore likely to be conserved across different groups of animals. Removing sheaths in fly embryos led to nerve cells becoming unstable; the animals were also less sensitive to touch. This confirmed that ensheathment was indeed necessary for sensory nerve cells to work properly. By revealing how ensheathment first emerges, these findings shed new light on how the sensory nervous system develops and how its activity is controlled. In humans, skin cells ensheath the nerve cells responsible for sensing pain. A better understanding of how ensheathments first arise could therefore lead to new avenues for treating chronic pain and related conditions.
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Affiliation(s)
- Nan Jiang
- Department of Biology, University of Washington, Seattle, United States
| | - Jeffrey P Rasmussen
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Joshua A Clanton
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Marci F Rosenberg
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Kory P Luedke
- Department of Biology, University of Washington, Seattle, United States
| | - Mark R Cronan
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Edward D Parker
- Department of Opthalmology, University of Washington, Seattle, United States
| | - Hyeon-Jin Kim
- Department of Chemistry, University of Washington, Seattle, United States.,Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, United States.,Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Alvaro Sagasti
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Jay Z Parrish
- Department of Biology, University of Washington, Seattle, United States
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20
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Chen Y, Xie W, Glaser AK, Reder NP, Mao C, Dintzis SM, Vaughan JC, Liu JTC. Rapid pathology of lumpectomy margins with open-top light-sheet (OTLS) microscopy. Biomed Opt Express 2019; 10:1257-1272. [PMID: 30891344 PMCID: PMC6420271 DOI: 10.1364/boe.10.001257] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/11/2019] [Accepted: 01/25/2019] [Indexed: 05/18/2023]
Abstract
Open-top light-sheet microscopy is a technique that can potentially enable rapid ex vivo inspection of large tissue surfaces and volumes. Here, we have optimized an open-top light-sheet (OTLS) microscope and image-processing workflow for the comprehensive examination of surgical margin surfaces, and have also developed a novel fluorescent analog of H&E staining that is robust for staining fresh unfixed tissues. Our tissue-staining method can be achieved within 2.5 minutes followed by OTLS microscopy of lumpectomy surfaces at a rate of up to 1.5 cm2/minute. An image atlas is presented to show that OTLS image quality surpasses that of intraoperative frozen sectioning and can approximate that of gold-standard H&E histology of formalin-fixed paraffin-embedded (FFPE) tissues. Qualitative evidence indicates that these intraoperative methods do not interfere with downstream post-operative H&E histology and immunohistochemistry. These results should facilitate the translation of OTLS microscopy for intraoperative guidance of lumpectomy and other surgical oncology procedures.
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Affiliation(s)
- Ye Chen
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98195, USA
- These authors contributed equally
| | - Weisi Xie
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98195, USA
- These authors contributed equally
| | - Adam K. Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Nicholas P. Reder
- Department of Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Chenyi Mao
- Department of Chemistry, University of Washington Seattle, WA 98195, USA
| | - Suzanne M. Dintzis
- Department of Pathology, University of Washington School of Medicine, Seattle, WA 98195, 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
| | - Jonathan T. C. Liu
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98195, USA
- Department of Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
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21
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Xie W, Chen Y, Wang Y, Wei L, Yin C, Glaser AK, Fauver ME, Seibel EJ, Dintzis SM, Vaughan JC, Reder NP, Liu JTC. Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins. J Biomed Opt 2019; 24:1-11. [PMID: 30737911 PMCID: PMC6368047 DOI: 10.1117/1.jbo.24.2.026501] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 01/21/2019] [Indexed: 05/06/2023]
Abstract
Intraoperative assessment of breast surgical margins will be of value for reducing the rate of re-excision surgeries for lumpectomy patients. While frozen-section histology is used for intraoperative guidance of certain cancers, it provides limited sampling of the margin surface (typically <1 % of the margin) and is inferior to gold-standard histology, especially for fatty tissues that do not freeze well, such as breast specimens. Microscopy with ultraviolet surface excitation (MUSE) is a nondestructive superficial optical-sectioning technique that has the potential to enable rapid, high-resolution examination of excised margin surfaces. Here, a MUSE system is developed with fully automated sample translation to image fresh tissue surfaces over large areas and at multiple levels of defocus, at a rate of ∼5 min / cm2. Surface extraction is used to improve the comprehensiveness of surface imaging, and 3-D deconvolution is used to improve resolution and contrast. In addition, an improved fluorescent analog of conventional H&E staining is developed to label fresh tissues within ∼5 min for MUSE imaging. We compare the image quality of our MUSE system with both frozen-section and conventional H&E histology, demonstrating the feasibility to provide microscopic visualization of breast margin surfaces at speeds that are relevant for intraoperative use.
