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Jha R, Kinna A, Hotblack A, Bughda R, Bulek A, Gannon I, Ilca T, Allen C, Lamb K, Dolor A, Scott I, Parekh F, Sillibourne J, Cordoba S, Onuoha S, Thomas S, Ferrari M, Pule M. Designer Small-Molecule Control System Based on Minocycline-Induced Disruption of Protein-Protein Interaction. ACS Chem Biol 2024; 19:308-324. [PMID: 38243811 PMCID: PMC10877577 DOI: 10.1021/acschembio.3c00521] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/01/2024] [Accepted: 01/04/2024] [Indexed: 01/22/2024]
Abstract
A versatile, safe, and effective small-molecule control system is highly desirable for clinical cell therapy applications. Therefore, we developed a two-component small-molecule control system based on the disruption of protein-protein interactions using minocycline, an FDA-approved antibiotic with wide availability, excellent biodistribution, and low toxicity. The system comprises an anti-minocycline single-domain antibody (sdAb) and a minocycline-displaceable cyclic peptide. Here, we show how this versatile system can be applied to OFF-switch split CAR systems (MinoCAR) and universal CAR adaptors (MinoUniCAR) with reversible, transient, and dose-dependent suppression; to a tunable T cell activation module based on MyD88/CD40 signaling; to a controllable cellular payload secretion system based on IL12 KDEL retention; and as a cell/cell inducible junction. This work represents an important step forward in the development of a remote-controlled system to precisely control the timing, intensity, and safety of therapeutic interventions.
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Affiliation(s)
- Ram Jha
- Autolus
Therapeutics, London W12 7FP, U.K.
- Research
Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, U.K.
| | | | - Alastair Hotblack
- Research
Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, U.K.
| | | | - Anna Bulek
- Autolus
Therapeutics, London W12 7FP, U.K.
| | | | - Tudor Ilca
- Autolus
Therapeutics, London W12 7FP, U.K.
| | | | | | | | - Ian Scott
- Autolus
Therapeutics, London W12 7FP, U.K.
| | | | | | | | | | | | | | - Martin Pule
- Autolus
Therapeutics, London W12 7FP, U.K.
- Research
Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, U.K.
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2
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Woodruff R, Parekh F, Lamb K, Mekkaoui L, Allen C, Smetanova K, Huang J, Williams A, Toledo GS, Lilova K, Roddie C, Sillibourne J, Pule M. Large-scale manufacturing of base-edited chimeric antigen receptor T cells. Mol Ther Methods Clin Dev 2023; 31:101123. [PMID: 37886606 PMCID: PMC10597784 DOI: 10.1016/j.omtm.2023.101123] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023]
Abstract
Base editing is a revolutionary gene-editing technique enabling the introduction of point mutations into the genome without generating detrimental DNA double-stranded breaks. Base-editing enzymes are commonly delivered in the form of modified linear messenger RNA (mRNA) that is costly to produce. Here, we address this problem by developing a simple protocol for manufacturing base-edited cells using circular RNA (circRNA), which is less expensive to synthesize. Compared with linear mRNA, higher editing efficiencies were achieved with circRNA, enabling an 8-fold reduction in the amount of RNA required. We used this protocol to manufacture a clinical dose (1 × 108 cells) of base-edited chimeric antigen receptor (CAR) T cells lacking expression of the inhibitory receptor, PD-1. Editing efficiencies of up to 86% were obtained using 0.25 μg circRNA/1 × 106 cells. Increased editing efficiencies with circRNA were attributed to more efficient translation. These results suggest that circRNA, which is less expensive to produce than linear mRNA, is a viable option for reducing the cost of manufacturing base-edited cells at scale.
