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Poirson J, Cho H, Dhillon A, Haider S, Imrit AZ, Lam MHY, Alerasool N, Lacoste J, Mizan L, Wong C, Gingras AC, Schramek D, Taipale M. Proteome-scale discovery of protein degradation and stabilization effectors. Nature 2024; 628:878-886. [PMID: 38509365 DOI: 10.1038/s41586-024-07224-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/22/2024] [Indexed: 03/22/2024]
Abstract
Targeted protein degradation and stabilization are promising therapeutic modalities because of their potency, versatility and their potential to expand the druggable target space1,2. However, only a few of the hundreds of E3 ligases and deubiquitinases in the human proteome have been harnessed for this purpose, which substantially limits the potential of the approach. Moreover, there may be other protein classes that could be exploited for protein stabilization or degradation3-5, but there are currently no methods that can identify such effector proteins in a scalable and unbiased manner. Here we established a synthetic proteome-scale platform to functionally identify human proteins that can promote the degradation or stabilization of a target protein in a proximity-dependent manner. Our results reveal that the human proteome contains a large cache of effectors of protein stability. The approach further enabled us to comprehensively compare the activities of human E3 ligases and deubiquitinases, identify and characterize non-canonical protein degraders and stabilizers and establish that effectors have vastly different activities against diverse targets. Notably, the top degraders were more potent against multiple therapeutically relevant targets than the currently used E3 ligases cereblon and VHL. Our study provides a functional catalogue of stability effectors for targeted protein degradation and stabilization and highlights the potential of induced proximity screens for the discovery of new proximity-dependent protein modulators.
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Affiliation(s)
- Juline Poirson
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Hanna Cho
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Akashdeep Dhillon
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Shahan Haider
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ahmad Zoheyr Imrit
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Mandy Hiu Yi Lam
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Nader Alerasool
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jessica Lacoste
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Lamisa Mizan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Cassandra Wong
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Daniel Schramek
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Mikko Taipale
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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2
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Rabbitts TH. Intracellular Antibodies for Drug Discovery and as Drugs of the Future. Antibodies (Basel) 2023; 12:24. [PMID: 36975371 PMCID: PMC10044824 DOI: 10.3390/antib12010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
The application of antibodies in cells was first shown in the early 1990s, and subsequently, the field of intracellular antibodies has expanded to encompass antibody fragments and their use in target validation and as engineered molecules that can be fused to moieties (referred to as warheads) to replace the Fc effector region of a whole immunoglobulin to elicit intracellular responses, such as cell death pathways or protein degradation. These various forms of intracellular antibodies have largely been used as research tools to investigate function within cells by perturbing protein activity. New applications of such molecules are on the horizon, namely their use as drugs per se and as templates for small-molecule drug discovery. The former is a potential new pharmacology that could harness the power and flexibility of molecular biology to generate new classes of drugs (herein referred to as macrodrugs when used in the context of disease control). Delivery of engineered intracellular antibodies, and other antigen-binding macromolecules formats, into cells to produce a therapeutic effect could be applied to any therapeutic area where regulation, degradation or other kinds of manipulation of target proteins can produce a therapeutic effect. Further, employing single-domain antibody fragments as competitors in small-molecule screening has been shown to enable identification of drug hits from diverse chemical libraries. Compounds selected in this way can mimic the effects of the intracellular antibodies that have been used for target validation. The capability of intracellular antibodies to discriminate between closely related proteins lends a new dimension to drug screening and drug development.
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3
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Mezentsev Y, Ershov P, Yablokov E, Kaluzhskiy L, Kupriyanov K, Gnedenko O, Ivanov A. Protein Interactome Profiling of Stable Molecular Complexes in Biomaterial Lysate. Int J Mol Sci 2022; 23:ijms232415697. [PMID: 36555337 PMCID: PMC9779103 DOI: 10.3390/ijms232415697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Most proteins function as part of various complexes, forming via stable and dynamic protein-protein interactions (PPIs). The profiling of PPIs expands the fundamental knowledge about the structures, functions, and regulation patterns of protein complexes and intracellular molecular machineries. Protein interactomics aims at solving three main tasks: (1) identification of protein partners and parts of complex intracellular structures; (2) analysis of PPIs parameters (affinity, molecular-recognition specificity, kinetic rate constants, and thermodynamic-parameters determination); (3) the study of the functional role of novel PPIs. The purpose of this work is to update the current state and prospects of multi-omics approaches to profiling of proteins involved in the formation of stable complexes. Methodological paradigm includes a development of protein-extraction and -separation techniques from tissues or cellular lysates and subsequent identification of proteins using mass-spectrometry analysis. In addition, some aspects of authors' experimental platforms, based on high-performance size-exclusion chromatography, procedures of molecular fishing, and protein identification, as well as the possibilities of interactomic taxonomy of each protein, are discussed.
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4
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Mucke HA. Patent Highlights February-March 2022. Pharm Pat Anal 2022. [PMID: 35861060 DOI: 10.4155/ppa-2022-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A snapshot of noteworthy recent developments in the patent literature of relevance to pharmaceutical and medical research and development.
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5
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Bery N, Rabbitts T. A Cell-based Screening Method Using an Intracellular Antibody for Discovering Small Molecules Targeting Hard-to-drug Proteins. Bio Protoc 2022; 12:e4324. [DOI: 10.21769/bioprotoc.4324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 08/19/2021] [Accepted: 01/12/2022] [Indexed: 11/02/2022] Open
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6
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Asaadi Y, Jouneghani FF, Janani S, Rahbarizadeh F. A comprehensive comparison between camelid nanobodies and single chain variable fragments. Biomark Res 2021; 9:87. [PMID: 34863296 PMCID: PMC8642758 DOI: 10.1186/s40364-021-00332-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022] Open
Abstract
By the emergence of recombinant DNA technology, many antibody fragments have been developed devoid of undesired properties of natural immunoglobulins. Among them, camelid heavy-chain variable domains (VHHs) and single-chain variable fragments (scFvs) are the most favored ones. While scFv is used widely in various applications, camelid antibodies (VHHs) can serve as an alternative because of their superior chemical and physical properties such as higher solubility, stability, smaller size, and lower production cost. Here, these two counterparts are compared in structure and properties to identify which one is more suitable for each of their various therapeutic, diagnosis, and research applications.