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Affiliation(s)
- Weisi Xie
- University of Washington, Department of Mechanical Engineering, Seattle, Washington, United States
| | - Ye Chen
- University of Washington, Department of Mechanical Engineering, Seattle, Washington, United States
| | - Yu Wang
- University of Washington, Department of Mechanical Engineering, Seattle, Washington, United States
| | - Linpeng Wei
- University of Washington, Department of Mechanical Engineering, Seattle, Washington, United States
| | - Chengbo Yin
- University of Washington, Department of Mechanical Engineering, Seattle, Washington, United States
| | - Adam K. Glaser
- University of Washington, Department of Mechanical Engineering, Seattle, Washington, United States
| | - Mark E. Fauver
- University of Washington, Department of Mechanical Engineering, Seattle, Washington, United States
| | - Eric J. Seibel
- University of Washington, Department of Mechanical Engineering, Seattle, Washington, United States
| | - Suzanne M. Dintzis
- University of Washington, School of Medicine, Department of Pathology, Seattle, Washington, United States
| | - Joshua C. Vaughan
- University of Washington, Department of Chemistry, Seattle, Washington, United States
| | - Nicholas P. Reder
- University of Washington, School of Medicine, Department of Pathology, Seattle, Washington, United States
| | - Jonathan T. C. Liu
- University of Washington, Department of Mechanical Engineering, Seattle, Washington, United States
- University of Washington, School of Medicine, Department of Pathology, Seattle, Washington, United States
- Address all correspondence to Jonathan T. C. Liu, E-mail:
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22
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Harrison GR, Vaughan JC, Hidle B, Laurent GM. Erratum: "DAVIS: A direct algorithm for velocity-map imaging system" [J. Chem. Phys. 148, 194101 (2018)]. J Chem Phys 2018; 149:129901. [PMID: 30278653 DOI: 10.1063/1.5055385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- G R Harrison
- Physics Department, Auburn University, Auburn, Alabama 36849, USA
| | - J C Vaughan
- Physics Department, Auburn University, Auburn, Alabama 36849, USA
| | - B Hidle
- Physics Department, Auburn University, Auburn, Alabama 36849, USA
| | - G M Laurent
- Physics Department, Auburn University, Auburn, Alabama 36849, USA
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23
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Abstract
The past decade has witnessed an explosion in the use of super-resolution fluorescence microscopy methods in biology and other fields. Single-molecule localization microscopy (SMLM) is one of the most widespread of these methods and owes its success in large part to the ability to control the on-off state of fluorophores through various chemical, photochemical, or binding-unbinding mechanisms. We provide here a comprehensive overview of switchable fluorophores in SMLM including a detailed review of all major classes of SMLM fluorophores, and we also address strategies for labeling specimens, considerations for multichannel and live-cell imaging, potential pitfalls, and areas for future development.
