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Sim J, Lee A, Kim D, Kim KL, Park BJ, Park KM, Kim K. A Combination of Bio-Orthogonal Supramolecular Clicking and Proximity Chemical Tagging as a Supramolecular Tool for Discovery of Putative Proteins Associated with Laminopathic Disease. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2208088. [PMID: 36843266 DOI: 10.1002/smll.202208088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/08/2023] [Indexed: 05/25/2023]
Abstract
Protein mutations alter protein-protein interactions that can lead to a number of illnesses. Mutations in lamin A (LMNA) have been reported to cause laminopathies. However, the proteins associated with the LMNA mutation have mostly remained unexplored. Herein, a new chemical tool for proximal proteomics is reported, developed by a combination of proximity chemical tagging and a bio-orthogonal supramolecular latching based on cucurbit[7]uril (CB[7])-based host-guest interactions. As this host-guest interaction acts as a noncovalent clickable motif that can be unclicked on-demand, this new chemical tool is exploited for reliable detection of the proximal proteins of LMNA and its mutant that causes laminopathic dilated cardiomyopathy (DCM). Most importantly, a comparison study reveals, for the first time, mutant-dependent alteration in LMNA proteomic environments, which allows to identify putative laminopathic DCM-linked proteins including FOXJ3 and CELF2. This study demonstrates the feasibility of this chemical tool for reliable proximal proteomics, and its immense potential as a new research platform for discovering biomarkers associated with protein mutation-linked diseases.
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Affiliation(s)
- Jaehwan Sim
- Center for Self-assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Ara Lee
- Center for Self-assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 37673, Republic of Korea
- Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Dasom Kim
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Kyung Lock Kim
- Center for Self-assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 37673, Republic of Korea
| | - Bum-Joon Park
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Kyeng Min Park
- Department of Biochemistry, Daegu Catholic University School of Medicine, Daegu, 42471, Republic of Korea
| | - Kimoon Kim
- Center for Self-assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
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2
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Fluorochromized tyramide-glucose oxidase as a multiplex fluorescent tyramide signal amplification system for histochemical analysis. Sci Rep 2022; 12:14807. [PMID: 36097273 PMCID: PMC9468149 DOI: 10.1038/s41598-022-19085-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/24/2022] [Indexed: 11/08/2022] Open
Abstract
Tyramide signal amplification (TSA) is a highly sensitive method for histochemical analysis. Previously, we reported a TSA system, biotinyl tyramine-glucose oxidase (BT-GO), for bright-filed imaging. Here, we develop fluorochromized tyramide-glucose oxidase (FT-GO) as a multiplex fluorescent TSA system. FT-GO involves peroxidase-catalyzed deposition of fluorochromized tyramide (FT) with hydrogen peroxide produced by enzymatic reaction between glucose and glucose oxidase. We showed that FT-GO enhanced immunofluorescence signals while maintaining low background signals. Compared with indirect immunofluorescence detections, FT-GO demonstrated a more widespread distribution of monoaminergic projection systems in mouse and marmoset brains. For multiplex labeling with FT-GO, we quenched antibody-conjugated peroxidase using sodium azide. We applied FT-GO to multiplex fluorescent in situ hybridization, and succeeded in labeling neocortical interneuron subtypes by coupling with immunofluorescence. FT-GO immunofluorescence further increased the detectability of an adeno-associated virus tracer. Given its simplicity and a staining with a high signal-to-noise ratio, FT-GO would provide a versatile platform for histochemical analysis.
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3
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Dual amplification enabled counting based ultrasensitive enzyme-linked immunosorbent assay. Anal Chim Acta 2022; 1198:339510. [DOI: 10.1016/j.aca.2022.339510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 11/17/2022]
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4
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Chen Y, Zhou W, Li X, Yang K, Liang Z, Zhang L, Zhang Y. Research Progress of Protein-Protein Interaction Based on Liquid Chromatography Mass Spectrometry ※. ACTA CHIMICA SINICA 2022. [DOI: 10.6023/a22010055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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5
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Kaneda H, Ida Y, Kuwahara R, Sato I, Nakano T, Tokuda H, Sato T, Murakoshi T, Honke K, Kotani N. Proximity Proteomics Has Potential for Extracellular Vesicle Identification. J Proteome Res 2021; 20:3519-3531. [PMID: 34115501 DOI: 10.1021/acs.jproteome.1c00149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Extracellular vesicles (EVs) are biomarkers and mediators of intercellular communication. In biological samples, EVs are secreted by various types of cells. The proteomic identification of proteins expressed in EVs has potential to contribute to research and clinical applications, particularly for cancer. In this study, the proximity-labeling method-based proteomic approach was used for EV identification, labeling membrane components proximal to a given molecule on the EV membrane surface. Due to the small labeling range, proteins on the surface of the same EVs are likely to be labeled by selecting a given EV surface antigen. The protein group of cancer cell-secreted EV (cEV), which abundantly expresses a close homologue of L1 (CHL1), was examined using a model mouse for lung cancer (LC). cEV-expressed proteins were identified by proteomic analysis of enzyme-mediated activation of radical sources by comparing serum EVs from wild-type and LC mice. SLC4A1 was found to be co-expressed in CHL1-expressing EVs, highlighting EVs expressing both CHL1 and SLC4A1 as candidates for cEVs. Serum EVs expressing both CHL1 and caspase 14 were significantly elevated in LC patients compared with healthy individuals. Thus, the combination of proximity labeling and proteomic analysis allows for effective EV identification.
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Affiliation(s)
- Hisako Kaneda
- Department of Biochemistry, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan.,Department of Oral and Maxillofacial Surgery, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Yui Ida
- Department of Biochemistry, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Ryusuke Kuwahara
- Quantum Wave Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Izumi Sato
- Department of Biochemistry, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Takanari Nakano
- Department of Biochemistry, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Haruhiko Tokuda
- Medical Genome Center Biobank, National Center for Geriatrics and Gerontology, 7-430 Morioka-cho, Obu, Aichi 474-8511, Japan
| | - Tsuyoshi Sato
- Department of Oral and Maxillofacial Surgery, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Takayuki Murakoshi
- Department of Biochemistry, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Koichi Honke
- Department of Biochemistry, Kochi University Medical School, Nankoku, Kochi 783-8505, Japan
| | - Norihiro Kotani
- Department of Biochemistry, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
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6
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Zapatero-Belinchón FJ, Carriquí-Madroñal B, Gerold G. Proximity labeling approaches to study protein complexes during virus infection. Adv Virus Res 2021; 109:63-104. [PMID: 33934830 DOI: 10.1016/bs.aivir.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cellular compartmentalization of proteins and protein complex formation allow cells to tightly control biological processes. Therefore, understanding the subcellular localization and interactions of a specific protein is crucial to uncover its biological function. The advent of proximity labeling (PL) has reshaped cellular proteomics in infection biology. PL utilizes a genetically modified enzyme that generates a "labeling cloud" by covalently labeling proteins in close proximity to the enzyme. Fusion of a PL enzyme to a specific antibody or a "bait" protein of interest in combination with affinity enrichment mass spectrometry (AE-MS) enables the isolation and identification of the cellular proximity proteome, or proxisome. This powerful methodology has been paramount for the mapping of membrane or membraneless organelles as well as for the understanding of hard-to-purify protein complexes, such as those of transmembrane proteins. Unsurprisingly, more and more infection biology research groups have recognized the potential of PL for the identification of host-pathogen interactions. In this chapter, we introduce the enzymes commonly used for PL labeling as well as recent promising advancements and summarize the major achievements in organelle mapping and nucleic acid PL. Moreover, we comprehensively describe the research on host-pathogen interactions using PL, giving special attention to studies in the field of virology.