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Affiliation(s)
- Yasaman Asaadi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Fatemeh Fazlollahi Jouneghani
- Department of Cell & Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Sara Janani
- Department of Cell & Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran.
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7
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Benn JA, Mukadam AS, McEwan WA. Targeted protein degradation using intracellular antibodies and its application to neurodegenerative disease. Semin Cell Dev Biol 2021; 126:138-149. [PMID: 34654628 DOI: 10.1016/j.semcdb.2021.09.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 01/10/2023]
Abstract
Antibodies mediate the majority of their effects in the extracellular domain, or in intracellular compartments isolated from the cytosol. Under a growing list of circumstances, however, antibodies are found to gain access to the cytoplasm. Cytosolic immune complexes are bound by the atypical antibody receptor TRIM21, which mediates the rapid degradation of the immune complexes at the proteasome. These discoveries have informed the development of TRIM-Away, a technique to selectively deplete proteins using delivery of antibodies into cells. A range of related approaches that elicit selective protein degradation using intracellular constructs linking antibody fragments to degradative effector functions have also been developed. These methods hold promise for inducing the degradation of proteins as both research tools and as a novel therapeutic approach. Protein aggregates are a pathophysiological feature of neurodegenerative diseases and are considered to have a causal role in pathology. Immunotherapy is emerging as a promising route towards their selective targeting, and a role of antibodies in the cytosol has been demonstrated in cell-based assays. This review will explore the mechanisms by which therapeutic antibodies engage and eliminate intracellularly aggregated proteins. We will discuss how future developments in intracellular antibody technology may enhance the therapeutic potential of such antibody-derived therapies.
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Affiliation(s)
- Jonathan A Benn
- UK Dementia Research Institute at the University of Cambridge, Department of Clinical Neurosciences, Cambridge, UK
| | - Aamir S Mukadam
- UK Dementia Research Institute at the University of Cambridge, Department of Clinical Neurosciences, Cambridge, UK
| | - William A McEwan
- UK Dementia Research Institute at the University of Cambridge, Department of Clinical Neurosciences, Cambridge, UK.
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8
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Abdulla H, Vo A, Shields BJ, Davies TJ, Jackson JT, Alserihi R, Viney EM, Wong T, Yan F, Wong NC, Demoen L, Curtis DJ, Alexander WS, Van Vlierberghe P, Dickins RA, McCormack MP. T-ALL can evolve to oncogene independence. Leukemia 2021; 35:2205-19. [PMID: 33483615 DOI: 10.1038/s41375-021-01120-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 09/09/2020] [Accepted: 01/07/2021] [Indexed: 01/29/2023]
Abstract
The majority of cases of T-cell acute lymphoblastic leukemia (T-ALL) contain chromosomal abnormalities that drive overexpression of oncogenic transcription factors. However, whether these initiating oncogenes are required for leukemia maintenance is poorly understood. To address this, we developed a tetracycline-regulated mouse model of T-ALL driven by the oncogenic transcription factor Lmo2. This revealed that whilst thymus-resident pre-Leukemic Stem Cells (pre-LSCs) required continuous Lmo2 expression, the majority of leukemias relapsed despite Lmo2 withdrawal. Relapse was associated with a mature phenotype and frequent mutation or loss of tumor suppressor genes including Ikzf1 (Ikaros), with targeted deletion Ikzf1 being sufficient to transform Lmo2-dependent leukemias to Lmo2-independence. Moreover, we found that the related transcription factor TAL1 was dispensable in several human T-ALL cell lines that contain SIL-TAL1 chromosomal deletions driving its overexpression, indicating that evolution to oncogene independence can also occur in human T-ALL. Together these results indicate an evolution of oncogene addiction in murine and human T-ALL and show that loss of Ikaros is a mechanism that can promote self-renewal of T-ALL lymphoblasts in the absence of an initiating oncogenic transcription factor.
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9
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Canning P, Bataille C, Bery N, Milhas S, Hayes A, Raynaud F, Miller A, Rabbitts T. Competitive SPR using an intracellular anti-LMO2 antibody identifies novel LMO2-interacting compounds. J Immunol Methods 2021; 494:113051. [PMID: 33794223 PMCID: PMC8208243 DOI: 10.1016/j.jim.2021.113051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/10/2021] [Accepted: 03/26/2021] [Indexed: 01/13/2023]
Abstract
The use of intracellular antibodies as templates to derive surrogate compounds is an important objective because intracellular antibodies can be employed initially for target validation in pre-clinical assays and subsequently employed in compound library screens. LMO2 is a T cell oncogenic protein activated in the majority of T cell acute leukaemias. We have used an inhibitory intracellular antibody fragment as a competitor in a small molecule library screen using competitive surface plasmon resonance (cSPR) to identify compounds that bind to LMO2. We selected four compounds that bind to LMO2 but not when the anti-LMO2 intracellular antibody fragment is bound to it. These findings further illustrate the value of intracellular antibodies in the initial stages of drug discovery campaigns and more generally antibodies, or antibody fragments, can be the starting point for chemical compound development as surrogates of the antibody combining site.
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Affiliation(s)
- Peter Canning
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Carole Bataille
- Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK
| | - Nicolas Bery
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Sabine Milhas
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Angela Hayes
- Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Florence Raynaud
- Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Ami Miller
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Terry Rabbitts
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK.