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Affiliation(s)
- Honglin Li
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA, 98195
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24
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Dou J, Vorobieva AA, Sheffler W, Doyle LA, Park H, Bick MJ, Mao B, Foight GW, Lee MY, Gagnon LA, Carter L, Sankaran B, Ovchinnikov S, Marcos E, Huang PS, Vaughan JC, Stoddard BL, Baker D. De novo design of a fluorescence-activating β-barrel. Nature 2018; 561:485-491. [PMID: 30209393 PMCID: PMC6275156 DOI: 10.1038/s41586-018-0509-0] [Citation(s) in RCA: 201] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 08/10/2018] [Indexed: 01/07/2023]
Abstract
The regular arrangements of β-strands around a central axis in β-barrels and of α-helices in coiled coils contrast with the irregular tertiary structures of most globular proteins, and have fascinated structural biologists since they were first discovered. Simple parametric models have been used to design a wide range of α-helical coiled-coil structures, but to date there has been no success with β-barrels. Here we show that accurate de novo design of β-barrels requires considerable symmetry-breaking to achieve continuous hydrogen-bond connectivity and eliminate backbone strain. We then build ensembles of β-barrel backbone models with cavity shapes that match the fluorogenic compound DFHBI, and use a hierarchical grid-based search method to simultaneously optimize the rigid-body placement of DFHBI in these cavities and the identities of the surrounding amino acids to achieve high shape and chemical complementarity. The designs have high structural accuracy and bind and fluorescently activate DFHBI in vitro and in Escherichia coli, yeast and mammalian cells. This de novo design of small-molecule binding activity, using backbones custom-built to bind the ligand, should enable the design of increasingly sophisticated ligand-binding proteins, sensors and catalysts that are not limited by the backbone geometries available in known protein structures.
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Affiliation(s)
- Jiayi Dou
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Anastassia A. Vorobieva
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Lindsey A. Doyle
- Division of Basic Science, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Hahnbeom Park
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Matthew J. Bick
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Binchen Mao
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Glenna W. Foight
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Min Yen Lee
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Lauren A. Gagnon
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Sergey Ovchinnikov
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Enrique Marcos
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Po-Ssu Huang
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Barry L. Stoddard
- Division of Basic Science, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA,# corresponding author
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25
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Chozinski TJ, Mao C, Halpern AR, Pippin JW, Shankland SJ, Alpers CE, Najafian B, Vaughan JC. Volumetric, Nanoscale Optical Imaging of Mouse and Human Kidney via Expansion Microscopy. Sci Rep 2018; 8:10396. [PMID: 29991751 PMCID: PMC6039510 DOI: 10.1038/s41598-018-28694-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/21/2018] [Indexed: 01/19/2023] Open
Abstract
Although light microscopy is a powerful tool for the assessment of kidney physiology and pathology, it has traditionally been unable to resolve structures separated by less than the ~250 nm diffraction limit of visible light. Here, we report on the optimization, validation, and application of a recently developed super-resolution fluorescence microscopy method, called expansion microscopy (ExM), for volumetric interrogation of mouse and human kidney tissue with 70-75 nm lateral and ~250 nm axial spatial resolution. Using ExM with a standard confocal microscope, we resolve fine details of structures that have traditionally required visualization by electron microscopy, including podocyte foot processes, the glomerular basement membrane, and the cytoskeleton. This inexpensive and accessible approach to volumetric, nanoscale imaging enables visualization of fine structural details of kidney tissues that were previously difficult or impossible to measure by conventional methodologies.
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Affiliation(s)
- Tyler J Chozinski
- Department of Chemistry, University of Washington, Seattle, Washington, 98195, USA
| | - Chenyi Mao
- Department of Chemistry, University of Washington, Seattle, Washington, 98195, USA
| | - Aaron R Halpern
- Department of Chemistry, University of Washington, Seattle, Washington, 98195, USA
| | - Jeffrey W Pippin
- Department of Medicine, Division of Nephrology, University of Washington, Seattle, Washington, 98195, USA
| | - Stuart J Shankland
- Department of Medicine, Division of Nephrology, University of Washington, Seattle, Washington, 98195, USA
| | - Charles E Alpers
- Department of Pathology, University of Washington, Seattle, Washington, 98195, USA
| | - Behzad Najafian
- Department of Pathology, University of Washington, Seattle, Washington, 98195, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, 98195, USA.
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, 98195, USA.
