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Frecot DI, Froehlich T, Rothbauer U. 30 years of nanobodies - an ongoing success story of small binders in biological research. J Cell Sci 2023; 136:jcs261395. [PMID: 37937477 DOI: 10.1242/jcs.261395] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
A milestone in the field of recombinant binding molecules was achieved 30 years ago with the discovery of single-domain antibodies from which antigen-binding variable domains, better known as nanobodies (Nbs), can be derived. Being only one tenth the size of conventional antibodies, Nbs feature high affinity and specificity, while being highly stable and soluble. In addition, they display accessibility to cryptic sites, low off-target accumulation and deep tissue penetration. Efficient selection methods, such as (semi-)synthetic/naïve or immunized cDNA libraries and display technologies, have facilitated the isolation of Nbs against diverse targets, and their single-gene format enables easy functionalization and high-yield production. This Review highlights recent advances in Nb applications in various areas of biological research, including structural biology, proteomics and high-resolution and in vivo imaging. In addition, we provide insights into intracellular applications of Nbs, such as live-cell imaging, biosensors and targeted protein degradation.
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Affiliation(s)
- Desiree I Frecot
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Reutlingen, Germany
| | - Theresa Froehlich
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
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2
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De Pauw T, De Mey L, Debacker JM, Raes G, Van Ginderachter JA, De Groof TWM, Devoogdt N. Current status and future expectations of nanobodies in oncology trials. Expert Opin Investig Drugs 2023; 32:705-721. [PMID: 37638538 DOI: 10.1080/13543784.2023.2249814] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/16/2023] [Indexed: 08/29/2023]
Abstract
INTRODUCTION Monoclonal antibodies have revolutionized personalized medicine for cancer in recent decades. Despite their broad application in oncology, their large size and complexity may interfere with successful tumor targeting for certain applications of cancer diagnosis and therapy. Nanobodies have unique structural and pharmacological features compared to monoclonal antibodies and have successfully been used as complementary anti-cancer diagnostic and/or therapeutic tools. AREAS COVERED Here, an overview is given of the nanobody-based diagnostics and therapeutics that have been or are currently being tested in oncological clinical trials. Furthermore, preclinical developments, which are likely to be translated into the clinic in the near future, are highlighted. EXPERT OPINION Overall, the presented studies show the application potential of nanobodies in the field of oncology, making it likely that more nanobodies will be clinically approved in the upcoming future.
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Affiliation(s)
- Tessa De Pauw
- In vivo Cellular and Molecular Imaging Laboratory, Department of Medical Imaging, Vrije Universiteit Brussel, Brussels, Belgium
| | - Lynn De Mey
- In vivo Cellular and Molecular Imaging Laboratory, Department of Medical Imaging, Vrije Universiteit Brussel, Brussels, Belgium
- Nuclear Medicine Department, UZ Brussel, Brussels, Belgium
| | - Jens M Debacker
- In vivo Cellular and Molecular Imaging Laboratory, Department of Medical Imaging, Vrije Universiteit Brussel, Brussels, Belgium
- Nuclear Medicine Department, UZ Brussel, Brussels, Belgium
| | - Geert Raes
- Cellular and Molecular Immunology Lab, Vrije Universiteit Brussel, Brussels, Belgium
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium
| | - Jo A Van Ginderachter
- Cellular and Molecular Immunology Lab, Vrije Universiteit Brussel, Brussels, Belgium
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium
| | - Timo W M De Groof
- In vivo Cellular and Molecular Imaging Laboratory, Department of Medical Imaging, Vrije Universiteit Brussel, Brussels, Belgium
| | - Nick Devoogdt
- In vivo Cellular and Molecular Imaging Laboratory, Department of Medical Imaging, Vrije Universiteit Brussel, Brussels, Belgium
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3
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Ekwujuru EU, Olatunde AM, Klink MJ, Ssemakalu CC, Chili MM, Peleyeju MG. Electrochemical and Photoelectrochemical Immunosensors for the Detection of Ovarian Cancer Biomarkers. SENSORS (BASEL, SWITZERLAND) 2023; 23:4106. [PMID: 37112447 PMCID: PMC10142013 DOI: 10.3390/s23084106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/20/2023] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
Photoelectrochemical (PEC) sensing is an emerging technological innovation for monitoring small substances/molecules in biological or non-biological systems. In particular, there has been a surge of interest in developing PEC devices for determining molecules of clinical significance. This is especially the case for molecules that are markers for serious and deadly medical conditions. The increased interest in PEC sensors to monitor such biomarkers can be attributed to the many apparent advantages of the PEC system, including an enhanced measurable signal, high potential for miniaturization, rapid testing, and low cost, amongst others. The growing number of published research reports on the subject calls for a comprehensive review of the various findings. This article is a review of studies on electrochemical (EC) and PEC sensors for ovarian cancer biomarkers in the last seven years (2016-2022). EC sensors were included because PEC is an improved EC; and a comparison of both systems has, expectedly, been carried out in many studies. Specific attention was given to the different markers of ovarian cancer and the EC/PEC sensing platforms developed for their detection/quantification. Relevant articles were sourced from the following databases: Scopus, PubMed Central, Web of Science, Science Direct, Academic Search Complete, EBSCO, CORE, Directory of open Access Journals (DOAJ), Public Library of Science (PLOS), BioMed Central (BMC), Semantic Scholar, Research Gate, SciELO, Wiley Online Library, Elsevier and SpringerLink.