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10
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Bery N, Bataille CJR, Russell A, Hayes A, Raynaud F, Milhas S, Anand S, Tulmin H, Miller A, Rabbitts TH. A cell-based screening method using an intracellular antibody for discovering small molecules targeting the translocation protein LMO2. Sci Adv 2021; 7:eabg1950. [PMID: 33837087 PMCID: PMC8034850 DOI: 10.1126/sciadv.abg1950] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/19/2021] [Indexed: 05/07/2023]
Abstract
Intracellular antibodies are tools that can be used directly for target validation by interfering with properties like protein-protein interactions. An alternative use of intracellular antibodies in drug discovery is developing small-molecule surrogates using antibody-derived (Abd) technology. We previously used this strategy with an in vitro competitive surface plasmon resonance method that relied on high-affinity antibody fragments to obtain RAS-binding compounds. We now describe a novel implementation of the Abd method with a cell-based intracellular antibody-guided screening method that we have applied to the chromosomal translocation protein LMO2. We have identified a chemical series of anti-LMO2 Abd compounds that bind at the same LMO2 location as the inhibitory anti-LMO2 intracellular antibody combining site. Intracellular antibodies could therefore be used in cell-based screens to identify chemical surrogates of their binding sites and potentially be applied to any challenging proteins, such as transcription factors that have been considered undruggable.
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Affiliation(s)
- Nicolas Bery
- Weatherall Institute of Molecular Medicine MRC Molecular Haematology Unit, University of Oxford John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Carole J R Bataille
- University of Oxford Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Angela Russell
- University of Oxford Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Angela Hayes
- Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Florence Raynaud
- Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Sabine Milhas
- Weatherall Institute of Molecular Medicine MRC Molecular Haematology Unit, University of Oxford John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Sneha Anand
- Weatherall Institute of Molecular Medicine MRC Molecular Haematology Unit, University of Oxford John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Hanna Tulmin
- Weatherall Institute of Molecular Medicine MRC Molecular Haematology Unit, University of Oxford John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Ami Miller
- Weatherall Institute of Molecular Medicine MRC Molecular Haematology Unit, University of Oxford John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Terence H Rabbitts
- Weatherall Institute of Molecular Medicine MRC Molecular Haematology Unit, University of Oxford John Radcliffe Hospital, Oxford OX3 9DS, UK.
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11
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Tanaka T, Thomas J, Van Montfort R, Miller A, Rabbitts T. Pan RAS-binding compounds selected from a chemical library by inhibiting interaction between RAS and a reduced affinity intracellular antibody. Sci Rep 2021; 11:1712. [PMID: 33462327 PMCID: PMC7814043 DOI: 10.1038/s41598-021-81262-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/28/2020] [Indexed: 02/07/2023] Open
Abstract
Intracellular antibodies are valuable tools for target validation studies for clinical situations such as cancer. Recently we have shown that antibodies can be used for drug discovery in screening for chemical compounds surrogates by showing that compounds could be developed to the so-called undruggable RAS protein family. This method, called Antibody-derived compound (Abd) technology, employed intracellular antibodies binding to RAS in a competitive surface plasmon resonance chemical library screen. Success with this method requires a high affinity interaction between the antibody and the target. We now show that reduction in the affinity (dematuration) of the anti-active RAS antibody facilitates the screening of a chemical library using an in vitro AlphaScreen method. This identified active RAS specific-binding Abd compounds that inhibit the RAS-antibody interaction. One compound is shown to be a pan-RAS binder to KRAS,
HRAS and NRAS-GTP proteins with a Kd of average 37 mM, offering the possibility of a new chemical series that interacts with RAS in the switch region where the intracellular antibody binds. This simple approach shows the druggability of RAS and is generally applicable to antibody-derived chemical library screening by affording flexibility through simple antibody affinity variation. This approach can be applied to find Abd compounds as surrogates of antibody-combining sites for novel drug development in a range of human diseases.
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Affiliation(s)
- Tomoyuki Tanaka
- Leeds Institute of Medical Research, St James Hospital, Brenner Building, Beckett St., Leeds, LS9 7TF, UK.,Sanofi K.K. Tokyo Opera City Tower, Shinjuku-ku, Tokyo, 163-1488, Japan
| | - Jemima Thomas
- Institute of Cancer Research, Division of Cancer Therapeutics, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Rob Van Montfort
- Institute of Cancer Research, Division of Cancer Therapeutics, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Ami Miller
- Institute of Cancer Research, Division of Cancer Therapeutics, 15 Cotswold Road, Sutton, London, SM2 5NG, UK.,, 114 Innovation Dr, Milton Park, Abingdon, OX14 4RZ, UK
| | - Terry Rabbitts
- Leeds Institute of Medical Research, St James Hospital, Brenner Building, Beckett St., Leeds, LS9 7TF, UK. .,Institute of Cancer Research, Division of Cancer Therapeutics, 15 Cotswold Road, Sutton, London, SM2 5NG, UK.
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12
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Jain AK, Bataille CJR, Milhas S, Miller A, Zhang J, Rabbitts TH. Immunopolymer Lipid Nanoparticles for Delivery of Macromolecules to Antigen-Expressing Cells. ACS Appl Bio Mater 2020; 3:8481-8495. [PMID: 35019618 DOI: 10.1021/acsabm.0c00857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Macromolecules such as antibodies and antibody fragments have been reported to interfere with intracellular targets, but their use is limited to delivery systems where expression is achieved from vectors such as plasmids or viruses. We have developed PEGylated nanoparticles of poly-lactic acid (PLA), including the cationic lipid 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP), which are functionalized with monoclonal anti-CD7, anti-CD53, or anti-GPR56 antibodies for receptor-mediated endocytic delivery into T-cell leukemia cell lines. Incorporation of DOTAP as the lipid component of the PLA nanoparticles enhanced the release of the immuno-nanoparticles from the endosomes into the cytosol compared to nanoparticles made from PLA alone. Systemic delivery of these anti-CD7 immuno-nanoparticles into humanized CD7 transgenic mice resulted in localization in the spleen, enhanced uptake into CD7-expressing splenocytes, and release of low amounts of reporter mRNA for translation. These functionalized polymer lipid nanoparticles are the basis for elaboration and optimization for realizing their potential in therapeutic applications to carry specific macromolecules such as mRNAs for translation into therapeutic proteins that can target intracellular proteins which mediate disease.
