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1
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Guo E, Dobrovolny HM. Mathematical Modeling of Oncolytic Virus Therapy Reveals Role of the Immune Response. Viruses 2023; 15:1812. [PMID: 37766219 PMCID: PMC10536413 DOI: 10.3390/v15091812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Oncolytic adenoviruses (OAds) present a promising path for cancer treatment due to their selectivity in infecting and lysing tumor cells and their ability to stimulate the immune response. In this study, we use an ordinary differential equation (ODE) model of tumor growth inhibited by oncolytic virus activity to parameterize previous research on the effect of genetically re-engineered OAds in A549 lung cancer tumors in murine models. We find that the data are best fit by a model that accounts for an immune response, and that the immune response provides a mechanism for elimination of the tumor. We also find that parameter estimates for the most effective OAds share characteristics, most notably a high infection rate and low viral clearance rate, that might be potential reasons for these viruses' efficacy in delaying tumor growth. Further studies observing E1A and P19 recombined viruses in different tumor environments may further illuminate the extent of the effects of these genetic modifications.
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Affiliation(s)
| | - Hana M. Dobrovolny
- Department of Physics & Astronomy, Texas Christian University, Fort Worth, TX 76109, USA
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2
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Eidenberger L, Kogelmann B, Steinkellner H. Plant-based biopharmaceutical engineering. NATURE REVIEWS BIOENGINEERING 2023; 1:426-439. [PMID: 37317690 PMCID: PMC10030082 DOI: 10.1038/s44222-023-00044-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/13/2023] [Indexed: 03/24/2023]
Abstract
Plants can be engineered to recombinantly produce high-quality proteins such as therapeutic proteins and vaccines, also known as molecular farming. Molecular farming can be established in various settings with minimal cold-chain requirements and could thus ensure rapid and global-scale deployment of biopharmaceuticals, promoting equitable access to pharmaceuticals. State of the art plant-based engineering relies on rationally assembled genetic circuits, engineered to enable the high-throughput and rapid expression of multimeric proteins with complex post-translational modifications. In this Review, we discuss the design of expression hosts and vectors, including Nicotiana benthamiana, viral elements and transient expression vectors, for the production of biopharmaceuticals in plants. We examine engineering of post-translational modifications and highlight the plant-based expression of monoclonal antibodies and nanoparticles, such as virus-like particles and protein bodies. Techno-economic analyses suggest a cost advantage of molecular farming compared with mammalian cell-based protein production systems. However, regulatory challenges remain to be addressed to enable the widespread translation of plant-based biopharmaceuticals.
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Affiliation(s)
- Lukas Eidenberger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Benjamin Kogelmann
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
- acib — Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Herta Steinkellner
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
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3
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Bais P, Alidrissi L, Blilou I. Detecting Protein-Protein Interactions Using Bimolecular Fluorescence Complementation (BiFC) and Luciferase Complementation Assays (LCA). Methods Mol Biol 2023; 2690:121-131. [PMID: 37450143 DOI: 10.1007/978-1-0716-3327-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
In multicellular organisms, establishing the full body plane involves cell-cell signaling where protein associations are important for the diverse cellular functions within the cells. For the study of protein-protein interactions (PPI), bimolecular fluorescence complementation (BiFC) and luciferase complementation assays (LCA) have proven to be reliable tools that can be used to confirm the physical association of two proteins in a semi-in vivo environment. This chapter provides a detailed description of these two techniques using Nicotiana benthamiana as a semi-in vivo transient expression system. As an example, we will use the interaction of the two well-described transcription factors SHORT-ROOT (SHR) and SCARECROW (SCR), which are known as regulators of asymmetric cell division and stem cell specification in the root meristem of the model plant Arabidopsis thaliana. While the BiFC assay provides subcellular information by displaying a fluorescence signal, nuclear in this case, resulting from the reconstituted fluorophore, the LCA generates a quantitative readout of the SCR-SHR interaction. The combination of both assays provides information on the localization and strength of the PPI.
