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An ultra-stable cytoplasmic antibody engineered for in vivo applications. Nat Commun 2020; 11:336. [PMID: 31953402 PMCID: PMC6969036 DOI: 10.1038/s41467-019-13654-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/08/2019] [Indexed: 11/16/2022] Open
Abstract
Targeting cytoplasmic protein–protein interactions with antibodies remains technically challenging, since antibodies expressed in the cytosol frequently form insoluble aggregates. Existing engineering methods are based on the notion that the estimated net charge at pH 7.4 affects stability; as such, they are unable to overcome this problem. Herein, we report a versatile method for engineering an ultra-stable cytoplasmic antibody (STAND), with a strong estimated net negative charge at pH 6.6, by fusing peptide tags with a highly negative charge and a low isoelectric point. Without the need for complicated amino acid substitutions, we convert aggregation-prone antibodies to STANDs that are useful for inhibiting in vivo transmitter release, modulating animal behaviour, and inhibiting in vivo cancer proliferation driven by mutated Kras—long recognised as an “undruggable” oncogenic protein. The STAND method shows promise for targeting endogenous cytoplasmic proteins in basic biology and for developing future disease treatments. Antibodies expressed in the cytosol often form insoluble aggregates, which makes it hard to target intracellular proteins. Here the authors engineer an ultra-stable cytoplasmic antibody (STAND) with a low isoelectric point that can be used in vivo.
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Rhodes DA, Isenberg DA. TRIM21 and the Function of Antibodies inside Cells. Trends Immunol 2017; 38:916-926. [PMID: 28807517 DOI: 10.1016/j.it.2017.07.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/28/2017] [Accepted: 07/18/2017] [Indexed: 11/26/2022]
Abstract
Therapeutic antibodies targeting disease-associated antigens are key tools in the treatment of cancer and autoimmunity. So far, therapeutic antibodies have targeted antigens that are, or are presumed to be, extracellular. A largely overlooked property of antibodies is their functional activity inside cells. The diverse literature dealing with intracellular antibodies emerged historically from studies of the properties of some autoantibodies. The identification of tripartite motif (TRIM) 21 as an intracellular Fc receptor linking cytosolic antibody recognition to the ubiquitin proteasome system brings this research into sharper focus. We review critically the research related to intracellular antibodies, link this to the TRIM21 effector mechanism, and highlight how this work is exposing the previously restricted intracellular space to the potential of therapeutic antibodies.
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Affiliation(s)
- David A Rhodes
- Department of Pathology, Immunology Division, University of Cambridge, Cambridge, UK.
| | - David A Isenberg
- Centre for Rheumatology, Division of Medicine, University College London, London, UK
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Cardinale A, Filesi I, Singh PB, Biocca S. Intrabody-mediated diverting of HP1β to the cytoplasm induces co-aggregation of H3-H4 histones and lamin-B receptor. Exp Cell Res 2015; 338:70-81. [PMID: 26364738 DOI: 10.1016/j.yexcr.2015.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 12/12/2022]
Abstract
Diverting a protein from its intracellular location is a unique property of intrabodies. To interfere with the intracellular traffic of heterochromatin protein 1β (HP1β) in living cells, we have generated a cytoplasmic targeted anti-HP1β intrabody, specifically directed against the C-terminal portion of the molecule. HP1β is a conserved component of mouse and human constitutive heterochromatin involved in diverse nuclear functions including gene silencing, DNA repair and nuclear membrane assembly. We found that the anti-HP1β intrabody sequesters HP1β into cytoplasmic aggregates, inhibiting its traffic to the nucleus. Lamin B receptor (LBR) and a subset of core histones (H3/H4) are also specifically co-sequestered in the cytoplasm of anti-HP1β intrabody-expressing cells. Methylated histone H3 at K9 (Me9H3), a marker of constitutive heterochromatin, is not affected by the anti-HP1β intrabody expression. Hyper-acetylating conditions completely dislodge H3 from HP1β:LBR containing aggregates. The expression of anti-HP1β scFv fragments induces apoptosis, associated with an alteration of nuclear morphology. Both these phenotypes are specifically rescued either by overexpression of recombinant full length HP1β or by HP1β mutant containing the chromoshadow domain, but not by recombinant LBR protein. The HP1β-chromodomain mutant, on the other hand, does not rescue the phenotypes, but does compete with LBR for binding to HP1β. These findings provide new insights into the mode of action of cytoplasmic-targeted intrabodies and the interaction between HP1β and its binding partners involved in peripheral heterochromatin organisation.