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Affiliation(s)
- Arvind K Jain
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, U.K
| | - Carole J R Bataille
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Rd, Oxford OX1 3TA, U.K
| | - Sabine Milhas
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, U.K
| | - Ami Miller
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, U.K
| | - Jing Zhang
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, U.K
| | - Terry H Rabbitts
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, U.K
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13
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Abstract
Tumour-associated KRAS mutations are the most prevalent in the three RAS-family isoforms and involve many different amino-acids. Therefore, molecules able to interfere with mutant KRAS protein are potentially important for wide-ranging tumour therapy. We describe the engineering of two RAS degraders based on protein macromolecules (macrodrugs) fused to specific E3 ligases. A KRAS-specific DARPin fused to the VHL E3 ligase is compared to a pan-RAS intracellular single domain antibody (iDAb) fused to the UBOX domain of the CHIP E3 ligase. We demonstrate that while the KRAS-specific DARPin degrader induces specific proteolysis of both mutant and wild type KRAS, it only inhibits proliferation of cancer cells expressing mutant KRAS in vitro and in vivo. Pan-RAS protein degradation, however, affects proliferation irrespective of the RAS mutation. These data show that specific KRAS degradation is an important therapeutic strategy to affect tumours expressing any of the range of KRAS mutations.
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Affiliation(s)
- Nicolas Bery
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Cancer Research Centre of Toulouse, INSERM - Université Toulouse III Paul Sabatier - CNRS, 2 avenue Hubert Curien, Toulouse, 31037, France
| | - Ami Miller
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Institute of Cancer Research, Division of Cancer Therapeutics, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Terry Rabbitts
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK.
- Institute of Cancer Research, Division of Cancer Therapeutics, 15 Cotswold Road, Sutton, London, SM2 5NG, UK.
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14
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Chambers JS, Brend T, Rabbitts TH. Cancer cell killing by target antigen engagement with engineered complementary intracellular antibody single domains fused to pro-caspase3. Sci Rep 2019; 9:8553. [PMID: 31189945 PMCID: PMC6561968 DOI: 10.1038/s41598-019-44908-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/27/2019] [Indexed: 12/31/2022] Open
Abstract
Many tumour causing proteins, such as those expressed after chromosomal translocations or from point mutations, are intracellular and are not enzymes per se amenable to conventional drug targeting. We previously demonstrated an approach (Antibody-antigen Interaction Dependent Apoptosis (AIDA)) whereby a single anti-β-galactosidase intracellular single chain Fv antibody fragment, fused to inactive procaspase-3, induced auto-activation of caspase-3 after binding to the tetrameric β-galactosidase protein. We now demonstrate that co-expressing an anti-RAS heavy chain single VH domain, that binds to mutant RAS several thousand times more strongly than to wild type RAS, with a complementary light chain VL domain, caused programmed cell death (PCD) in mutant RAS expressing cells when each variable region is fused to procaspase-3. The effect requires binding of both anti-RAS variable region fragments and is RAS-specific, producing a tri-molecular complex that auto-activates the caspase pathway leading to cell death. AIDA can be generally applicable for any target protein inside cells by involving appropriate pairs of antigen-specific intracellular antibodies.
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Affiliation(s)
- Jennifer S Chambers
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Oxford, OX3 9DS, UK
| | - Tim Brend
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Oxford, OX3 9DS, UK.,Leeds Institute of Medical Research at St. James's, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Terence H Rabbitts
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Oxford, OX3 9DS, UK.
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15
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Abstract
Protein silencing is often employed as a means to aid investigations in protein function and is increasingly desired as a therapeutic approach. Several types of protein silencing methodologies have been developed, including targeting the encoding genes, transcripts, the process of translation or the protein directly. Despite these advances, most silencing systems suffer from limitations. Silencing protein expression through genetic ablation, for example by CRISPR/Cas9 genome editing, is irreversible, time consuming and not always feasible. Similarly, RNA interference approaches warrant prolonged treatments, can lead to incomplete protein depletion and are often associated with off-target effects. Targeted proteolysis has the potential to overcome some of these limitations. The field of targeted proteolysis has witnessed the emergence of many methodologies aimed at targeting specific proteins for degradation in a spatio-temporal manner. In this review, we provide an appraisal of the different targeted proteolytic systems and discuss their applications in understanding protein function, as well as their potential in therapeutics.
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Affiliation(s)
- Sascha Röth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Luke J Fulcher
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Gopal P Sapkota
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
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16
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Bery N, Cruz-Migoni A, Bataille CJ, Quevedo CE, Tulmin H, Miller A, Russell A, Phillips SE, Carr SB, Rabbitts TH. BRET-based RAS biosensors that show a novel small molecule is an inhibitor of RAS-effector protein-protein interactions. eLife 2018; 7:37122. [PMID: 29989546 PMCID: PMC6039175 DOI: 10.7554/elife.37122] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/16/2018] [Indexed: 12/13/2022] Open
Abstract
The RAS family of proteins is amongst the most highly mutated in human cancers and has so far eluded drug therapy. Currently, much effort is being made to discover mutant RAS inhibitors and in vitro screening for RAS-binding drugs must be followed by cell-based assays. Here, we have developed a robust set of bioluminescence resonance energy transfer (BRET)-based RAS biosensors that enable monitoring of RAS-effector interaction inhibition in living cells. These include KRAS, HRAS and NRAS and a variety of different mutations that mirror those found in human cancers with the major RAS effectors such as CRAF, PI3K and RALGDS. We highlighted the utility of these RAS biosensors by showing a RAS-binding compound is a potent pan-RAS-effector interactions inhibitor in cells. The RAS biosensors represent a useful tool to investigate and characterize the potency of anti-RAS inhibitors in cells and more generally any RAS protein-protein interaction (PPI) in cells. A group of proteins known as the RAS family plays a critical role in controlling animal cell growth and division. RAS proteins are normally active only some of the time, but genetic mutations can create permanently active forms of the proteins. These constantly interact with other proteins called effectors. In response, cells multiply uncontrollably and give rise to cancers. In an attempt to find new cancer treatments, researchers across the globe are trying to develop inhibitor drugs that prevent RAS and effector proteins from interacting. New drugs are often tested in laboratory experiments that directly apply the drugs to the proteins that they are designed to work on. But in some cases a drug may work wellin the laboratory but fail to work when used in cells. Unfortunately, there are few ways to judge how well inhibitor drugs work inside living cells. Bery et al. have now developed RAS biosensors – a collection of proteins that bind to RAS and produce light more brightly when RAS interacts with effector proteins in living cells. Tests on cells treated with an antibody that works inside cells and is known to prevent interactions between RAS and effector proteins confirmed that the RAS biosensors work well. Bery et al. then used the RAS biosensors to show that a new RAS inhibitor works in human cancer cells. The RAS biosensors are available upon request to researchers across the globe. They should form an important tool for testing potential treatments for cancers that contain mutated RAS proteins.
