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Tsuneoka Y, Atsumi Y, Makanae A, Yashiro M, Funato H. Fluorescence quenching by high-power LEDs for highly sensitive fluorescence in situ hybridization. Front Mol Neurosci 2022; 15:976349. [PMID: 36117911 PMCID: PMC9479452 DOI: 10.3389/fnmol.2022.976349] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022] Open
Abstract
Recent technical advances have made fluorescent in situ hybridization (ISH) a pivotal method to analyze neural tissue. In a highly sensitive ISH, it is important to reduce tissue autofluorescence. We developed a photobleaching device using a light-emitting diode (LED) illuminator to quench autofluorescence in neural tissue. This device was equipped with 12 high-power LEDs (30 W per single LED) and an evaporative cooling system, and these features achieved highly efficient bleaching of autofluorescence and minimized tissue damage. Even after 60 min of photobleaching with evaporative cooling, the temperature gain of the tissue slide was suppressed almost completely. The autofluorescence of lipofuscin-like granules completely disappeared after 60 min of photobleaching, as did other background autofluorescence observed in the mouse cortex and hippocampus. In combination with the recently developed fluorescent ISH method using the hybridization chain reaction (HCR), high signal/noise ratio imaging was achieved without reduction of ISH sensitivity to visualize rare mRNA at single copy resolution by quenching autofluorescence. Photobleaching by the LED illuminator was also effective in quenching the fluorescent staining of ISH-HCR. We performed multiround ISH by repeating the cycle of HCR staining, confocal imaging, and photobleaching. In addition to the two-round ISH, fluorescent immunohistochemistry or fluorescent Nissl staining was conducted on the same tissue. This LED illuminator provides a quick and simple way to reduce autofluorescence and quench fluorescent dyes for multiround ISH with minimum tissue degradation.
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Affiliation(s)
- Yousuke Tsuneoka
- Department of Anatomy, Faculty of Medicine, Toho University, Tokyo, Japan
- *Correspondence: Yousuke Tsuneoka Hiromasa Funato
| | - Yusuke Atsumi
- Department of Anatomy, Faculty of Medicine, Toho University, Tokyo, Japan
- Center for Research and Product Development, Nepa Gene Co., Ltd., Chiba, Japan
| | - Aki Makanae
- Department of Anatomy, Faculty of Medicine, Toho University, Tokyo, Japan
- Center for Research and Product Development, Nepa Gene Co., Ltd., Chiba, Japan
| | - Mitsuru Yashiro
- Department of Anatomy, Faculty of Medicine, Toho University, Tokyo, Japan
- Center for Research and Product Development, Nepa Gene Co., Ltd., Chiba, Japan
| | - Hiromasa Funato
- Department of Anatomy, Faculty of Medicine, Toho University, Tokyo, Japan
- International Institutes for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Ibaraki, Japan
- *Correspondence: Yousuke Tsuneoka Hiromasa Funato
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2
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Fang R, Xia C, Close JL, Zhang M, He J, Huang Z, Halpern AR, Long B, Miller JA, Lein ES, Zhuang X. Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH. Science 2022; 377:56-62. [PMID: 35771910 PMCID: PMC9262715 DOI: 10.1126/science.abm1741] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The human cerebral cortex has tremendous cellular diversity. How different cell types are organized in the human cortex and how cellular organization varies across species remain unclear. In this study, we performed spatially resolved single-cell profiling of 4000 genes using multiplexed error-robust fluorescence in situ hybridization (MERFISH), identified more than 100 transcriptionally distinct cell populations, and generated a molecularly defined and spatially resolved cell atlas of the human middle and superior temporal gyrus. We further explored cell-cell interactions arising from soma contact or proximity in a cell type-specific manner. Comparison of the human and mouse cortices showed conservation in the laminar organization of cells and differences in somatic interactions across species. Our data revealed human-specific cell-cell proximity patterns and a markedly increased enrichment for interactions between neurons and non-neuronal cells in the human cortex.