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Affiliation(s)
- Pepijn Bais
- BESE Division, Plant Cell and Developmental Biology, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Louai Alidrissi
- BESE Division, Plant Cell and Developmental Biology, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ikram Blilou
- BESE Division, Plant Cell and Developmental Biology, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
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4
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Doerner J, Sallard E, Zhang W, Solanki M, Liu J, Ehrke-Schulz E, Zirngibl H, Lieber A, Ehrhardt A. Novel Group C Oncolytic Adenoviruses Carrying a miRNA Inhibitor Demonstrate Enhanced Oncolytic Activity In Vitro and In Vivo. Mol Cancer Ther 2022; 21:460-470. [PMID: 35027480 PMCID: PMC9377726 DOI: 10.1158/1535-7163.mct-21-0240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/10/2021] [Accepted: 01/03/2022] [Indexed: 01/07/2023]
Abstract
Oncolytic adenoviruses (OAd) represent an attractive treatment option for cancer. Clinical efficacy of commonly utilized human adenovirus type 5 (Ad5)-based oncolytic viruses is limited by variable expression levels of the coxsackie- and adenovirus receptor (CAR) in tumor cells and high prevalence of neutralizing antibodies against human Ad5. However, previous studies have highlighted alternative human Ad types as promising candidates for oncolytic therapy. In this study, we generated novel OAds based on Ad1, -2, -5, and -6 derived from species C Ads. These OAds contain a 24-bp deletion in the early gene E1A for tumor selective replication and express the RNAi inhibitor P19. We examined these OAds for in vitro anticancer activity on various cancer cell lines derived from lung, colon, gynecologic, bone, and pancreatic carcinoma. In most surveyed cell lines, OAds based on Ad1, -2, and -6 demonstrated higher cell lysis capability compared with Ad5, suggesting enhanced oncolytic potential. Moreover, enhanced oncolytic activity was associated with P19 expression in a cell type-dependent manner. We further explored a A549 tumor xenograft mouse model to compare the novel OAds directly with Ad5 and H101, an oncolytic adenovirus used in clinical trials. These P19-containing OAds based on Ad1, -2, and -6 showed significantly decelerated tumor progression compared with H101, indicating better antitumor potency in vivo. Our studies provide a novel path for OAd development based on alternative Ad types with improved effectiveness by RNA interference suppression.
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Affiliation(s)
- Johannes Doerner
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany.,Chair for Surgery II, Helios University Hospital Wuppertal, Department Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Erwan Sallard
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Wenli Zhang
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Manish Solanki
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Jing Liu
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Eric Ehrke-Schulz
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Hubert Zirngibl
- Chair for Surgery II, Helios University Hospital Wuppertal, Department Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - André Lieber
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington
| | - Anja Ehrhardt
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany.,Corresponding Author: Anja Ehrhardt, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Stockumer Strasse 10, Witten 58453, Germany. Phone: +49 23902 926 273; Fax: +49 2302 926 44278; E-mail:
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5
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Choi SH, Reeves RE, Romano Ibarra GS, Lynch TJ, Shahin WS, Feng Z, Gasser GN, Winter MC, Evans TIA, Liu X, Luo M, Zhang Y, Stoltz DA, Devor EJ, Yan Z, Engelhardt JF. Detargeting Lentiviral-Mediated CFTR Expression in Airway Basal Cells Using miR-106b. Genes (Basel) 2020; 11:E1169. [PMID: 33036232 PMCID: PMC7601932 DOI: 10.3390/genes11101169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 09/29/2020] [Accepted: 10/02/2020] [Indexed: 12/12/2022] Open
Abstract
Lentiviral-mediated integration of a CFTR transgene cassette into airway basal cells is a strategy being considered for cystic fibrosis (CF) cell-based therapies. However, CFTR expression is highly regulated in differentiated airway cell types and a subset of intermediate basal cells destined to differentiate. Since basal stem cells typically do not express CFTR, suppressing the CFTR expression from the lentiviral vector in airway basal cells may be beneficial for maintaining their proliferative capacity and multipotency. We identified miR-106b as highly expressed in proliferating airway basal cells and extinguished in differentiated columnar cells. Herein, we developed lentiviral vectors with the miR-106b-target sequence (miRT) to both study miR-106b regulation during basal cell differentiation and detarget CFTR expression in basal cells. Given that miR-106b is expressed in the 293T cells used for viral production, obstacles of viral genome integrity and titers were overcome by creating a 293T-B2 cell line that inducibly expresses the RNAi suppressor B2 protein from flock house virus. While miR-106b vectors effectively detargeted reporter gene expression in proliferating basal cells and following differentiation in the air-liquid interface and organoid cultures, the CFTR-miRT vector produced significantly less CFTR-mediated current than the non-miR-targeted CFTR vector following transduction and differentiation of CF basal cells. These findings suggest that miR-106b is expressed in certain airway cell types that contribute to the majority of CFTR anion transport in airway epithelium.