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Affiliation(s)
- Nicolas Bery
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Abimael Cruz-Migoni
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.,Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, United Kingdom
| | | | - Camilo E Quevedo
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Hanna Tulmin
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Ami Miller
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Simon Ev Phillips
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Stephen B Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, United Kingdom.,Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Terence H Rabbitts
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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17
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Miyashita K, Kitajima K, Goyama S, Kitamura T, Hara T. Overexpression of Lhx2 suppresses proliferation of human T cell acute lymphoblastic leukemia-derived cells, partly by reducing LMO2 protein levels. Biochem Biophys Res Commun 2018; 495:2310-6. [DOI: 10.1016/j.bbrc.2017.12.135] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 12/22/2017] [Indexed: 11/23/2022]
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18
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Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a hematological malignancy characterized by the clonal proliferation of immature T-cell precursors. T-ALL has many similar pathophysiological features to acute myeloid leukemia, which has been extensively studied in the establishment of the cancer stem cell (CSC) theory, but the CSC concept in T-ALL is still debatable. Although leukemia-initiating cells (LICs), which can generate leukemia in a xenograft setting, have been found in both human T-ALL patients and animal models, the nature and origin of LICs are largely unknown. In this review, we discuss recent studies on LICs in T-ALL and the potential mechanisms of LIC emergence in this disease. We focus on the oncogenic transcription factors TAL1, LMO2, and NOTCH1 and highlight the significance of the transcriptional regulatory programs in normal hematopoietic stem cells and T-ALL.
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Affiliation(s)
- Shi Hao Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Fatima Carla Bertulfo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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19
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Sanda T, Leong WZ. TAL1 as a master oncogenic transcription factor in T-cell acute lymphoblastic leukemia. Exp Hematol 2017; 53:7-15. [PMID: 28652130 DOI: 10.1016/j.exphem.2017.06.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 06/11/2017] [Indexed: 11/29/2022]
Abstract
In hematopoietic cell development, the transcriptional program is strictly regulated in a lineage- and stage-specific manner that requires a number of transcription factors to work in a cascade or in a loop, in addition to interactions with nonhematopoietic cells in the microenvironment. Disruption of the transcriptional program alters the cellular state and may predispose cells to the acquisition of genetic abnormalities. Early studies have shown that proteins that promote cell differentiation often serve as tumor suppressors, whereas inhibitors of those proteins act as oncogenes in the context of acute leukemia. A prime example is T-cell acute lymphoblastic leukemia (T-ALL), a malignant disorder characterized by clonal proliferation of immature stage thymocytes. Although a relatively small number of genetic abnormalities are observed in T-ALL, these abnormalities are crucial for leukemogenesis. Many oncogenes and tumor suppressors in T-ALL are transcription factors that are required for normal hematopoiesis. The transformation process in T-ALL is efficient and orchestrated; the oncogene disrupts the transcriptional program directing T-cell differentiation and also uses its native ability as a master transcription factor in hematopoiesis. This imbalance in the transcriptional program is a primary determinant underlying the molecular pathogenesis of T-ALL. In this review, we focus on the oncogenic transcription factor TAL1 and the tumor-suppressor E-proteins and discuss the malignant cell state, the transcriptional circuit, and the consequence of molecular abnormalities in T-ALL.
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Affiliation(s)
- Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
| | - Wei Zhong Leong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
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20
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Abstract
Single domain antibodies (sdAbs) from camels or sharks comprise only the variable heavy chain domain. Human sdAbs comprise the variable domain of the heavy chain (VH) or light chain (VL) and can be selected from human antibodies. SdAbs are stable, nonaggregating molecules in vitro and in vivo compared to complete antibodies and scFv fragments. They are excellent novel inhibitors of cytosolic/nuclear proteins because they are correctly folded inside the cytosol in contrast to scFv fragments. SdAbs are unique because of their excellent specificity and possibility to target posttranslational modifications such as phosphorylation sites, conformers or interaction regions of proteins that cannot be targeted with genetic knockout techniques and are impossible to knockdown with RNAi. The number of inhibiting cytosolic/nuclear sdAbs is increasing and usage of synthetic single pot single domain antibody libraries will boost the generation of these fascinating molecules without the need of immunization. The most frequently selected antigenic epitopes belong to viral and oncogenic proteins, followed by toxins, proteins of the nervous system as well as plant- and drosophila proteins. It is now possible to select functional sdAbs against virtually every cytosolic/nuclear protein and desired epitope. The development of new endosomal escape protein domains and cell-penetrating peptides for efficient transfection broaden the application of inhibiting sdAbs. Last but not least, the generation of relatively new cell-specific nanoparticles such as polymersomes and polyplexes carrying cytosolic/nuclear sdAb-DNA or -protein will pave the way to apply cytosolic/nuclear sdAbs for inhibition of viral infection and cancer in the clinic.