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Affiliation(s)
- Ezinne U. Ekwujuru
- Department of Biotechnology and Chemistry, Vaal University of Technology, Vanderbijlpark 1911, South Africa
| | | | - Michael J. Klink
- Department of Biotechnology and Chemistry, Vaal University of Technology, Vanderbijlpark 1911, South Africa
| | - Cornelius C. Ssemakalu
- Department of Biotechnology and Chemistry, Vaal University of Technology, Vanderbijlpark 1911, South Africa
| | - Muntuwenkosi M. Chili
- Department of Biotechnology and Chemistry, Vaal University of Technology, Vanderbijlpark 1911, South Africa
- Centre for Academic Development, Vaal University of Technology, Vanderbijlpark 1911, South Africa
| | - Moses G. Peleyeju
- Department of Biotechnology and Chemistry, Vaal University of Technology, Vanderbijlpark 1911, South Africa
- Centre for Academic Development, Vaal University of Technology, Vanderbijlpark 1911, South Africa
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4
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Raynaud P, Gauthier C, Jugnarain V, Jean-Alphonse F, Reiter E, Bruneau G, Crépieux P. Intracellular VHHs to monitor and modulate GPCR signaling. Front Endocrinol (Lausanne) 2022; 13:1048601. [PMID: 36465650 PMCID: PMC9708903 DOI: 10.3389/fendo.2022.1048601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022] Open
Abstract
Single-domain antibody fragments, also known as VHHs or nanobodies, have opened promising avenues in therapeutics and in exploration of intracellular processes. Because of their unique structural properties, they can reach cryptic regions in their cognate antigen. Intracellular VHHs/antibodies primarily directed against cytosolic proteins or transcription factors have been described. In contrast, few of them target membrane proteins and even less recognize G protein-coupled receptors. These receptors are major therapeutic targets, which reflects their involvement in a plethora of physiological responses. Hence, they elicit a tremendous interest in the scientific community and in the industry. Comprehension of their pharmacology has been obscured by their conformational complexity, that has precluded deciphering their structural properties until the early 2010's. To that respect, intracellular VHHs have been instrumental in stabilizing G protein-coupled receptors in active conformations in order to solve their structure, possibly bound to their primary transducers, G proteins or β-arrestins. In contrast, the modulatory properties of VHHs recognizing the intracellular regions of G protein-coupled receptors on the induced signaling network have been poorly studied. In this review, we will present the advances that the intracellular VHHs have permitted in the field of GPCR signaling and trafficking. We will also discuss the methodological hurdles that linger the discovery of modulatory intracellular VHHs directed against GPCRs, as well as the opportunities they open in drug discovery.
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Affiliation(s)
- Pauline Raynaud
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l’Equitation (IFCE), Université de Tours, Nouzilly, France
| | - Camille Gauthier
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l’Equitation (IFCE), Université de Tours, Nouzilly, France
| | - Vinesh Jugnarain
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l’Equitation (IFCE), Université de Tours, Nouzilly, France
| | - Frédéric Jean-Alphonse
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l’Equitation (IFCE), Université de Tours, Nouzilly, France
- Inria, Inria Saclay-Ile-de-France, Palaiseau, France
| | - Eric Reiter
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l’Equitation (IFCE), Université de Tours, Nouzilly, France
- Inria, Inria Saclay-Ile-de-France, Palaiseau, France
| | - Gilles Bruneau
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l’Equitation (IFCE), Université de Tours, Nouzilly, France
| | - Pascale Crépieux
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l’Equitation (IFCE), Université de Tours, Nouzilly, France
- Inria, Inria Saclay-Ile-de-France, Palaiseau, France
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Hatano T, Lim TC, Billault-Chaumartin I, Dhar A, Gu Y, Massam-Wu T, Scott W, Adishesha S, Chapa-y-Lazo B, Springall L, Sivashanmugam L, Mishima M, Martin SG, Oliferenko S, Palani S, Balasubramanian MK. mNG-tagged fusion proteins and nanobodies to visualize tropomyosins in yeast and mammalian cells. J Cell Sci 2022; 135:jcs260288. [PMID: 36148799 PMCID: PMC9592052 DOI: 10.1242/jcs.260288] [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: 05/27/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Tropomyosins are structurally conserved α-helical coiled-coil proteins that bind along the length of filamentous actin (F-actin) in fungi and animals. Tropomyosins play essential roles in the stability of actin filaments and in regulating myosin II contractility. Despite the crucial role of tropomyosin in actin cytoskeletal regulation, in vivo investigations of tropomyosin are limited, mainly due to the suboptimal live-cell imaging tools currently available. Here, we report on an mNeonGreen (mNG)-tagged tropomyosin, with native promoter and linker length configuration, that clearly reports tropomyosin dynamics in Schizosaccharomyces pombe (Cdc8), Schizosaccharomyces japonicus (Cdc8) and Saccharomyces cerevisiae (Tpm1 and Tpm2). We also describe a fluorescent probe to visualize mammalian tropomyosin (TPM2 isoform). Finally, we generated a camelid nanobody against S. pombe Cdc8, which mimics the localization of mNG-Cdc8 in vivo. Using these tools, we report the presence of tropomyosin in previously unappreciated patch-like structures in fission and budding yeasts, show flow of tropomyosin (F-actin) cables to the cytokinetic actomyosin ring and identify rearrangements of the actin cytoskeleton during mating. These powerful tools and strategies will aid better analyses of tropomyosin and F-actin cables in vivo.