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Affiliation(s)
- Rosie Woodruff
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | - Farhaan Parekh
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | - Katarina Lamb
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | - Leila Mekkaoui
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | - Christopher Allen
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | | | - Jasmine Huang
- Imperial College London, South Kensington Campus, SW7 2AZ London, UK
| | - Alex Williams
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | | | - Koki Lilova
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | - Claire Roddie
- Deparment of Haematology, Cancer Institute, 72 Huntley Street, WC1E 6BT London, UK
| | - James Sillibourne
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | - Martin Pule
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
- Deparment of Haematology, Cancer Institute, 72 Huntley Street, WC1E 6BT London, UK
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McKenzie C, El-Kholy M, Parekh F, Robson M, Lamb K, Allen C, Sillibourne J, Cordoba S, Thomas S, Pule M. Novel Fas-TNFR chimeras that prevent Fas ligand-mediated kill and signal synergistically to enhance CAR T cell efficacy. Mol Ther Nucleic Acids 2023; 32:603-621. [PMID: 37200859 PMCID: PMC10185706 DOI: 10.1016/j.omtn.2023.04.017] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/18/2023] [Indexed: 05/20/2023]
Abstract
The hostile tumor microenvironment limits the efficacy of adoptive cell therapies. Activation of the Fas death receptor initiates apoptosis and disrupting these receptors could be key to increasing CAR T cell efficacy. We screened a library of Fas-TNFR proteins identifying several novel chimeras that not only prevented Fas ligand-mediated kill, but also enhanced CAR T cell efficacy by signaling synergistically with the CAR. Upon binding Fas ligand, Fas-CD40 activated the NF-κB pathway, inducing greatest proliferation and IFN-γ release out of all Fas-TNFRs tested. Fas-CD40 induced profound transcriptional modifications, particularly genes relating to the cell cycle, metabolism, and chemokine signaling. Co-expression of Fas-CD40 with either 4-1BB- or CD28-containing CARs increased in vitro efficacy by augmenting CAR T cell proliferation and cancer target cytotoxicity, and enhanced tumor killing and overall mouse survival in vivo. Functional activity of the Fas-TNFRs were dependent on the co-stimulatory domain within the CAR, highlighting crosstalk between signaling pathways. Furthermore, we show that a major source for Fas-TNFR activation derives from CAR T cells themselves via activation-induced Fas ligand upregulation, highlighting a universal role of Fas-TNFRs in augmenting CAR T cell responses. We have identified Fas-CD40 as the optimal chimera for overcoming Fas ligand-mediated kill and enhancing CAR T cell efficacy.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Martin Pule
- Autolus Therapeutics, London W12 7FP, UK
- Department of Haematology, UCL Cancer Institute, University College, 72 Huntley Street, London WC1E 6DD, UK
- Corresponding author Martin Pule, Autolus Therapeutics, London W12 7FP, UK.
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Ferrari M, Mekkaoui L, Ilca FT, Akbar Z, Bughda R, Lamb K, Ward K, Parekh F, Karattil R, Allen C, Wu P, Baldan V, Mattiuzzo G, Bentley EM, Takeuchi Y, Sillibourne J, Datta P, Kinna A, Pule M, Onuoha SC. Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. J Virol 2021; 95:e0068521. [PMID: 34287040 PMCID: PMC8432736 DOI: 10.1128/jvi.00685-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/14/2021] [Indexed: 12/15/2022] Open
Abstract
The human angiotensin-converting enzyme 2 acts as the host cell receptor for SARS-CoV-2 and the other members of the Coronaviridae family SARS-CoV-1 and HCoV-NL63. Here, we report the biophysical properties of the SARS-CoV-2 spike variants D614G, B.1.1.7, B.1.351, and P.1 with affinities to the ACE2 receptor and infectivity capacity, revealing weaknesses in the developed neutralizing antibody approaches. Furthermore, we report a preclinical characterization package for a soluble receptor decoy engineered to be catalytically inactive and immunologically inert, with broad neutralization capacity, that represents an attractive therapeutic alternative in light of the mutational landscape of COVID-19. This construct efficiently neutralized four SARS-CoV-2 variants of concern. The decoy also displays antibody-like biophysical properties and manufacturability, strengthening its suitability as a first-line treatment option in prophylaxis or therapeutic regimens for COVID-19 and related viral infections. IMPORTANCE Mutational drift of SARS-CoV-2 risks rendering both therapeutics and vaccines less effective. Receptor decoy strategies utilizing soluble human ACE2 may overcome the risk of viral mutational escape since mutations disrupting viral interaction with the ACE2 decoy will by necessity decrease virulence, thereby preventing meaningful escape. The solution described here of a soluble ACE2 receptor decoy is significant for the following reasons: while previous ACE2-based therapeutics have been described, ours has novel features, including (i) mutations within ACE2 to remove catalytical activity and systemic interference with the renin/angiotensin system, (ii) abrogated FcγR engagement, reduced risk of antibody-dependent enhancement of infection, and reduced risk of hyperinflammation, and (iii) streamlined antibody-like purification process and scale-up manufacturability indicating that this receptor decoy could be produced quickly and easily at scale. Finally, we demonstrate that ACE2-based therapeutics confer a broad-spectrum neutralization potency for ACE2-tropic viruses, including SARS-CoV-2 variants of concern in contrast to therapeutic MAb.