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Affiliation(s)
- Rongxin Fang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Chenglong Xia
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | | | - Meng Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Jiang He
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Zhengkai Huang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Aaron R. Halpern
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Brian Long
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Ed S. Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
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3
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Sanchez-Arias JC, Carrier M, Frederiksen SD, Shevtsova O, McKee C, van der Slagt E, Gonçalves de Andrade E, Nguyen HL, Young PA, Tremblay MÈ, Swayne LA. A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy. Front Neuroanat 2021; 15:722443. [PMID: 34949993 PMCID: PMC8691181 DOI: 10.3389/fnana.2021.722443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/28/2021] [Indexed: 02/03/2023] Open
Abstract
The ever-expanding availability and evolution of microscopy tools has enabled ground-breaking discoveries in neurobiology, particularly with respect to the analysis of cell-type density and distribution. Widespread implementation of many of the elegant image processing tools available continues to be impeded by the lack of complete workflows that span from experimental design, labeling techniques, and analysis workflows, to statistical methods and data presentation. Additionally, it is important to consider open science principles (e.g., open-source software and tools, user-friendliness, simplicity, and accessibility). In the present methodological article, we provide a compendium of resources and a FIJI-ImageJ-based workflow aimed at improving the quantification of cell density in mouse brain samples using semi-automated open-science-based methods. Our proposed framework spans from principles and best practices of experimental design, histological and immunofluorescence staining, and microscopy imaging to recommendations for statistical analysis and data presentation. To validate our approach, we quantified neuronal density in the mouse barrel cortex using antibodies against pan-neuronal and interneuron markers. This framework is intended to be simple and yet flexible, such that it can be adapted to suit distinct project needs. The guidelines, tips, and proposed methodology outlined here, will support researchers of wide-ranging experience levels and areas of focus in neuroscience research.
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Affiliation(s)
| | - Micaël Carrier
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Axe Neurosciences, Centre de Recherche du CHU de Québec, Université de Laval, Québec City, QC, Canada
| | | | - Olga Shevtsova
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Chloe McKee
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Emma van der Slagt
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | | | - Hai Lam Nguyen
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Penelope A Young
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Marie-Ève Tremblay
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Axe Neurosciences, Centre de Recherche du CHU de Québec, Université de Laval, Québec City, QC, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada.,Department of Molecular Medicine, Université de Laval, Québec City, QC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.,Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Leigh Anne Swayne
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada.,Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, QC, Canada
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4
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Ren M, Tian J, Sun Q, Chen S, Luo T, Jia X, Jiang T, Luo Q, Gong H, Li X. Plastic embedding for precise imaging of large-scale biological tissues labeled with multiple fluorescent dyes and proteins. BIOMEDICAL OPTICS EXPRESS 2021; 12:6730-6745. [PMID: 34858677 PMCID: PMC8606158 DOI: 10.1364/boe.435120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/03/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Resin embedding of multi-color labeled whole organs is the primary step to preserve structural information for visualization of fine structures in three dimensions. It is essential to study the morphological characteristics, spatial and positional relationships of the millions of neurons, and the intricate network of blood vessels with fluorescent labels in the brain. However, the current resin embedding method is inadequate because of incompatibilities with fluorescent dyes, making it difficult to reconstruct a variety of structures for the interpretation of their complex spatial relationships. We modified the resin embedding method for large biological tissues labeled with multiple fluorescent dyes and proteins through different labeling strategies. With TrueBlack as the background fluorescence inhibitor in the glycol methacrylate (GMA) embedding, we referred to the method as GMA-T (Glycol methacrylate with TB). In the GMA-T embedded mouse brains, structures labeled with fluorescent proteins and dyes were visualized in millimeter-scale networks with sub-cellular resolution, allowing quantitative analysis of different anatomical structures in the same brain, including neurons and blood vessels. In combination with high-resolution whole-brain imaging, it is possible to obtain a variety of fluorescence labeled structures in just a few days. We quantified the distribution and morphology of the tdTomato-labeled vasoactive intestinal polypeptide (VIP) neurons and the BSA-FITC labeled blood vessels in the same brain. These results demonstrated that VIP neurons and blood vessels have their own unique distribution patterns and morphological characteristics among cortical regions and different layers in cerebral cortex, and there was no significant correlation between VIP neurons and vessels. This approach provides a novel approach to study the interaction among different anatomical structures within large-volume biological samples labeled with multiple fluorescent dyes and proteins, which helps elucidating the complex anatomical characteristics of biological organs.