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Affiliation(s)
- Tomoyuki Hatano
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, Warwick CV4 7AL, UK
| | - Tzer Chyn Lim
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, Warwick CV4 7AL, UK
| | - Ingrid Billault-Chaumartin
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Anubhav Dhar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Ying Gu
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK
| | - Teresa Massam-Wu
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, Warwick CV4 7AL, UK
| | - William Scott
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, Warwick CV4 7AL, UK
| | - Sushmitha Adishesha
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Bernardo Chapa-y-Lazo
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, Warwick CV4 7AL, UK
| | - Luke Springall
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, Warwick CV4 7AL, UK
| | - Lavanya Sivashanmugam
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, Warwick CV4 7AL, UK
| | - Masanori Mishima
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, Warwick CV4 7AL, UK
| | - Sophie G. Martin
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK
| | - Saravanan Palani
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Mohan K. Balasubramanian
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, Warwick CV4 7AL, UK
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6
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Wang M, Wei L, Xiang H, Ren B, Liu X, Jiang L, Yang N, Shi J. A megadiverse naïve library derived from numerous camelids for efficient and rapid development of VHH antibodies. Anal Biochem 2022; 657:114871. [PMID: 36108795 DOI: 10.1016/j.ab.2022.114871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 07/20/2022] [Accepted: 08/17/2022] [Indexed: 11/01/2022]
Abstract
The field of antibody development is under pressure to meet rising demands for speed, cost-effectiveness, efficacy, reliability, and large-scale production. It is costly and time-consuming to immunize animals and build a single-domain antibody (sdAb) library for each target. Using the variable domain (VHH) of heavy-chain only antibodies (HcAbs) derived from blood samples of 75 non-immunized camelid animals (51 alpacas, 13 llamas, 11 Bactrian camels), and spleens from two Bactrian camels, a naïve sdAb library with extensive megadiversity and reusability was constructed. The library was evaluated using next-generation DNA sequencing (NGS) and was found to contain hundreds of billions of unique clones. To confirm the availability of target-specific VHHs, a naive library was screened for a variety of targets. At least two VHH candidates were extracted for each target using a 20-day selection pipeline. Some binders had ultrahigh potencies, with binding affinities in the nanomolar range. This naïve library, in particular, offers the possibility of acquiring unique antibodies targeting antigens of interest with low feasible dissociation constant (kD) without the time, effort, and price associated in producing antibodies in animals via antigen injection. Overall, the study shows that the megadiverse naïve library provides a rapid, adaptable, and easy platform for antibody creation, emphasizing its therapeutic and diagnostic implications.
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Affiliation(s)
- Meiniang Wang
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Likun Wei
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China; Biotechnology and Health Centre, City University of Hong Kong, Shenzhen Research Institute, Shenzhen, China
| | - Haitao Xiang
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Bingzhao Ren
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xiaopan Liu
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Lin Jiang
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Naibo Yang
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China; Complete Genomics, Inc., 2904 Orchard Parkway, San Jose, CA, 95134, USA.