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Affiliation(s)
| | | | - F Tudor Ilca
- Autolus Limited, The MediaWorks, London, United Kingdom
| | | | - Reyisa Bughda
- Autolus Limited, The MediaWorks, London, United Kingdom
| | - Katarina Lamb
- Autolus Limited, The MediaWorks, London, United Kingdom
| | | | | | | | | | - Philip Wu
- Autolus Limited, The MediaWorks, London, United Kingdom
| | - Vania Baldan
- Autolus Limited, The MediaWorks, London, United Kingdom
| | - Giada Mattiuzzo
- National Institute for Biological Standards and Controlgrid.70909.37, Herts, United Kingdom
| | - Emma M Bentley
- National Institute for Biological Standards and Controlgrid.70909.37, Herts, United Kingdom
| | - Yasuhiro Takeuchi
- National Institute for Biological Standards and Controlgrid.70909.37, Herts, United Kingdom
- Division of Infection and Immunity, University College Londongrid.83440.3b, London, United Kingdom
| | | | - Preeta Datta
- Autolus Limited, The MediaWorks, London, United Kingdom
| | | | - Martin Pule
- Autolus Limited, The MediaWorks, London, United Kingdom
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Nannini F, Senicar L, Parekh F, Kong KJ, Kinna A, Bughda R, Sillibourne J, Hu X, Ma B, Bai Y, Ferrari M, Pule MA, Onuoha SC. Combining phage display with SMRTbell next-generation sequencing for the rapid discovery of functional scFv fragments. MAbs 2021; 13:1864084. [PMID: 33382949 PMCID: PMC7781620 DOI: 10.1080/19420862.2020.1864084] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/06/2020] [Accepted: 12/10/2020] [Indexed: 12/18/2022] Open
Abstract
Phage display technology in combination with next-generation sequencing (NGS) currently is a state-of-the-art method for the enrichment and isolation of monoclonal antibodies from diverse libraries. However, the current NGS methods employed for sequencing phage display libraries are limited by the short contiguous read lengths associated with second-generation sequencing platforms. Consequently, the identification of antibody sequences has conventionally been restricted to individual antibody domains or to the analysis of single domain binding moieties such as camelid VHH or cartilaginous fish IgNAR antibodies. In this study, we report the application of third-generation sequencing to address this limitation. We used single molecule real time (SMRT) sequencing coupled with hairpin adaptor loop ligation to facilitate the accurate interrogation of full-length single-chain Fv (scFv) libraries. Our method facilitated the rapid isolation and testing of scFv antibodies enriched from phage display libraries within days following panning. Two libraries against CD160 and CD123 were panned and monitored by NGS. Analysis of NGS antibody data sets led to the isolation of several functional scFv antibodies that were not identified by conventional panning and screening strategies. Our approach, which combines phage display selection of immune libraries with the full-length interrogation of scFv fragments, is an easy method to discover functional antibodies, with a range of affinities and biophysical characteristics.
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Affiliation(s)
| | | | | | - Khai J. Kong
- Cancer Institute, University College London, London, UK
| | | | | | | | - Xihao Hu
- GV20 Therapeutics LLC, Cambridge, MA, USA
| | - Biao Ma
- Autolus Therapeutics, London, UK
| | | | | | - Martin A. Pule
- Cancer Institute, University College London, London, UK
- Autolus Therapeutics, London, UK
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Nannini F, Parekh F, Wawrzyniecka P, Mekkaoui L, Righi M, Dastjerdi FV, Yeung J, Roddie C, Bai Y, Ma B, Ferrari M, Onuoha S, Chester K, Pule M. A primer set for the rapid isolation of scFv fragments against cell surface antigens from immunised rats. Sci Rep 2020; 10:19168. [PMID: 33154441 PMCID: PMC7644676 DOI: 10.1038/s41598-020-76069-3] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/21/2020] [Indexed: 12/20/2022] Open
Abstract
Antibody phage display is a powerful platform for discovery of clinically applicable high affinity monoclonal antibodies against a broad range of targets. Libraries generated from immunized animals offer the advantage of in vivo affinity-maturation of V regions prior to library generation. Despite advantages, few studies have described isolation of antibodies from rats using immune phage display. In our study, we describe a novel primer set, covering the full rat heavy chain variable and kappa light chain variable regions repertoire for the generation of an unbiased immune libraries. Since the immune repertoire of rats is poorly understood, we first performed a deep sequencing analysis of the V(D)J regions of VH and VLK genes, demonstrating the high abundance of IGVH2 and IGVH5 families for VH and IGVLK12 and IGVLK22 for VLK. The comparison of gene's family usage in naïve rats have been used to validate the frequency's distribution of the primer set, confirming the absence of PCR-based biases. The primers were used to generate and assemble a phage display library from human CD160-vaccinated rats. CD160 represents a valid therapeutic target as it has been shown to be expressed on chronic lymphocytic leukaemia cells and on the surface of newly formed vessels. We utilised a novel phage display panning strategy to isolate a high affinity pool (KD range: 0.399-233 nM) of CD160 targeting monoclonal antibodies. Subsequently, identified binders were tested for function as third generation Chimeric Antigen Receptors (CAR) T cells demonstrating specific cytolytic activity. Our novel primer set coupled with a streamlined strategy for phage display panning enable the rapid isolation and identification of high affinity antibodies from immunised rats. The therapeutic utility of these antibodies was demonstrated in CAR format.