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26
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Jiang N, Kim HJ, Chozinski TJ, Azpurua JE, Eaton BA, Vaughan JC, Parrish JZ. Superresolution imaging of Drosophila tissues using expansion microscopy. Mol Biol Cell 2018; 29:1413-1421. [PMID: 29688792 PMCID: PMC6014096 DOI: 10.1091/mbc.e17-10-0583] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The limited resolving power of conventional diffraction-limited microscopy hinders analysis of small, densely packed structural elements in cells. Expansion microscopy (ExM) provides an elegant solution to this problem, allowing for increased resolution with standard microscopes via physical expansion of the specimen in a swellable polymer hydrogel. Here, we apply, validate, and optimize ExM protocols that enable the study of Drosophila embryos, larval brains, and larval and adult body walls. We achieve a lateral resolution of ∼70 nm in Drosophila tissues using a standard confocal microscope, and we use ExM to analyze fine intracellular structures and intercellular interactions. First, we find that ExM reveals features of presynaptic active zone (AZ) structure that are observable with other superresolution imaging techniques but not with standard confocal microscopy. We further show that synapses known to exhibit age-dependent changes in activity also exhibit age-dependent changes in AZ structure. Finally, we use the significantly improved axial resolution of ExM to show that dendrites of somatosensory neurons are inserted into epithelial cells at a higher frequency than previously reported in confocal microscopy studies. Altogether, our study provides a foundation for the application of ExM to Drosophila tissues and underscores the importance of tissue-specific optimization of ExM procedures.
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Affiliation(s)
- Nan Jiang
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Hyeon-Jin Kim
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Tyler J Chozinski
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Jorge E Azpurua
- Department of Physiology, University of Texas Health Sciences Center, San Antonio, TX 78229
| | - Benjamin A Eaton
- Department of Physiology, University of Texas Health Sciences Center, San Antonio, TX 78229
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Jay Z Parrish
- Department of Biology, University of Washington, Seattle, WA 98195
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27
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Halpern AR, Alas GCM, Chozinski TJ, Paredez AR, Vaughan JC. Hybrid Structured Illumination Expansion Microscopy Reveals Microbial Cytoskeleton Organization. ACS Nano 2017; 11:12677-12686. [PMID: 29165993 PMCID: PMC5752594 DOI: 10.1021/acsnano.7b07200] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Recently developed tissue-hydrogel methods for specimen expansion now enable researchers to perform super-resolution microscopy with ∼65 nm lateral resolution using ordinary microscopes, standard fluorescent probes, and inexpensive reagents. Here we use the combination of specimen expansion and the optical super-resolution microscopy technique structured illumination microscopy (SIM) to extend the spatial resolution to ∼30 nm. We apply this hybrid method, which we call ExSIM, to study the cytoskeleton of the important human pathogen Giardia lamblia including the adhesive disc and flagellar axonemes. We determined the localization of two recently identified disc-associated proteins, including DAP86676 , which localizes to disc microribbons, and the functionally unknown DAP16263 , which primarily localizes to dorsal microtubules of the disc overlap zone and the paraflagellar rod of ventral axonemes. Based on its strong performance in revealing known and unknown details of the ultrastructure of Giardia, we find that ExSIM is a simple, rapid, and powerful super-resolution method for the study of fixed specimens, and it should be broadly applicable to other biological systems of interest.
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Affiliation(s)
- Aaron R. Halpern
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Germain C. M. Alas
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Tyler J. Chozinski
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Alexander R. Paredez
- Department of Biology, University of Washington, Seattle, Washington, USA
- Corresponding Authors A. R. Paredez (); J. C. Vaughan ()
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA
- Corresponding Authors A. R. Paredez (); J. C. Vaughan ()
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28
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Decarreau J, Wagenbach M, Lynch E, Halpern AR, Vaughan JC, Kollman J, Wordeman L. Corrigendum: The tetrameric kinesin Kif25 suppresses pre-mitotic centrosome separation to establish proper spindle orientation. Nat Cell Biol 2017; 19:740. [PMID: 28561052 DOI: 10.1038/ncb3546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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29
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Decarreau J, Wagenbach M, Lynch E, Halpern AR, Vaughan JC, Kollman J, Wordeman L. The tetrameric kinesin Kif25 suppresses pre-mitotic centrosome separation to establish proper spindle orientation. Nat Cell Biol 2017; 19:384-390. [PMID: 28263957 PMCID: PMC5376238 DOI: 10.1038/ncb3486] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 02/03/2017] [Indexed: 12/17/2022]
Abstract
Microtubules tether centrosomes together during interphase. How this is accomplished and what benefit it provides to the cell is not known. We have identified a bipolar, minus-end-directed kinesin, Kif25, that suppresses centrosome separation. Kif25 is required to prevent premature centrosome separation during interphase. We show that premature centrosome separation leads to microtubule-dependent nuclear translocation, culminating in eccentric nuclear positioning that disrupts the cortical spindle positioning machinery. The activity of Kif25 during interphase is required to maintain a centred nucleus to ensure the spindle is stably oriented at the onset of mitosis.