| | - Jiahai Shi
- Synthetic Biology Translational Research Programmes, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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Keller L, Tardy C, Ligat L, Le Pennec S, Bery N, Koraïchi F, Chinestra P, David M, Gence R, Favre G, Cabantous S, Olichon A. Tripartite split-GFP assay to identify selective intracellular nanobody that suppresses GTPase RHOA subfamily downstream signaling. Front Immunol 2022; 13:980539. [PMID: 36059552 PMCID: PMC9433928 DOI: 10.3389/fimmu.2022.980539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/29/2022] [Indexed: 11/24/2022] Open
Abstract
Strategies based on intracellular expression of artificial binding domains present several advantages over manipulating nucleic acid expression or the use of small molecule inhibitors. Intracellularly-functional nanobodies can be considered as promising macrodrugs to study key signaling pathways by interfering with protein-protein interactions. With the aim of studying the RAS-related small GTPase RHOA family, we previously isolated, from a synthetic phage display library, nanobodies selective towards the GTP-bound conformation of RHOA subfamily proteins that lack selectivity between the highly conserved RHOA-like and RAC subfamilies of GTPases. To identify RHOA/ROCK pathway inhibitory intracellular nanobodies, we implemented a stringent, subtractive phage display selection towards RHOA-GTP followed by a phenotypic screen based on F-actin fiber loss. Intracellular interaction and intracellular selectivity between RHOA and RAC1 proteins was demonstrated by adapting the sensitive intracellular protein-protein interaction reporter based on the tripartite split-GFP method. This strategy led us to identify a functional intracellular nanobody, hereafter named RH28, that does not cross-react with the close RAC subfamily and blocks/disrupts the RHOA/ROCK signaling pathway in several cell lines without further engineering or functionalization. We confirmed these results by showing, using SPR assays, the high specificity of the RH28 nanobody towards the GTP-bound conformation of RHOA subfamily GTPases. In the metastatic melanoma cell line WM266-4, RH28 expression triggered an elongated cellular phenotype associated with a loss of cellular contraction properties, demonstrating the efficient intracellular blocking of RHOA/B/C proteins downstream interactions without the need of manipulating endogenous gene expression. This work paves the way for future therapeutic strategies based on protein-protein interaction disruption with intracellular antibodies.
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Affiliation(s)
- Laura Keller
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Laboratoire de Biologie Médicale Oncologique, IUCT-Oncopôle, Toulouse, France
| | - Claudine Tardy
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Laetitia Ligat
- Le Pôle Technologique du Centre de Recherches en Cancérologie de Toulouse, Plateau de Protéomique, Toulouse, France
| | - Soazig Le Pennec
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Nicolas Bery
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Faten Koraïchi
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Patrick Chinestra
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Mélissa David
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Rémi Gence
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Gilles Favre
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Laboratoire de Biologie Médicale Oncologique, IUCT-Oncopôle, Toulouse, France
| | - Stéphanie Cabantous
- Laboratoire de Biologie Médicale Oncologique, IUCT-Oncopôle, Toulouse, France
- *Correspondence: Stéphanie Cabantous, ; Aurélien Olichon,
| | - Aurélien Olichon
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1188 Diabète athérothrombose Réunion Océan Indien (DéTROI), Université de La Réunion, Saint Denis de La Réunion, France
- *Correspondence: Stéphanie Cabantous, ; Aurélien Olichon,
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8
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Structural insights into the binding of nanobody Rh57 to active RhoA-GTP. Biochem Biophys Res Commun 2022; 616:122-128. [DOI: 10.1016/j.bbrc.2022.05.084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 05/27/2022] [Indexed: 11/21/2022]
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9
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Cordell P, Carrington G, Curd A, Parker F, Tomlinson D, Peckham M. Affimers and nanobodies as molecular probes and their applications in imaging. J Cell Sci 2022; 135:276020. [PMID: 35848463 PMCID: PMC9450889 DOI: 10.1242/jcs.259168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antibodies are the most widely used, traditional tool for labelling molecules in cells. In the past five to ten years, many new labelling tools have been developed with significant advantages over the traditional antibody. Here, we focus on nanobodies and the non-antibody binding scaffold proteins called Affimers. We explain how they are generated, selected and produced, and we describe how their small size, high binding affinity and specificity provides them with many advantages compared to antibodies. Of particular importance, their small size enables them to better penetrate dense cytoskeletal regions within cells, as well as tissues, providing them with specific advantage for super-resolution imaging, as they place the fluorophore with a few nanometres of the target protein being imaged. We expect these novel tools to be of broad interest to many cell biologists and anticipate them becoming the tools of choice for super-resolution imaging.
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10
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Wang Z, Ren D, Zheng P. The role of Rho/ROCK in epileptic seizure-related neuronal damage. Metab Brain Dis 2022; 37:881-887. [PMID: 35119588 PMCID: PMC9042975 DOI: 10.1007/s11011-022-00909-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 01/06/2022] [Indexed: 01/09/2023]
Abstract
Epilepsy is one of the most severe neurological disorders characterized by spontaneous recurrent seizures. Although more than two-thirds of patients can be cured with anti-epileptic drugs (AEDs), the rest one-third of epilepsy patients are resistant to AEDs. A series of studies have demonstrated Rho/Rho-associated kinase (ROCK) pathway might be involved in the pathogenesis of epilepsy in the recent twenty years. Several related pathway inhibitors of Rho/ROCK have been used in the treatment of epilepsy. We searched PubMed from Jan 1, 2000 to Dec 31, 2020, using the terms "epilepsy AND Rho AND ROCK" and "seizure AND Rho AND ROCK". We selected articles that characterized Rho/ROCK in animal models of epilepsy and patients. We then chose the most relevant research studies including in-vitro, in-vivo and clinical trials. The expression of Rho/ROCK could be a potential non-invasive biomarker to apply in treatment for patients with epilepsy. RhoA and ROCK show significant upregulation in the acute and chronic stage of epilepsy. ROCK inhibitors can reduce the epilepsy, epileptic seizure-related neuronal death and comorbidities. These findings demonstrate the novel development for diagnosis and treatment for patients with epilepsy. Rho/ROCK signaling pathway inhibitors may show more promising effects in epilepsy and related neurological diseases.
