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In vitro and in vivo comparison of viral and cellular internal ribosome entry sites for bicistronic vector expression

Abstract

Bicistronic vectors are essential to achieve efficient expression of multiple genes in gene therapy protocols and biomedical applications. Internal ribosome entry site (IRES) elements have been utilized to initiate expression of an additional protein from a bicistronic vector. The IRES element commonly used in current bicistronic vectors originates from the encephalomyocarditis virus (EMCV). As IRES-mediated translation is dependent on availability of IRES trans-acting factors, which vary between cell types and species, adequate gene expression from the EMCV IRES element is not always achieved. To identify a novel IRES element that mediates gene expression consistently with a higher efficiency than the EMCV IRES, we tested 13 bicistronic reporter constructs containing different viral and cellular IRES elements. The in vitro screening in human and mouse fibroblast and hepatocarcinoma cells revealed that the vascular endothelial growth factor and type 1 collagen-inducible protein (VCIP) IRES was the only IRES element that directed translation more efficiently than the EMCV IRES in all cell lines. Furthermore, the VCIP IRES initiated greater reporter expression levels than the EMCV IRES in transfected mouse livers. These results suggest that VCIP-IRES containing vectors improve gene expression compared with those harboring an EMCV-IRES. This could increase the potential benefits of bicistronic vectors for experimental and therapeutic purposes.

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References

  1. Shatkin AJ . Capping of eucaryotic mRNAs. Cell 1976; 9: 645–653.

    Article  CAS  PubMed  Google Scholar 

  2. Shatkin AJ . mRNA cap binding proteins: essential factors for initiating translation. Cell 1985; 40: 223–224.

    Article  CAS  PubMed  Google Scholar 

  3. Pestova TV, Kolupaeva VG, Lomakin IB, Pilipenko EV, Shatsky IN, Agol VI et al. Molecular mechanisms of translation initiation in eukaryotes. Proc Natl Acad Sci USA 2001; 98: 7029–7036.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  4. Hellen CU, Sarnow P . Internal ribosome entry sites in eukaryotic mRNA molecules. Genes Dev 2001; 15: 1593–1612.

    Article  CAS  PubMed  Google Scholar 

  5. Pelletier J, Sonenberg N . Internal initiation of translation of eukaryotic messenger-RNA directed by a sequence derived from poliovirus RNA. Nature 1988; 334: 320–325.

    Article  CAS  PubMed  Google Scholar 

  6. de Felipe P . Skipping the co-expression problem: the new 2A ‘CHYSEL’ technology. Genet Vaccines Ther 2004; 2: 13.

    Article  PubMed Central  PubMed  Google Scholar 

  7. Ryan MD, Drew J . Foot-and-mouth disease virus 2A oligopeptide mediated cleavage of an artificial polyprotein. EMBO J 1994; 13: 928–933.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  8. de Felipe P, Izquierdo M . Construction and characterization of pentacistronic retrovirus vectors. J Gen Virol 2003; 84: 1281–1285.

    Article  CAS  Google Scholar 

  9. De Felipe P, Izquierdo M . Tricistronic and tetracistronic retroviral vectors for gene transfer. Hum Gene Ther 2000; 11: 1921–1931.

    Article  CAS  PubMed  Google Scholar 

  10. Belsham GJ, Sonenberg N . RNA–protein interactions in regulation of picornavirus RNA translation. Microbiol Rev 1996; 60: 499–511.

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Vagner S, Galy B, Pyronnet S . Irresistible IRES—attracting the translation machinery to internal ribosome entry sites. EMBO Rep 2001; 2: 893–898.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  12. Stoneley M, Paulin FEM, Le Quesne JPC, Chappell SA, Willis AE . C-Myc 5′ untranslated region contains an internal ribosome entry segment. Oncogene 1998; 16: 423–428.

