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Godbold GD, Hewitt FC, Kappell AD, Scholz MB, Agar SL, Treangen TJ, Ternus KL, Sandbrink JB, Koblentz GD. Improved understanding of biorisk for research involving microbial modification using annotated sequences of concern. Front Bioeng Biotechnol 2023; 11:1124100. [PMID: 37180048 PMCID: PMC10167326 DOI: 10.3389/fbioe.2023.1124100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/11/2023] [Indexed: 05/15/2023] Open
Abstract
Regulation of research on microbes that cause disease in humans has historically been focused on taxonomic lists of 'bad bugs'. However, given our increased knowledge of these pathogens through inexpensive genome sequencing, 5 decades of research in microbial pathogenesis, and the burgeoning capacity of synthetic biologists, the limitations of this approach are apparent. With heightened scientific and public attention focused on biosafety and biosecurity, and an ongoing review by US authorities of dual-use research oversight, this article proposes the incorporation of sequences of concern (SoCs) into the biorisk management regime governing genetic engineering of pathogens. SoCs enable pathogenesis in all microbes infecting hosts that are 'of concern' to human civilization. Here we review the functions of SoCs (FunSoCs) and discuss how they might bring clarity to potentially problematic research outcomes involving infectious agents. We believe that annotation of SoCs with FunSoCs has the potential to improve the likelihood that dual use research of concern is recognized by both scientists and regulators before it occurs.
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Affiliation(s)
| | | | | | | | - Stacy L. Agar
- Signature Science, LLC, Charlottesville, VA, United States
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX, United States
| | | | - Jonas B. Sandbrink
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gregory D. Koblentz
- Schar School of Policy and Government, George Mason University, Arlington, VA, United States
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Li D, Tian G, Wang J, Zhao LY, Co O, Underill ZC, Mymryk JS, Claessens F, Dehm SM, Daaka Y, Liao D. Inhibition of androgen receptor transactivation function by adenovirus type 12 E1A undermines prostate cancer cell survival. Prostate 2018; 78:1140-1156. [PMID: 30009471 PMCID: PMC6424568 DOI: 10.1002/pros.23689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/26/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Mutations or truncation of the ligand-binding domain (LBD) of androgen receptor (AR) underlie treatment resistance for prostate cancer (PCa). Thus, targeting the AR N-terminal domain (NTD) could overcome such resistance. METHODS Luciferase reporter assays after transient transfection of various DNA constructs were used to assess effects of E1A proteins on AR-mediated transcription. Immunofluorescence microscopy and subcellular fractionation were applied to assess intracellular protein localization. Immunoprecipitation and mammalian two-hybrid assays were used to detect protein-protein interactions. qRT-PCR was employed to determine RNA levels. Western blotting was used to detect protein expression in cells. Effects of adenoviruses on prostate cancer cell survival were evaluated with CellTiter-Glo assays. RESULTS Adenovirus 12 E1A (E1A12) binds specifically to the AR. Interestingly, the full-length E1A12 (266 aa) preferentially binds to full-length AR, while the small E1A12 variant (235 aa) interacts more strongly with AR-V7. E1A12 promotes AR nuclear translocation, likely through mediating intramolecular AR NTD-LBD interactions. In the nucleus, AR and E1A12 co-expression in AR-null PCa cells results in E1A12 redistribution from nuclear foci containing CBX4 (also known as Pc2), suggesting a preferential AR-E1A12 interaction over other E1A12 interactors. E1A12 represses AR-mediated transcription in reporter gene assays and endogenous AR target genes such as ATAD2 and MYC in AR-expressing PCa cells. AR-expressing PCa cells are more sensitive to death induced by a recombinant adenovirus expressing E1A12 (Ad-E1A12) than AR-deficient PCa cells, which could be attributed to the increased viral replication promoted by androgen stimulation. Targeting the AR by E1A12 promotes apoptosis in PCa cells that express the full-length AR or C-terminally truncated AR variants. Importantly, inhibition of mTOR signaling that blocks the expression of anti-apoptotic proteins markedly augments Ad-E1A12-induced apoptosis of AR-expressing cells. Mechanistically, Ad-E1A12 infection triggers apoptotic response while activating the PI3K-AKT-mTOR signaling axis; thus, mTOR inhibition enhances apoptosis in AR-expressing PCa cells infected by Ad-E1A12. CONCLUSION Ad12 E1A inhibits AR-mediated transcription and suppresses PCa cell survival, suggesting that targeting the AR by E1A12 might have therapeutic potential for treating advanced PCa with heightened AR signaling.
