1
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Nishihara T, Motohashi Y, Mio R, Sugawara M, Tanabe K. A detection system using sensing motif-tethered oligodeoxynucleotides for multiplex biomolecular analysis. Chem Commun (Camb) 2024; 60:6059-6062. [PMID: 38780054 DOI: 10.1039/d4cc01470g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
We developed a system to detect multiple target biomolecules through sensing motif-tethered oligodeoxynucleotides. DNA-based molecular probes gave the primary amine motif upon reaction with the target biomolecules, glutathione (GSH) and H2O2. After labelling with biotin, the product DNAs were selectively collected to be quantified by qPCR.
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Affiliation(s)
- Tatsuya Nishihara
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan.
| | - Yuto Motohashi
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan.
| | - Reoto Mio
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan.
| | - Masato Sugawara
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan.
| | - Kazuhito Tanabe
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan.
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2
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Yazaki J, Yamanashi T, Nemoto S, Kobayashi A, Han YW, Hasegawa T, Iwase A, Ishikawa M, Konno R, Imami K, Kawashima Y, Seita J. Mapping adipocyte interactome networks by HaloTag-enrichment-mass spectrometry. Biol Methods Protoc 2024; 9:bpae039. [PMID: 38884001 PMCID: PMC11180226 DOI: 10.1093/biomethods/bpae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/19/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024] Open
Abstract
Mapping protein interaction complexes in their natural state in vivo is arguably the Holy Grail of protein network analysis. Detection of protein interaction stoichiometry has been an important technical challenge, as few studies have focused on this. This may, however, be solved by artificial intelligence (AI) and proteomics. Here, we describe the development of HaloTag-based affinity purification mass spectrometry (HaloMS), a high-throughput HaloMS assay for protein interaction discovery. The approach enables the rapid capture of newly expressed proteins, eliminating tedious conventional one-by-one assays. As a proof-of-principle, we used HaloMS to evaluate the protein complex interactions of 17 regulatory proteins in human adipocytes. The adipocyte interactome network was validated using an in vitro pull-down assay and AI-based prediction tools. Applying HaloMS to probe adipocyte differentiation facilitated the identification of previously unknown transcription factor (TF)-protein complexes, revealing proteome-wide human adipocyte TF networks and shedding light on how different pathways are integrated.
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Affiliation(s)
- Junshi Yazaki
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Faculty of Agriculture, Laboratory for Genome Biology, Setsunan University, Osaka, 573-0101, Japan
| | - Takashi Yamanashi
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Medical Data Deep Learning Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Tokyo, 103-0027, Japan
- School of Integrative and Global Majors, University of Tsukuba, Tsukuba, 305-8577, Japan
| | - Shino Nemoto
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Atsuo Kobayashi
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Yong-Woon Han
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Tomoko Hasegawa
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Akira Iwase
- Cell Function Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Masaki Ishikawa
- Department of Applied Genomics, Technology Development Team, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Ryo Konno
- Department of Applied Genomics, Technology Development Team, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Koshi Imami
- Proteome Homeostasis Research Unit, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Technology Development Team, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Jun Seita
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Medical Data Deep Learning Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Tokyo, 103-0027, Japan
- School of Integrative and Global Majors, University of Tsukuba, Tsukuba, 305-8577, Japan
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3
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Medeiros AT, Gratz S, Delgado A, Ritt J, O’Connor-Giles KM. Ca 2+ channel and active zone protein abundance intersects with input-specific synapse organization to shape functional synaptic diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.02.535290. [PMID: 37034654 PMCID: PMC10081318 DOI: 10.1101/2023.04.02.535290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Synaptic heterogeneity is a hallmark of nervous systems that enables complex and adaptable communication in neural circuits. To understand circuit function, it is thus critical to determine the factors that contribute to the functional diversity of synapses. We investigated the contributions of voltage-gated calcium channel (VGCC) abundance, spatial organization, and subunit composition to synapse diversity among and between synapses formed by two closely related Drosophila glutamatergic motor neurons with distinct neurotransmitter release probabilities (Pr). Surprisingly, VGCC levels are highly predictive of heterogeneous Pr among individual synapses of either low- or high-Pr inputs, but not between inputs. We find that the same number of VGCCs are more densely organized at high-Pr synapses, consistent with tighter VGCC-synaptic vesicle coupling. We generated endogenously tagged lines to investigate VGCC subunits in vivo and found that the α2δ-3 subunit Straightjacket along with the CAST/ELKS active zone (AZ) protein Bruchpilot, both key regulators of VGCCs, are less abundant at high-Pr inputs, yet positively correlate with Pr among synapses formed by either input. Consistently, both Straightjacket and Bruchpilot levels are dynamically increased across AZs of both inputs when neurotransmitter release is potentiated to maintain stable communication following glutamate receptor inhibition. Together, these findings suggest a model in which VGCC and AZ protein abundance intersects with input-specific spatial and molecular organization to shape the functional diversity of synapses.