    Article  CAS  PubMed  Google Scholar 

  13. Palmenberg AC, Kirby EM, Janda MR, Drake NL, Duke GM, Potratz KF et al. The nucleotide and deduced amino acid sequences of the encephalomyocarditis viral polyprotein coding region. Nucleic Acids Res 1984; 12: 2969–2985.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  14. Jang SK, Krausslich HG, Nicklin MJ, Duke GM, Palmenberg AC, Wimmer E . A segment of the 5′ nontranslated region of encephalomyocarditis virus RNA directs internal entry of ribosomes during in vitro translation. J Virol 1988; 62: 2636–2643.

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Wong ET, Ngoi SM, Lee CGL . Improved co-expression of multinle genes in vectors containing internal ribosome entry sites (IRESes) from human genes. Gene Therapy 2002; 9: 337–344.

    Article  CAS  PubMed  Google Scholar 

  16. Li JD, Menzel C, Meier D, Zhang C, Dubel S, Jostock T . A comparative study of different vector designs for the mammalian expression of recombinant IgG antibodies. J Immunol Methods 2007; 318: 113–124.

    Article  CAS  PubMed  Google Scholar 

  17. Wang YL, Iyer M, Annala AJ, Chappell S, Mauro V, Gambhir SS . Noninvasive monitoring of target gene expression by imaging reporter gene expression in living animals using improved bicistronic vectors. J Nuclear Med 2005; 46: 667–674.

    CAS  Google Scholar 

  18. Mizuguchi H, Xu ZL, Ishii-Watabe A, Uchida E, Hayakawa T . IRES-dependent second gene expression is significantly lower than cap-dependent first gene expression in a bicistronic vector. Mol Ther 2000; 1: 376–382.

    Article  CAS  PubMed  Google Scholar 

  19. Douin V, Bornes S, Creancier L, Rochaix P, Favre G, Prats AC et al. Use and comparison of different internal ribosomal entry sites (IRES) in tricistronic retroviral vectors. BMC Biotechnol 2004; 4: 16.

    Article  PubMed Central  PubMed  Google Scholar 

  20. Hennecke M, Kwissa M, Metzger K, Oumard A, Kroger A, Schirmbeck R et al. Composition and arrangement of genes define the strength of IRES-driven translation in bicistronic mRNAs. Nucleic Acids Res 2001; 29: 3327–3334.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  21. Allera-Moreau C, Delluc-Clavieres A, Castano C, Van den Berghe L, Golzio M, Moreau M et al. Long term expression of bicistronic vector driven by the FGF-1 IRES in mouse muscle. BMC Biotechnol 2007; 7: 74.

    Article  PubMed Central  PubMed  Google Scholar 

  22. Harries M, Phillipps N, Anderson R, Prentice G, Collins M . Comparison of bicistronic retroviral vectors containing internal ribosome entry sites (IRES) using expression of human interleukin-12 (IL-12) as a readout. J Gene Med 2000; 2: 243–249.

    Article  CAS  PubMed  Google Scholar 

  23. Fux C, Langer D, Kelm JM, Weber W, Fussenegger M . New-generation multicistronic expression platform: pTRIDENT vectors containing size-optimized IRES elements enable homing endonuclease-based cistron swapping into lentiviral expression vectors. Biotechnol Bioeng 2004; 86: 174–187.

    Article  CAS  PubMed  Google Scholar 

  24. Borman AM, Le Mercier P, Girard M, Kean KM . Comparison of picornaviral IRES-driven internal initiation of translation in cultured cells of different origins. Nucleic Acids Res 1997; 25: 925–932.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  25. Bernstein J, Sella O, Le SY, Elroy-Stein O . PDGF2/c-sis mRNA leader contains a differentiation-linked internal ribosomal entry site (D-IRES). J Biol Chem 1997; 272: 9356–9362.

    Article  CAS  PubMed  Google Scholar 

  26. Ramesh N, Kim ST, Wei MQ, Khalighi M, Osborne WR . High-titer bicistronic retroviral vectors employing foot-and-mouth disease virus internal ribosome entry site. Nucleic Acids Res 1996; 24: 2697–2700.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  27. Delluc-Clavieres A, Le Bec C, Van den Berghe L, Conte C, Allo V, Danos O et al. Efficient gene transfer in skeletal muscle with AAV-derived bicistronic vector using the FGF-1 IRES. Gene Therapy 2008; 15: 1090–1098.