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Affiliation(s)
- Francisco José Zapatero-Belinchón
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden.
| | - Belén Carriquí-Madroñal
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Gisa Gerold
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden.
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7
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Wang S, Lin CW, Carleton AE, Cortez CL, Johnson C, Taniguchi LE, Sekulovski N, Townshend RF, Basrur V, Nesvizhskii AI, Zou P, Fu J, Gumucio DL, Duncan MC, Taniguchi K. Spatially resolved cell polarity proteomics of a human epiblast model. SCIENCE ADVANCES 2021; 7:7/17/eabd8407. [PMID: 33893097 PMCID: PMC8064645 DOI: 10.1126/sciadv.abd8407] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 03/05/2021] [Indexed: 05/08/2023]
Abstract
Critical early steps in human embryonic development include polarization of the inner cell mass, followed by formation of an expanded lumen that will become the epiblast cavity. Recently described three-dimensional (3D) human pluripotent stem cell-derived cyst (hPSC-cyst) structures can replicate these processes. To gain mechanistic insights into the poorly understood machinery involved in epiblast cavity formation, we interrogated the proteomes of apical and basolateral membrane territories in 3D human hPSC-cysts. APEX2-based proximity bioinylation, followed by quantitative mass spectrometry, revealed a variety of proteins without previous annotation to specific membrane subdomains. Functional experiments validated the requirement for several apically enriched proteins in cyst morphogenesis. In particular, we found a key role for the AP-1 clathrin adaptor complex in expanding the apical membrane domains during lumen establishment. These findings highlight the robust power of this proximity labeling approach for discovering novel regulators of epithelial morphogenesis in 3D stem cell-based models.
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Affiliation(s)
- Sicong Wang
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Amber E Carleton
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chari L Cortez
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Craig Johnson
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Linnea E Taniguchi
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Nikola Sekulovski
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ryan F Townshend
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Deborah L Gumucio
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mara C Duncan
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Kenichiro Taniguchi
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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8
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Huang J, Zhao R, Qin S, Yang S, Li W, Mo J, Wang F, Du Y, Weng X, Zhou X. 4-Thiouridine-Enhanced Peroxidase-Generated Biotinylation of RNA. Chembiochem 2020; 22:212-216. [PMID: 32864814 DOI: 10.1002/cbic.202000567] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 08/28/2020] [Indexed: 12/21/2022]
Abstract
Peroxidase-generated proximity labeling is in widespread use to study subcellular proteomes and the protein interaction networks in living cells, but the development of subcellular RNA labeling is limited. APEX-seq has emerged as a new method to study subcellular RNA in living cells, but the labeling of RNA still has room to improve. In this work, we describe 4-thiouridine (s4 U)-enhanced peroxidase-generated biotinylation of RNA with high efficiency. The incorporation of s4 U could introduce additional sites for RNA labeling, enhanced biotinylation was observed on monomer, model oligo RNA and total RNA. Through the s4 U metabolic approach, the in vivo RNA biotinylation efficiency by peroxidase catalysis was also dramatically increased, which will benefit RNA isolation and study for the spatial transcriptome.
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Affiliation(s)
- Jinguo Huang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Ruiqi Zhao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Shanshan Qin
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Shixi Yang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Wei Li
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Jing Mo
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Fang Wang
- Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, P. R. China
| | - Yuhao Du
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
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9
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Li Y, Tian C, Liu K, Zhou Y, Yang J, Zou P. A Clickable APEX Probe for Proximity-Dependent Proteomic Profiling in Yeast. Cell Chem Biol 2020; 27:858-865.e8. [DOI: 10.1016/j.chembiol.2020.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/24/2019] [Accepted: 05/08/2020] [Indexed: 10/24/2022]
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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11
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Ummethum H, Hamperl S. Proximity Labeling Techniques to Study Chromatin. Front Genet 2020; 11:450. [PMID: 32477404 PMCID: PMC7235407 DOI: 10.3389/fgene.2020.00450] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/14/2020] [Indexed: 12/19/2022] Open
Abstract
Mammals contain over 200 different cell types, yet nearly all have the same genomic DNA sequence. It is a key question in biology how the genetic instructions in DNA are selectively interpreted by cells to specify various transcriptional programs and therefore cellular identity. The structural and functional organization of chromatin governs the transcriptional state of individual genes. To understand how genomic loci adopt different levels of gene expression, it is critical to characterize all local chromatin factors as well as long-range interactions in the 3D nuclear compartment. Much of our current knowledge regarding protein interactions in a chromatin context is based on affinity purification of chromatin components coupled to mass spectrometry (AP-MS). AP-MS has been invaluable to map strong protein-protein interactions in the nucleus. However, the interaction is detected after cell lysis and biochemical enrichment, allowing for loss or gain of false positive or negative interaction partners. Recently, proximity-dependent labeling methods have emerged as powerful tools for studying chromatin in its native context. These methods take advantage of engineered enzymes that are fused to a chromatin factor of interest and can directly label all factors in proximity. Subsequent pull-down assays followed by mass spectrometry or sequencing approaches provide a comprehensive snapshot of the proximal chromatin interactome. By combining this method with dCas9, this approach can also be extended to study chromatin at specific genomic loci. Here, we review and compare current proximity-labeling approaches available for studying chromatin, with a particular focus on new emerging technologies that can provide important insights into the transcriptional and chromatin interaction networks essential for cellular identity.
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Affiliation(s)
- Henning Ummethum
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Stephan Hamperl
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
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12
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Samavarchi-Tehrani P, Samson R, Gingras AC. Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches. Mol Cell Proteomics 2020; 19:757-773. [PMID: 32127388 PMCID: PMC7196579 DOI: 10.1074/mcp.r120.001941] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/25/2020] [Indexed: 12/12/2022] Open
Abstract
The study of protein subcellular distribution, their assembly into complexes and the set of proteins with which they interact with is essential to our understanding of fundamental biological processes. Complementary to traditional assays, proximity-dependent biotinylation (PDB) approaches coupled with mass spectrometry (such as BioID or APEX) have emerged as powerful techniques to study proximal protein interactions and the subcellular proteome in the context of living cells and organisms. Since their introduction in 2012, PDB approaches have been used in an increasing number of studies and the enzymes themselves have been subjected to intensive optimization. How these enzymes have been optimized and considerations for their use in proteomics experiments are important questions. Here, we review the structural diversity and mechanisms of the two main classes of PDB enzymes: the biotin protein ligases (BioID) and the peroxidases (APEX). We describe the engineering of these enzymes for PDB and review emerging applications, including the development of PDB for coincidence detection (split-PDB). Lastly, we briefly review enzyme selection and experimental design guidelines and reflect on the labeling chemistries and their implication for data interpretation.
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Affiliation(s)
| | - Reuben Samson
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada.
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Abstract
Siglecs are known to be bound and regulated by membrane molecules that display specific sialic acid-containing ligands and are present on the same cell (cis-ligands). Because of the low-affinity binding of Siglecs to the glycan ligands, conventional methods such as immunoprecipitation are not suitable for identification of Siglec cis-ligands. Here we describe efficient and specific labeling of cis-ligands of CD22 (also known as Siglec-2) on B lymphocytes by proximity labeling using tyramide. This method may also be applicable to labeling of cis-ligands of other Siglecs.