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Affiliation(s)
- A. T. Medeiros
- Neuroscience Graduate Training Program, Brown University, Providence, RI
| | - S.J. Gratz
- Department of Neuroscience, Brown University, Providence, RI
| | - A. Delgado
- Department of Neuroscience, Brown University, Providence, RI
| | - J.T. Ritt
- Department of Neuroscience, Brown University, Providence, RI
- Carney Institute for Brain Science, Brown University, Providence, RI
| | - Kate M. O’Connor-Giles
- Neuroscience Graduate Training Program, Brown University, Providence, RI
- Department of Neuroscience, Brown University, Providence, RI
- Carney Institute for Brain Science, Brown University, Providence, RI
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4
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Komiya E, Takamatsu S, Miura D, Tsukakoshi K, Tsugawa W, Sode K, Ikebukuro K, Asano R. Exploration and Application of DNA-Binding Proteins to Make a Versatile DNA-Protein Covalent-Linking Patch (D-Pclip): The Case of a Biosensing Element. J Am Chem Soc 2024; 146:4087-4097. [PMID: 38295327 PMCID: PMC10870700 DOI: 10.1021/jacs.3c12668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/02/2024]
Abstract
DNA-protein complexes are attractive components with broad applications in various research fields, such as DNA aptamer-enzyme complexes as biosensing elements. However, noncovalent DNA-protein complexes often decrease detection sensitivity because they are highly susceptible to environmental conditions. In this study, we developed a versatile DNA-protein covalent-linking patch (D-Pclip) for fabricating covalent and stoichiometric DNA-protein complexes. We comprehensively explored the database to determine the DNA-binding ability of the candidates and selected UdgX as the only uracil-DNA glycosylase known to form covalent bonds with DNA via uracil, with a binding efficiency >90%. We integrated a SpyTag/SpyCatcher protein-coupling system into UdgX to create a universal and convenient D-Pclip. The usability of D-Pclip was shown by preparing a stoichiometric model complex of a hemoglobin (Hb)-binding aptamer and glucose oxidase (GOx) by mixing at 4 °C. The prepared aptamer-GOx complexes detected Hb in a dose-dependent manner within the clinically required detection range in buffer and human serum without any washing procedures. D-Pclip covalently connects any uracil-inserted DNA sequence and any SpyCatcher-fused protein stoichiometrically; therefore, it has a high potential for various applications.
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Affiliation(s)
- Erika Komiya
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Shouhei Takamatsu
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Daimei Miura
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kaori Tsukakoshi
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Wakako Tsugawa
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koji Sode
- Joint
Department of Biomedical Engineering, University
of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina 27599, United States
- Institute
of Global Innovation Research, Tokyo University
of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo 183-8509, Japan
| | - Kazunori Ikebukuro
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Ryutaro Asano
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Institute
of Global Innovation Research, Tokyo University
of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo 183-8509, Japan
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5
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Song L, Rauf F, Hou CW, Qiu J, Murugan V, Chung Y, Lai H, Adam D, Magee DM, Trivino Soto G, Peterson M, Anderson KS, Rice SG, Readhead B, Park JG, LaBaer J. Quantitative assessment of multiple pathogen exposure and immune dynamics at scale. Microbiol Spectr 2024; 12:e0239923. [PMID: 38063388 PMCID: PMC10783028 DOI: 10.1128/spectrum.02399-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/13/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Serology reveals exposure to pathogens, as well as the state of autoimmune and other clinical conditions. It is used to evaluate individuals and their histories and as a public health tool to track epidemics. Employing a variety of formats, studies nearly always perform serology by testing response to only one or a few antigens. However, clinical outcomes of new infections also depend on which previous infections may have occurred. We developed a high-throughput serology method that evaluates responses to hundreds of antigens simultaneously. It can be used to evaluate thousands of samples at a time and provide a quantitative readout. This tool will enable doctors to monitor which pathogens an individual has been exposed to and how that changes in the future. Moreover, public health officials could track populations and look for infectious trends among large populations. Testing many potential antigens at a time may also aid in vaccine development.