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Affiliation(s)
- Zhihan Wang
- Department of Neurosurgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, China
| | - Dabin Ren
- Department of Neurusurgery & Key Laboratory, Shanghai Pudong New area People's Hospital, Shanghai, 201299, China
| | - Ping Zheng
- Department of Neurusurgery & Key Laboratory, Shanghai Pudong New area People's Hospital, Shanghai, 201299, China.
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11
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Koh SP, Pham NP, Piekny A. Seeing is believing: tools to study the role of Rho GTPases during cytokinesis. Small GTPases 2022; 13:211-224. [PMID: 34405757 PMCID: PMC9707540 DOI: 10.1080/21541248.2021.1957384] [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] [Indexed: 02/06/2023] Open
Abstract
Cytokinesis is required to cleave the daughter cells at the end of mitosis and relies on the spatiotemporal control of RhoA GTPase. Cytokinesis failure can lead to changes in cell fate or aneuploidy, which can be detrimental during development and/or can lead to cancer. However, our knowledge of the pathways that regulate RhoA during cytokinesis is limited, and the role of other Rho family GTPases is not clear. This is largely because the study of Rho GTPases presents unique challenges using traditional cell biological and biochemical methods, and they have pleiotropic functions making genetic studies difficult to interpret. The recent generation of optogenetic tools and biosensors that control and detect active Rho has overcome some of these challenges and is helping to elucidate the role of RhoA in cytokinesis. However, improvements are needed to reveal the role of other Rho GTPases in cytokinesis, and to identify the molecular mechanisms that control Rho activity. This review examines some of the outstanding questions in cytokinesis, and explores tools for the imaging and control of Rho GTPases.
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Affiliation(s)
- Su Pin Koh
- Department of Biology, Concordia University, Montreal, QC, Canada
| | - Nhat Phi Pham
- Department of Biology, Concordia University, Montreal, QC, Canada
| | - Alisa Piekny
- Department of Biology, Concordia University, Montreal, QC, Canada,CONTACT Alisa Piekny Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC, Canada
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12
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Kazemi-Lomedasht F, Karami E. Biosensors: Types, features, and application in biomedicine. Asian Pac J Trop Biomed 2022. [DOI: 10.4103/2221-1691.354427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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13
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Wagner TR, Rothbauer U. Nanobodies - Little helpers unravelling intracellular signaling. Free Radic Biol Med 2021; 176:46-61. [PMID: 34536541 DOI: 10.1016/j.freeradbiomed.2021.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/26/2021] [Accepted: 09/08/2021] [Indexed: 11/21/2022]
Abstract
The identification of diagnostic and therapeutic targets requires a comprehensive understanding of cellular processes, for which advanced technologies in biomedical research are needed. The emergence of nanobodies (Nbs) derived from antibody fragments of camelid heavy chain-only antibodies as intracellular research tools offers new possibilities to study and modulate target antigens in living cells. Here we summarize this rapidly changing field, beginning with a brief introduction of Nbs, followed by an overview of how target-specific Nbs can be generated, and introduce the selection of intrabodies as research tools. Intrabodies, by definition, are intracellular functional Nbs that target ectopic or endogenous intracellular antigens within living cells. Such binders can be applied in various formats, e.g. as chromobodies for live cell microscopy or as biosensors to decipher complex intracellular signaling pathways. In addition, protein knockouts can be achieved by target-specific Nbs, while modulating Nbs have the potential as future therapeutics. The development of fine-tunable and switchable Nb-based systems that simultaneously provide spatial and temporal control has recently taken the application of these binders to the next level.
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Affiliation(s)
- Teresa R Wagner
- Pharmaceutical Biotechnology, Eberhard Karls University, Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University, Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University, Tübingen, Germany.
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14
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Targeting small GTPases and their downstream pathways with intracellular macromolecule binders to define alternative therapeutic strategies in cancer. Biochem Soc Trans 2021; 49:2021-2035. [PMID: 34623375 DOI: 10.1042/bst20201059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 11/17/2022]
Abstract
The RAS superfamily of small GTPases regulates major physiological cellular processes. Mutation or deregulation of these small GTPases, their regulators and/or their effectors are associated with many diseases including cancer. Hence, targeting these classes of proteins is an important therapeutic strategy in cancer. This has been recently achieved with the approval of the first KRASG12C covalent inhibitors for the clinic. However, many other mutants and small GTPases are still considered as 'undruggable' with small molecule inhibitors because of a lack of well-defined pocket(s) at their surface. Therefore, alternative therapeutic strategies have been developed to target these proteins. In this review, we discuss the use of intracellular antibodies and derivatives - reagents that bind their antigen inside the cells - for the discovery of novel inhibitory mechanisms, targetable features and therapeutic strategies to inhibit small GTPases and their downstream pathways. These reagents are also versatile tools used to better understand the biological mechanisms regulated by small GTPases and to accelerate the drug discovery process.