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Affiliation(s)
- Thomas Böldicke
- Helmholtz Centre for Infection Research, Structure and Function of ProteinsInhoffenstraße 7, D‐38124BraunschweigGermany
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21
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Porcher C, Chagraoui H, Kristiansen MS. SCL/TAL1: a multifaceted regulator from blood development to disease. Blood 2017; 129:2051-60. [DOI: 10.1182/blood-2016-12-754051] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 01/17/2017] [Indexed: 12/12/2022] Open
Abstract
Abstract
SCL/TAL1 (stem cell leukemia/T-cell acute lymphoblastic leukemia [T-ALL] 1) is an essential transcription factor in normal and malignant hematopoiesis. It is required for specification of the blood program during development, adult hematopoietic stem cell survival and quiescence, and terminal maturation of select blood lineages. Following ectopic expression, SCL contributes to oncogenesis in T-ALL. Remarkably, SCL’s activities are all mediated through nucleation of a core quaternary protein complex (SCL:E-protein:LMO1/2 [LIM domain only 1 or 2]:LDB1 [LIM domain-binding protein 1]) and dynamic recruitment of conserved combinatorial associations of additional regulators in a lineage- and stage-specific context. The finely tuned control of SCL’s regulatory functions (lineage priming, activation, and repression of gene expression programs) provides insight into fundamental developmental and transcriptional mechanisms, and highlights mechanistic parallels between normal and oncogenic processes. Importantly, recent discoveries are paving the way to the development of innovative therapeutic opportunities in SCL+ T-ALL.
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22
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Wang Y, Fan Z, Shao L, Kong X, Hou X, Tian D, Sun Y, Xiao Y, Yu L. Nanobody-derived nanobiotechnology tool kits for diverse biomedical and biotechnology applications. Int J Nanomedicine 2016; 11:3287-303. [PMID: 27499623 PMCID: PMC4959585 DOI: 10.2147/ijn.s107194] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Owing to peculiar properties of nanobody, including nanoscale size, robust structure, stable and soluble behaviors in aqueous solution, reversible refolding, high affinity and specificity for only one cognate target, superior cryptic cleft accessibility, and deep tissue penetration, as well as a sustainable source, it has been an ideal research tool for the development of sophisticated nanobiotechnologies. Currently, the nanobody has been evolved into versatile research and application tool kits for diverse biomedical and biotechnology applications. Various nanobody-derived formats, including the nanobody itself, the radionuclide or fluorescent-labeled nanobodies, nanobody homo- or heteromultimers, nanobody-coated nanoparticles, and nanobody-displayed bacteriophages, have been successfully demonstrated as powerful nanobiotechnological tool kits for basic biomedical research, targeting drug delivery and therapy, disease diagnosis, bioimaging, and agricultural and plant protection. These applications indicate a special advantage of these nanobody-derived technologies, already surpassing the “me-too” products of other equivalent binders, such as the full-length antibodies, single-chain variable fragments, antigen-binding fragments, targeting peptides, and DNA-based aptamers. In this review, we summarize the current state of the art in nanobody research, focusing on the nanobody structural features, nanobody production approach, nanobody-derived nanobiotechnology tool kits, and the potentially diverse applications in biomedicine and biotechnology. The future trends, challenges, and limitations of the nanobody-derived nanobiotechnology tool kits are also discussed.
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Affiliation(s)
- Yongzhong Wang
- School of Life Sciences, Collaborative Innovation Center of Modern Bio-manufacture, Anhui University, Hefei, People's Republic of China
| | - Zhen Fan
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, USA
| | - Lei Shao
- State Key Laboratory of New Drugs and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, Shanghai
| | - Xiaowei Kong
- School of Life Sciences, Collaborative Innovation Center of Modern Bio-manufacture, Anhui University, Hefei, People's Republic of China
| | - Xianjuan Hou
- School of Life Sciences, Collaborative Innovation Center of Modern Bio-manufacture, Anhui University, Hefei, People's Republic of China
| | - Dongrui Tian
- School of Life Sciences, Collaborative Innovation Center of Modern Bio-manufacture, Anhui University, Hefei, People's Republic of China
| | - Ying Sun
- School of Life Sciences, Collaborative Innovation Center of Modern Bio-manufacture, Anhui University, Hefei, People's Republic of China
| | - Yazhong Xiao
- School of Life Sciences, Collaborative Innovation Center of Modern Bio-manufacture, Anhui University, Hefei, People's Republic of China
| | - Li Yu
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Microbiology and Parasitology, Anhui Key Laboratory of Zoonoses, Anhui Medical University, Hefei, People's Republic of China
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23
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Abstract
LMO2 was first discovered through proximity to frequently occurring chromosomal translocations in T cell acute lymphoblastic leukaemia (T-ALL). Subsequent studies on its role in tumours and in normal settings have highlighted LMO2 as an archetypical chromosomal translocation oncogene, activated by association with antigen receptor gene loci and a paradigm for translocation gene activation in T-ALL. The normal function of LMO2 in haematopoietic cell fate and angiogenesis suggests it is a master gene regulator exerting a dysfunctional control on differentiation following chromosomal translocations. Its importance in T cell neoplasia has been further emphasized by the recurrent findings of interstitial deletions of chromosome 11 near LMO2 and of LMO2 as a target of retroviral insertion gene activation during gene therapy trials for X chromosome-linked severe combined immuno-deficiency syndrome, both types of event leading to similar T cell leukaemia. The discovery of LMO2 in some B cell neoplasias and in some epithelial cancers suggests a more ubiquitous function as an oncogenic protein, and that the current development of novel inhibitors will be of great value in future cancer treatment. Further, the role of LMO2 in angiogenesis and in haematopoietic stem cells (HSCs) bodes well for targeting LMO2 in angiogenic disorders and in generating autologous induced HSCs for application in various clinical indications.