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Affiliation(s)
- Lusheng Song
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Femina Rauf
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Ching-Wen Hou
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Ji Qiu
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Vel Murugan
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Yunro Chung
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- College of Health Solutions, Arizona State University, Tempe, Arizona, USA
| | - Huafang Lai
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Deborah Adam
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - D. Mitchell Magee
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Guillermo Trivino Soto
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Milene Peterson
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Karen S. Anderson
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Stephen G. Rice
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Benjamin Readhead
- Arizona State University-Banner Neurodegenerative Disease Research Center, Tempe, Arizona, USA
| | - Jin G. Park
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Joshua LaBaer
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
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6
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Single-cell proteomics enabled by next-generation sequencing or mass spectrometry. Nat Methods 2023; 20:363-374. [PMID: 36864196 DOI: 10.1038/s41592-023-01791-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/24/2023] [Indexed: 03/04/2023]
Abstract
In the last decade, single-cell RNA sequencing routinely performed on large numbers of single cells has greatly advanced our understanding of the underlying heterogeneity of complex biological systems. Technological advances have also enabled protein measurements, further contributing to the elucidation of cell types and states present in complex tissues. Recently, there have been independent advances in mass spectrometric techniques bringing us one step closer to characterizing single-cell proteomes. Here we discuss the challenges of detecting proteins in single cells by both mass spectrometry and sequencing-based methods. We review the state of the art for these techniques and propose that there is a space for technological advancements and complementary approaches that maximize the advantages of both classes of technologies.
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7
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Credle JJ, Gunn J, Sangkhapreecha P, Monaco DR, Zheng XA, Tsai HJ, Wilbon A, Morgenlander WR, Rastegar A, Dong Y, Jayaraman S, Tosi L, Parekkadan B, Baer AN, Roederer M, Bloch EM, Tobian AAR, Zyskind I, Silverberg JI, Rosenberg AZ, Cox AL, Lloyd T, Mammen AL, Benjamin Larman H. Unbiased discovery of autoantibodies associated with severe COVID-19 via genome-scale self-assembled DNA-barcoded protein libraries. Nat Biomed Eng 2022; 6:992-1003. [PMID: 35986181 PMCID: PMC10034860 DOI: 10.1038/s41551-022-00925-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/14/2022] [Indexed: 12/13/2022]
Abstract
Pathogenic autoreactive antibodies that may be associated with life-threatening coronavirus disease 2019 (COVID-19) remain to be identified. Here, we show that self-assembled genome-scale libraries of full-length proteins covalently coupled to unique DNA barcodes for analysis by sequencing can be used for the unbiased identification of autoreactive antibodies in plasma samples. By screening 11,076 DNA-barcoded proteins expressed from a sequence-verified human ORFeome library, the method, which we named MIPSA (for Molecular Indexing of Proteins by Self-Assembly), allowed us to detect circulating neutralizing type-I and type-III interferon (IFN) autoantibodies in five plasma samples from 55 patients with life-threatening COVID-19. In addition to identifying neutralizing type-I IFN-α and IFN-ω autoantibodies and other previously known autoreactive antibodies in patient plasma, MIPSA enabled the detection of as yet unidentified neutralizing type-III anti-IFN-λ3 autoantibodies that were not seen in healthy plasma samples or in convalescent plasma from ten non-hospitalized individuals with COVID-19. The low cost and simple workflow of MIPSA will facilitate unbiased high-throughput analyses of protein-antibody, protein-protein and protein-small-molecule interactions.
