Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Enabling Technologies
  • Published:

Improved antibiotic-free plasmid vector design by incorporation of transient expression enhancers

Abstract

Methods to improve plasmid-mediated transgene expression are needed for gene medicine and gene vaccination applications. To maintain a low risk of insertional mutagenesis-mediated gene activation, expression-augmenting sequences would ideally function to improve transgene expression from transiently transfected intact plasmid, but not from spurious genomically integrated vectors. We report herein the development of potent minimal, antibiotic-free, high-manufacturing-yield mammalian expression vectors incorporating rationally designed additive combinations of expression enhancers. The SV40 72 bp enhancer incorporated upstream of the cytomegalovirus (CMV) enhancer selectively improved extrachromosomal transgene expression. The human T-lymphotropic virus type I (HTLV-I) R region, incorporated downstream of the CMV promoter, dramatically increased mRNA translation efficiency, but not overall mRNA levels, after transient transfection. A similar mRNA translation efficiency increase was observed with plasmid vectors incorporating and expressing the protein kinase R-inhibiting adenoviral viral associated (VA)1 RNA. Strikingly, HTLV-I R and VA1 did not increase transgene expression or mRNA translation efficiency from plasmid DNA after genomic integration. The vector platform, when combined with electroporation delivery, further increased transgene expression and improved HIV-1 gp120 DNA vaccine-induced neutralizing antibody titers in rabbits. These antibiotic-free vectors incorporating transient expression enhancers are safer, more potent alternatives to improve transgene expression for DNA therapy or vaccination.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5

Similar content being viewed by others

References

  1. Liu L, Marti GP, Wei X, Zhang X, Zhang H, Liu YV et al. Age-dependent impairment of HIF-1α expression in diabetic mice: correction with electroporation-facilitated gene therapy increases wound healing, angiogenesis, and circulating angiogenic cells. J Cell Physiol 2008; 217: 319–327.

    Article  CAS  Google Scholar 

  2. Bodles-Brakhop AM, Heller R, Draghia-Akli R . Electroporation for the delivery of DNA-based vaccines and immunotherapeutics: current clinical developments. Mol Ther 2009; 17: 585–592.

    Article  CAS  Google Scholar 

  3. Luke J, Carnes AE, Hodgson CP, Williams JA . Improved antibiotic-free DNA vaccine vectors utilizing a novel RNA based plasmid selection system. Vaccine 2009; 27: 6454–6459.

    Article  CAS  Google Scholar 

  4. Williams JA, Luke J, Johnson L, Hodgson CP . pDNAVACCultra vector family: high throughput intracellular targeting DNA vaccine plasmids. Vaccine 2006; 24: 4671–4676.

    Article  CAS  Google Scholar 

  5. Williams JA, Carnes AE, Hodgson CP . Plasmid DNA vector design; impact on efficacy, safety and upstream production. Biotechnol Adv 2009; 27: 353–370.

    Article  CAS  Google Scholar 

  6. Williams JA, Luke J, Langtry S, Anderson S, Hodgson CP, Carnes AE . Generic plasmid DNA production platform incorporating low metabolic burden seed-stock and fed-batch fermentation processes. Biotechnol Bioeng 2009; 103: 1129–1143.

    Article  CAS  Google Scholar 

  7. Carnes AE, Williams JA . Low metabolic burden plasmid production. Genetic Eng Biotech News 2009; 29: 56–57.

    Google Scholar 

  8. Carnes AE, Hodgson CP, Luke J, Vincent J, Williams JA . Plasmid DNA production combining antibiotic-free selection, inducible high yield fermentation, and novel autolytic purification. Biotechnol Bioeng 2009; 104: 505–515.

    Article  CAS  Google Scholar 

  9. FDA. Guidance for Industry: Considerations for Plasmid DNA Vaccines for Infectious Disease Indications 2007: US Food and Drug Administration: Rockville, MD, USA.

  10. EMA. Non-clinical Studies Required before First Clinical use of Gene Therapy Medicinal Products 2008: European Medicines Agency: London, England.