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14
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Protein Chemical Labeling Using Biomimetic Radical Chemistry. Molecules 2019; 24:molecules24213980. [PMID: 31684188 PMCID: PMC6864698 DOI: 10.3390/molecules24213980] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 01/17/2023] Open
Abstract
Chemical labeling of proteins with synthetic low-molecular-weight probes is an important technique in chemical biology. To achieve this, it is necessary to use chemical reactions that proceed rapidly under physiological conditions (i.e., aqueous solvent, pH, low concentration, and low temperature) so that protein denaturation does not occur. The radical reaction satisfies such demands of protein labeling, and protein labeling using the biomimetic radical reaction has recently attracted attention. The biomimetic radical reaction enables selective labeling of the C-terminus, tyrosine, and tryptophan, which is difficult to achieve with conventional electrophilic protein labeling. In addition, as the radical reaction proceeds selectively in close proximity to the catalyst, it can be applied to the analysis of protein–protein interactions. In this review, recent trends in protein labeling using biomimetic radical reactions are discussed.
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15
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Cho IT, Adelmant G, Lim Y, Marto JA, Cho G, Golden JA. Ascorbate peroxidase proximity labeling coupled with biochemical fractionation identifies promoters of endoplasmic reticulum-mitochondrial contacts. J Biol Chem 2017; 292:16382-16392. [PMID: 28760823 PMCID: PMC5625067 DOI: 10.1074/jbc.m117.795286] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 07/14/2017] [Indexed: 11/06/2022] Open
Abstract
To maintain cellular homeostasis, subcellular organelles communicate with each other and form physical and functional networks through membrane contact sites coupled by protein tethers. In particular, endoplasmic reticulum (ER)-mitochondrial contacts (EMC) regulate diverse cellular activities such as metabolite exchange (Ca2+ and lipids), intracellular signaling, apoptosis, and autophagy. The significance of EMCs has been highlighted by reports indicating that EMC dysregulation is linked to neurodegenerative diseases. Therefore, obtaining a better understanding of the physical and functional components of EMCs should provide new insights into the pathogenesis of several neurodegenerative diseases. Here, we applied engineered ascorbate peroxidase (APEX) to map the proteome at EMCs in live HEK293 cells. APEX was targeted to the outer mitochondrial membrane, and proximity-labeled proteins were analyzed by stable isotope labeling with amino acids in culture (SILAC)-LC/MS-MS. We further refined the specificity of the proteins identified by combining biochemical subcellular fractionation to the protein isolation method. We identified 405 proteins with a 2.0-fold cutoff ratio (log base 2) in SILAC quantification from replicate experiments. We performed validation screening with a Split-Rluc8 complementation assay that identified reticulon 1A (RTN1A), an ER-shaping protein localized to EMCs as an EMC promoter. Proximity mapping augmented with biochemical fractionation and additional validation methods reported here could be useful to discover other components of EMCs, identify mitochondrial contacts with other organelles, and further unravel their communication.
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Affiliation(s)
- Il-Taeg Cho
- From the Department of Pathology, Brigham and Women's Hospital, and
| | - Guillaume Adelmant
- the Departments of Cancer Biology and Pathology, Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Youngshin Lim
- From the Department of Pathology, Brigham and Women's Hospital, and
| | - Jarrod A Marto
- From the Department of Pathology, Brigham and Women's Hospital, and
- the Departments of Cancer Biology and Pathology, Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Ginam Cho
- From the Department of Pathology, Brigham and Women's Hospital, and
| | - Jeffrey A Golden
- From the Department of Pathology, Brigham and Women's Hospital, and
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16
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Lee SW, Lee SE, Ko SH, Hong EK, Nam KI, Nakamura KI, Imayama S, Park YJ, Ahn KY, Bae CS, Kim BY, Park SS. Introduction of Tyramide Signal Amplification (TSA) to Pre-embedding Nanogold-Silver Staining at the Electron Microscopic Level. J Histochem Cytochem 2016; 53:249-52. [PMID: 15684338 DOI: 10.1369/jhc.3b6194.2005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The tyramide signal amplification (TSA) technique has been shown to detect scarce tissue antigens in light and electron microscopy. In this study we applied the TSA technique at the electron microscopic level to pre-embedding immunocytochemistry. This protocol was compared to the non-amplified protocol. With the TSA protocol, the labeling of GM130, a cis-Golgi matrix protein, was tested in a cell line and found to be highly sensitive and more enhanced than that with the simple protocol. Moreover, the gold particles were well localized to the cis-side of the Golgi apparatus in both the TSA and the simple protocol.
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Affiliation(s)
- Seung-won Lee
- Department of Anatomy, Chonnam National University Medical School, Gwangju, Korea.
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17
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Huang R, Kiss MM, Batonick M, Weiner MP, Kay BK. Generating Recombinant Antibodies to Membrane Proteins through Phage Display. Antibodies (Basel) 2016; 5:antib5020011. [PMID: 31557992 PMCID: PMC6698964 DOI: 10.3390/antib5020011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 04/21/2016] [Accepted: 04/21/2016] [Indexed: 01/03/2023] Open
Abstract
One of the most important classes of proteins in terms of drug targets is cell surface membrane proteins, and yet it is a challenging set of proteins for generating high-quality affinity reagents. In this review, we focus on the use of phage libraries, which display antibody fragments, for generating recombinant antibodies to membrane proteins. Such affinity reagents generally have high specificity and affinity for their targets. They have been used for cell staining, for promoting protein crystallization to solve three-dimensional structures, for diagnostics, and for treating diseases as therapeutics. We cover publications on this topic from the past 10 years, with a focus on the various formats of membrane proteins for affinity selection and the diverse affinity selection strategies used. Lastly, we discuss the challenges faced in this field and provide possible directions for future efforts.
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Affiliation(s)
- Renhua Huang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607-7060, USA.
| | - Margaret M Kiss
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Melissa Batonick
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Michael P Weiner
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Brian K Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607-7060, USA.
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18
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Proteomic mapping in live Drosophila tissues using an engineered ascorbate peroxidase. Proc Natl Acad Sci U S A 2015; 112:12093-8. [PMID: 26362788 DOI: 10.1073/pnas.1515623112] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Characterization of the proteome of organelles and subcellular domains is essential for understanding cellular organization and identifying protein complexes as well as networks of protein interactions. We established a proteomic mapping platform in live Drosophila tissues using an engineered ascorbate peroxidase (APEX). Upon activation, the APEX enzyme catalyzes the biotinylation of neighboring endogenous proteins that can then be isolated and identified by mass spectrometry. We demonstrate that APEX labeling functions effectively in multiple fly tissues for different subcellular compartments and maps the mitochondrial matrix proteome of Drosophila muscle to demonstrate the power of APEX for characterizing subcellular proteomes in live cells. Further, we generate "MitoMax," a database that provides an inventory of Drosophila mitochondrial proteins with subcompartmental annotation. Altogether, APEX labeling in live Drosophila tissues provides an opportunity to characterize the organelle proteome of specific cell types in different physiological conditions.