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Affiliation(s)
- Justin Decarreau
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195, USA
| | - Michael Wagenbach
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195, USA
| | - Eric Lynch
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Aaron R Halpern
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Joshua C Vaughan
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195, USA.,Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Justin Kollman
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Linda Wordeman
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195, USA
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30
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Abstract
Here we report the direct observation and quantitative analysis of single redox events on a modified indium-tin oxide (ITO) electrode. The key in the observation of single redox events are the use of a fluorogenic redox species and the nanoconfinement and hindered redox diffusion inside 3-nm-diameter silica nanochannels. A simple electrochemical process was used to grow an ultrathin silica film (∼100 nm) consisting of highly ordered parallel nanochannels exposing the electrode surface from the bottom. The electrode-supported 3-nm-diameter nanochannels temporally trap fluorescent resorufin molecules resulting in hindered molecular diffusion in the vicinity of the electrode surface. Adsorption, desorption, and heterogeneous redox events of individual resorufin molecules can be studied using total-internal reflection fluorescence (TIRF). The rate constants of adsorption and desorption processes of resorufin were characterized from single-molecule analysis to be (1.73 ± 0.08) × 10-4 cm·s-1 and 15.71 ± 0.76 s-1, respectively. The redox events of resorufin to the non-fluorescent dihydroresorufin were investigated by analyzing the change in surface population of single resorufin molecules with applied potential. The scan-rate-dependent molecular counting results (single-molecule fluorescence voltammetry) indicated a surface-controlled electrochemical kinetics of the resorufin reduction on the modified ITO electrode. This study demonstrates the great potential of mesoporous silica as a useful modification scheme for studying single redox events on a variety of transparent substrates such as ITO electrodes and gold or carbon film coated glass electrodes. The ability to electrochemically grow and transfer mesoporous silica films onto other substrates makes them an attractive material for future studies in spatial heterogeneity of electrocatalytic surfaces.
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Affiliation(s)
- Jin Lu
- Department of Chemistry, University of Washington , Seattle, Washington 98195-1700, United States
| | - Yunshan Fan
- Department of Chemistry, University of Washington , Seattle, Washington 98195-1700, United States
| | - Marco D Howard
- Department of Chemistry, University of Washington , Seattle, Washington 98195-1700, United States
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington , Seattle, Washington 98195-1700, United States
| | - Bo Zhang
- Department of Chemistry, University of Washington , Seattle, Washington 98195-1700, United States
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31
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Chozinski TJ, Halpern AR, Okawa H, Kim HJ, Tremel GJ, Wong RO, Vaughan JC. Expansion microscopy with conventional antibodies and fluorescent proteins. Nat Methods 2016; 13:485-8. [PMID: 27064647 PMCID: PMC4929147 DOI: 10.1038/nmeth.3833] [Citation(s) in RCA: 252] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/18/2016] [Indexed: 11/09/2022]
Abstract
Expansion microscopy is a technique in which fluorophores on fixed specimens are linked to a swellable polymer that is physically expanded to enable super-resolution microscopy with ordinary microscopes. We have developed and characterized new methods for linking fluorophores to the polymer that now enable expansion microscopy with conventional fluorescently labeled antibodies and fluorescent proteins. Our methods simplify the procedure and expand the palette of compatible labels, allowing rapid dissemination of the technique.