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Affiliation(s)
- Joel J Credle
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jonathan Gunn
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Puwanat Sangkhapreecha
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel R Monaco
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xuwen Alice Zheng
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hung-Ji Tsai
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Azaan Wilbon
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - William R Morgenlander
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andre Rastegar
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yi Dong
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sahana Jayaraman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lorenzo Tosi
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Biju Parekkadan
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Alan N Baer
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Evan M Bloch
- Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aaron A R Tobian
- Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Israel Zyskind
- Department of Pediatrics, NYU Langone Medical Center, New York City, NY, USA
- Department of Pediatrics, Maimonides Medical Center, Brooklyn, NY, USA
| | - Jonathan I Silverberg
- Department of Dermatology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Avi Z Rosenberg
- Division of Kidney-Urologic Pathology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrea L Cox
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tom Lloyd
- Department of Neurology and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew L Mammen
- Department of Neurology and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - H Benjamin Larman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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8
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Tseng CY, Wang WX, Douglas TR, Chou LYT. Engineering DNA Nanostructures to Manipulate Immune Receptor Signaling and Immune Cell Fates. Adv Healthc Mater 2022; 11:e2101844. [PMID: 34716686 DOI: 10.1002/adhm.202101844] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/14/2021] [Indexed: 12/19/2022]
Abstract
Immune cells sense, communicate, and logically integrate a multitude of environmental signals to make important cell-fate decisions and fulfill their effector functions. These processes are initiated and regulated by a diverse array of immune receptors and via their dynamic spatiotemporal organization upon ligand binding. Given the widespread relevance of the immune system to health and disease, there have been significant efforts toward understanding the biophysical principles governing immune receptor signaling and activation, as well as the development of biomaterials which exploit these principles for therapeutic immune engineering. Here, how advances in the field of DNA nanotechnology constitute a growing toolbox for further pursuit of these endeavors is discussed. Key cellular players involved in the induction of immunity against pathogens or diseased cells are first summarized. How the ability to design DNA nanostructures with custom shapes, dynamics, and with site-specific incorporation of diverse guests can be leveraged to manipulate the signaling pathways that regulate these processes is then presented. It is followed by highlighting emerging applications of DNA nanotechnology at the crossroads of immune engineering, such as in vitro reconstitution platforms, vaccines, and adjuvant delivery systems. Finally, outstanding questions that remain for further advancing immune-modulatory DNA nanodevices are outlined.
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Affiliation(s)
- Chung Yi Tseng
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Wendy Xueyi Wang
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Travis Robert Douglas
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Leo Y. T. Chou
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
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9
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CHEN W, YOUNIS MH, ZHAO Z, CAI W. Recent biomedical advances enabled by HaloTag technology. BIOCELL 2022; 46:1789-1801. [PMID: 35601815 PMCID: PMC9119580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The knowledge of interactions among functional proteins helps researchers understand disease mechanisms and design potential strategies for treatment. As a general approach, the fluorescent and affinity tags were employed for exploring this field by labeling the Protein of Interest (POI). However, the autofluorescence and weak binding strength significantly reduce the accuracy and specificity of these tags. Conversely, HaloTag, a novel self-labeling enzyme (SLE) tag, could quickly form a covalent bond with its ligand, enabling fast and specific labeling of POI. These desirable features greatly increase the accuracy and specificity, making the HaloTag a valuable system for various applications ranging from imaging to immobilization of POI. Notably, the HaloTag technique has already been successfully employed in a series of studies with excellent efficiency. In this review, we summarize the development of HaloTag and recent advanced investigations associated with HaloTag, including in vitro imaging (e.g., POI imaging, cellular condition monitoring, microorganism imaging, system development), in vivo imaging, biomolecule immobilization (e.g., POI collection, protein/nuclear acid interaction and protein structure analysis), targeted degradation (e.g., L-AdPROM), and more. We also present a systematic discussion regarding the future direction and challenges of the HaloTag technique.
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Affiliation(s)
- Weiyu CHEN
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China,International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, 322000, China
| | - Muhsin H. YOUNIS
- Departments of Radiology and Medical Physics, University of Wisconsin—Madison, Madison, WI, 53705, USA
| | - Zhongkuo ZHAO
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China,Address correspondence to: Zhongkuo Zhao, ; Weibo Cai,
| | - Weibo CAI
- Departments of Radiology and Medical Physics, University of Wisconsin—Madison, Madison, WI, 53705, USA,Address correspondence to: Zhongkuo Zhao, ; Weibo Cai,
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10
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Motone K, Cardozo N, Nivala J. Herding cats: Label-based approaches in protein translocation through nanopore sensors for single-molecule protein sequence analysis. iScience 2021; 24:103032. [PMID: 34527891 PMCID: PMC8433247 DOI: 10.1016/j.isci.2021.103032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Proteins carry out life's essential functions. Comprehensive proteome analysis technologies are thus required for a full understanding of the operating principles of biological systems. While current proteomics techniques suffer from limitations in sensitivity and/or throughput, nanopore technology has the potential to enable de novo protein identification through single-molecule sequencing. However, a significant barrier to achieving this goal is controlling protein/peptide translocation through the nanopore sensor for processive strand analysis. Here, we review recent approaches that use a range of techniques, from oligonucleotide conjugation to molecular motors, aimed at driving protein strands and peptides through protein nanopores. We further discuss site-specific protein conjugation chemistry that could be combined with these translocation approaches as future directions to achieve single-molecule protein detection and sequencing of native proteins.