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Affiliation(s)
- Jennifer Chambers
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Terence H Rabbitts
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
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24
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Zhang J, Rabbitts TH. Intracellular antibody capture: A molecular biology approach to inhibitors of protein-protein interactions. Biochim Biophys Acta 2014; 1844:1970-6. [PMID: 24881582 DOI: 10.1016/j.bbapap.2014.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/19/2014] [Accepted: 05/20/2014] [Indexed: 01/10/2023]
Abstract
Many proteins of interest in basic biology, translational research studies and for clinical targeting in diseases reside inside the cell and function by interacting with other macromolecules. Protein complexes control basic processes such as development and cell division but also abnormal cell growth when mutations occur such as found in cancer. Interfering with protein-protein interactions is an important aspiration in both basic and disease biology but small molecule inhibitors have been difficult and expensive to isolate. Recently, we have adapted molecular biology techniques to develop a simple set of protocols for isolation of high affinity antibody fragments (in the form of single VH domains) that function within the reducing environment of higher organism cells and can bind to their target molecules. The method called Intracellular Antibody Capture (IAC) has been used to develop inhibitory anti-RAS and anti-LMO2 single domains that have been used for target validation of these antigens in pre-clinical cancer models and illustrate the efficacy of the IAC approach to generation of drug surrogates. Future use of inhibitory VH antibody fragments as drugs in their own right (we term these macrodrugs to distinguish them from small molecule drugs) requires their delivery to target cells in vivo but they can also be templates for small molecule drug development that emulate the binding sites of the antibody fragments. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody.
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25
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Sewell H, Tanaka T, El Omari K, Mancini EJ, Cruz A, Fernandez-Fuentes N, Chambers J, Rabbitts TH. Conformational flexibility of the oncogenic protein LMO2 primes the formation of the multi-protein transcription complex. Sci Rep 2014; 4:3643. [PMID: 24407558 DOI: 10.1038/srep03643] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 12/09/2013] [Indexed: 01/07/2023] Open
Abstract
LMO2 was discovered via chromosomal translocations in T-cell leukaemia and shown normally to be essential for haematopoiesis. LMO2 is made up of two LIM only domains (thus it is a LIM-only protein) and forms a bridge in a multi-protein complex. We have studied the mechanism of formation of this complex using a single domain antibody fragment that inhibits LMO2 by sequestering it in a non-functional form. The crystal structure of LMO2 with this antibody fragment has been solved revealing a conformational difference in the positioning and angle between the two LIM domains compared with its normal binding. This contortion occurs by bending at a central helical region of LMO2. This is a unique mechanism for inhibiting an intracellular protein function and the structural contusion implies a model in which newly synthesized, intrinsically disordered LMO2 binds to a partner protein nucleating further interactions and suggests approaches for therapeutic targeting of LMO2.
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26
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Abstract
Nanobodies are recombinant, antigen-specific, single-domain, variable fragments of camelid heavy chain-only antibodies. The innate supremacy of nanobodies as a renewable source of affinity reagents, together with their high production yield in a broad variety of expression systems, minimal size, great stability, reversible refolding and outstanding solubility in aqueous solutions, and ability to specifically recognize unique epitopes with subnanomolar affinity, have combined to make them a useful class of biomolecules for research and various medical diagnostic and therapeutic applications. This article speculates on a number of technological innovations that might be introduced in the nanobody identification platform to streamline the generation of more potent nanobodies and to expand their application range.
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27
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McCormack MP, Shields BJ, Jackson JT, Nasa C, Shi W, Slater NJ, Tremblay CS, Rabbitts TH, Curtis DJ. Requirement for Lyl1 in a model of Lmo2-driven early T-cell precursor ALL. Blood 2013; 122:2093-103. [PMID: 23926305 DOI: 10.1182/blood-2012-09-458570] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Lmo2 is an oncogenic transcription factor that is frequently overexpressed in T-cell acute lymphoblastic leukemia (T-ALL), including early T-cell precursor ALL (ETP-ALL) cases with poor prognosis. Lmo2 must be recruited to DNA by binding to the hematopoietic basic helix-loop-helix factors Scl/Tal1 or Lyl1. However, it is unknown which of these factors can mediate the leukemic activity of Lmo2. To address this, we have generated Lmo2-transgenic mice lacking either Scl or Lyl1 in the thymus. We show that although Scl is dispensable for Lmo2-driven leukemia, Lyl1 is critical for all oncogenic functions of Lmo2, including upregulation of a stem cell-like gene signature, aberrant self-renewal of thymocytes, and subsequent generation of T-cell leukemia. Lyl1 expression is restricted to preleukemic and leukemic stem cell populations in this model, providing a molecular explanation for the stage-specific expression of the Lmo2-induced gene expression program. Moreover, LMO2 and LYL1 are coexpressed in ETP-ALL patient samples, and LYL1 is required for growth of ETP-ALL cell lines. Thus, the LMO2-LYL1 interaction is a promising therapeutic target for inhibiting self-renewing cancer stem cells in T-ALL, including poor-prognosis ETP-ALL cases.
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Zeng J, Zhang J, Tanaka T, Rabbitts T. Single Domain Antibody Fragments as Drug Surrogates Targeting Protein–Protein Interactions inside Cells. Antibodies (Basel) 2013; 2:306-20. [DOI: 10.3390/antib2020306] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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29
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Abstract
Sera of camelids contain both conventional heterotetrameric antibodies and unique functional heavy (H)-chain antibodies (HCAbs). The H chain of these homodimeric antibodies consists of one antigen-binding domain, the VHH, and two constant domains. HCAbs fail to incorporate light (L) chains owing to the deletion of the first constant domain and a reshaped surface at the VHH side, which normally associates with L chains in conventional antibodies. The genetic elements composing HCAbs have been identified, but the in vivo generation of these antibodies from their dedicated genes into antigen-specific and affinity-matured bona fide antibodies remains largely underinvestigated. However, the facile identification of antigen-specific VHHs and their beneficial biochemical and economic properties (size, affinity, specificity, stability, production cost) supported by multiple crystal structures have encouraged antibody engineering of these single-domain antibodies for use as a research tool and in biotechnology and medicine.