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Affiliation(s)
- Alessio Cardinale
- Laboratory of Molecular and Cellular Neurobiology, IRCCS San Raffaele Pisana, Via di Val Cannuta 247, 00166 Rome, Italy
| | - Ilaria Filesi
- Department of Systems Medicine, University of Roma Tor Vergata, Via Montpellier 1, 00133 Roma, Italy
| | - Prim B Singh
- Department of Natural Sciences and Psychology, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom
| | - Silvia Biocca
- Department of Systems Medicine, University of Roma Tor Vergata, Via Montpellier 1, 00133 Roma, Italy.
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Hypothesis: A role for EBV-induced molecular mimicry in Parkinson's disease. Parkinsonism Relat Disord 2014; 20:685-94. [DOI: 10.1016/j.parkreldis.2014.02.031] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 02/18/2014] [Accepted: 02/22/2014] [Indexed: 12/12/2022]
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5
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Intrabody Expression in Mammalian Cells. ANTIBODY EXPRESSION AND PRODUCTION 2011. [PMCID: PMC7120103 DOI: 10.1007/978-94-007-1257-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/30/2022]
Abstract
The intracellular expression of antibodies or antibody fragments (intrabodies) in different compartments of mammalian cells allows to block or modulate the function of endogenous molecules. Intrabodies can alter protein folding, protein-protein, protein-DNA, protein-RNA interactions and protein modification. They can induce a phenotypic knockout and work as neutralizing agents by direct binding to the target antigen, by diverting its intracellular traffic or by inhibiting its association with binding partners. They have been largely employed as research tools and are emerging as therapeutic molecules for the treatment of human diseases as viral pathologies, cancer and misfolding diseases. The fast growing bio-market of recombinant antibodies provides intrabodies with enhanced binding specificity, stability and solubility, together with lower immunogenicity, for their use in therapy. This chapter describes the crucial aspects required to express intrabodies in different intracellular compartments of mammalian cells, their various modes of action and gives an update on the applications of intrabodies in human diseases.
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Sudol KL, Mastrangelo MA, Narrow WC, Frazer ME, Levites YR, Golde TE, Federoff HJ, Bowers WJ. Generating differentially targeted amyloid-beta specific intrabodies as a passive vaccination strategy for Alzheimer's disease. Mol Ther 2009; 17:2031-40. [PMID: 19638957 DOI: 10.1038/mt.2009.174] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Amyloid-beta (A beta) has been identified as a key component in Alzheimer's disease (AD). Significant in vitro and human pathological data suggest that intraneuronal accumulation of A beta peptides plays an early role in the neurodegenerative cascade. We hypothesized that targeting an antibody-based therapeutic to specifically abrogate intracellular A beta accumulation could prevent or slow disease onset. A beta 42-specific intracellular antibodies (intrabodies) with and without an intracellular trafficking signal were engineered from a previously characterized single-chain variable fragment (scFv) antibody. The intrabodies, one with an endoplasmic reticulum (ER) targeting signal and one devoid of a targeting sequence, were assessed in cells harboring a doxycycline (Dox)-regulated mutant human amyloid precursor protein Swedish mutant (hAPP(swe)) transcription unit for their abilities to prevent A beta peptide egress. Adeno-associated virus (AAV) vectors expressing the engineered intrabodies were administered to young adult 3xTg-AD mice, a model that develops amyloid and Tau pathologies, prior to the initial appearance of intraneuronal A beta. Chronic expression of the ER-targeted intrabody (IB) led to partial clearance of A beta 42 deposits and interestingly, in reduced staining for a pathologic phospho-Tau epitope (Thr231). This approach may provide insights into the functional relevance of intraneuronal A beta accumulation in early AD and potentially lead to the development of new therapeutics.