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Affiliation(s)
- Soon H. Choi
- Department of Anatomy and Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, IA 52242, USA; (S.H.C.); (R.E.R.); (T.J.L.); (W.S.S.); (Z.F.); (G.N.G.); (M.C.W.); (T.I.A.E.); (X.L.); (M.L.); (Y.Z.); (Z.Y.)
| | - Rosie E. Reeves
- Department of Anatomy and Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, IA 52242, USA; (S.H.C.); (R.E.R.); (T.J.L.); (W.S.S.); (Z.F.); (G.N.G.); (M.C.W.); (T.I.A.E.); (X.L.); (M.L.); (Y.Z.); (Z.Y.)
| | | | - Thomas J. Lynch
- Department of Anatomy and Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, IA 52242, USA; (S.H.C.); (R.E.R.); (T.J.L.); (W.S.S.); (Z.F.); (G.N.G.); (M.C.W.); (T.I.A.E.); (X.L.); (M.L.); (Y.Z.); (Z.Y.)
| | - Weam S. Shahin
- Department of Anatomy and Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, IA 52242, USA; (S.H.C.); (R.E.R.); (T.J.L.); (W.S.S.); (Z.F.); (G.N.G.); (M.C.W.); (T.I.A.E.); (X.L.); (M.L.); (Y.Z.); (Z.Y.)
| | - Zehua Feng
- Department of Anatomy and Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, IA 52242, USA; (S.H.C.); (R.E.R.); (T.J.L.); (W.S.S.); (Z.F.); (G.N.G.); (M.C.W.); (T.I.A.E.); (X.L.); (M.L.); (Y.Z.); (Z.Y.)
| | - Grace N. Gasser
- Department of Anatomy and Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, IA 52242, USA; (S.H.C.); (R.E.R.); (T.J.L.); (W.S.S.); (Z.F.); (G.N.G.); (M.C.W.); (T.I.A.E.); (X.L.); (M.L.); (Y.Z.); (Z.Y.)
| | - Michael C. Winter
- Department of Anatomy and Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, IA 52242, USA; (S.H.C.); (R.E.R.); (T.J.L.); (W.S.S.); (Z.F.); (G.N.G.); (M.C.W.); (T.I.A.E.); (X.L.); (M.L.); (Y.Z.); (Z.Y.)
| | - T. Idil Apak Evans
- Department of Anatomy and Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, IA 52242, USA; (S.H.C.); (R.E.R.); (T.J.L.); (W.S.S.); (Z.F.); (G.N.G.); (M.C.W.); (T.I.A.E.); (X.L.); (M.L.); (Y.Z.); (Z.Y.)
| | - Xiaoming Liu
- Department of Anatomy and Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, IA 52242, USA; (S.H.C.); (R.E.R.); (T.J.L.); (W.S.S.); (Z.F.); (G.N.G.); (M.C.W.); (T.I.A.E.); (X.L.); (M.L.); (Y.Z.); (Z.Y.)
