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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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Wan Q, Song D, Li H, He ML. Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development. Signal Transduct Target Ther 2020; 5:125. [PMID: 32661235 PMCID: PMC7356129 DOI: 10.1038/s41392-020-00233-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/26/2020] [Accepted: 06/13/2020] [Indexed: 02/06/2023] Open
Abstract
Stress proteins (SPs) including heat-shock proteins (HSPs), RNA chaperones, and ER associated stress proteins are molecular chaperones essential for cellular homeostasis. The major functions of HSPs include chaperoning misfolded or unfolded polypeptides, protecting cells from toxic stress, and presenting immune and inflammatory cytokines. Regarded as a double-edged sword, HSPs also cooperate with numerous viruses and cancer cells to promote their survival. RNA chaperones are a group of heterogeneous nuclear ribonucleoproteins (hnRNPs), which are essential factors for manipulating both the functions and metabolisms of pre-mRNAs/hnRNAs transcribed by RNA polymerase II. hnRNPs involve in a large number of cellular processes, including chromatin remodelling, transcription regulation, RNP assembly and stabilization, RNA export, virus replication, histone-like nucleoid structuring, and even intracellular immunity. Dysregulation of stress proteins is associated with many human diseases including human cancer, cardiovascular diseases, neurodegenerative diseases (e.g., Parkinson’s diseases, Alzheimer disease), stroke and infectious diseases. In this review, we summarized the biologic function of stress proteins, and current progress on their mechanisms related to virus reproduction and diseases caused by virus infections. As SPs also attract a great interest as potential antiviral targets (e.g., COVID-19), we also discuss the present progress and challenges in this area of HSP-based drug development, as well as with compounds already under clinical evaluation.
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Affiliation(s)
- Qianya Wan
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Dan Song
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Huangcan Li
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Ming-Liang He
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, China. .,CityU Shenzhen Research Institute, Shenzhen, China.
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Sprague L, Lee JM, Hutzen BJ, Wang PY, Chen CY, Conner J, Braidwood L, Cassady KA, Cripe TP. High Mobility Group Box 1 Influences HSV1716 Spread and Acts as an Adjuvant to Chemotherapy. Viruses 2018; 10:v10030132. [PMID: 29543735 PMCID: PMC5869525 DOI: 10.3390/v10030132] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/06/2018] [Accepted: 03/12/2018] [Indexed: 01/07/2023] Open
Abstract
High Mobility Group Box 1 (HMGB1) is a multifunctional protein that plays various roles in the processes of inflammation, cancer, and other diseases. Many reports document abundant HMGB1 release following infection with oncolytic viruses (OVs). Further, other groups including previous reports from our laboratory highlight the synergistic effects of OVs with chemotherapy drugs. Here, we show that virus-free supernatants have varying cytotoxic potential, and HMGB1 is actively secreted by two established fibroblast cell lines (NIH 3T3 and 3T6-Swiss albino) following HSV1716 infection in vitro. Further, pharmacologic inhibition or genetic knock-down of HMGB1 reveals a role for HMGB1 in viral restriction, the ability to modulate bystander cell proliferation, and drug sensitivity in 3T6 cells. These data further support the multifactorial role of HMGB1, and suggest it could be a target for modulating the efficacy of oncolytic virus therapies alone or in combination with other frontline cancer treatments.
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Affiliation(s)
- Leslee Sprague
- The Ohio State University College of Medicine, Biomedical Sciences Graduate Program, Columbus, OH 43210, USA.
| | - Joel M Lee
- The Ohio State University College of Medicine, Biomedical Sciences Graduate Program, Columbus, OH 43210, USA.
| | - Brian J Hutzen
- Nationwide Children's Hospital, Division of Hematology/Oncology/BMT and Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA.
| | - Pin-Yi Wang
- Nationwide Children's Hospital, Division of Hematology/Oncology/BMT and Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA.
| | - Chun-Yu Chen
- Nationwide Children's Hospital, Division of Hematology/Oncology/BMT and Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA.
| | - Joe Conner
- Virttu Biologics, BioCity Glasgow, Newhouse ML1 5UH, UK.
| | | | - Kevin A Cassady
- The Ohio State University College of Medicine, Biomedical Sciences Graduate Program, Columbus, OH 43210, USA.
- Nationwide Children's Hospital, Division of Infectious Diseases and Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA.
| | - Timothy P Cripe
- The Ohio State University College of Medicine, Biomedical Sciences Graduate Program, Columbus, OH 43210, USA.
- Nationwide Children's Hospital, Division of Hematology/Oncology/BMT and Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA.