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19
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Jing J, He L, Sun A, Quintana A, Ding Y, Ma G, Tan P, Liang X, Zheng X, Chen L, Shi X, Zhang SL, Zhong L, Huang Y, Dong MQ, Walker CL, Hogan PG, Wang Y, Zhou Y. Proteomic mapping of ER-PM junctions identifies STIMATE as a regulator of Ca²⁺ influx. Nat Cell Biol 2015; 17:1339-47. [PMID: 26322679 PMCID: PMC4589512 DOI: 10.1038/ncb3234] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 07/29/2015] [Indexed: 12/19/2022]
Abstract
Specialized junctional sites that connect the plasma membrane (PM) and endoplasmic reticulum (ER) play critical roles in controlling lipid metabolism and Ca2+ signaling1–4. Store operated Ca2+ entry mediated by dynamic STIM1-ORAI1 coupling represents a classical molecular event occurring at ER-PM junctions, but the protein composition and how previously-unrecognized protein regulators facilitate this process remain ill-defined. Using a combination of spatially-restricted biotin-labelling in situ coupled with mass spectrometry5, 6 and a secondary screen based on bimolecular fluorescence complementation7, we mapped the proteome of intact ER-PM junctions in living cells without disrupting their architectural integrity. Our approaches lead to the discovery of an ER-resident multi-transmembrane protein that we call STIMATE (STIM-activating enhancer, encoded by TMEM110) as a positive regulator of Ca2+ influx in vertebrates. STIMATE physically interacts with STIM1 to promote STIM1 conformational switch. Genetic depletion of STIMATE substantially reduces STIM1 puncta formation at ER-PM junctions and suppresses the Ca2+-NFAT signaling. Our findings enable further genetic studies to elucidate the function of STIMATE in normal physiology and disease, and set the stage to uncover more uncharted functions of hitherto underexplored ER-PM junctions.
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Affiliation(s)
- Ji Jing
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas 77030, USA
| | - Lian He
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas 77030, USA
| | - Aomin Sun
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ariel Quintana
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA
| | - Yuehe Ding
- National Institute of Biological Sciences, Beijing 102206, China
| | - Guolin Ma
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas 77030, USA
| | - Peng Tan
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas 77030, USA
| | - Xiaowen Liang
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas 77030, USA
| | - Xiaolu Zheng
- Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Liangyi Chen
- Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Xiaodong Shi
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, USA
| | - Shenyuan L Zhang
- Department of Medical Physiology, College of Medicine, Texas A&M University Health Science Center, Temple, Texas 76504, USA
| | - Ling Zhong
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas 77030, USA
| | - Yun Huang
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas 77030, USA
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Cheryl L Walker
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas 77030, USA
| | - Patrick G Hogan
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA
| | - Youjun Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Yubin Zhou
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas 77030, USA.,Department of Medical Physiology, College of Medicine, Texas A&M University Health Science Center, Temple, Texas 76504, USA
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20
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Abstract
Enzyme-linked signal amplification is a key technique used to enhance the immunohistochemical detection of protein, mRNA, and other molecular species. Tyramide signal amplification (TSA) is based on a catalytic reporter deposit in close vicinity to the epitope of interest. The advantages of this technique are its simplicity, enhanced sensitivity, high specificity, and compatibility with modern multi-label fluorescent microscopy. Here, we describe the use of a TSA kit to increase the signal of enhanced green fluorescent protein (eGFP) expressed under the control of Slc17a6 regulatory elements in the brain of a transgenic mouse. The labeling procedure consists of 6 basic steps: (1) tissue preparation, (2) blocking of nonspecific epitopes, (3) binding with primary antibody, (4) binding with horseradish peroxidase-conjugated secondary antibody, (5) reacting with fluorescent tyramide substrate, and (6) imaging of the signal. The procedures described herein detail these steps and provide additional guidance and background to assist novice users.
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21
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Rhee HW, Zou P, Udeshi ND, Martell JD, Mootha VK, Carr SA, Ting AY. Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. Science 2013; 339:1328-1331. [PMID: 23371551 DOI: 10.1126/science.1230593] [Citation(s) in RCA: 875] [Impact Index Per Article: 79.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Microscopy and mass spectrometry (MS) are complementary techniques: The former provides spatiotemporal information in living cells, but only for a handful of recombinant proteins at a time, whereas the latter can detect thousands of endogenous proteins simultaneously, but only in lysed samples. Here, we introduce technology that combines these strengths by offering spatially and temporally resolved proteomic maps of endogenous proteins within living cells. Our method relies on a genetically targetable peroxidase enzyme that biotinylates nearby proteins, which are subsequently purified and identified by MS. We used this approach to identify 495 proteins within the human mitochondrial matrix, including 31 not previously linked to mitochondria. The labeling was exceptionally specific and distinguished between inner membrane proteins facing the matrix versus the intermembrane space (IMS). Several proteins previously thought to reside in the IMS or outer membrane, including protoporphyrinogen oxidase, were reassigned to the matrix by our proteomic data and confirmed by electron microscopy. The specificity of peroxidase-mediated proteomic mapping in live cells, combined with its ease of use, offers biologists a powerful tool for understanding the molecular composition of living cells.
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Affiliation(s)
- Hyun-Woo Rhee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peng Zou
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Jeffrey D Martell
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Vamsi K Mootha
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Molecular Biology, Massachusetts General Hospital, and Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alice Y Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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22
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DNA microarrays for visual detection of human pathogenic microorganisms based on tyramine signal amplification coupled with gold label silver stain. Anal Bioanal Chem 2010; 398:2745-50. [DOI: 10.1007/s00216-010-4189-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 08/29/2010] [Accepted: 09/01/2010] [Indexed: 11/26/2022]
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23
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Detection of endogenous and immuno-bound peroxidase — The status Quo in histochemistry. ACTA ACUST UNITED AC 2010; 45:81-139. [DOI: 10.1016/j.proghi.2009.11.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2009] [Indexed: 11/22/2022]
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24
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Bendayan M. A Review of the Potential and Versatility of Colloidal Gold Cytochemical Labeling for Molecular Morphology. Biotech Histochem 2010. [DOI: 10.1080/10520290009068433] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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25
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Bobrow MN, Moen PT. Tyramide signal amplification (TSA) systems for the enhancement of ISH signals in cytogenetics. ACTA ACUST UNITED AC 2008; Chapter 8:Unit 8.9. [PMID: 18770747 DOI: 10.1002/0471142956.cy0809s11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This unit provides a series of techniques that dramatically improve the sensitivity of direct and indirect in situ detection. TSA is a peroxidase-based signal amplification system which is compatible with all in situ hybridization as well as immunocytochemical detection systems. The assay is performed on a glass slide and combines the use of fluorescent probes in either direct or indirect format using either an enzyme-labeled streptavidin or antibody. Protocols are provided for brightfield and fluorescent detection of single DNA targets, DNA or RNA in cultured cells, multitarget detection for DNA/RNA and DNA and RNA. In addition a protocol is included for the TSA plus system, a DNP-based detection system using horseradish peroxidase and alkaline phosphatase.
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Affiliation(s)
- M N Bobrow
- NEN Life Science Products, Boston, Massachusetts, USA
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26
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A simplified, sensitive immunohistochemical detection system employing signal amplification based on fluorescyl-tyramide/antifluorescein antibody reaction: its application to pathologic testing and research. Appl Immunohistochem Mol Morphol 2008; 16:87-93. [PMID: 18091313 DOI: 10.1097/pai.0b013e31802ca9ea] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The catalyzed signal amplification (CSA) technique, based on the peroxidase-mediated deposition of haptenized tyramide and also known as tyramide signal amplification and catalyzed reportor deposition systems, is widely accepted as a signal amplification method for immunohistochemistry and in situ hybridization. In this study, we examined the applicability of a new simplified CSA system employing fluorescyl-tyramide (FT) to pathologic testing and research with formalin-fixed, paraffin-embedded tissues. By using the FT, instead of biotinyl-tyramide (BT) that is commonly employed in the CSA system with chromogen, nonspecific staining caused by endogenous biotin was completely avoided. The FT-CSA system loaded on the automated immunostaining equipment also allowed for more reproducible detection in short times. When applied to cyclin D1 immunostaining that is important in differentiation among small B-cell lymphomas, the system was useful in demonstrating its protein expression in mantle cell lymphomas considered negative or equivocally positive for cyclin D1 in a conventional immunodetection. In immunohistochemistry for phosphorylated proteins and murine hematologic markers that often require higher sensitivity than conventional methods, the FT-CSA system provided desirable staining results with intense signal amplification. Our results indicate that the simplified CSA system employing the FT can be useful in enlarging the target range for routine immunohistochemistry due to its high applicability.