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15
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Mahlandt EK, Arts JJG, van der Meer WJ, van der Linden FH, Tol S, van Buul JD, Gadella TWJ, Goedhart J. Visualizing endogenous Rho activity with an improved localization-based, genetically encoded biosensor. J Cell Sci 2021; 134:272101. [PMID: 34357388 PMCID: PMC8445605 DOI: 10.1242/jcs.258823] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/26/2021] [Indexed: 12/05/2022] Open
Abstract
Rho GTPases are regulatory proteins, which orchestrate cell features such as morphology, polarity and movement. Therefore, probing Rho GTPase activity is key to understanding processes such as development and cell migration. Localization-based reporters for active Rho GTPases are attractive probes to study Rho GTPase-mediated processes in real time with subcellular resolution in living cells and tissue. Until now, relocation Rho biosensors (sensors that relocalize to the native location of active Rho GTPase) seem to have been only useful in certain organisms and have not been characterized well. In this paper, we systematically examined the contribution of the fluorescent protein and Rho-binding peptides on the performance of localization-based sensors. To test the performance, we compared relocation efficiency and specificity in cell-based assays. We identified several improved localization-based, genetically encoded fluorescent biosensors for detecting endogenous Rho activity. This enables a broader application of Rho relocation biosensors, which was demonstrated by using the improved biosensor to visualize Rho activity during several cellular processes, such as cell division, migration and G protein-coupled receptor signaling. Owing to the improved avidity of the new biosensors for Rho activity, cellular processes regulated by Rho can be better understood. This article has an associated First Person interview with the first author of the paper. Summary: The dT-2xrGBD location-based Rho biosensor relocalizes more efficiently than other sensors of this type, and this sensor enables the observation of endogenous Rho activity in cultured cells.
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Affiliation(s)
- Eike K Mahlandt
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Janine J G Arts
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.,Molecular Cell Biology Lab at Dept. Molecular Hematology, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Werner J van der Meer
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Franka H van der Linden
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Simon Tol
- Molecular Cell Biology Lab at Dept. Molecular Hematology, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Jaap D van Buul
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.,Molecular Cell Biology Lab at Dept. Molecular Hematology, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Theodorus W J Gadella
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Joachim Goedhart
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
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16
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A Novel Nanobody Precisely Visualizes Phosphorylated Histone H2AX in Living Cancer Cells under Drug-Induced Replication Stress. Cancers (Basel) 2021; 13:cancers13133317. [PMID: 34282773 PMCID: PMC8267817 DOI: 10.3390/cancers13133317] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary γ-H2AX, a phosphorylated variant of histone H2A, is a widely used biomarker of DNA replication stress. To develop an immunological probe able to detect and track γ-H2AX in live cancer cells, we have isolated single domain antibodies (called nanobodies) that are easily expressed as functional recombinant proteins and here we report the extensive characterization of a novel nanobody that specifically recognizes γ-H2AX. The interaction of this nanobody with the C-terminal end of γ-H2AX was determined by X-ray crystallography. Moreover, the generation of a bivalent nanobody allowed us to precisely detect γ-H2AX foci in drug-treated cells as efficiently as with commercially available conventional antibodies. Furthermore, we tracked γ-H2AX foci in live cells upon intracellular delivery of the bivalent nanobody fused to the red fluorescent protein dTomato, making, consequently, this new cost-effective reagent useful for studying drug-induced replication stress in both fixed and living cancer cells. Abstract Histone H2AX phosphorylated at serine 139 (γ-H2AX) is a hallmark of DNA damage, signaling the presence of DNA double-strand breaks and global replication stress in mammalian cells. While γ-H2AX can be visualized with antibodies in fixed cells, its detection in living cells was so far not possible. Here, we used immune libraries and phage display to isolate nanobodies that specifically bind to γ-H2AX. We solved the crystal structure of the most soluble nanobody in complex with the phosphopeptide corresponding to the C-terminus of γ-H2AX and show the atomic constituents behind its specificity. We engineered a bivalent version of this nanobody and show that bivalency is essential to quantitatively visualize γ-H2AX in fixed drug-treated cells. After labelling with a chemical fluorophore, we were able to detect γ-H2AX in a single-step assay with the same sensitivity as with validated antibodies. Moreover, we produced fluorescent nanobody-dTomato fusion proteins and applied a transduction strategy to visualize with precision γ-H2AX foci present in intact living cells following drug treatment. Together, this novel tool allows performing fast screenings of genotoxic drugs and enables to study the dynamics of this particular chromatin modification in individual cancer cells under a variety of conditions.
