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Sallard E, Fischer J, Schroeer K, Dawson LM, Beaude N, Affes A, Ehrke-Schulz E, Zhang W, Westhaus A, Cabanes-Creus M, Lisowski L, Ruszics Z, Ehrhardt A. ADEVO: Proof-of-concept of adenovirus-directed EVOlution by random peptide display on the fiber knob. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200867. [PMID: 39346764 PMCID: PMC11439537 DOI: 10.1016/j.omton.2024.200867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 08/02/2024] [Accepted: 08/27/2024] [Indexed: 10/01/2024]
Abstract
Directed evolution of viral vectors involves the generation of randomized libraries followed by artificial selection of improved variants. Directed evolution only yielded limited results in adenovirus (AdV) engineering until now, mainly due to insufficient complexities of randomized libraries. Meanwhile, clinical applications of AdVs as gene therapy or oncolytic vectors are still hampered by the predetermined tropism of natural types. To overcome this challenge, we hypothesized that randomized peptide insertions on the capsid surface can be incorporated into the AdV bioengineering toolbox for retargeting. Here we developed AdV-directed EVOlution protocols based on fiber knob peptide display. Human AdV-C5-derived libraries were constructed following three distinct protocols and selected on a panel of cancer cell lines, with the goal of identifying variants able to infect and lyse these tumor cells more efficiently. All protocols enabled the construction of high complexity libraries with up to 9.6 × 105 unique variants, an approximate 100-fold improvement compared with previously published AdV libraries. After selection, the most enriched variants, which were robustly selected in various cancer cell lines, did not display enhanced infectivity but rather more efficient replication and cell lysis. Selected inserts also conferred enhanced lysis ability to oncolytic AdVs restricted to telomerase-expressing cell lines.
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Affiliation(s)
- Erwan Sallard
- Virology and Microbiology, Centre for Biomedical Education & Research (ZBAF), Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Julian Fischer
- Institute of Virology, Faculty of Medicine, University Medical Center Freiburg, University of Freiburg, Freiburg, Germany
| | - Katrin Schroeer
- Virology and Microbiology, Centre for Biomedical Education & Research (ZBAF), Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Lisa-Marie Dawson
- Virology and Microbiology, Centre for Biomedical Education & Research (ZBAF), Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Nissai Beaude
- Virology and Microbiology, Centre for Biomedical Education & Research (ZBAF), Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
- AgroParisTech, Paris-Saclay University, Palaiseau, France
| | - Arsalene Affes
- Virology and Microbiology, Centre for Biomedical Education & Research (ZBAF), Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
- AgroParisTech, Paris-Saclay University, Palaiseau, France
| | - Eric Ehrke-Schulz
- Virology and Microbiology, Centre for Biomedical Education & Research (ZBAF), Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Wenli Zhang
- Virology and Microbiology, Centre for Biomedical Education & Research (ZBAF), Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Adrian Westhaus
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Marti Cabanes-Creus
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
- Australian Genome Therapeutics Centre, Children’s Medical Research Institute and Sydney Children’s Hospitals Network, Westmead, NSW 2145, Australia
- Military Institute of Medicine – National Research Institute, Laboratory of Molecular Oncology and Innovative Therapies, 04-141 Warsaw, Poland
| | - Zsolt Ruszics
- Institute of Virology, Faculty of Medicine, University Medical Center Freiburg, University of Freiburg, Freiburg, Germany
| | - Anja Ehrhardt
- Virology and Microbiology, Centre for Biomedical Education & Research (ZBAF), Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
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Lu SC, Lee YY, Andres FG, Moyer DA, Barry MA. FastAd: A versatile toolkit for rapid generation of single adenoviruses or diverse adenoviral vector libraries. Mol Ther Methods Clin Dev 2024; 32:101356. [PMID: 39559559 PMCID: PMC11570478 DOI: 10.1016/j.omtm.2024.101356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Accepted: 10/15/2024] [Indexed: 11/20/2024]
Abstract
Adenoviruses (Ads) are potent gene delivery vectors for in vitro and in vivo applications. However, current methods for their construction are time-consuming and inefficient, limiting their rapid production and utility in generating complex genetic libraries. Here, we introduce FastAd, a rapid and easy-to-use technology for inserting recombinant "donor" DNA directly into infectious "receiver" Ads in mammalian cells by the concerted action of two efficient recombinases: Cre and Bxb1. Subsequently, the resulting mixed recombinant Ad population is subjected to negative selections by flippase recombinase to remove viruses that missed the initial recombination. With this approach, recombinant Ad production time is reduced from 2 months to 10 days or less. FastAd can be applied for inserting complex genetic DNA libraries into Ad genomes, as demonstrated by the generation of barcode libraries with over 3 million unique clones from a T25 flask-scale transfection of 3 million cells. Furthermore, we leveraged FastAd to construct an Ad library containing a comprehensive genome-wide CRISPR-Cas9 guide RNA library and demonstrated its effectiveness in uncovering novel virus-host interactions. In summary, FastAd enables the rapid generation of single Ad vectors or complex genetic libraries, facilitating not only novel applications of Ad vectors but also research in foundamental virology.