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Affiliation(s)
- Kelly L Sudol
- Center for Neural Development and Disease, University of Rochester Medical Center, Rochester, New York 14642, USA
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Liao HI, Olson CA, Hwang S, Deng H, Wong E, Baric RS, Roberts RW, Sun R. mRNA display design of fibronectin-based intrabodies that detect and inhibit severe acute respiratory syndrome coronavirus nucleocapsid protein. J Biol Chem 2009; 284:17512-20. [PMID: 19364769 PMCID: PMC2719390 DOI: 10.1074/jbc.m901547200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The nucleocapsid (N) protein of severe acute respiratory syndrome (SARS) coronavirus plays important roles in both viral replication and modulation of host cell processes. New ligands that target the N protein may thus provide tools to track the protein inside cells, detect interaction hot spots on the protein surface, and discover sites that could be used to develop new anti-SARS therapies. Using mRNA display selection and directed evolution, we designed novel antibody-like protein affinity reagents that target SARS N protein with high affinity and selectivity. Our libraries were based on an 88-residue variant of the 10th fibronectin type III domain from human fibronectin (10Fn3). This selection resulted in eight independent 10Fn3 intrabodies, two that require the N-terminal domain for binding and six that recognize the C terminus, one with Kd = 1.7 nm. 10Fn3 intrabodies are well expressed in mammalian cells and are relocalized by N in SARS-infected cells. Seven of the selected intrabodies tested do not perturb cellular function when expressed singly in vivo and inhibit virus replication from 11- to 5900-fold when expressed in cells prior to infection. Targeting two sites on SARS-N simultaneously using two distinct 10Fn3s results in synergistic inhibition of virus replication.
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Affiliation(s)
- Hsiang-I Liao
- Department of Molecular and Medical Pharmacology, California Nano System Institute, UCLA, Los Angeles, CA 90095, USA
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Cardinale A, Biocca S. Can intrabodies targeted to the secretory compartment interact with a cytosolic protein? A comment on the article by Sawahata et al. "Cytoplasmic expression and specific binding of the VH/VL single domain intrabodies in transfected NIH3T3 cells", Exp. Mol. Pathol. 2008 Nov 27; Epub ahead of print. Exp Mol Pathol 2009; 86:138. [PMID: 19348064 DOI: 10.1016/j.yexmp.2009.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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9
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The potential of intracellular antibodies for therapeutic targeting of protein-misfolding diseases. Trends Mol Med 2008; 14:373-80. [DOI: 10.1016/j.molmed.2008.07.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Revised: 07/04/2008] [Accepted: 07/04/2008] [Indexed: 12/25/2022]
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Mulugeta S, Maguire JA, Newitt JL, Russo SJ, Kotorashvili A, Beers MF. Misfolded BRICHOS SP-C mutant proteins induce apoptosis via caspase-4- and cytochrome c-related mechanisms. Am J Physiol Lung Cell Mol Physiol 2007; 293:L720-9. [PMID: 17586700 DOI: 10.1152/ajplung.00025.2007] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Several mutations within the BRICHOS domain of surfactant protein C (SP-C) have been linked to interstitial lung disease. Recent studies have suggested that these mutations cause misfolding of the proprotein (proSP-C), which initiates the unfolded protein response to resolve improper folding or promote protein degradation. We have reported that in vitro expression of one of these proteins, the exon 4 deletion mutant (hSP-CΔexon4), causes endoplasmic reticulum (ER) stress, inhibits proteasome function, and activates caspase-3-mediated apoptosis. To further elucidate mechanisms and common pathways for cellular dysfunction, various assays were performed by transiently expressing two SP-C BRICHOS domain mutant (BRISPC) proteins (hSP-CΔexon4, hSP-CL188Q) and control proteins in lung epithelium-derived A549 and kidney epithelium-derived (HEK-293) GFPu-1 cell lines. Compared with controls, cells expressing either BRICHOS mutant protein consistently exhibited increased formation of insoluble aggregates, enhanced promotion of inositol-requiring enzyme 1-dependent splicing of X-box binding protein-1 (XBP-1), significant inhibition of proteasome activity, enhanced induction of mitochondrial cytochrome c release, and increased activations of caspase-4 and caspase-3, leading to apoptosis. These results suggest common cellular responses, including initiation of cell-death signaling pathways, to these lung disease-associated BRISPC proteins.