    Article  CAS  PubMed  Google Scholar 

  28. Lafuente E, Ramos R, Martinez-Salas E . Long-range RNA–RNA interactions between distant regions of the hepatitis C virus internal ribosome entry site element. J Gen Virol 2002; 83: 1113–1121.

    Article  CAS  PubMed  Google Scholar 

  29. Johansen LK, Morrow CD . Inherent instability of poliovirus genomes containing two internal ribosome entry site (IRES) elements supports a role for the IRES in encapsidation. J Virol 2000; 74: 8335–8342.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  30. Chappell SA, Owens GC, Mauro VP . A 5′ leader of Rbm3, a cold stress-induced mRNA, mediates internal initiation of translation with increased efficiency under conditions of mild hypothermia. J Biol Chem 2001; 276: 36917–36922.

    Article  CAS  PubMed  Google Scholar 

  31. Oumard A, Hennecke M, Hauser H, Nourbakhsh M . Translation of NRF mRNA is mediated by highly efficient internal ribosome entry. Mol Cell Biol 2000; 20: 2755–2759.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  32. Holcik M, Gordon BW, Korneluk RG . The internal ribosome entry site-mediated translation of antiapoptotic protein XIAP is modulated by the heterogeneous nuclear ribonucleoproteins C1 and C2. Mol Cell Biol 2003; 23: 280–288.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  33. Nevins TA, Harder ZM, Korneluk RG, Holcik M . Distinct regulation of internal ribosome entry site-mediated translation following cellular stress is mediated by apoptotic fragments of eIF4G translation initiation factor family members eIF4GI and p97lDAP5/NAT1. J Biol Chem 2003; 278: 3572–3579.

    Article  CAS  PubMed  Google Scholar 

  34. Blais JD, Addison CL, Edge R, Falls T, Zhao H, Wary K et al. Perk-dependent translational regulation promotes tumor cell adaptation and angiogenesis in response to hypoxic stress. Mol Cell Biol 2006; 26: 9517–9532.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  35. Baird SD, Lewis SM, Turcotte M, Holcik M . A search for structurally similar cellular internal ribosome entry sites. Nucleic Acids Res 2007; 35: 4664–4677.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  36. Fernandez J, Yaman I, Mishra R, Merrick WC, Snider MD, Lamers WH et al. Internal ribosome entry site-mediated translation of a mammalian mRNA is regulated by amino acid availability. J Biol Chem 2001; 276: 12285–12291.

    Article  CAS  PubMed  Google Scholar 

  37. Holcik M, Graber T, Lewis SM, Lefebvre CA, Lacasse E, Baird S . Spurious splicing within the XIAP 5′ UTR occurs in the Rluc/Fluc but not the beta gal/CAT bicistronic reporter system. Rna-A Publ Rna Soc 2005; 11: 1605–1609.

    Article  CAS  Google Scholar 

  38. Van Eden ME, Byrd MP, Sherrill KW, Lloyd RE . Demonstrating internal ribosome entry sites in eukaryotic mRNAs using stringent RNA test procedures. Rna-A Publ Rna Soc 2004; 10: 720–730.

    Article  CAS  Google Scholar 

  39. Kozak M . Alternative ways to think about mRNA sequences and proteins that appear to promote internal initiation of translation. Gene 2003; 318: 1–23.

    Article  CAS  PubMed  Google Scholar 

  40. Bert AG, Grepin R, Vadas MA, Goodall GJ . Assessing IRES activity in the HIF-1 alpha and other cellular 5′ UTRs. Rna-A Publ Rna Soc 2006; 12: 1074–1083.

    Article  CAS  Google Scholar 

  41. Albagli-Curiel O, Lecluse Y, Pognonec P, Boulukos KE, Martin P . A new generation of pPRIG-based retroviral vectors. BMC Biotechnol 2007; 7: 85.