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Affiliation(s)
- Francesco Nannini
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | - Farhaan Parekh
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | - Patrycja Wawrzyniecka
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | - Leila Mekkaoui
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | - Matteo Righi
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | | | - Jenny Yeung
- Research Department of Oncology, UCL Cancer Institute, London, UK
| | - Claire Roddie
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | | | - Biao Ma
- Autolus Therapeutics, London, UK
| | | | | | - Kerry Chester
- Research Department of Oncology, UCL Cancer Institute, London, UK
| | - Martin Pule
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK.
- Autolus Therapeutics, London, UK.
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Mekkaoui L, Parekh F, Kotsopoulou E, Darling D, Dickson G, Cheung GW, Chan L, MacLellan-Gibson K, Mattiuzzo G, Farzaneh F, Takeuchi Y, Pule M. Lentiviral Vector Purification Using Genetically Encoded Biotin Mimic in Packaging Cell. Mol Ther Methods Clin Dev 2018; 11:155-165. [PMID: 30547049 PMCID: PMC6258877 DOI: 10.1016/j.omtm.2018.10.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/17/2018] [Indexed: 11/17/2022]
Abstract
Lentiviral vectors (LVs) have recently witnessed an increasing demand in research and clinical applications. Their current purification processes represent the main bottleneck in their widespread use, as the methods used are cumbersome and yield low recoveries. We aimed to develop a one-step method to specifically purify LVs, with high yields and reduced levels of impurities, using the biotin-streptavidin system. Herein, packaging HEK293T cells were genetically engineered with a cyclical biotin-mimicking peptide displayed on a CD8α stalk, termed cTag8. LVs were modified with cTag8 by its passive incorporation onto viral surfaces during budding, without viral protein engineering or hindrance on infectivity. Expression of cTag8 on LVs allowed complete capture of infectious particles by streptavidin magnetic beads. As cTag8 binds streptavidin in the nanomolar range, the addition of micromolar concentrations of biotin resulted in the release of captured LVs by competitive elution, with overall yields of ≥60%. Analysis of eluted LVs revealed high purity with a >3-log and 2-log reduction in DNA contamination and host cell proteins, respectively. This one-step purification was also tested for scalable vector processing using monolith affinity chromatography, with an encouraging preliminary overall yield of 20%. This method will be of valuable use for both research and clinical applications of LVs.
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Affiliation(s)
- Leila Mekkaoui
- UCL Cancer Institute, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Farhaan Parekh
- UCL Cancer Institute, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | | | - David Darling
- School of Cancer & Pharmaceutical Sciences, King’s College London, Molecular Medicine Group, The Rayne Institute, 123 Coldharbour Lane, London SE5 9NU, UK
| | - Glenda Dickson
- School of Cancer & Pharmaceutical Sciences, King’s College London, Molecular Medicine Group, The Rayne Institute, 123 Coldharbour Lane, London SE5 9NU, UK
| | - Gordon W. Cheung
- UCL Cancer Institute, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Lucas Chan
- School of Cancer & Pharmaceutical Sciences, King’s College London, Molecular Medicine Group, The Rayne Institute, 123 Coldharbour Lane, London SE5 9NU, UK
| | - Kirsty MacLellan-Gibson
- National Institute for Biological Standards and Control-MHRA, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QC, UK
| | - Giada Mattiuzzo
- National Institute for Biological Standards and Control-MHRA, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QC, UK
| | - Farzin Farzaneh
- School of Cancer & Pharmaceutical Sciences, King’s College London, Molecular Medicine Group, The Rayne Institute, 123 Coldharbour Lane, London SE5 9NU, UK
| | - Yasuhiro. Takeuchi
- National Institute for Biological Standards and Control-MHRA, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QC, UK
- Division of Infection and Immunity, University College London, Rayne Building, 5 University Street, London WC1E 6JF, UK
| | - Martin Pule
- UCL Cancer Institute, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
- Corresponding author: Martin Pule, UCL Cancer Institute, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6BT, UK.
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Whitney C, Cotter A, Festin M, Parekh F, Limpongsanurak S, Gaitan H, Tolosa J. 404 International multicenter study of group B streptococcal colonization in pregnant women. Am J Obstet Gynecol 2001. [DOI: 10.1016/s0002-9378(01)80436-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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