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27
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Saha D, Acharya D, Roy D, Dhar TK. Filtration-based tyramide amplification technique—a new simple approach for rapid detection of aflatoxin B1. Anal Bioanal Chem 2006; 387:1121-30. [PMID: 17151856 DOI: 10.1007/s00216-006-0943-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2006] [Revised: 10/11/2006] [Accepted: 10/12/2006] [Indexed: 11/29/2022]
Abstract
The catalyzed reporter deposition (CARD) method of signal amplification, also called "tyramide signal amplification", has been used in immunoassays not only to increase sensitivity but also to reduce assay time. The current approach to tyramide amplification in immunoassays involves slow incubation with agitation. In this paper we describe new filtration-based tyramide amplification and substrate visualization techniques. Compared with the standard method, this new approach greatly enhances spot intensities in membrane immunoassay and reduces biotinylated tyramide (B-T) and substrate consumption approximately fiftyfold, without loss of specificity. An improved test device and a cost-effective method for preparation of membranes for Super-CARD amplification have also been developed. The techniques have been used for rapid detection of aflatoxin B(1) (AFB(1)) in a variety of foodstuffs with a detection limit of 12.5 microg kg(-1). The assay procedure involves sequential addition of standards or sample, AFB(1)-horseradish peroxidase (HRP) conjugate, B-T, avidin-HRP, and substrate solution over anti-AFB(1) antibody-spotted zones of the membrane surface. The method saves time, improves reproducibility, eliminates many washing steps and avoids manipulation of the membranes between the different steps, while maintaining the sensitivity of the standard method. Average recoveries from different non-infected food samples spiked with AFB(1) at concentrations from 25 to 100 mg kg(-1) were between 95 and 105%. AFB(1) results obtained on different days for Aspergillus parasiticus infection of corn and groundnut samples correlated well with estimates obtained by HPLC.
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Affiliation(s)
- Debjani Saha
- Drug Development, Diagnostics and Biotechnology Division, Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Calcutta, 700 032, India
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28
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Hasui K, Murata F. A new simplified catalyzed signal amplification system for minimizing non-specific staining in tissues with supersensitive immunohistochemistry. ACTA ACUST UNITED AC 2005; 68:1-17. [PMID: 15827374 DOI: 10.1679/aohc.68.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We investigated non-specific staining in a catalyzed reporter deposition (CARD) reaction and improved its blocking methods in supersensitive immunohistochemistry, based on our simplified catalyzed signal amplification (CSA) system (Hasui et al. 2002). In the CARD reaction using biotinyl tyramide, non-specific staining could be reduced by pretreatment with a casein solution or 3% bovine serum albumin (BSA)-phosphate buffer saline (PBS) with 0.1% Tween 20. In the CARD reaction using FITC-labeled tyramide, non-specific staining could be blocked by pretreatment with 0.3% BSA-PBS with 0.1% Tween 20 or 3% polyethylene glycol-PBS with 01% Tween 20. Thus, our new simplified CSA system features: 1) destruction of the endogenous peroxidase activity; 2) blocking of the nonspecific reaction of the primary antibody; 3) a primary antibody reaction; 4) blocking of the non-specific reaction of the polymer reagent by casein treatment; 5) a polymer reaction; 6) blocking of the non-specific reaction of CARD reaction by casein treatment; 7) a CARD reaction; and 8) detection of deposited tyramide. This new system proved useful for detecting an extremely low amount of antigen in the endogenous biotin-rich tissues such as the gastrointestinal tract and liver. By this method, the Ki67 antigen in the G1 phase cell cycle could be detected and a metabolic disorder of the Ki67 antigen was implicated in a carcinoid tumor in the stomach. We believe that this new simplified CSA system represents a new standard of supersensitive immunohistochemistry for use in light-microscopic investigation.
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Affiliation(s)
- Kazuhisa Hasui
- Department of Structural Cell Biology, Field of Musculo-Skeletal Disorder, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima 890-8544, Japan.
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29
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Chakalova L, Carter D, Fraser P. RNA fluorescence in situ hybridization tagging and recovery of associated proteins to analyze in vivo chromatin interactions. Methods Enzymol 2004; 375:479-93. [PMID: 14870684 DOI: 10.1016/s0076-6879(03)75029-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Affiliation(s)
- Lyubomira Chakalova
- Laboratory of Chromatin and Gene Expression, Babraham Institute, Cambridge CB2 4AT, United Kingdom
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30
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Andras SC, Power JB, Cocking EC, Davey MR. Strategies for signal amplification in nucleic acid detection. Mol Biotechnol 2001; 19:29-44. [PMID: 11697219 DOI: 10.1385/mb:19:1:029] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Many aspects of molecular genetics necessitate the detection of nucleic acid sequences. Current approaches involving target amplification (in situ PCR, Primed in situ Labeling, Self-Sustained Sequence Replication, Strand Displacement Amplification), probe amplification (Ligase Chain Reaction, Padlock Probes, Rolling Circle Amplification) and signal amplification (Tyramide Signal Amplification, Branched DNA Amplification) are summarized in the present review, together with their advantages and limitations.
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Affiliation(s)
- S C Andras
- Babes-Boylai University, Faculty of Biology and Geology, Ecology and Genetics Department, Str. Clinicilor 5-7, Cluj-Napoca 3400, Romania
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31
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Mayer G, Bendayan M. Amplification methods for the immunolocalization of rare molecules in cells and tissues. PROGRESS IN HISTOCHEMISTRY AND CYTOCHEMISTRY 2001; 36:3-85. [PMID: 11194866 DOI: 10.1016/s0079-6336(01)80002-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The needs to precisely assign macromolecules to specific locations and domains within tissues and cells and to reveal antigens which are present in low or even in trace amounts, led to the elaboration of a wide spectrum of immunocytochemical amplification procedures. These arise from the successive improvements of tissue preparation techniques, of antigen retrieval procedures and of immunological or non-immunological detection systems. Improvement of detection systems may be the most active in the development of amplification techniques. Since the early work of Coons, in which by the introduction of the indirect technique has started amplifying the signal, different systems have succeeded in increasing the sensitivity of antigens detection. Indeed, amplification techniques such as the multiple antibody layers, the multiple bridges, the enzyme complexes, the avidin-biotin, the silver intensification, and the numerous variations and combinations among these have increased the sensitivity for the detection of scarce tissue antigens. However, as shown by the recent progress carried out with new approaches such as the catalyzed reporter deposition (CARD) and the enhanced polymer one-step staining (EPOS), more efficient methods are still needed. In electron microscopy, few techniques have reached the resolution afforded by the post-embedding immunogold approach. In spite of this and in order to further increase its sensitivity, new probes and novel approaches are allowing combination of the gold marker with the amplification capacity of enzymes afforded by the CARD technique. Immunogold amplification strategies, such as the multiple incubations with the primary antibody and the use of an anti-protein A antibody have also led to enhanced signals displaying the advantages in terms of resolution and possibilities of quantification inherent to the colloidal gold marker.