  11. Wang Z, Troilo PJ, Wang X, Griffiths TG, Pacchione SJ, Barnum AB et al. Detection of integration of plasmid DNA into host genomic DNA following intramuscular injection and electroporation. Gene Ther 2004; 11: 711–721.

    Article  CAS  Google Scholar 

  12. van Hall T, van de Rhee NE, Schoenberger SP, Vierboom MP, Verreck FA, Melief CJ et al. Cryptic open reading frames in plasmid vector backbone sequences can provide highly immunogenic cytotoxic T-lymphocyte epitopes. Cancer Res 1998; 58: 3087–3093.

    CAS  PubMed  Google Scholar 

  13. Schirmbeck R, Riedl P, Fissolo N, Lemonnier FA, Bertoleti A, Reimann J . Translation from cryptic reading frames of DNA vaccines generates an extended repertoire of immunogenic, MHC class I-restricted epitopes. J Immunol 2005; 174: 4647–4656.

    Article  CAS  Google Scholar 

  14. Maness NJ, Wilson NA, Reed JS, Piaskowski SM, Sacha JB, Walsh AD et al. Robust, vaccine-induced CD8+ T lymphocyte response against an out-of-frame epitope. J Immunol 2010; 184: 67–72.

    Article  CAS  Google Scholar 

  15. Yuh CH, Ting LP . The genome of hepatitis B virus contains a second enhancer: cooperation of two elements within this enhancer is required for its function. J Virol 1990; 64: 4281–4287.

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Mariati Ho SC, Yap MG, Yang Y . Evaluating post-transcriptional regulatory elements for enhancing transient gene expression levels in CHO K1 and HEK293. Protein Expr Purif 2010; 69: 9–15.

    Article  Google Scholar 

  17. Takebe Y, Seiki M, Fujisawa J, Hoy P, Yokata K, Arai K et al. SR alpha promoter: an efficient and versatile mammalian cDNA expression system composed of the simian virus 40 early promoter and the R-U5 segment of human T-cell leukemia virus type 1 long terminal repeat. Mol Cell Biol 1988; 8: 466–472.

    Article  CAS  Google Scholar 

  18. Barouch DH, Yang ZY, Kong WP, Korioth-Schmitz B, Sumida SM, Truitt DM et al. A human T-cell leukemia virus type 1 regulatory element enhances the immunogenicity of human immunodeficiency virus type 1 DNA vaccines in mice and nonhuman primates. J Virol 2005; 79: 8828–8834.

    Article  CAS  Google Scholar 

  19. Williams BR . PKR; a sentinel kinase for cellular stress. Oncogene 1999; 18: 6112–6120.

    Article  CAS  Google Scholar 

  20. Garcia MA, Gil J, Ventoso I, Guerra S, Domingo E, Rivas C et al. Impact of protein kinase PKR in cell biology: from antiviral to antiproliferative action. Microbiol Mol Biol Rev 2006; 70: 1032–1060.

    Article  CAS  Google Scholar 

  21. Lee ES, Yoon CH, Kim YS, Bae YS . The double-strand RNA-dependent protein kinase PKR plays a significant role in a sustained ER stress-induced apoptosis. FEBS Lett 2007; 581: 4325–4332.

    Article  CAS  Google Scholar 

  22. Groskreutz D, Schenborn E . Increased gene expression in mammalian cell lines using pAdVAntage DNA as a cotransfectant. Promega Notes 1994; 48: 8–13.

    Google Scholar 

  23. Lei M, Liu Y, Samuel CE . Adenovirus VAI RNA antagonizes the RNA-editing activity of the ADAR adenosine deaminase. Virology 1998; 245: 188–196.

    Article  CAS  Google Scholar 

  24. Andersson MG, Haasnoot PCJ, Xu N, Berenjian S, Berkhout B, Akusjarvi G . Suppression of RNA interference by adenovirus virus-associated RNA. J Virol 2005; 79: 9556–9565.