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Affiliation(s)
- Miao Ren
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou 570228, China
- These authors contributed equally to this paper
| | - Jiaojiao Tian
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
- These authors contributed equally to this paper
| | - Qingtao Sun
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Siqi Chen
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Ting Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xueyan Jia
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou 215125, China
| | - Tao Jiang
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou 215125, China
| | - Qingming Luo
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou 570228, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou 215125, China
| | - Xiangning Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou 215125, China
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5
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Nolta NF, Liberti A, Makol R, Han M. Gelatin embedding and LED autofluorescence reduction for rodent spinal cord histology. J Neurosci Methods 2020; 346:108924. [PMID: 32918967 DOI: 10.1016/j.jneumeth.2020.108924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 11/20/2022]
Abstract
We present two innovations in histological technique for rodent spinal cord: gelatin embedding and LED photobleaching. Gelatin embedding uses liquid gelatin solution to permeate delicate biological structures then solidify to provide mechanical support throughout dissection, vibratome sectioning, and staining. LED photobleaching uses high-intensity visible light during blocking and primary incubations to reduce autofluorescence in tissue sections before fluorescent secondaries are added. We found gelatin embedding improved mechanical stability without interfering with immunohistochemical staining. Gelatin embedding also preserved some spinal roots and provided an opportunity for dye-less and cut-less tracking of left/right orientation during free-floating staining, which is valuable for tissue samples that have no spare areas that can be marked. LED photobleaching greatly reduced autofluorescence and added essentially no extra time or labor to the process. Descriptions of the techniques and characterization data are provided.
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Affiliation(s)
- Nicholas F Nolta
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Alexandra Liberti
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Rohit Makol
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Martin Han
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA; Institute of Materials Science, University of Connecticut, Storrs, CT, 06269, USA.
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6
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Powell JM, Plummer NW, Scappini EL, Tucker CJ, Jensen P. DEFiNE: A Method for Enhancement and Quantification of Fluorescently Labeled Axons. Front Neuroanat 2019; 12:117. [PMID: 30687025 PMCID: PMC6336715 DOI: 10.3389/fnana.2018.00117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/17/2018] [Indexed: 11/29/2022] Open
Abstract
Visualization and quantification of fluorescently labeled axonal fibers are widely employed in studies of neuronal connectivity in the brain. However, accurate analysis of axon density is often confounded by autofluorescence and other fluorescent artifacts. By the time these problems are detected in labeled tissue sections, significant time and resources have been invested, and the tissue may not be easy to replace. In response to these difficulties, we have developed Digital Enhancement of Fibers with Noise Elimination (DEFiNE), a method for eliminating fluorescent artifacts from digital images based on their morphology and fluorescence spectrum, thus permitting enhanced visualization and quantification of axonal fibers. Application of this method is facilitated by a DEFiNE macro, written using ImageJ Macro Language (IJM), which includes an automated and customizable procedure for image processing and a semi-automated quantification method that accounts for any remaining local variation in background intensity. The DEFiNE macro is open-source and used with the widely available FIJI software for maximum accessibility.