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Affiliation(s)
- Tyler J. Chozinski
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Aaron R. Halpern
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Haruhisa Okawa
- Department of Biological Structure, University of Washington, Seattle, Washington, USA
| | - Hyeon-Jin Kim
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Grant J. Tremel
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Rachel O.L. Wong
- Department of Biological Structure, 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
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Halpern AR, Howard MD, Vaughan JC. Point by Point: An Introductory Guide to Sample Preparation for Single-Molecule, Super-Resolution Fluorescence Microscopy. ACTA ACUST UNITED AC 2015; 7:103-20. [DOI: 10.1002/9780470559277.ch140241] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Aaron R. Halpern
- Department of Chemistry, University of Washington; Seattle Washington
| | - Marco D. Howard
- Department of Chemistry, University of Washington; Seattle Washington
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington; Seattle Washington
- Department of Physiology and Biophysics, University of Washington; Seattle Washington
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Chozinski TJ, Gagnon LA, Vaughan JC. Twinkle, twinkle little star: photoswitchable fluorophores for super-resolution imaging. FEBS Lett 2014; 588:3603-12. [PMID: 25010263 DOI: 10.1016/j.febslet.2014.06.043] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/14/2014] [Accepted: 06/16/2014] [Indexed: 01/01/2023]
Abstract
Photoswitchable fluorescent probes are key elements of newly developed super-resolution fluorescence microscopy techniques that enable far-field interrogation of biological systems with a resolution of 50 nm or better. In contrast to most conventional fluorescence imaging techniques, the performance achievable by most super-resolution techniques is critically impacted by the photoswitching properties of the fluorophores. Here we review photoswitchable fluorophores for super-resolution imaging with discussion of the fundamental principles involved, a focus on practical implementation with available tools, and an outlook on future directions.
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Affiliation(s)
| | - Lauren A Gagnon
- Department of Chemistry, 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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Abstract
Airy beams maintain their intensity profiles over a large propagation distance without substantial diffraction and exhibit lateral bending during propagation1-5. This unique property has been exploited for micromanipulation of particles6, generation of plasma channels7 and guidance of plasmonic waves8, but has not been explored for high-resolution optical microscopy. Here, we introduce a self-bending point spread function (SB-PSF) based on Airy beams for three-dimensional (3D) super-resolution fluorescence imaging. We designed a side-lobe-free SB-PSF and implemented a two-channel detection scheme to enable unambiguous 3D localization of fluorescent molecules. The lack of diffraction and the propagation-dependent lateral bending make the SB-PSF well suited for precise 3D localization of molecules over a large imaging depth. Using this method, we obtained super-resolution imaging with isotropic 3D localization precision of 10-15 nm over a 3 μm imaging depth from ∼2000 photons per localization.
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Affiliation(s)
- Shu Jia
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Joshua C. Vaughan
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Physics, Harvard University, Cambridge, Massachusetts, USA
- To whom correspondence should be addressed.
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Abstract
We report that the cyanine dye Cy5 and several of its structural relatives are reversibly quenched by the phosphine tris(2-carboxyethyl)phosphine (TCEP). Using Cy5 as a model, we show that the quenching reaction occurs by 1,4-addition of the phosphine to the polymethine bridge of Cy5 to form a covalent adduct. Illumination with UV light dissociates the adduct and returns the dye to the fluorescent state. We demonstrate that TCEP quenching can be used for super-resolution imaging as well as for other applications, such as differentiating between molecules inside and outside the cell.
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Affiliation(s)
- Joshua C Vaughan
- Howard Hughes Medical Institute, and Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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Abstract
Sub-diffraction-limit imaging can be achieved by sequential localization of photoactivatable fluorophores, where the image resolution depends on the number of photons detected per localization. Here, we report a strategy for fluorophore caging that creates photoactivatable probes with high photon yields. Upon photoactivation, these probes can provide 104–106 photons per localization and allow imaging of fixed samples with resolutions of several nanometers. This strategy can be applied to many fluorophores across the visible spectrum.