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Affiliation(s)
- Dawei Li
- Department of Urology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012, P. R. China
- Department of Anatomy and Cell Biology, UF Health Cancer Center and UF Genetics Institute, University of Florida College of Medicine, Gainesville, Florida 32610
| | - Guimei Tian
- Department of Anatomy and Cell Biology, UF Health Cancer Center and UF Genetics Institute, University of Florida College of Medicine, Gainesville, Florida 32610
| | - Jia Wang
- Department of Anatomy and Cell Biology, UF Health Cancer Center and UF Genetics Institute, University of Florida College of Medicine, Gainesville, Florida 32610
- Affiliated Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, P. R. China
| | - Lisa Y. Zhao
- Department of Anatomy and Cell Biology, UF Health Cancer Center and UF Genetics Institute, University of Florida College of Medicine, Gainesville, Florida 32610
- Present address: Department of Medicine, University of Florida, Gainesville, FL 32610
| | - Olivia Co
- Department of Anatomy and Cell Biology, UF Health Cancer Center and UF Genetics Institute, University of Florida College of Medicine, Gainesville, Florida 32610
| | - Zoe C. Underill
- Department of Anatomy and Cell Biology, UF Health Cancer Center and UF Genetics Institute, University of Florida College of Medicine, Gainesville, Florida 32610
| | - Joe S. Mymryk
- Department of Microbiology and Immunology, the University of Western Ontario, London Regional Cancer Centre, Ontario, Canada
| | - Frank Claessens
- Laboratory of Molecular Endocrinology, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 PO box 901, 3000 Leuven, Belgium
| | - Scott M. Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Yehia Daaka
- Department of Anatomy and Cell Biology, UF Health Cancer Center and UF Genetics Institute, University of Florida College of Medicine, Gainesville, Florida 32610
| | - Daiqing Liao
- Department of Anatomy and Cell Biology, UF Health Cancer Center and UF Genetics Institute, University of Florida College of Medicine, Gainesville, Florida 32610
- Corresponding author: Department of Anatomy and Cell Biology, University of Florida, 1333 Center Drive, Gainesville, Florida, 32610-0235, , Phone: 352-273-8188, Fax: 352-846-1248
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Ning Z, Zheng Z, Hao W, Duan C, Li W, Wang Y, Li M, Luo S. The N terminus of orf virus-encoded protein 002 inhibits acetylation of NF-κB p65 by preventing Ser(276) phosphorylation. PLoS One 2013; 8:e58854. [PMID: 23536830 PMCID: PMC3594181 DOI: 10.1371/journal.pone.0058854] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 02/08/2013] [Indexed: 01/01/2023] Open
Abstract
Orf virus-encoded protein 002 (ORFV002) inhibits NF-κB signaling pathway by decreasing the acetylation of NF-κB-p65 through interference of NF-κB p65′s association with NF-κB p300. However, the precise mechanism of how ORFV002 interferes with the NF-κB p65/p300 association is still unknown. Due to similarities of the amino acid sequences of ORFV002 and the adenovirus type 12 (Ad12) E1A protein (E1A-12), we hypothesized that the N-terminal 52 amino acids of ORFV002 might play an important role in this inhibition and constructed several in-frame fusions of ORFV002 to an enhanced green fluorescent protein (EGFP) reporter, including C-terminal and N-terminal deletion mutants of ORFV002. When the N-terminus of ORFV002 was absent, the localization of ORFV002 shifted mainly from the nucleus to the cytoplasm, and it's inhibition of NF-κB transactivation was lost. NF-κB p65 Lys310 acetylation and Ser276 phosphorylation were detected in co-transfection experiments with NF-κB p65 and ORFV002 or its mutants with, or without, the N-terminal region. The results showed that the N-terminus of ORFV002 plays a crucial role in inhibiting both the acetylation and phosphorylation of NF-κB p65. Further investigation indicated that ORFV002 and its C-terminal deletion mutants interfered with NF-κB p65 (Ser276) phosphorylation induced by mitogen- and stress-activated protein kinase-1 (MSK1) and the interaction between NF-κB p65 and MSK1. Since phosphorylated NF-κB p65 recruits transcriptional co-activators such as p300 and CBP, we concluded that the N-terminus of ORFV002 inhibits acetylation of NF-κB p65 by blocking phosphorylation of NF-κB p65 at Ser276.