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Affiliation(s)
- Serge Muyldermans
- Research Group Cellular and Molecular Immunology, Vrije Universiteit Brussel, 1050 Brussels, Belgium.
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30
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Tanaka T, Rabbitts TH. Selection of functional single domain antibody fragments for interfering with protein-protein interactions inside cells: a "one plasmid" mammalian two-hybrid system. Methods Mol Biol 2012; 911:175-82. [PMID: 22886252 DOI: 10.1007/978-1-61779-968-6_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
As a complement to the intracellular antibody capture method to isolate intracellular single domain antibody fragments (iDabs) from high diverse libraries, we describe here a simple mammalian two-hybrid (M2H) protocol using a "bait-prey hybrid single plasmid" to assess those interfering iDabs that will block protein-protein interactions of a target with its natural partner proteins. This rapid method identifies interfering iDabs in one step and improves the reproducibility of the results between experiments and samples (e.g., different single domain antibody clones) compared to traditional M2H. This method yields functional, interfering iDabs and can be applied to any interfering molecule for use as a research tool or template for clinical inhibitor production.
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Affiliation(s)
- Tomoyuki Tanaka
- Leeds Institute of Molecular Medicine, St. James's University Hospital, University of Leeds, Leeds, UK
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31
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Butler DC, McLear JA, Messer A. Engineered antibody therapies to counteract mutant huntingtin and related toxic intracellular proteins. Prog Neurobiol 2012; 97:190-204. [PMID: 22120646 PMCID: PMC3908675 DOI: 10.1016/j.pneurobio.2011.11.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 11/03/2011] [Accepted: 11/08/2011] [Indexed: 02/07/2023]
Abstract
The engineered antibody approach to Huntington's disease (HD) therapeutics is based on the premise that significantly lowering the levels of the primary misfolded mutant protein will reduce abnormal protein interactions and direct toxic effects of the misfolded huntingtin (HTT). This will in turn reduce the pathologic stress on cells, and normalize intrinsic proteostasis. Intracellular antibodies (intrabodies) are single-chain (scFv) and single-domain (dAb; nanobody) variable fragments that can retain the affinity and specificity of full-length antibodies, but can be selected and engineered as genes. Functionally, they represent a protein-based approach to the problem of aberrant mutant protein folding, post-translational modifications, protein-protein interactions, and aggregation. Several intrabodies that bind on either side of the expanded polyglutamine tract of mutant HTT have been reported to improve the mutant phenotype in cell and organotypic cultures, fruit flies, and mice. Further refinements to the difficult challenges of intraneuronal delivery, cytoplasmic folding, and long-term efficacy are in progress. This review covers published studies and emerging approaches on the choice of targets, selection and engineering methods, gene and protein delivery options, and testing of candidates in cell and animal models. The resultant antibody fragments can be used as direct therapeutics and as target validation/drug discovery tools for HD, while the technology is also applicable to a wide range of neurodegenerative and other diseases that are triggered by toxic proteins.
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Affiliation(s)
- David C. Butler
- Wadsworth Center, New York State Dept. of Health, Albany, NY, United States, 12208
| | | | - Anne Messer
- Wadsworth Center, New York State Dept. of Health, Albany, NY, United States, 12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, NY 12201
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32
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Dixon AS, Constance JE, Tanaka T, Rabbitts TH, Lim CS. Changing the subcellular location of the oncoprotein Bcr-Abl using rationally designed capture motifs. Pharm Res 2011; 29:1098-109. [PMID: 22183511 DOI: 10.1007/s11095-011-0654-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 12/06/2011] [Indexed: 11/30/2022]
Abstract
PURPOSE Bcr-Abl, the causative agent of chronic myelogenous leukemia (CML), localizes in the cytoplasm where its oncogenic signaling leads to proliferation of cells. If forced into the nucleus Bcr-Abl causes apoptosis. To achieve nuclear translocation, binding domains for capture of Bcr-Abl were generated and attached to proteins with signals destined for the nucleus. These resulting proteins would be capable of binding and translocating endogenous Bcr-Abl to the nucleus. METHODS Bcr-Abl was targeted at 3 distinct domains for capture: by construction of high affinity intracellular antibody domains (iDabs) to regions of Bcr-Abl known to promote cytoplasmic retention, via its coiled coil domain (CC), and through a naturally occurring protein-protein interaction domain (RIN1). These binding domains were then tested for their ability to escort Bcr-Abl into the nucleus using a "protein switch" or attachment of 4 nuclear localization signals (NLSs). RESULTS Although RIN1, ABI7-iDab, and CCmut3 constructs all produced similar colocalization with Bcr-Abl, only 4NLS-CCmut3 produced efficient nuclear translocation of Bcr-Abl. CONCLUSIONS We demonstrate that a small binding domain can be used to control the subcellular localization of Bcr-Abl, which may have implications for CML therapy. Our ultimate future goal is to change the location of critical proteins to alter their function.
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Affiliation(s)
- Andrew S Dixon
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, 421 Wakara Way, Rm. 318, Salt Lake City, Utah 84108, USA
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33
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Abstract
BACKGROUND Single-domain antibody fragments possess structural features, such as a small dimension, an elevated stability, and the singularity of recognizing epitopes non-accessible for conventional antibodies that make them interesting for several research and biotechnological applications. RESULTS The discovery of the single-domain antibody's potentials has stimulated their use in an increasing variety of fields. The rapid accumulation of articles describing new applications and further developments of established approaches has made it, therefore, necessary to update the previous reviews with a new and more complete summary of the topic. CONCLUSIONS Beside the necessary task of updating, this work analyses in detail some applicative aspects of the single-domain antibodies that have been overseen in the past, such as their efficacy in affinity chromatography, as co-crystallization chaperones, protein aggregation controllers, enzyme activity tuners, and the specificities of the unconventional single-domain fragments.
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Affiliation(s)
- Ario de Marco
- University of Nova Gorica (UNG), Vipavska 13, PO Box 301-SI-5000, Rožna Dolina (Nova Gorica), Slovenia.
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