| | - Meihui Luo
- Department of Anatomy and Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, IA 52242, USA; (S.H.C.); (R.E.R.); (T.J.L.); (W.S.S.); (Z.F.); (G.N.G.); (M.C.W.); (T.I.A.E.); (X.L.); (M.L.); (Y.Z.); (Z.Y.)
| | - Yulong Zhang
- Department of Anatomy and Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, IA 52242, USA; (S.H.C.); (R.E.R.); (T.J.L.); (W.S.S.); (Z.F.); (G.N.G.); (M.C.W.); (T.I.A.E.); (X.L.); (M.L.); (Y.Z.); (Z.Y.)
| | - David A. Stoltz
- Department of Internal Medicine, University of Iowa, Carver College of Medicine, Iowa City, IA 52246, USA;
| | - Eric J. Devor
- Department of Obstetrics and Gynecology, University of Iowa, Carver College of Medicine, Iowa City, IA 52246, USA;
| | - Ziying Yan
- Department of Anatomy and Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, IA 52242, USA; (S.H.C.); (R.E.R.); (T.J.L.); (W.S.S.); (Z.F.); (G.N.G.); (M.C.W.); (T.I.A.E.); (X.L.); (M.L.); (Y.Z.); (Z.Y.)
| | - John F. Engelhardt
- Department of Anatomy and Cell Biology, University of Iowa, Carver College of Medicine, Iowa City, IA 52242, USA; (S.H.C.); (R.E.R.); (T.J.L.); (W.S.S.); (Z.F.); (G.N.G.); (M.C.W.); (T.I.A.E.); (X.L.); (M.L.); (Y.Z.); (Z.Y.)
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6
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Stepanenko AA, Chekhonin VP. A compendium of adenovirus genetic modifications for enhanced replication, oncolysis, and tumor immunosurveillance in cancer therapy. Gene 2018; 679:11-18. [PMID: 30171937 DOI: 10.1016/j.gene.2018.08.069] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/19/2018] [Accepted: 08/27/2018] [Indexed: 12/23/2022]
Abstract
In this review, we specifically focus on genetic modifications of oncolytic adenovirus 5 (Ad5)-based vectors that enhance replication, oncolysis/spread, and virus-mediated tumor immunosurveillance. The finding of negative regulation of minor core protein V by SUMOylation led to the identification of amino acid residues, which when mutated increase adenovirus replication and progeny yield. Suppression of Dicer and/or RNAi pathway with shRNA or p19 tomato bushy stunt protein also results in significant enhancement of adenovirus replication and progeny yield. Truncation mutations in E3-19K or i-leader sequence or overexpression of adenovirus death protein (ADP) potently increase adenovirus progeny release and spread without affecting virus yield. Moreover, E3-19K protein, which was found to inhibit both major histocompatibility complex I (MHCI) and MHC-I chain-related A and B proteins (MICA/MICB) expression on the cell surface, protecting infected cells from T-lymphocyte and natural killer (NK) cell attack, may be tailored to selectively target only MHCI or MICA/MICB, or to lose the ability to downregulate both. At last, E3-19K protein may be exploited to deliver tumor-associated epitopes directly to the endoplasmic reticulum for loading MHCI in the transporter associated with antigen processing (TAP)-deregulated cells.
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Affiliation(s)
- Aleksei A Stepanenko
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky Federal Medical Research Center of Psychiatry and Narcology, the Ministry of Health of the Russian Federation, Kropotkinsky lane 23, 119034 Moscow, Russia.