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Affiliation(s)
- Zhangyong Ning
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, People's Republic of China
| | - Zewei Zheng
- Institute of Antibody Engineering, School of Biotechnology, Southern Medical University, Guangzhou, People's Republic of China
| | - Wenbo Hao
- Institute of Antibody Engineering, School of Biotechnology, Southern Medical University, Guangzhou, People's Republic of China
| | - Chaohui Duan
- Laboratory of Clinical Immunology, The Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Wei Li
- Institute of Antibody Engineering, School of Biotechnology, Southern Medical University, Guangzhou, People's Republic of China
| | - Yuanyuan Wang
- Institute of Antibody Engineering, School of Biotechnology, Southern Medical University, Guangzhou, People's Republic of China
| | - Ming Li
- Institute of Antibody Engineering, School of Biotechnology, Southern Medical University, Guangzhou, People's Republic of China
| | - Shuhong Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, People's Republic of China
- Institute of Antibody Engineering, School of Biotechnology, Southern Medical University, Guangzhou, People's Republic of China
- * E-mail:
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Carl JW, Trgovcich J, Hannenhalli S. Widespread evidence of viral miRNAs targeting host pathways. BMC Bioinformatics 2013; 14 Suppl 2:S3. [PMID: 23369080 PMCID: PMC3549839 DOI: 10.1186/1471-2105-14-s2-s3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background MicroRNAs (miRNA) are regulatory genes that target and repress other RNA molecules via sequence-specific binding. Several biological processes are regulated across many organisms by evolutionarily conserved miRNAs. Plants and invertebrates employ their miRNA in defense against viruses by targeting and degrading viral products. Viruses also encode miRNAs and there is evidence to suggest that virus-encoded miRNAs target specific host genes and pathways that may be beneficial for their infectivity and/or proliferation. However, it is not clear whether there are general patterns underlying cellular targets of viral miRNAs. Results Here we show that for several of the 135 known viral miRNAs in human viruses, the human genes targeted by the viral miRNA are enriched for specific host pathways whose targeting is likely beneficial to the virus. Given that viral miRNAs continue to be discovered as technologies evolve, we extended the investigation to 6809 putative miRNAs encoded by 23 human viruses. Our analysis further suggests that human viruses have evolved their miRNA repertoire to target specific human pathways, such as cell growth, axon guidance, and cell differentiation. Interestingly, many of the same pathways are also targeted in mice by miRNAs encoded by murine viruses. Furthermore, Human Cytomegalovirus (CMV) miRNAs that target specific human pathways exhibit increased conservation across CMV strains. Conclusions Overall, our results suggest that viruses may have evolved their miRNA repertoire to target specific host pathways as a means for their survival.
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Affiliation(s)
- Joseph W Carl
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
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Chan JK, Greene WC. Dynamic roles for NF-κB in HTLV-I and HIV-1 retroviral pathogenesis. Immunol Rev 2012; 246:286-310. [DOI: 10.1111/j.1600-065x.2012.01094.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Heyward CY, Patel R, Mace EM, Grier JT, Guan H, Makrigiannis AP, Orange JS, Ricciardi RP. Tumorigenic adenovirus 12 cells evade NK cell lysis by reducing the expression of NKG2D ligands. Immunol Lett 2012; 144:16-23. [PMID: 22445355 DOI: 10.1016/j.imlet.2012.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 02/25/2012] [Accepted: 03/04/2012] [Indexed: 11/17/2022]
Abstract
Activation of natural killer (NK) cells depends on a balance between signals received from activation and inhibitory ligands expressed on the surface of target cells. Tumorigenic human adenovirus 12 (Ad12) transformed cells express low levels of the NK cell inhibitory ligand MHC I, but do not exhibit increased sensitivity to NK cell lysis compared to their non-tumorigenic counterparts. Analysis of the expression of activation ligands that bind to the NKG2D receptor revealed that RAE1β and H60 were reduced on the surface of Ad12 mouse cells as well as at the level of transcription. In accord with these results, RAE1 localization to the synapse and sensitivity to NK cell cytotoxicity were also diminished. The reduced transcription of the rat NKG2D ligands, RAEt1L and RRTL, in tumorigenic rat cells compared to non-tumorigenic counterparts implies that both mouse and rat cell lines share a common mechanism of NKG2D ligand activation subverted by Ad12.
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Affiliation(s)
- Christa Y Heyward
- Abramson Cancer Center, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
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Abstract
The nuclear factor-κB (NF-κB) family of transcription factors plays a central part in the host response to infection by microbial pathogens, by orchestrating the innate and acquired host immune responses. The NF-κB proteins are activated by diverse signalling pathways that originate from many different cellular receptors and sensors. Many successful pathogens have acquired sophisticated mechanisms to regulate the NF-κB signalling pathways by deploying subversive proteins or hijacking the host signalling molecules. Here, we describe the mechanisms by which viruses and bacteria micromanage the host NF-κB signalling circuitry to favour the continued survival of the pathogen.
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Affiliation(s)
- Masmudur M Rahman
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100266, Gainesville, Florida, USA
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