    Article  PubMed Central  PubMed  Google Scholar 

  42. Wagstaff MJ, Lilley CE, Smith J, Robinson MJ, Coffin RS, Latchman DS . Gene transfer using a disabled herpes virus vector containing the EMCV IRES allows multiple gene expression in vitro and in vivo. Gene Therapy 1998; 5: 1566–1570.

    Article  CAS  PubMed  Google Scholar 

  43. Gallardo HF, Tan C, Sadelain M . The internal ribosomal entry site of the encephalomyocarditis virus enables reliable coexpression of two transgenes in human primary T lymphocytes. Gene Therapy 1997; 4: 1115–1119.

    Article  CAS  PubMed  Google Scholar 

  44. Ngoi SM, Chien AC, Lee CGL . Exploiting internal ribosome entry sites in gene therapy vector design. Curr Gene Ther 2004; 4: 15–31.

    Article  CAS  PubMed  Google Scholar 

  45. Kai M, Wada I, Imai S, Sakane F, Kanoh H . Cloning and characterization of two human isozymes of Mg2+-independent phosphatidic acid phosphatase. J Biol Chem 1997; 272: 24572–24578.

    Article  CAS  PubMed  Google Scholar 

  46. Shmueli O, Horn-Saban S, Chalifa-Caspi V, Shmoish M, Ophir R, Benjamin-Rodrig H et al. GeneNote: whole genome expression profiles in normal human tissues. C R Biol 2003; 326: 1067–1072.

    Article  CAS  PubMed  Google Scholar 

  47. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 2004; 101: 6062–6067.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  48. Escalante-Alcalde D, Hernandez L, Le Stunff H, Maeda R, Lee HS, Gang Jr C et al. The lipid phosphatase LPP3 regulates extra-embryonic vasculogenesis and axis patterning. Development 2003; 130: 4623–4637.

    Article  CAS  PubMed  Google Scholar 

  49. Wary KK, Humtsoe JO . Anti-lipid phosphate phosphohydrolase-3 (LPP3) antibody inhibits bFGF- and VEGF-induced capillary morphogenesis of endothelial cells. Cell Commun Signal 2005; 3: 9.

    Article  PubMed Central  PubMed  Google Scholar 

  50. Humtsoe JO, Feng S, Thakker GD, Yang J, Hong J, Wary KK . Regulation of cell-cell interactions by phosphatidic acid phosphatase 2b/VCIP. EMBO Journal 2003; 22: 1539–1554.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  51. Martinez-Salas E . Internal ribosome entry site biology and its use in expression vectors. Curr Opin Biotechnol 1999; 10: 458–464.

    Article  CAS  PubMed  Google Scholar 

  52. Carmeliet P, Jain RK . Angiogenesis in cancer and other diseases. Nature 2000; 407: 249–257.

    Article  CAS  PubMed  Google Scholar 

  53. Graeber TG, Osmanian C, Jacks T, Housman DE, Koch CJ, Lowe SW et al. Hypoxia-mediated selection of cells with diminished apoptotic potential in solid tumours. Nature 1996; 379: 88–91.

    Article  CAS  PubMed  Google Scholar 

  54. Bochkov YA, Palmenberg AC . Translational efficiency of EMCV IRES in bicistronic vectors is dependent upon IRES sequence and gene location. Biotechniques 2006; 41: 283–284.

    Article  CAS  PubMed  Google Scholar 

  55. Liu F, Song YK, Liu D . Hydrodynamics-based transfection in animals by systemic administration of plasmid DNA. Gene Therapy 1999; 6: 1258–1266.

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This work was supported by an NSERC Discovery Grant to KH and a post-doctoral fellowship award to SLC from the Cancer Research Training Program with support from the Beatrice Hunter Cancer Research Institute and the Terry Fox Foundation. We thank Paul Crocker for technical assistance.

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Correspondence to K Hirasawa.

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Licursi, M., Christian, S., Pongnopparat, T. et al. In vitro and in vivo comparison of viral and cellular internal ribosome entry sites for bicistronic vector expression. Gene Ther 18, 631–636 (2011). https://doi.org/10.1038/gt.2011.11

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