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Affiliation(s)
- Keisuke Motone
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Nicolas Cardozo
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Jeff Nivala
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
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11
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van der Sleen LM, Tych KM. Bioconjugation Strategies for Connecting Proteins to DNA-Linkers for Single-Molecule Force-Based Experiments. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:2424. [PMID: 34578744 PMCID: PMC8464727 DOI: 10.3390/nano11092424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 01/10/2023]
Abstract
The mechanical properties of proteins can be studied with single molecule force spectroscopy (SMFS) using optical tweezers, atomic force microscopy and magnetic tweezers. It is common to utilize a flexible linker between the protein and trapped probe to exclude short-range interactions in SMFS experiments. One of the most prevalent linkers is DNA due to its well-defined properties, although attachment strategies between the DNA linker and protein or probe may vary. We will therefore provide a general overview of the currently existing non-covalent and covalent bioconjugation strategies to site-specifically conjugate DNA-linkers to the protein of interest. In the search for a standardized conjugation strategy, considerations include their mechanical properties in the context of SMFS, feasibility of site-directed labeling, labeling efficiency, and costs.
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Affiliation(s)
| | - Katarzyna M. Tych
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands;
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Credle JJ, Gunn J, Sangkhapreecha P, Monaco DR, Zheng XA, Tsai HJ, Wilbon A, Morgenlander WR, Dong Y, Jayaraman S, Tosi L, Parekkadan B, Baer AN, Roederer M, Bloch EM, Tobian AAR, Zyskind I, Silverberg JI, Rosenberg AZ, Cox AL, Lloyd T, Mammen AL, Larman HB. Neutralizing IFNL3 Autoantibodies in Severe COVID-19 Identified Using Molecular Indexing of Proteins by Self-Assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.02.432977. [PMID: 33688651 PMCID: PMC7941622 DOI: 10.1101/2021.03.02.432977] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Unbiased antibody profiling can identify the targets of an immune reaction. A number of likely pathogenic autoreactive antibodies have been associated with life-threatening SARS-CoV-2 infection; yet, many additional autoantibodies likely remain unknown. Here we present Molecular Indexing of Proteins by Self Assembly (MIPSA), a technique that produces ORFeome-scale libraries of proteins covalently coupled to uniquely identifying DNA barcodes for analysis by sequencing. We used MIPSA to profile circulating autoantibodies from 55 patients with severe COVID-19 against 11,076 DNA-barcoded proteins of the human ORFeome library. MIPSA identified previously known autoreactivities, and also detected undescribed neutralizing interferon lambda 3 (IFN-λ3) autoantibodies. At-risk individuals with anti- IFN-λ3 antibodies may benefit from interferon supplementation therapies, such as those currently undergoing clinical evaluation.
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Affiliation(s)
- Joel J. Credle
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Jonathan Gunn
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Puwanat Sangkhapreecha
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Daniel R. Monaco
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Xuwen Alice Zheng
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Hung-Ji Tsai
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston; Birmingham, United Kingdom
| | - Azaan Wilbon
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - William R. Morgenlander
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Yi Dong
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Sahana Jayaraman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Lorenzo Tosi
- Department of Biomedical Engineering, Rutgers University; Piscataway, NJ, USA
| | - Biju Parekkadan
- Department of Biomedical Engineering, Rutgers University; Piscataway, NJ, USA
| | - Alan N. Baer
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH; Bethesda, MD, USA
| | - Evan M. Bloch
- Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Aaron A. R. Tobian
- Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Israel Zyskind
- Department of Pediatrics, NYU Langone Medical Center, New York, NY and Maimonides Medical Center; Brooklyn, NY, USA
| | - Jonathan I. Silverberg
- Department of Dermatology, George Washington University School of Medicine and Health Sciences; Washington, DC, USA
| | - Avi Z. Rosenberg
- Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University; Baltimore, MD, USA
| | - Andrea L. Cox
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University; Baltimore, MD, USA
| | - Tom Lloyd
- Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Andrew L. Mammen
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH; Bethesda, MD, USA and Departments of Neurology and Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - H. Benjamin Larman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
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Yazaki J. Novel Protein-oligonucleotide Conjugation Method Involving a High-affinity Capture HaloTag. Bio Protoc 2020; 10:e3759. [DOI: 10.21769/bioprotoc.3759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/29/2020] [Accepted: 07/22/2020] [Indexed: 11/02/2022] Open
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