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17
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Keller L, Tardy C, Ligat L, Gilhodes J, Filleron T, Bery N, Rochaix P, Aquilina A, Bdioui S, Roux T, Trinquet E, Favre G, Olichon A. Nanobody-Based Quantification of GTP-Bound RHO Conformation Reveals RHOA and RHOC Activation Independent from Their Total Expression in Breast Cancer. Anal Chem 2021; 93:6104-6111. [PMID: 33825439 DOI: 10.1021/acs.analchem.0c05137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
As key regulators of the actin cytoskeleton, RHO GTPase expression and/or activity are deregulated in tumorigenesis and metastatic progression. Nevertheless, the vast majority of experiments supporting this conclusion was conducted on cell lines but not on human tumor samples that were mostly studied at the expression level only. Up to now, the activity of RHO proteins remains poorly investigated in human tumors. In this article, we present the development of a robust nanobody-based ELISA assay, with a high selectivity that allows an accurate quantification of RHO protein GTP-bound state in the nanomolar range (1 nM; 20 μg/L), not only in cell lines after treatment but also in tumor samples. Of note, we present here a fine analysis of RHOA-like and RAC1 active state in tumor samples with the most comprehensive study of RHOA-GTP and RHOC-GTP levels performed on human breast tumor samples. We revealed increased GTP-bound RHOA and RHOC protein activities in tumors compared to normal tissue counterparts, and demonstrated that the RHO active state and RHO expression are two independent parameters among different breast cancer subtypes. Our results further highlight the regulation of RHO protein activation in tumor samples and the relevance of directly studying RHO GTPase activities involvement in molecular pathways.
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Affiliation(s)
- Laura Keller
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, UPS, Toulouse 31037, France.,Laboratoire de Biologie Médicale Oncologique, Institut Claudius Regaud, IUCT-Oncopôle, Toulouse 31037, France
| | - Claudine Tardy
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, UPS, Toulouse 31037, France
| | - Laetitia Ligat
- Le Pôle Technologique du Centre de Recherches en Cancérologie de Toulouse, plateau de protéomique, Toulouse 31037, France
| | - Julia Gilhodes
- Service de Biostatistiques, Institut Claudius Regaud, IUCT-Oncopôle, Toulouse 31059, France
| | - Thomas Filleron
- Service de Biostatistiques, Institut Claudius Regaud, IUCT-Oncopôle, Toulouse 31059, France
| | - Nicolas Bery
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, UPS, Toulouse 31037, France
| | - Philippe Rochaix
- Laboratoire de Biologie Médicale Oncologique, Institut Claudius Regaud, IUCT-Oncopôle, Toulouse 31037, France
| | | | | | | | | | - Gilles Favre
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, UPS, Toulouse 31037, France.,Laboratoire de Biologie Médicale Oncologique, Institut Claudius Regaud, IUCT-Oncopôle, Toulouse 31037, France
| | - Aurélien Olichon
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, UPS, Toulouse 31037, France.,INSERM, UMR 1188 Diabète athérothrombose Réunion Océan Indien (DéTROI), Université de La Réunion, Saint-Denis de La Réunion 97487, France
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18
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Soetens E, Ballegeer M, Saelens X. An Inside Job: Applications of Intracellular Single Domain Antibodies. Biomolecules 2020; 10:biom10121663. [PMID: 33322697 PMCID: PMC7764588 DOI: 10.3390/biom10121663] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Sera of camelid species contain a special kind of antibody that consists only of heavy chains. The variable antigen binding domain of these heavy chain antibodies can be expressed as a separate entity, called a single domain antibody that is characterized by its small size, high solubility and oftentimes exceptional stability. Because of this, most single domain antibodies fold correctly when expressed in the reducing environment of the cytoplasm, and thereby retain their antigen binding specificity. Single domain antibodies can thus be used to target a broad range of intracellular proteins. Such intracellular single domain antibodies are also known as intrabodies, and have proven to be highly useful tools for basic research by allowing visualization, disruption and even targeted degradation of intracellular proteins. Furthermore, intrabodies can be used to uncover prospective new therapeutic targets and have the potential to be applied in therapeutic settings in the future. In this review we provide a brief overview of recent advances in the field of intracellular single domain antibodies, focusing on their use as research tools and potential therapeutic applications. Special attention is given to the available methods that allow delivery of single domain antibodies into cells.
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Affiliation(s)
- Eline Soetens
- VIB-UGent Center for Medical Biotechnology, VIB, B-9052 Ghent, Belgium; (E.S.); (M.B.)
- Department of Biochemistry and Microbiology, Ghent University, B-9000 Ghent, Belgium
| | - Marlies Ballegeer
- VIB-UGent Center for Medical Biotechnology, VIB, B-9052 Ghent, Belgium; (E.S.); (M.B.)
- Department of Biochemistry and Microbiology, Ghent University, B-9000 Ghent, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, B-9052 Ghent, Belgium; (E.S.); (M.B.)