    Article  CAS  Google Scholar 

  25. Lu S, Cullen BR . Adenovirus VA1 noncoding RNA can inhibit small interfering RNA and microRNA biogenesis. J Virol 2004; 78: 12868–12876.

    Article  CAS  Google Scholar 

  26. Ma Y, Mathews MB . Secondary and tertiary structure in the central domain of adenovirus type 2 VA RNA I. RNA 1996; 2: 937–951.

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Rahman A, Malhotra P, Shar R, Kewalramani T, Thimmapaya B . Effect of single-base substitutions in the central domain of virus-associated RNA I on its function. J Virol 1995; 69: 4299–4307.

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Lam AP, Dean DA . Progress and prospects: nuclear import of nonviral vectors. Gene Ther 2010; 61: 603–613.

    Google Scholar 

  29. Wagstaff KM, Jans DA . Nucleocytoplasmic transport of DNA: enhancing non-viral gene transfer. Biochem J 2007; 406: 185–202.

    Article  CAS  Google Scholar 

  30. Miller AM, Munkonge FM, Alton EW, Dean DA . Identification of protein cofactors necessary for sequence-specific plasmid DNA nuclear import. Mol Ther 2009; 17: 1897–1903.

    Article  CAS  Google Scholar 

  31. Li S, MacLaughlin FC, Fewell JG, Gondo M, Wang J, Nicol F et al. Muscle-specific enhancement of gene expression by incorporation of SV40 enhancer in the expression plasmid. Gene Ther 2001; 8: 494–497.

    Article  CAS  Google Scholar 

  32. Blomberg P, Eskandarpour M, Xia S, Sylven C, Islam KB . Electroporation in combination with a plasmid vector containing SV40 enhancer elements results in increased and persistent gene expression in mouse muscle. Biochem Biophys Res Commun 2002; 298: 505–510.

    Article  CAS  Google Scholar 

  33. Williams JA . Vectors and methods for genetic immunization. World Patent Application 2006; WO2006078979.

  34. Angulo A, Kerry D, Huang H, Borst EM, Razinsky A, Wu J et al. Identification of a boundary domain adjacent to the potent human cytomegalovirus enhancer that represses transcription from the divergent UL127 promoter. J Virol 2000; 74: 2826–2839.

    Article  CAS  Google Scholar 

  35. Chao SH, Harada JN, Hyndman F, Gao X, Nelson CG, Chanda SK et al. PDX1, a cellular homeoprotein, binds to and regulates the activity of human cytomegalovirus immediate early promoter. J Biol Chem 2004; 279: 16111–16120.

    Article  CAS  Google Scholar 

  36. Lee J, Klase Z, Gao X, Caldwell JS, Stinski MJ, Kashanchi F et al. Cellular homeoproteins, SATB1 and CDP, bind to the unique region between the human cytomegalovirus UL127 and major immediate-early genes. Virology 2007; 366: 117–125.

    Article  CAS  Google Scholar 

  37. Mesika A, Grigoreva I, Zohar M, Reich Z . A regulated NFkB-assisted import of plasmid DNA into mammalian cell nuclei. Mol Ther 2001; 3: 653–657.

    Article  CAS  Google Scholar 

  38. Munkonge FM, Amin V, Hyde SC, Green AM, Pringle IA, Gill DR et al. Identification and functional characterization of cytoplasmic determinants of plasmid DNA nuclear import. J Biol Chem 2009; 284: 26978–26987.

    Article  CAS  Google Scholar 

  39. Hilton TL, Li Y, Dunphy EL, Wang EH . TAF1 histone acetyltransferase activity in Sp1 activation of the cyclin D1 promoter. Mol Cell Biol 2005; 25: 4321–4332.

    Article  CAS  Google Scholar 

  40. Thakur RK, Kumar P, Halder K, Verma A, Kar A, Parent JL et al. Metastases suppressor NM23-H2 interaction with G-quadruplex DNA within c-MYC promoter nuclease hypersensitive element induces c-MYC expression. Nucleic Acids Res 2009; 37: 172–183.