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Affiliation(s)
- Jeanne M Powell
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, United States Department of Health and Human Services, Durham, NC, United States
| | - Nicholas W Plummer
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, United States Department of Health and Human Services, Durham, NC, United States
| | - Erica L Scappini
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, United States Department of Health and Human Services, Durham, NC, United States
| | - Charles J Tucker
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, United States Department of Health and Human Services, Durham, NC, United States
| | - Patricia Jensen
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, United States Department of Health and Human Services, Durham, NC, United States
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7
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Sun Y, Medina Cruz A, Hadley KC, Galant NJ, Law R, Vernon RM, Morris VK, Robertson J, Chakrabartty A. Physiologically Important Electrolytes as Regulators of TDP-43 Aggregation and Droplet-Phase Behavior. Biochemistry 2018; 58:590-607. [DOI: 10.1021/acs.biochem.8b00842] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yulong Sun
- University Health Network, Princess Margaret Cancer Centre, University of Toronto, TMDT 4-305, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Alison Medina Cruz
- Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, TMDT 4-305, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Kevin C. Hadley
- University Health Network, Princess Margaret Cancer Centre, University of Toronto, TMDT 4-305, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Natalie J. Galant
- University Health Network, Princess Margaret Cancer Centre, University of Toronto, TMDT 4-305, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Ryan Law
- Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, TMDT 4-305, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Robert M. Vernon
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Vanessa K. Morris
- University Health Network, Princess Margaret Cancer Centre, University of Toronto, TMDT 4-305, 101 College Street, Toronto, ON M5G 1L7, Canada
- School of Biological Sciences, University of Canterbury, Ilam, Christchurch 8041, New Zealand
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Avijit Chakrabartty
- University Health Network, Princess Margaret Cancer Centre, University of Toronto, TMDT 4-305, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, TMDT 4-305, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Biochemistry, University of Toronto, TMDT 4-305, 101 College Street, Toronto, ON M5G 1L7, Canada
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8
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Sato A, Kim JD, Mizukami H, Nakashima M, Kako K, Ishida J, Itakura A, Takeda S, Fukamizu A. Gestational changes in PRMT1 expression of murine placentas. Placenta 2018; 65:47-54. [PMID: 29908641 DOI: 10.1016/j.placenta.2018.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/24/2018] [Accepted: 04/06/2018] [Indexed: 10/17/2022]
Abstract
INTRODUCTION In mammals, the placenta is an organ that is required to maintain the development of fetus during pregnancy. Although the proper formation of placenta is in part regulated by the post-translational modifications of proteins, little is known regarding protein arginine methylation during placental development. Here, we characterized developmental expression of protein arginine methyltransferase 1 (PRMT1) in mouse placentas. METHODS Expression levels of PRMT1 mRNA and protein in placentas were investigated using the real-time quantitative PCR and Western blot, respectively. Next, the localization of PRMT1 was determined by immunohistochemistry and immunofluorescence analyses. In addition, the levels of methylarginines of placental proteins were quantified using liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS PRMT1 mRNA and its protein were expressed at highest levels in mid-gestation stages, and their expression showed stepwise decrease in the late gestation. At embryonic (E) day 9, PRMT1 was observed in several different trophoblast cell (TC) subtypes. Furthermore, PRMT1 was mainly expressed in the labyrinth zone of TCs at E13. Finally, total methylarginines of proteins were significantly reduced in late gestation of placentas compared with mid-gestation stages. DISCUSSION In this study, we found developmental changes in the placental expression of PRMT1 and in protein arginine methylation status during pregnancy. These findings provide fundamental information regarding placental PRMT1-mediated arginine methylation during the development.
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Affiliation(s)
- Anna Sato
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyoku, Tokyo 113-8421, Japan
| | - Jun-Dal Kim
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Hayase Mizukami
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Misaki Nakashima
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Koichiro Kako
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Junji Ishida
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Atsuo Itakura
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyoku, Tokyo 113-8421, Japan
| | - Satoru Takeda
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyoku, Tokyo 113-8421, Japan
| | - Akiyoshi Fukamizu
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
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Sun Y, Ip P, Chakrabartty A. Simple Elimination of Background Fluorescence in Formalin-Fixed Human Brain Tissue for Immunofluorescence Microscopy. J Vis Exp 2017. [PMID: 28892031 DOI: 10.3791/56188] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Immunofluorescence is a common method used to visualize subcellular compartments and to determine the localization of specific proteins within a tissue sample. A great hindrance to the acquisition of high quality immunofluorescence images is endogenous autofluorescence of the tissue caused by aging pigments such as lipofuscin or by common sample preparation processes such as aldehyde fixation. This protocol describes how background fluorescence can be greatly reduced through photobleaching using white phosphor light emitting diode (LED) arrays prior to treatment with fluorescent probes. The broad-spectrum emission of white phosphor LEDs allow for bleaching of fluorophores across a range of emission peaks. The photobleaching apparatus can be constructed from off-the-shelf components at very low cost and offers an accessible alternative to commercially available chemical quenchers. A photobleaching pre-treatment of the tissue followed by conventional immunofluorescence staining generates images free of background autofluorescence. Compared to established chemical quenchers which reduced probe as well as background signals, photobleaching treatment had no effect on probe fluorescence intensity while it effectively reduced background and lipofuscin fluorescence. Although photobleaching requires more time for pre-treatment, higher intensity LED arrays may be used to reduce photobleaching time. This simple method can potentially be applied to a variety of tissues, particularly postmitotic tissues that accumulate lipofuscin such as the brain and cardiac or skeletal muscles.