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Affiliation(s)
- Joshua C Vaughan
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
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Dempsey GT, Vaughan JC, Chen KH, Bates M, Zhuang X. Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging. Nat Methods 2011; 8:1027-36. [PMID: 22056676 PMCID: PMC3272503 DOI: 10.1038/nmeth.1768] [Citation(s) in RCA: 913] [Impact Index Per Article: 70.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 10/05/2011] [Indexed: 01/14/2023]
Abstract
One approach to super-resolution fluorescence imaging uses sequential activation and localization of individual fluorophores to achieve high spatial resolution. Essential to this technique is the choice of fluorescent probes; the properties of the probes, including photons per switching event, on-off duty cycle, photostability and number of switching cycles, largely dictate the quality of super-resolution images. Although many probes have been reported, a systematic characterization of the properties of these probes and their impact on super-resolution image quality has been described in only a few cases. Here we quantitatively characterized the switching properties of 26 organic dyes and directly related these properties to the quality of super-resolution images. This analysis provides guidelines for characterization of super-resolution probes and a resource for selecting probes based on performance. Our evaluation identified several photoswitchable dyes with good to excellent performance in four independent spectral ranges, with which we demonstrated low-cross-talk, four-color super-resolution imaging.
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Affiliation(s)
- Graham T Dempsey
- Graduate program in Biophysics, Harvard University, Cambridge, Massachusetts, USA
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Abstract
Newly developed photoswitchable fluorescent proteins exhibit hundreds to thousands of switching cycles and facilitate live-cell super-resolution imaging at low light intensity.
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Vaughan JC, Brandenburg B, Hogle JM, Zhuang X. Rapid actin-dependent viral motility in live cells. Biophys J 2009; 97:1647-56. [PMID: 19751669 PMCID: PMC3297771 DOI: 10.1016/j.bpj.2009.07.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 06/23/2009] [Accepted: 07/07/2009] [Indexed: 01/21/2023] Open
Abstract
During the course of an infection, viruses take advantage of a variety of mechanisms to travel in cells, ranging from diffusion within the cytosol to active transport along cytoskeletal filaments. To study viral motility within the intrinsically heterogeneous environment of the cell, we have developed a motility assay that allows for the global and unbiased analysis of tens of thousands of virus trajectories in live cells. Using this assay, we discovered that poliovirus exhibits anomalously rapid intracellular movement that was independent of microtubules, a common track for fast and directed cargo transport. Such rapid motion, with speeds of up to 5 microm/s, allows the virus particles to quickly explore all regions of the cell with the exception of the nucleus. The rapid, microtubule-independent movement of poliovirus was observed in multiple human-derived cell lines, but appeared to be cargo-specific. Other cargo, including a closely related picornavirus, did not exhibit similar motility. Furthermore, the motility is energy-dependent and requires an intact actin cytoskeleton, suggesting an active transport mechanism. The speed of this microtubule-independent but actin-dependent movement is nearly an order of magnitude faster than the fastest speeds reported for actin-dependent transport in animal cells, either by actin polymerization or by myosin motor proteins.
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Affiliation(s)
- Joshua C. Vaughan
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Boerries Brandenburg
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - James M. Hogle
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
- Department of Physics, Harvard University, Cambridge, Massachusetts
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Abstract
A novel approach to coherent nonlinear optical spectroscopy based on two-dimensional femtosecond pulse shaping is introduced. Multiple phase-stable output beams are created and overlapped at the sample in a phase-matched boxcars geometry via two-dimensional femtosecond pulse shaping. The pulse timing, shape, phase, and spectral content within all beams may be specified, yielding an unprecedented level of control over the interacting fields in nonlinear spectroscopic experiments. Heterodyne detection and phase cycling of the nonlinear signal are easily implemented due to the excellent phase stability among all output beams. This approach combines the waveform generation capabilities of magnetic resonance spectroscopy with the wavevector specification and phase matching of nonlinear optical spectroscopy, yielding the control capabilities and signal selectivity of both. Results on four prototype systems are used to illustrate some of the novel possibilities of this method.
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Affiliation(s)
- Joshua C Vaughan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Vaughan JC, Hornung T, Feurer T, Nelson KA. Diffraction-based femtosecond pulse shaping with a two-dimensional spatial light modulator. Opt Lett 2005; 30:323-325. [PMID: 15751899 DOI: 10.1364/ol.30.000323] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A new diffraction-based method is proposed and demonstrated for simultaneous shaping of both the phase and amplitude of femtosecond laser pulses by use of a phase-only two-dimensional spatial light modulator. The method suppresses certain types of temporal replica features ordinarily observed in femtosecond pulse shaping owing to imperfections in modulator devices and allows for multiplexed outputs suitable for use in various applications.