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Affiliation(s)
- Shao-Chia Lu
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Yi-Yuan Lee
- Department of Computational Biology, Cornell University, Ithaca, NY 14850, USA
| | - Felix G.M. Andres
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Daniel A. Moyer
- Immunology Track, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Michael A. Barry
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
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Fischer J, Fedotova A, Jaki L, Sallard E, Erhardt A, Fuchs J, Ruzsics Z. Combining CRISPR-Cas-mediated terminal resolution with a novel genetic workflow to achieve high-diversity adenoviral libraries. Mol Ther Methods Clin Dev 2024; 32:101241. [PMID: 38585687 PMCID: PMC10995876 DOI: 10.1016/j.omtm.2024.101241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/14/2024] [Indexed: 04/09/2024]
Abstract
While recombinant adenoviruses (rAds) are widely used in both laboratory and medical gene transfer, library-based applications using this vector platform are not readily available. Recently, we developed a new method, the CRISPR-Cas9 mediated in vivo terminal resolution aiding high-efficiency rescue of rAds from recombinant DNA. Here we report on a genetic workflow that allows construction of bacterial artificial chromosome-based rAd libraries reconstituted using highly efficient terminal resolution. We utilized frequent, pre-existing genomic sequences to allow the insertion of a selection marker, complementing two selected target sites into novel endonuclease recognition sites. In the second step, this selection marker is replaced with a transgene or mutation of interest via Gibson assembly. Our approach does not cause unwanted genomic off-target mutations while providing substantial flexibility for the site and nature of the genetic modification. This new genetic workflow, which we termed half site-directed fragment replacement (HFR) allows the introduction of more than 106 unique modifications into rAd encoding BACs using laboratory scale methodology. To demonstrate the power of HFR, we rescued barcoded viral vector libraries yielding a diversity of approximately 2.5 × 104 unique rAds per cm2 of transfected cell culture.
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Affiliation(s)
- Julian Fischer
- Institute of Virology, University Medical Center Freiburg, Medical Faculty, University of Freiburg, 79104 Freiburg, Germany
| | - Ariana Fedotova
- Institute of Virology, University Medical Center Freiburg, Medical Faculty, University of Freiburg, 79104 Freiburg, Germany
| | - Lena Jaki
- Institute of Virology, University Medical Center Freiburg, Medical Faculty, University of Freiburg, 79104 Freiburg, Germany
| | - Erwan Sallard
- Virology and Microbiology, Centre for Biomedical Education & Research (ZBAF), Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Anja Erhardt
- Virology and Microbiology, Centre for Biomedical Education & Research (ZBAF), Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Jonas Fuchs
- Institute of Virology, University Medical Center Freiburg, Medical Faculty, University of Freiburg, 79104 Freiburg, Germany
| | - Zsolt Ruzsics
- Institute of Virology, University Medical Center Freiburg, Medical Faculty, University of Freiburg, 79104 Freiburg, Germany
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Fischer J, Fedotova A, Bühler C, Darriba L, Schreiner S, Ruzsics Z. Expanding the Scope of Adenoviral Vectors by Utilizing Novel Tools for Recombination and Vector Rescue. Viruses 2024; 16:658. [PMID: 38793540 PMCID: PMC11125593 DOI: 10.3390/v16050658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
Recombinant adenoviruses are widely used in clinical and laboratory applications. Despite the wide variety of available sero- and genotypes, only a fraction is utilized in vivo. As adenoviruses are a large group of viruses, displaying many different tropisms, immune epitopes, and replication characteristics, the merits of translating these natural benefits into vector applications are apparent. This translation, however, proves difficult, since while research has investigated the application of these viruses, there are no universally applicable rules in vector design for non-classical adenovirus types. In this paper, we describe a generalized workflow that allows vectorization, rescue, and cloning of all adenoviral species to enable the rapid development of new vector variants. We show this using human and simian adenoviruses, further modifying a selection of them to investigate their gene transfer potential and build potential vector candidates for future applications.