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Affiliation(s)
- Surafel Mulugeta
- Pulmonary, Allergy, and Critical Care Division, Univ. of Pennsylvania School of Medicine, Vernon & Shirley Hill Pavilion, Suite H418, 380 South Univ. Ave., Philadelphia, PA 19104, USA.
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Tanaka T, Williams RL, Rabbitts TH. Tumour prevention by a single antibody domain targeting the interaction of signal transduction proteins with RAS. EMBO J 2007; 26:3250-9. [PMID: 17568777 PMCID: PMC1914092 DOI: 10.1038/sj.emboj.7601744] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Accepted: 05/09/2007] [Indexed: 12/31/2022] Open
Abstract
Many disease-related processes occur via protein complexes that are considered undruggable with small molecules. An example is RAS, which is frequently mutated in cancer and contributes to initiation and maintenance of the disease by constitutive signal transduction through protein interaction with effector proteins, like PI3K, RAF and RALGDS. Such protein interactions are therefore significant targets for therapy. We describe a single immunoglobulin variable region domain that specifically binds to activated GTP-bound RAS and prevents RAS-dependent tumorigenesis in a mouse model. The crystal structure of the immunoglobulin-RAS complex shows that the variable region competitively binds to the conformationally variant regions of RAS, where its signalling effector molecules interact. This allows the plasma membrane targeted single domain intrabody to inhibit signalling by mutant RAS. This mode of action is a novel advance to directly interfere with oncogenic RAS function in human cancer and shows a universally applicable approach to develop macromolecules to combat cancer. In addition, this method illustrates a general means for interfering with protein interactions that are commonly considered intractable as conventional drug targets.
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MESH Headings
- Animals
- Antibodies, Neoplasm/chemistry
- Antibodies, Neoplasm/immunology
- Cell Line
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Chlorocebus aethiops
- Crystallography, X-Ray
- Disease Models, Animal
- Humans
- Mice
- Models, Molecular
- Neoplasms/genetics
- Neoplasms/immunology
- Neoplasms/metabolism
- Neoplasms/pathology
- Phenotype
- Protein Binding
- Protein Structure, Quaternary
- Protein Structure, Tertiary
- Signal Transduction
- Surface Plasmon Resonance
- Xenograft Model Antitumor Assays
- ras Proteins/chemistry
- ras Proteins/genetics
- ras Proteins/immunology
- ras Proteins/metabolism
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Affiliation(s)
- Tomoyuki Tanaka
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK
| | | | - Terence H Rabbitts
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK
- Present address: Leeds Institute of Molecular Medicine, Section of Experimental Therapeutics, Wellcome Trust Brenner Building, St James's University Hospital, Leeds LS9 7TF, UK. Tel.: +44 (0) 113 343 8518; Fax: +44 (0) 113 343 8601; E-mail:
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12
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Filesi I, Cardinale A, Mattei S, Biocca S. Selective re-routing of prion protein to proteasomes and alteration of its vesicular secretion prevent PrPScformation. J Neurochem 2007; 101:1516-26. [PMID: 17542810 DOI: 10.1111/j.1471-4159.2006.04439.