| | - Vladimir P Chekhonin
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky Federal Medical Research Center of Psychiatry and Narcology, the Ministry of Health of the Russian Federation, Kropotkinsky lane 23, 119034 Moscow, Russia; Department of Medical Nanobiotechnologies, Medico-Biological Faculty, N. I. Pirogov Russian National Research Medical University, the Ministry of Health of the Russian Federation, Ostrovitianov str. 1, 117997 Moscow, Russia
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7
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Yang NJ, Kauke MJ, Sun F, Yang LF, Maass KF, Traxlmayr MW, Yu Y, Xu Y, Langer RS, Anderson DG, Wittrup KD. Cytosolic delivery of siRNA by ultra-high affinity dsRNA binding proteins. Nucleic Acids Res 2017. [PMID: 28641400 PMCID: PMC5570165 DOI: 10.1093/nar/gkx546] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Protein-based methods of siRNA delivery are capable of uniquely specific targeting, but are limited by technical challenges such as low potency or poor biophysical properties. Here, we engineered a series of ultra-high affinity siRNA binders based on the viral protein p19 and developed them into siRNA carriers targeted to the epidermal growth factor receptor (EGFR). Combined in trans with a previously described endosome-disrupting agent composed of the pore-forming protein Perfringolysin O (PFO), potent silencing was achieved in vitro with no detectable cytotoxicity. Despite concerns that excessively strong siRNA binding could prevent the discharge of siRNA from its carrier, higher affinity continually led to stronger silencing. We found that this improvement was due to both increased uptake of siRNA into the cell and improved pharmacodynamics inside the cell. Mathematical modeling predicted the existence of an affinity optimum that maximizes silencing, after which siRNA sequestration decreases potency. Our study characterizing the affinity dependence of silencing suggests that siRNA-carrier affinity can significantly affect the intracellular fate of siRNA and may serve as a handle for improving the efficiency of delivery. The two-agent delivery system presented here possesses notable biophysical properties and potency, and provide a platform for the cytosolic delivery of nucleic acids.
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Affiliation(s)
- Nicole J Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Monique J Kauke
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Fangdi Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lucy F Yang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Katie F Maass
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael W Traxlmayr
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yao Yu
- Protein Analytics, Adimab LLC, Lebanon, NH 03766, USA
| | - Yingda Xu
- Protein Analytics, Adimab LLC, Lebanon, NH 03766, USA
| | - Robert S Langer
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel G Anderson
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - K Dane Wittrup
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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8
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Machitani M, Sakurai F, Wakabayashi K, Tachibana M, Fujiwara T, Mizuguchi H. Enhanced Oncolytic Activities of the Telomerase-Specific Replication-Competent Adenovirus Expressing Short-Hairpin RNA against Dicer. Mol Cancer Ther 2016; 16:251-259. [PMID: 27760834 DOI: 10.1158/1535-7163.mct-16-0383] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/21/2016] [Accepted: 10/13/2016] [Indexed: 11/16/2022]
Abstract
Oncolytic viruses have been receiving much attention as potential agents for cancer treatment. Among the various types of oncolytic viruses, the telomerase-specific replication-competent adenovirus (TRAD), which carries the tumor-specific promoter-driven E1 gene expression cassette, exhibits efficient antitumor effects. The development of a novel TRAD that shows higher replication efficiency and antitumor activity would be highly beneficial for safer and more efficient cancer therapy. We recently demonstrated that the endoribonuclease Dicer significantly inhibits the replication of wild-type adenovirus (Ad) via the processing of viral-associated (VA)-RNAs, which are Ad-encoded small noncoding RNAs, and that the knockdown of Dicer leads to enhanced VA-RNA expression and Ad replication after infection with wild-type Ad. Based on these findings, we herein developed a novel TRAD expressing short-hairpin RNA against Dicer (shDicer; TRAD-shDicer). After infection, TRAD-shDicer efficiently induced the knockdown of Dicer. TRAD-shDicer showed significantly higher replication efficiency and tumor cell lysis activity compared with the conventional TRAD in tumor cells. The Dicer expression levels and viabilities of normal cells were not altered by infection with TRAD-shDicer. These results indicate that TRAD-shDicer is a potent antitumor reagent by virtue of its enhanced oncolytic activity. Mol Cancer Ther; 16(1); 251-9. ©2016 AACR.