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Affiliation(s)
- G Mayer
- Département de Pathologie et Biologie Cellulaire, Université de Montréal C.P. 6128, Succ. Centre-ville, Montréal, Quebec H3C 3J7, Canada.
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32
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Hand GM, Martone ME, Stelljes A, Ellisman MH, Sosinsky GE. Specific labeling of connexin43 in NRK cells using tyramide-based signal amplification and fluorescence photooxidation. Microsc Res Tech 2001; 52:331-43. [PMID: 11180624 DOI: 10.1002/1097-0029(20010201)52:3<331::aid-jemt1017>3.0.co;2-h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Imaging of gap junction proteins, the connexins, has been performed in tissue culture cells both by labeling of connexins with immunocytochemical tags and by cloning and expressing chimeras of connexins and fluorescent proteins such as Green Fluorescent Protein. These two approaches have been used to gain information about protein localization or trafficking at light microscopic resolution. Electron microscopy provides higher resolution; however, analysis of electron micrographs of unlabeled connexins has been generally limited to recognition of gap junction structures. Immunolabeling of gap junction proteins in whole cells at the electron microscopic level has been difficult to achieve because of the fixation sensitivity of most gap junction antibodies. To obtain reasonable sensitivity, immunoperoxidase procedures are typically employed, and these suffer from relatively poor resolution. Here we describe the combination of tyramide signal amplification techniques and fluorescence photooxidation for higher resolution immunolocalization studies for correlative light and electron microscopic imaging. By using correlative microscopy, we can not only localize connexin pools or structures, but also discover what other cellular substructures interact with gap junction proteins. The use of tyramide signal amplification techniques is necessary to increase fluorescence levels that have decreased due to increased specimen fixation required to maintain cell ultrastructure. The fluorescence photooxidation technique provides a high-resolution method for staining of proteins in cells. Unlike colloidal gold-based methods, fluorescence photooxidation allows for three-dimensional localization using high-voltage electron microscopy.
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Affiliation(s)
- G M Hand
- National Center for Microscopy and Imaging Research, Dept. of Neurosciences, University of California, San Diego, La Jolla, California 92093-0608, USA
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33
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Zerbini M, Cricca M, Gentilomi G, Venturoli S, Gallinella G, Musiani M. Tyramide signal amplification of biotinylated probe in dot-blot hybridization assay for the detection of parvovirus B19 DNA in serum samples. Clin Chim Acta 2000; 302:79-87. [PMID: 11074066 DOI: 10.1016/s0009-8981(00)00354-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Highly sensitive assay systems are necessary for large-scale virological screenings. We evaluated the use of tyramide signal amplification (TSA) for biotinylated probe in dot-blot hybridization assay to detect B19 DNA in serum samples. The probe was constructed by PCR and directly labeled with biotin during amplification reaction. The sensitivity of the dot-blot hybridization assay with TSA detection method was evaluated in comparison with a hybridization assay using the direct detection of biotinylated probe by streptavidin-biotin-alkaline phosphatase substrate. The TSA detection was able to detect 1 pg of B19 DNA and proved to be 10-50 times more sensitive than the hybridization assay with the direct detection of biotinylated probe. The analysis of 720 serum samples by TSA detection of biotinylated probe showed that the assay may be a valid diagnostic tool in routine testing of B19 DNA in serum samples.
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Affiliation(s)
- M Zerbini
- Department of Clinical and Experimental Medicine, Division of Microbiology, Osp. S. Orsola, University of Bologna, Via Massarenti 9, 40138, Bologna, Italy.
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Köhler A, Lauritzen B, Van Noorden CJ. Signal amplification in immunohistochemistry at the light microscopic level using biotinylated tyramide and nanogold-silver staining. J Histochem Cytochem 2000; 48:933-41. [PMID: 10858270 DOI: 10.1177/002215540004800706] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Signal amplification techniques greatly enhance the sensitivity of immunohistochemical (IHC) and in situ hybridization (ISH) methods. In particular, catalyzed signal amplification (CSA) using labeled tyramide or Nanogold-silver staining is an important signal amplification tool. We have applied a combination of both techniques, as has been introduced for ISH, for a further increase in sensitivity of an IHC method to detect cathepsin B. This lysosomal proteinase can also be expressed extracellularly, particularly in relation to cancer metastasis. Higher sensitivity of the IHC method was needed because existing methods failed to demonstrate cathepsin B protein where cathepsin B activity was found with a fluorescence enzyme histochemical method. Combined CSA and Nanogold-silver staining provided the sensitivity that was required. Moreover, this signal amplification method enabled the use of a 10-fold lower concentration of primary antibody (1 microg/ml). Nonspecific background staining was low provided that endogenous biotin, avidin, and peroxidase were completely blocked. The method was reproducible when all steps, and particularly the silver enhancement step, were rigidly controlled. The method resulted in localization patterns of cathepsin B protein that were in agreement with those of cathepsin B activity in serial sections of rat liver containing colon cancer metastases. We concluded that combined application of CSA and Nanogold-silver staining provides high sensitivity for immunohistochemical methods and that activity localization by an enzyme histochemical method is a very attractive alternative to IHC localization of an enzyme because it is at least as sensitive, it is rapid and simple, and it provides direct information on the function of an enzyme.
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Affiliation(s)
- A Köhler
- Department of Ecophysiology and Toxicology, Biologische Anstalt Helgoland in the Alfred Wegener Institute, Hamburg, Germany
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Herrera GA, Lowery MC, Turbat-Herrera EA. Immunoelectron microscopy in the age of molecular pathology. Appl Immunohistochem Mol Morphol 2000; 8:87-97. [PMID: 10937055 DOI: 10.1097/00129039-200006000-00002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The introduction of molecular biology-based diagnostic procedures in pathology has created substantial expectations in regard to screening, characterization, monitoring, and detection of predisposition to a variety of diseases, most notably malignant neoplasms. It should be emphasized, however, that molecular studies are only one component of the diagnostic process and that more traditional methods are still required in the evaluation of tumors and management of patients. The data obtained from the molecular biology-based studies must be always interpreted in conjunction with the clinical history, immunomorphologic findings, and other pertinent ancillary data. Routine evaluation of tissues using traditional light microscopy remains the backbone of pathologic evaluation. The additive role of molecular diagnostics often depends on how accurate the initial evaluation has been. Ancillary techniques such as immunohistochemistry and electron microscopy remain essential in properly characterizing diseased tissues and in speciation of tumors. Ultrastructural immunolabeling capitalizes on combining these two techniques and providing exquisite immunomorphologic evaluation. The extra time and effort required are more than compensated by the degree of sophistication that can be achieved when this diagnostic technique is utilized and the added expense is rather reasonable. The value of molecular biology-based diagnostics is potentially questionable if the tissue samples are not initially accurately characterized. The question that molecular diagnostics may be trying to answer may be the wrong one or the answer obtained may be interpreted incorrectly if the context of the clinicopathologic situation has not been clearly defined using traditional diagnostic techniques.
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Affiliation(s)
- G A Herrera
- Department of Pathology, Louisiana State University Health Sciences Center, Shreveport 71130, USA.