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Affiliation(s)
- Yulong Sun
- Department of Medical Biophysics, University of Toronto;
| | - Philbert Ip
- Department of Biochemistry, University of Toronto
| | - Avijit Chakrabartty
- Department of Medical Biophysics, University of Toronto; Department of Biochemistry, University of Toronto
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10
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Riew TR, Kim HL, Choi JH, Jin X, Shin YJ, Lee MY. Progressive accumulation of autofluorescent granules in macrophages in rat striatum after systemic 3-nitropropionic acid: a correlative light- and electron-microscopic study. Histochem Cell Biol 2017; 148:517-528. [PMID: 28597061 DOI: 10.1007/s00418-017-1589-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2017] [Indexed: 01/10/2023]
Abstract
A variety of tissue biomolecules and intracellular structures are known to be autofluorescent. However, autofluorescent signals in brain tissues often confound analysis of the fluorescent markers used for immunohistochemistry. While investigating tissue and cellular pathologies induced by 3-nitropropionic acid, a mitochondrial toxin selective for striatal neurons, we encountered many autofluorescent signals confined to the lesion core. These structures were excited by blue (wavelength = 488 nm) and yellow-orange (555 nm), but not by red (639 nm) or violet (405 nm) lasers, indicating that this autofluorescence overlaps with the emission spectra of commonly used fluorophores. Almost all of the autofluorescence was localized in activated microglia/macrophages, while reactive astrocytes emitted no detectable autofluorescence. Amoeboid brain macrophages filled with autofluorescent granules revealed very weak expression of the microglial marker, ionized calcium-binding adaptor molecule 1 (Iba1), while activated microglia with evident processes and intense Iba1 immunoreactivity contained scant autofluorescent granules. In addition, immunolabeling with two lysosomal markers, ED1/CD68 and lysosomal-associated membrane protein 1, showed a pattern complementary with autofluorescent signals in activated microglia/macrophages, implying that the autofluorescent structures reside within cytoplasm free of intact lysosomes. A correlative light- and electron-microscopic approach finally revealed the ultrastructural identity of the fluorescent granules, most of which matched to clusters of lipofuscin-like inclusions with varying morphology. Thus, autofluorescence in the damaged brain may reflect the presence of lipofuscin-laden brain macrophages, which should be taken into account when verifying any fluorescent signals that are likely to be correlated with activated microglia/macrophages after brain insults.
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Affiliation(s)
- Tae-Ryong Riew
- Department of Anatomy, Catholic Neuroscience Institute, Cell Death Disease Research Center, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06501, Republic of Korea
| | - Hong Lim Kim
- Integrative Research Support Center, Laboratory of Electron Microscope, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jeong-Heon Choi
- Department of Anatomy, Catholic Neuroscience Institute, Cell Death Disease Research Center, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06501, Republic of Korea
| | - Xuyan Jin
- Department of Anatomy, Catholic Neuroscience Institute, Cell Death Disease Research Center, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06501, Republic of Korea
| | - Yoo-Jin Shin
- Department of Anatomy, Catholic Neuroscience Institute, Cell Death Disease Research Center, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06501, Republic of Korea
| | - Mun-Yong Lee
- Department of Anatomy, Catholic Neuroscience Institute, Cell Death Disease Research Center, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06501, Republic of Korea.
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