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Affiliation(s)
- Mitsuhiro Machitani
- Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan.,Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Fuminori Sakurai
- Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan. .,Laboratory of Regulatory Sciences for Oligonucleotide Therapeutics, Clinical Drug Development Unit, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Keisaku Wakabayashi
- Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Masashi Tachibana
- Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Toshiyoshi Fujiwara
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Hiroyuki Mizuguchi
- Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan. .,Laboratory of Hepatocyte Regulation, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,iPS Cell-Based Research Project on Hepatic Toxicity and Metabolism, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan.,Global Center for Advanced Medical Engineering and Informatics, Osaka University, Osaka, Japan.,Graduate School of Medicine, Osaka University, Osaka, Japan
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9
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Inturi R, Kamel W, Akusjärvi G, Punga T. Complementation of the human adenovirus type 5 VA RNAI defect by the Vaccinia virus E3L protein and serotype-specific VA RNAIs. Virology 2015. [PMID: 26196231 DOI: 10.1016/j.virol.2015.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Human adenoviruses (HAdVs) encode for multifunctional non-coding virus-associated (VA) RNAs, which function as powerful suppressors of the cellular interferon (IFN) and RNA interference (RNAi) systems. In this study we tested the ability of various plant and animal virus encoded RNAi and IFN suppressor proteins to functionally substitute for the HAdV-5 VA RNAI. Our results revealed that only the Vaccinia virus (VACV) E3L protein was able to substitute for the HAdV-5 VA RNAI functions in virus-infected cells. Interestingly, the E3L protein rescues the translational defect but does not stimulate viral capsid mRNA accumulation observed with VA RNA. We further show that the E3L C-terminal region containing the dsRNA-binding domain is needed to enhance VA RNAI mutant virus replication. Additionally, we show that the HAdV-4 and HAdV-37 VA RNAI are more effective than the HAdV-5 VA RNAI in rescuing virus replication.
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Affiliation(s)
- Raviteja Inturi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, BMC, Box 582, Uppsala, Sweden
| | - Wael Kamel
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, BMC, Box 582, Uppsala, Sweden
| | - Göran Akusjärvi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, BMC, Box 582, Uppsala, Sweden
| | - Tanel Punga
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, BMC, Box 582, Uppsala, Sweden.
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10
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Functional analysis of RNAi suppressor P19 on improving baculovirus yield and transgene expression in Sf9 cells. Biotechnol Lett 2015; 37:2159-66. [PMID: 26187316 DOI: 10.1007/s10529-015-1910-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 07/08/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVE To investigate whether RNA interference suppressor P19 derived from tombusvirus can enhance baculovirus yield and transgene expression. RESULTS A number of recombinant baculoviruses with P19 under the control of white spot syndrome virus immediate-early promoter, baculovirus early-to-late promoter, or P10 late promoter were constructed The budded virus titer and the expression levels of eGFP and luciferase were determined. P19 was clearly functional in Sf9 cells and could enhance baculovirus yield, eGFP and luciferase expression levels up to 6.8-, 1.8-, and 2.1-fold respectively, at 72 h post infection. CONCLUSION P19 enhanced baculovirus production and transgene expression, and thus has potential applications in baculovirus-based gene therapy and vaccine studies.