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Mayer G, Leone RD, Hainfeld JF, Bendayan M. Introduction of a novel HRP substrate-Nanogold probe for signal amplification in immunocytochemistry. J Histochem Cytochem 2000; 48:461-70. [PMID: 10727287 DOI: 10.1177/002215540004800403] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Amplification of immunological signals with catalyzed reporter deposition (CARD) allows improved detection of scarce tissue antigens in light and electron microscopy. The technique takes advantage of the oxidation ability of horseradish peroxidase (HRP), in the presence of hydrogen peroxide, to yield the accumulation of one of its specific reporter-tagged substrates. This immunocytochemical approach continues to be improved by the introduction of new reporter molecules tagged to tyramine or to other HRP substrates. In this study we introduced a novel HRP substrate tagged to Nanogold particles. The amplification protocol is based on the application of a specific primary antibody, a biotinylated secondary antibody, streptavidin-HRP, and an HRP substrate coupled to Nanogold, followed by silver intensification. In addition to amplification of immunological signals of high resolution, direct accumulation of Nanogold particles at target sites by enzymatic activity of HRP improves the efficiency of the technique compared to other amplification protocols. Moreover, this approach combines the CARD amplification potentials with the ultrasmall gold probe and the silver intensification method. Immunolabeling obtained by light and electron microscopy, as well as immunodot assay using this new amplification strategy, appear to be highly sensitive, specific, and of enhanced intensity.
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Affiliation(s)
- G Mayer
- Department of Pathology, Université de Montréal, Montreal, Quebec, Canada
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Büki A, Walker SA, Stone JR, Povlishock JT. Novel application of tyramide signal amplification (TSA): ultrastructural visualization of double-labeled immunofluorescent axonal profiles. J Histochem Cytochem 2000; 48:153-61. [PMID: 10653596 DOI: 10.1177/002215540004800116] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Fluorescent immunocytochemistry (FICC) allows multiple labeling approaches when enzyme-based techniques are difficult to combine, such as in double-labeling experiments targeting small-caliber axonal segments. Nevertheless, the conversion of FICC to a product visible at the electron microscopic (EM) level requires labor-intensive procedures, thus justifying the development of more user-friendly conversion methods. This study was initiated to simplify the conversion of FICC to EM by employing the unique properties of tyramide signal amplification (TSA), which allowed the simultaneous targeting of a fluorescent tag and biotin label to the same antigenic site. Briefly, one of two antigenic sites typically co-localized in damaged axonal segments was visualized by the application of a fluorescent secondary antibody, with the other tagged via a biotinylated antibody. Next, an ABC kit was used, followed by the simultaneous application of fluorophore-tyramide and biotin-tyramide. After temporary mounting for fluorescent digital photomicroscopy, sections were incubated in ABC and reacted with diaminobenzidine before EM analysis. Double-labeling fluorescent immunocytochemistry with TSA clearly delineated damaged axonal segments. In addition, these same axonal segments yielded high-quality EM images with discrete electron-dense reaction products, thereby providing a simple and reproducible means for following fluorescent analysis with EM.
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Affiliation(s)
- A Büki
- Department of Anatomy, Medical College of Virginia, Virginia Commonwealth University, Richmond 23298-0709, USA
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Andersen-Beckh B, Dehe M, Schülein R, Wiesner B, Rutz C, Liebenhoff U, Rosenthal W, Oksche A. Polarized expression of the vasopressin V2 receptor in Madin-Darby canine kidney cells. Kidney Int 1999; 56:517-27. [PMID: 10432391 DOI: 10.1046/j.1523-1755.1999.00569.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND The vasopressin V2 receptor is expressed in the polarized principal cell of the renal collecting duct. Inactivating mutations of the vasopressin V2 receptor gene cause X-linked nephrogenic diabetes insipidus (NDI). Most of the mutant V2 receptors show transport defects, as analyzed in non-polarized cells, but data pertaining to polarized cells have not previously been presented. METHODS Madin-Darby canine kidney cell (MDCK) II clones stably expressing c-myc-tagged human V2 receptors were characterized for [3H]-arginine vasopressin (AVP)-binding and AVP-sensitive adenylyl cyclase activity. The V2 receptors were immunocytochemically localized using the tyramide signal amplification technique in conjunction with an anti-c-myc antibody. RESULTS The introduction of the c-myc epitope at the N- or C-terminus did not affect the functional properties of the V2 receptor expressed in MDCK II clones. However, the use of standard immunofluorescence methodology for these MDCK II clones yielded only weak signals. With the tyramide signal amplification technique, strong signals were obtained, showing the V2 receptor to be mainly localized within the lateral and, to a minor extent, apical membrane. In MDCK II clones stably expressing the c-myc-tagged V2 receptor NDI mutant L44P, fluorescent signals were found exclusively within the cell. CONCLUSION The wild-type V2 receptor is expressed mainly in the lateral membrane, whereas the L44P mutant is completely retained within the cell. In conjunction with tyramide signal amplification, MDCK II cells constitute a suitable model for the analysis of transport-defective mutants of the V2 receptor.
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Stanarius A, Faber-Zuschratter H, Töpel I, Schulz S, Wolf G. Tyramide signal amplification in brain immunocytochemistry: adaptation to electron microscopy. J Neurosci Methods 1999; 88:55-61. [PMID: 10379579 DOI: 10.1016/s0165-0270(99)00012-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The tyramide signal amplification (TSA) technique is well-established in light microscopic immunohistochemistry and in situ hybridization to improve the signal-to-noise ratio. The present study deals with its adaptation to the electron microscopic level using the pre-embedding technique and a modified protocol. The outcome of immunolabeling of most of the antigens tested in brain tissue, including endothelial and neuronal nitric oxide synthase, glial fibrillary acidic protein, and isolectin B4, was greatly improved. If signal amplification is required, the TSA-technique proved to be reliable with high specificity and good ultrastructural resolution.
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Affiliation(s)
- A Stanarius
- Institute of Medical Neurobiology, Otto-von-Guericke University Magdeburg, Germany
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Mayer G, Bendayan M. Immunogold signal amplification: Application of the CARD approach to electron microscopy. J Histochem Cytochem 1999; 47:421-30. [PMID: 10082744 DOI: 10.1177/002215549904700401] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Catalyzed reporter deposition (CARD) is a technique that allows amplification of routine immunolabeling in light microscopy. This procedure takes advantage of the horseradish peroxidase (HRP) from an HRP-avidin complex to catalyze the accumulation of reporter-conjugated tyramine (a phenolic compound) onto a surface displaying biotinylated antigen-antibody complexes. The large amount of labeled tyramine deposited allows the detection of an antigenic site with multiple reporter molecules. In this study we modified this amplification protocol to combine it with the immunogold technique for the ultrastructural localization of antigens in electron microscopy. We constructed various tyramide conjugates that permit the combination of this amplification method with a particulate colloidal gold marker. The new probes yield results of high specificity and enhanced intensity. Assessment of the level of resolution of the labeling has demonstrated that, in spite of the amplification, the resolution remains very good. Therefore, once associated, the immunogold and the CARD techniques lead to specific, high-resolution, sensitive and amplified signals that exhibit the advantages of both approaches.(J Histochem Cytochem 47:421-429, 1999)
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Affiliation(s)
- G Mayer
- Department of Pathology and Cell Biology, Université de Montréal, Montreal, Quebec, Canada
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Mengel M, Werner M, von Wasielewski R. Concentration dependent and adverse effects in immunohistochemistry using the tyramine amplification technique. THE HISTOCHEMICAL JOURNAL 1999; 31:195-200. [PMID: 10421419 DOI: 10.1023/a:1003554217994] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Although the tyramine amplification technique to enhance sensitivity in immunohistochemistry has been described in numerous methodological papers, it has not yet gained access to diagnostic immunohistochemistry. This is mainly due to problems and pitfalls occurring in adaptation of this method to routine application. In this study a monoclonal antibody and a polyclonal antiserum (pan-cytokeratin and anti-myoglobin) were tested in tissues with different amounts of epitopes, using a checkerboard table and testing a total of 133 different dilution combinations of both the tyramide solution and the primary antibodies. The specific tissue investigated, i.e. the amount of accessible epitope to be detected and the applied concentration of the tyramide solution mainly influenced the staining reaction. Several pitfalls such as an uneven distribution of the staining or dramatic overstaining (paradoxical overstaining) must be considered to achieve optimal results. In conclusion, our data confirm methodological studies that the tyramine amplification technique is a powerful method to enhance immunohistochemical sensitivity. However, for reliable daily practice several pitfalls of the technique have to be circumvented.