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Conversion of the cellular prion protein (PrP(C)) into the abnormal scrapie isoform (PrP(Sc)) is the hallmark of prion diseases, which are fatal and transmissible neurodegenerative disorders. ER-retained anti-prion recombinant single-chain Fv fragments have been proved to be an effective tool for inhibition of PrP(C) trafficking to the cell surface and antagonize PrP(Sc) formation and infectivity. In the present study, we have generated the secreted version of 8H4 intrabody (Sec-8H4) in order to compel PrP(C) outside the cells. The stable expression of the Sec-8H4 intrabodies induces proteasome degradation of endogenous prion protein but does not influence its glycosylation profile and maturation. Moreover, we found a dramatic diverting of PrP(C) traffic from its vesicular secretion and, most importantly, a total inhibition of PrP(Sc) accumulation in NGF-differentiated Sec-8H4 PC12 cells. These results confirm that perturbing the intracellular traffic of endogenous PrP(C) is an effective strategy to inhibit PrP(Sc) accumulation and provide convincing evidences for application of intracellular antibodies in prion diseases.
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Affiliation(s)
- Ilaria Filesi
- Department of Neuroscience and Laboratory of Clinical Biochemistry, University of Tor Vergata, Rome, Italy
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Visintin M, Meli GA, Cannistraci I, Cattaneo A. Intracellular antibodies for proteomics. J Immunol Methods 2004; 290:135-53. [PMID: 15261577 PMCID: PMC7126613 DOI: 10.1016/j.jim.2004.04.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2004] [Indexed: 11/03/2022]
Abstract
The intracellular antibody technology has many applications for proteomics studies. The potential of intracellular antibodies for the systematic study of the proteome has been made possible by the development of new experimental strategies that allow the selection of antibodies under conditions of intracellular expression. The Intracellular Antibody Capture Technology (IACT) is an in vivo two-hybrid-based method originally developed for the selection of antibodies readily folded for ectopic expression. IACT has been used for the rapid and effective identification of novel antigen-antibody pairs in intracellular compartments and for the in vivo identification of epitopes recognized by selected intracellular antibodies. IACT opens the way to the use of intracellular antibody technology for large-scale applications in proteomics. In its present format, its use is however somewhat limited by the need of a preselection of the input phage antibody libraries on protein antigens or by the construction of an antibody library from mice immunized against the target protein(s), to provide an enriched input library to compensate for the suboptimal efficiency of transformation of the yeast cells. These enrichment steps require expressing the corresponding proteins, which represents a severe bottleneck for the scaling up of the technology. We describe here the construction of a single pot library of intracellular antibodies (SPLINT), a naïve library of scFv fragments expressed directly in the yeast cytoplasm in a format such that antigen-specific intrabodies can be isolated directly from gene sequences, with no manipulation whatsoever of the corresponding proteins. We describe also the isolation from SPLINT of a panel of intrabodies against a number of different proteins. The application of SPLINT on a genome-wide scale should help the systematic study of the functional organization of cell proteome.
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Affiliation(s)
- Michela Visintin
- Lay Line Genomics SpA, Via di Castel Romano 100, 00128 Rome, Italy
| | - Giovanni Antonio Meli
- International School for Advanced Studies (SISSA), Padriciano 99, 34012 Trieste, Italy
| | | | - Antonino Cattaneo
- Lay Line Genomics SpA, Via di Castel Romano 100, 00128 Rome, Italy
- International School for Advanced Studies (SISSA), Padriciano 99, 34012 Trieste, Italy
- Corresponding author. Lay Line Genomics SpA, Via di Castel Romano 100, 00128 Rome, Italy
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