- Department of Biochemistry and Microbiology, Ghent University, B-9000 Ghent, Belgium
- Correspondence:
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19
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Cheloha RW, Harmand TJ, Wijne C, Schwartz TU, Ploegh HL. Exploring cellular biochemistry with nanobodies. J Biol Chem 2020; 295:15307-15327. [PMID: 32868455 PMCID: PMC7650250 DOI: 10.1074/jbc.rev120.012960] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/27/2020] [Indexed: 12/21/2022] Open
Abstract
Reagents that bind tightly and specifically to biomolecules of interest remain essential in the exploration of biology and in their ultimate application to medicine. Besides ligands for receptors of known specificity, agents commonly used for this purpose are monoclonal antibodies derived from mice, rabbits, and other animals. However, such antibodies can be expensive to produce, challenging to engineer, and are not necessarily stable in the context of the cellular cytoplasm, a reducing environment. Heavy chain-only antibodies, discovered in camelids, have been truncated to yield single-domain antibody fragments (VHHs or nanobodies) that overcome many of these shortcomings. Whereas they are known as crystallization chaperones for membrane proteins or as simple alternatives to conventional antibodies, nanobodies have been applied in settings where the use of standard antibodies or their derivatives would be impractical or impossible. We review recent examples in which the unique properties of nanobodies have been combined with complementary methods, such as chemical functionalization, to provide tools with unique and useful properties.
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Affiliation(s)
- Ross W Cheloha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Thibault J Harmand
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Charlotte Wijne
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA.
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20
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21
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Arp2/3-Branched Actin Maintains an Active Pool of GTP-RhoA and Controls RhoA Abundance. Cells 2019; 8:cells8101264. [PMID: 31623230 PMCID: PMC6830327 DOI: 10.3390/cells8101264] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/03/2019] [Accepted: 10/15/2019] [Indexed: 01/23/2023] Open
Abstract
Small GTPases regulate cytoskeletal dynamics, cell motility, and division under precise spatiotemporal control. Different small GTPases exhibit cross talks to exert feedback response or to act in concert during signal transduction. However, whether and how specific cytoskeletal components' feedback to upstream signaling factors remains largely elusive. Here, we report an intriguing finding that disruption of the Arp2/3-branched actin specifically reduces RhoA activity but upregulates its total protein abundance. We further dissect the mechanisms underlying these circumstances and identify the altered cortactin/p190RhoGAP interaction and weakened CCM2/Smurf1 binding to be involved in GTP-RhoA reduction and total RhoA increase, respectively. Moreover, we find that cytokinesis defects induced by Arp2/3 inhibition can be rescued by activating RhoA. Our study reveals an intricate feedback from the actin cytoskeleton to the small GTPase. Our work highlights the role of Arp2/3-branched actin in signal transduction aside from its function in serving as critical cytoskeletal components to maintain cell morphology and motility.
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22
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Bery N, Keller L, Soulié M, Gence R, Iscache AL, Cherier J, Cabantous S, Sordet O, Lajoie-Mazenc I, Pedelacq JD, Favre G, Olichon A. A Targeted Protein Degradation Cell-Based Screening for Nanobodies Selective toward the Cellular RHOB GTP-Bound Conformation. Cell Chem Biol 2019; 26:1544-1558.e6. [PMID: 31522999 DOI: 10.1016/j.chembiol.2019.08.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 11/22/2018] [Accepted: 08/23/2019] [Indexed: 01/10/2023]
Abstract
The selective downregulation of activated intracellular proteins is a key challenge in cell biology. RHO small GTPases switch between a guanosine diphosphate (GDP)-bound and a guanosine triphosphate (GTP)-bound state that drives downstream signaling. At present, no tool is available to study endogenous RHO-GTPinduced conformational changes in live cells. Here, we established a cell-based screen to selectively degrade RHOB-GTP using F-box-intracellular single-domain antibody fusion. We identified one intracellular antibody (intrabody) that shows selective targeting of endogenous RHOB-GTP mediated by interactions between the CDR3 loop of the domain antibody and the GTP-binding pocket of RHOB. Our results suggest that, while RHOB is highly regulated at the expression level, only the GTP-bound pool, but not its global expression, mediates RHOB functions in genomic instability and in cell invasion. The F-box/intrabody-targeted protein degradation represents a unique approach to knock down the active form of small GTPases or other proteins with multiple cellular activities.
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Affiliation(s)
- Nicolas Bery
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Laura Keller
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, UPS, Toulouse, France; Département de Biologie, Institut Claudius Regaud, Toulouse, France
| | - Marjorie Soulié
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Rémi Gence
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Anne-Laure Iscache
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, UPS, Toulouse, France; Département de Biologie, Institut Claudius Regaud, Toulouse, France
| | - Julia Cherier
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, UPS, Toulouse, France; Département de Biologie, Institut Claudius Regaud, Toulouse, France
| | - Stéphanie Cabantous
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Olivier Sordet
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Isabelle Lajoie-Mazenc
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jean-Denis Pedelacq
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France.
| | - Gilles Favre
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, UPS, Toulouse, France; Département de Biologie, Institut Claudius Regaud, Toulouse, France.
| | - Aurélien Olichon
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, UPS, Toulouse, France.
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