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Affiliation(s)
- M Mengel
- Institut für Pathologie der Medizinischen Hochschule Hannover, Germany
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42
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Speel EJ, Hopman AH, Komminoth P. Amplification methods to increase the sensitivity of in situ hybridization: play card(s). J Histochem Cytochem 1999; 47:281-8. [PMID: 10026231 DOI: 10.1177/002215549904700302] [Citation(s) in RCA: 142] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In situ hybridization (ISH) has proved to be an invaluable molecular tool in research and diagnosis to visualize nucleic acids in their cellular environment. However, its applicability can be limited by its restricted detection sensitivity. During the past 10 years, several strategies have been developed to improve the threshold levels of nucleic acid detection in situ by amplification of either target nucleic acid sequences before ISH (e.g., in situ PCR) or the detection signals after the hybridization procedures. Here we outline the principles of tyramide signal amplification using the catalyzed reporter deposition (CARD) technique, present practical suggestions to efficiently enhance the sensitivity of ISH with CARD, and discuss some applications and possible future directions of in situ nucleic acid detection using such an amplification strategy.
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Affiliation(s)
- E J Speel
- Department of Pathology, University of Zürich, Zürich, Switzerland
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Abstract
During the last decade, several strategies have been developed to improve the detection sensitivity of in situ hybridization (ISV) by amplification of either target nucleic acid sequences prior to ISH (e.g., in situ PCRX or the detection signals after the hybridization procedures (signal amplification). Here we outline the principles of tyramide signal amplification using the catalyzed reporter deposition (CARD) technique, summarize applications as well as possible limitations of CARD 15K, and discuss some future directions of in situ nucleic acid detection using this amplification strategy.
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Wong FS, Visintin I, Shanabrough M, Leranth C, Janeway CA. A novel method for concurrent visualization of immunostain under light and electron microscopy in pancreatic islets. J Histochem Cytochem 1998; 46:1341-6. [PMID: 9815274 DOI: 10.1177/002215549804601201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
We developed a simple method employing the use of flat-embedding techniques on thick frozen sections which allows correlation of light and electron microscopic immunohistochemistry. This method has been particularly useful in visualization of pancreas sections, an adaptation especially important because this tissue is not amenable to conventional vibratome sectioning. In this study we demonstrate the use of this technique to examine the same tissue section at the light and the electron microscopic level while maintaining morphology.
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Affiliation(s)
- F S Wong
- Section of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
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Loup F, Weinmann O, Yonekawa Y, Aguzzi A, Wieser HG, Fritschy JM. A highly sensitive immunofluorescence procedure for analyzing the subcellular distribution of GABAA receptor subunits in the human brain. J Histochem Cytochem 1998; 46:1129-39. [PMID: 9742069 DOI: 10.1177/002215549804601005] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We designed a protocol to improve the immunohistochemical analysis of human brain structures, which overcomes the limited detection sensitivity, high background, and intense autofluorescence commonly associated with human tissue. This procedure was evaluated by using antibodies against major GABAA receptor subunits (alpha1, alpha2, alpha3, gamma2) in autopsy and surgical specimens. Tissue blocks were briefly fixed by immersion and pretreated with microwave irradiation in sodium citrate buffer. Immunoperoxidase staining revealed a marked enhancement of cell surface immunoreactivity and reduction of background in microwave-irradiated tissue, irrespective of its origin. For confocal laser scanning microscopy, immunofluorescence staining was optimized with the tyramide signal amplification (TSA) technique. This procedure not only dramatically increased the sensitivity for antigen detection but also totally suppressed autofluorescence, thus revealing the cellular and subcellular distribution of GABAA receptor subunits. A distinct neuron-specific expression pattern of the alpha-subunit variants was observed in cerebral cortex and hippocampal formation, along with widespread expression of the gamma2-subunit. Of particular interest was the prominent alpha2- and alpha3-subunit staining on the initial axon segment of pyramidal neurons. This protocol represents a major improvement for high-resolution studies of human brain tissue aimed at investigating morphological alterations underlying neurological diseases.
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Affiliation(s)
- F Loup
- Institute of Pharmacology, University Hospital Zurich, Zurich, Switzerland
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Bruneau N, Lombardo D, Bendayan M. Participation of GRP94-related protein in secretion of pancreatic bile salt-dependent lipase and in its internalization by the intestinal epithelium. J Cell Sci 1998; 111 ( Pt 17):2665-79. [PMID: 9701565 DOI: 10.1242/jcs.111.17.2665] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In previous studies on the AR4-2J cell line, we have shown that secretion of bile salt-dependent lipase (BSDL) involves a multiprotein complex, including a protein of 94 kDa (p94) that is immunologically related to the chaperone Grp94, which seems to play essential roles in the folding process of BSDL. Combined biochemical and immunocytochemical investigations were carried out to study the secretion of BSDL by normal pancreatic cells and its transport to the small intestine where this enzyme is thought to exert its physiological function. Both BSDL and Grp94 antigenic sites were localized and found to be associated all along the pancreatic acinar cell secretory pathway. Grp94 and BSDL remain associated from leaving the pancreas until arriving at the intestinal lumen. In pancreatic juice, both proteins appear as a complex of high molecular mass (180 kDa) containing at least one each of p94 and BSDL molecules, interacting by hydrophobic forces. At the intestinal level, associated Grp94 and BSDL were detected on microvilli and in the endosomal compartment of enterocytes. The BSDL mRNA, however, was not expressed by the intestinal mucosa. The pancreatic Grp94-BSDL complex was internalized through the endosomal compartment of enterocytes. Finally, the two proteins dissociated in this compartment and BSDL, but not Grp94, was transferred to the basolateral membrane.
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Affiliation(s)
- N Bruneau
- Département de Pathologie et Biologie Cellulaire, Faculté de Médecine, Université de Montréal, Montréal, Quebec, H3C 3J7 Canada
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Abstract
The catalyze reporter deposition (CARD) method is a new technique to enhance signal detection in immunostaining, immunoelectron microscopy, and in situ hybridization. This technique, which uses a biotinylated tyramine amplification reagent, has been applied to endocrine cells and tumors, and has shown a marked increase in sensitivity in detecting small amounts of protein antigens in endocrine cells and tumors. Although some technical problems remain before widespread application of this method can be used the potential for more in depth understanding of normal and neoplastic endocrine tissue by CARD analysis is largely unexplored at this time.
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