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Abstract
Bovine herpesvirus 1 (BHV-1) infection is widespread and causes a variety of diseases. Although similar in many respects to the human immune response to human herpesvirus 1, the differences in the bovine virus proteins, immune system components and strategies, physiology, and lifestyle mean the bovine immune response to BHV-1 is unique. The innate immune system initially responds to infection, and primes a balanced adaptive immune response. Cell-mediated immunity, including cytotoxic T lymphocyte killing of infected cells, is critical to recovery from infection. Humoral immunity, including neutralizing antibody and antibody-dependent cell-mediated cytotoxicity, is important to prevention or control of (re-)infection. BHV-1 immune evasion strategies include suppression of major histocompatibility complex presentation of viral antigen, helper T-cell killing, and latency. Immune suppression caused by the virus potentiates secondary infections and contributes to the costly bovine respiratory disease complex. Vaccination against BHV-1 is widely practiced. The many vaccines reported include replicating and non-replicating, conventional and genetically engineered, as well as marker and non-marker preparations. Current development focuses on delivery of major BHV-1 glycoproteins to elicit a balanced, protective immune response, while excluding serologic markers and virulence or other undesirable factors. In North America, vaccines are used to prevent or reduce clinical signs, whereas in some European Union countries marker vaccines have been employed in the eradication of BHV-1 disease.
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Complete Genome Sequence of a UL96 Mutant Cytomegalovirus Towne-BAC (Bacterial Artificial Chromosome) Isolate Passaged in Fibroblasts To Allow Accumulation of Compensatory Mutations. GENOME ANNOUNCEMENTS 2013; 1:1/5/e00901-13. [PMID: 24158558 PMCID: PMC3813188 DOI: 10.1128/genomea.00901-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we present the complete genome sequence of a cytomegalovirus Towne-BAC (bacterial artificial chromosome) isolate that we first genetically engineered to mutate the UL96 gene and then serially passaged in human fibroblasts to allow for the accumulation of compensatory mutations. A total of 17 single-base substitutions were discovered in the passaged genome compared to the reference sequence (KF493877).
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Li G, Scull C, Ozcan L, Tabas I. NADPH oxidase links endoplasmic reticulum stress, oxidative stress, and PKR activation to induce apoptosis. Crit Rev Microbiol 2010; 41:150-64. [PMID: 25168431 PMCID: PMC7113905 DOI: 10.3109/1040841x.2013.813899] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The endoplasmic reticulum (ER) is a cellular membrane organelle that plays important roles in virus replication and maturation. Accumulating evidence indicates that virus infection often disturbs ER homeostasis and leads to ER stress, which is associated with a variety of prevalent diseases. To cope with the deleterious effects of virus-induced ER stress, cells activate critical signaling pathways including the unfolded protein response (UPR) and intrinsic mitochondrial apoptosis, which have complex effects on virus replication and pathogenesis. In this review, we present a comprehensive summary of recent research in this field, which revealed that about 36 viruses trigger ER stress and differentially activate ER stress-related signaling pathways. We also highlight the strategies evolved by viruses to modulate ER stress-related signaling networks including immune responses in order to ensure their survival and pathogenesis. Together, the knowledge gained from this field will shed light on unveiling the mechanisms of virus replication and pathogenesis and provide insight for future research as well as antiviral development.
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Affiliation(s)
- Gang Li
- Department of Medicine, Columbia University, New York, NY 10032, USA
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Hukkanen V, Paavilainen H, Mattila RK. Host responses to herpes simplex virus and herpes simplex virus vectors. Future Virol 2010. [DOI: 10.2217/fvl.10.35] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herpes simplex virus (HSV) is a well-known, ubiquitous pathogen of humans. Engineered mutants of HSV can also be exploited as vectors in gene therapy or for virotherapy of tumors. HSV has multiple abilities to evade and modulate the innate and adaptive responses of the host. The increasing knowledge on the mutual interactions of the invading HSV with the host defenses will contribute to our deeper understanding of the relationship between HSV and the host, and thereby lead to future development of more effective and specific HSV vectors for treatment of human diseases. The future advances of HSV vaccines and vaccine vectors are based on the knowlegde of the complex interplay between HSV and the host defenses.
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Affiliation(s)
| | - Henrik Paavilainen
- Department of Virology, University of Turku, Kiinamyllynkatu 13, FIN-20520 Turku, Finland
| | - Riikka K Mattila
- Institute of Diagnostics, University of Oulu, Aapistie 5A, FIN-90014, Finland
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