    Article  CAS  Google Scholar 

  41. Carnes AE, Luke JM, Vincent JM, Anderson S, Schukar A, Hodgson CP et al. Critical design criteria for minimal antibiotic-free plasmid vectors necessary to combine robust RNA Pol II and Pol III-mediated eukaryotic expression with high bacterial production yields. J Gene Med 2010; 12: 818–831.

    Article  CAS  Google Scholar 

  42. Kaufman RJ, Murtha P . Translational control mediated by eukaryotic initiation factor-2 is restricted to specific mRNAs in transfected cells. Mol Cell Biol 1987; 7: 1568–1571.

    Article  CAS  Google Scholar 

  43. Terenzi F, deVeer MJ, Ying H, Restifo NP, Williams BR, Silverman RH . The antiviral enzymes PKR and RNase L suppress gene expression from viral and non-viral based vectors. Nucleic Acids Res 1999; 27: 4369–4375.

    Article  CAS  Google Scholar 

  44. Breuzard G, Tertil M, Goncalves C, Cheradame H, Geguan P, Pichon C et al. Nuclear delivery of NFB-assisted DNA/polymer complexes: plasmid DNA quantification by confocal laser scanning microscopy and evidence of nuclear polyplexes by FRET imaging. Nucleic Acids Res 2008; 36: e71.

    Article  Google Scholar 

  45. Molnar MJ, Gilbert R, Lu Y, Liu AB, Guo A, Larochelle N et al. Factors influencing the efficacy, longevity, and safety of electroporation-assisted plasmid-based gene transfer into mouse muscles. Mol Ther 2004; 10: 447–455.

    Article  CAS  Google Scholar 

  46. Williams JA . Vectors and methods for genetic immunization. World Patent Application 2008; WO2008153733.

  47. Lednicky J, Folk WR . Two synthetic Sp1-binding sites functionally substitute for the 21-base-pair repeat region to activate simian virus 40 growth in CV-1 cells. J Virol 1992; 66: 6379–6390.

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Du SX, Idiart RJ, Mariano EB, Chen H, Jiang P, Xu L et al. Effect of trimerization motifs on quaternary structure, antigenicity, and immunogenicity of a noncleavable HIV-1 gp120 envelope glycoprotein. Virology 2009; 395: 33–44.

    Article  CAS  Google Scholar 

  49. Gerdemann U, Christin AS, Vera JF, Ramos CA, Fujita Y, Liu H et al. Nucleofection of DCs to generate multivirus-specific T cells for prevention or treatment of viral infections in the immunocompromised host. Mol Ther 2009; 17: 1616–1625.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank Marni England-Hill (Aldevron) and Jennifer Bath (Concordia College) for oversight of the rabbit study at Aldevron, and Danielle Shea (University of Nebraska, Lincoln) for performing flow cytometry. We also thank Kim Hanson (Nature Technology) for purifying the plasmid DNA used in this study and Sheryl Anderson (Nature Technology) for linear vector preparation. This paper described work supported by NIH grants R44 GM072141-03 and R43 GM080768-01 to JAW. AML is supported by a Specialized Centers for Cell-based Therapy Grant NIH-NHLBI 1 U54 HL081007 and an Amy Strelzer Manasevit Scholar Award. UG is supported by an Asbmt Young Investigator Award and a Leukemia and Lymphoma Society Special Fellow in Clinical Research Award.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to J A Williams.

Ethics declarations

Competing interests

JML, JMV, CPH and JAW have an equity interest in Nature Technology Corporation. SXD and RGW have an equity interest in AltraVax.

Additional information

Supplementary Information accompanies the paper on Gene Therapy website

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Cite this article

Luke, J., Vincent, J., Du, S. et al. Improved antibiotic-free plasmid vector design by incorporation of transient expression enhancers. Gene Ther 18, 334–343 (2011). https://doi.org/10.1038/gt.2010.149

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/gt.2010.149

Keywords

This article is cited by

Search

Quick links