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Affiliation(s)
| | | | | | | | | | - Zsolt Ruzsics
- Institute of Virology, University Medical Center Freiburg, Medical Faculty, University of Freiburg, 79104 Freiburg, Germany; (J.F.); (A.F.); (S.S.)
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Funk C, Uhlig N, Ruzsics Z, Baur F, Peindl M, Nietzer S, Epting K, Vacun G, Dandekar G, Botteron C, Werno C, Grunwald T, Bailer SM. TheraVision: Engineering platform technology for the development of oncolytic viruses based on herpes simplex virus type 1. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200784. [PMID: 38596296 PMCID: PMC10950833 DOI: 10.1016/j.omton.2024.200784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 07/20/2023] [Accepted: 02/26/2024] [Indexed: 04/11/2024]
Abstract
Viruses are able to efficiently penetrate cells, multiply, and eventually kill infected cells, release tumor antigens, and activate the immune system. Therefore, viruses are highly attractive novel agents for cancer therapy. Clinical trials with first generations of oncolytic viruses (OVs) are very promising but show significant need for optimization. The aim of TheraVision was to establish a broadly applicable engineering platform technology for combinatorial oncolytic virus and immunotherapy. Through genetic engineering, an attenuated herpes simplex virus type 1 (HSV1) was generated that showed increased safety compared to the wild-type strain. To demonstrate the modularity and the facilitated generation of new OVs, two transgenes encoding retargeting as well as immunomodulating single-chain variable fragments (scFvs) were integrated into the platform vector. The resulting virus selectively infected epidermal growth factor receptor (EGFR)-expressing cells and produced a functional immune checkpoint inhibitor against programmed cell death protein 1 (PD-1). Thus, both viral-mediated oncolysis and immune-cell-mediated therapy were combined into a single viral vector. Safety and functionality of the armed OVs have been shown in novel preclinical models ranging from patient-derived organoids and tissue-engineered human in vitro 3D tumor models to complex humanized mouse models. Consequently, a novel and proprietary engineering platform vector based on HSV1 is available for the facilitated preclinical development of oncolytic virotherapy.
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Affiliation(s)
- Christina Funk
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | - Nadja Uhlig
- Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Zsolt Ruzsics
- Department for Medical Microbiology and Hygiene, Institute of Virology, University Medical Center Freiburg, Freiburg, Germany
| | - Florentin Baur
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, Röntgenring, Würzburg, Germany
| | - Matthias Peindl
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, Röntgenring, Würzburg, Germany
| | - Sarah Nietzer
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, Röntgenring, Würzburg, Germany
- Fraunhofer Institute for Silicate Research ISC, Translational Center Regenerative Therapies, Würzburg, Germany
| | - Karina Epting
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | - Gabriele Vacun
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | - Gudrun Dandekar
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, Röntgenring, Würzburg, Germany
- Fraunhofer Institute for Silicate Research ISC, Translational Center Regenerative Therapies, Würzburg, Germany
| | - Catherine Botteron
- Fraunhofer Institute for Toxicology and Experimental Medicine, Regensburg, Germany
| | - Christian Werno
- Fraunhofer Institute for Toxicology and Experimental Medicine, Regensburg, Germany
| | - Thomas Grunwald
- Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Susanne M. Bailer
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
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