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Affiliation(s)
- Joshua C Vaughan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Popescu G, Deflores LP, Vaughan JC, Badizadegan K, Iwai H, Dasari RR, Feld MS. Fourier phase microscopy for investigation of biological structures and dynamics. Opt Lett 2004; 29:2503-5. [PMID: 15584275 DOI: 10.1364/ol.29.002503] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
By use of the Fourier decomposition of a low-coherence optical image field into two spatial components that can be controllably shifted in phase with respect to each other, a new high-transverse-resolution quantitative-phase microscope has been developed. The technique transforms a typical optical microscope into a quantitative-phase microscope, with high accuracy and a path-length sensitivity of lambda/5500, which is stable over several hours. The results obtained on epithelial and red blood cells demonstrate the potential of this instrument for quantitative investigation of the structure and dynamics associated with biological systems without sample preparation.
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Affiliation(s)
- Gabriel Popescu
- George R Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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Hornung T, Vaughan JC, Feurer T, Nelson KA. Degenerate four-wave mixing spectroscopy based on two-dimensional femtosecond pulse shaping. Opt Lett 2004; 29:2052-2054. [PMID: 15455777 DOI: 10.1364/ol.29.002052] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We report noncollinear, degenerate four-wave mixing experiments that employ a new device based on two-dimensional femtosecond pulse shaping that delays and modulates all incident fields. Heterodyne detection is easily implemented due to the full phase stability of the device.
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Affiliation(s)
- Thomas Hornung
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
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Feurer T, Vaughan JC, Hornung T, Nelson KA. Typesetting of terahertz waveforms. Opt Lett 2004; 29:1802-1804. [PMID: 15352375 DOI: 10.1364/ol.29.001802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We demonstrate programmable generation of temporally shaped terahertz waveforms in LiNbO3 by spatially shaping the beam profile of femtosecond excitation laser pulses with a spatial light modulator. The generated terahertz waveforms have amplitudes that are approximately proportional to the first spatial derivative of the excitation beam profile.
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Affiliation(s)
- T Feurer
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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Abstract
We exploit the close similarities between time-frequency and position-wave-vector correspondences to control the spatiotemporal diffraction pattern of ultrashort laser pulses. This approach permits novel, automated generation of sophisticated two-dimensional femtosecond waveforms. A two-dimensional space-time version of a Gerchberg-Saxton algorithm is used to iteratively determine the phase pattern in position-frequency space that produces a user-defined intensity profile in wave-vector-time space.
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Affiliation(s)
- Joshua C Vaughan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Abstract
We achieved automated optical control over coherent lattice responses that were both time- and position-dependent across macroscopic length scales. In our experiments, spatiotemporal femtosecond pulse shaping was used to generate excitation light fields that were directed toward distinct regions of crystalline samples, producing terahertz-frequency lattice vibrational waves that emanated outward from their multiple origins at lightlike speeds. Interferences among the waves resulted in fully specified far-field responses, including tilted, focusing, or amplified wavefronts. Generation and coherent amplification of terahertz traveling waves and terahertz phased-array generation also were demonstrated.
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Affiliation(s)
- T Feurer
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Feurer T, Vaughan JC, Koehl RM, Nelson KA. Multidimensional control of femtosecond pulses by use of a programmable liquid-crystal matrix. Opt Lett 2002; 27:652-654. [PMID: 18007892 DOI: 10.1364/ol.27.000652] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We report the automated generation of high-fidelity spatiotemporally shaped femtosecond pulses by use of an optically addressed, two-dimensional liquid-crystal spatial light modulator. A single input pulse was divided into many independent regions, and each region was shaped temporally. By changing the imaging geometry we accomplished either real-space or wave-vector shaping.
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50
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Johnson WV, Vaughan JC. Study of the American diet. Indiana Med 1986; 79:606-8. [PMID: 3745896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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