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Sekeli R, Abdullah JO, Namasivayam P, Muda P, Abu Bakar UK, Yeong WC, Pillai V. RNA interference of 1-aminocyclopropane-1-carboxylic acid oxidase (ACO1 and ACO2) genes expression prolongs the shelf life of Eksotika (Carica papaya L.) papaya fruit. Molecules 2014; 19:8350-62. [PMID: 24950439 PMCID: PMC6270959 DOI: 10.3390/molecules19068350] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/19/2014] [Accepted: 05/30/2014] [Indexed: 12/28/2022] Open
Abstract
The purpose of this study was to evaluate the effectiveness of using RNA interference in down regulating the expression of 1-aminocyclopropane-1-carboxylic acid oxidase gene in Eksotika papaya. One-month old embryogenic calli were separately transformed with Agrobacterium strain LBA 4404 harbouring the three different RNAi pOpOff2 constructs bearing the 1-aminocyclopropane-1-carboxylic acid oxidase gene. A total of 176 putative transformed lines were produced from 15,000 calli transformed, selected, then regenerated on medium supplemented with kanamycin. Integration and expression of the targeted gene in putatively transformed lines were verified by PCR and real-time RT-PCR. Confined field evaluation of a total of 31 putative transgenic lines planted showed a knockdown expression of the targeted ACO1 and ACO2 genes in 13 lines, which required more than 8 days to achieve the full yellow colour (Index 6). Fruits harvested from lines pRNAiACO2 L2-9 and pRNAiACO1 L2 exhibited about 20 and 14 days extended post-harvest shelf life to reach Index 6, respectively. The total soluble solids contents of the fruits ranged from 11 to 14° Brix, a range similar to fruits from non-transformed, wild type seed-derived plants.
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Affiliation(s)
- Rogayah Sekeli
- Malaysian Agricultural Research and Development Institute (MARDI), P.O. Box 12301, Kuala Lumpur 50774, Malaysia.
| | - Janna Ong Abdullah
- Department of Microbiology, Faculty of Biotechnology & Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang 43400, Selangor Darul Ehsan, Malaysia.
| | - Parameswari Namasivayam
- Department of Cell and Molecular Biology, Faculty of Biotechnology & Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang 43400, Selangor Darul Ehsan, Malaysia.
| | - Pauziah Muda
- Malaysian Agricultural Research and Development Institute (MARDI), P.O. Box 12301, Kuala Lumpur 50774, Malaysia.
| | - Umi Kalsom Abu Bakar
- Malaysian Agricultural Research and Development Institute (MARDI), P.O. Box 12301, Kuala Lumpur 50774, Malaysia.
| | - Wee Chien Yeong
- Malaysian Agricultural Research and Development Institute (MARDI), P.O. Box 12301, Kuala Lumpur 50774, Malaysia.
| | - Vilasini Pillai
- Ministry of Science, Technology and Innovation (MOSTI), Putrajaya 62574, Federal Territory, Malaysia.
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Supervised learning classification models for prediction of plant virus encoded RNA silencing suppressors. PLoS One 2014; 9:e97446. [PMID: 24828116 PMCID: PMC4020838 DOI: 10.1371/journal.pone.0097446] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 04/21/2014] [Indexed: 12/21/2022] Open
Abstract
Viral encoded RNA silencing suppressor proteins interfere with the host RNA silencing machinery, facilitating viral infection by evading host immunity. In plant hosts, the viral proteins have several basic science implications and biotechnology applications. However in silico identification of these proteins is limited by their high sequence diversity. In this study we developed supervised learning based classification models for plant viral RNA silencing suppressor proteins in plant viruses. We developed four classifiers based on supervised learning algorithms: J48, Random Forest, LibSVM and Naïve Bayes algorithms, with enriched model learning by correlation based feature selection. Structural and physicochemical features calculated for experimentally verified primary protein sequences were used to train the classifiers. The training features include amino acid composition; auto correlation coefficients; composition, transition, and distribution of various physicochemical properties; and pseudo amino acid composition. Performance analysis of predictive models based on 10 fold cross-validation and independent data testing revealed that the Random Forest based model was the best and achieved 86.11% overall accuracy and 86.22% balanced accuracy with a remarkably high area under the Receivers Operating Characteristic curve of 0.95 to predict viral RNA silencing suppressor proteins. The prediction models for plant viral RNA silencing suppressors can potentially aid identification of novel viral RNA silencing suppressors, which will provide valuable insights into the mechanism of RNA silencing and could be further explored as potential targets for designing novel antiviral therapeutics. Also, the key subset of identified optimal features may help in determining compositional patterns in the viral proteins which are important determinants for RNA silencing suppressor activities. The best prediction model developed in the study is available as a freely accessible web server pVsupPred at http://bioinfo.icgeb.res.in/pvsup/.
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