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Using Engineered Nucleases to Create HIV-Resistant Cells

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Part of the book series: Advances in Experimental Medicine and Biology ((AEMB))

Abstract

HIV-1/AIDS is often considered a priority disease in the development of genetic and cell based therapies because of the high burden imposed by current treatments, which require life-long adherence to antiretroviral drug regimens. Engineered nucleases have the capability to either disrupt a specific gene, or to promote precise gene edits or additions at the targeted gene. As one application for the gene disruption capabilities of the nucleases, HIV-1 infection provides an exceptional target in the CCR5 gene. This is the most commonly used entry co-receptor through which the virus enters into CD4+ T cells. Importantly, the loss of CCR5 is expected to be well-tolerated, since a relatively high percentage of individuals are naturally homozygous for a defective CCR5 allele. As a result, CCR5 disruption by zinc finger nuclease treatment of autologous T cells was the first-in-man use of engineered nucleases. Future applications to refine this therapy may include disrupting CCR5 in precursor hematopoietic stem cells, the additional disruption of the alternate HIV-1 co-receptor, CXCR4, in T cells, and the addition of other anti-HIV genes at a disrupted CCR5 locus to provide a combinatorial therapy. Finally, the gene disrupting actions of engineered nucleases could also be harnessed to inactivate the integrated HIV-1 genomes that persist in patients’ cells despite drug therapy, and which thereby prevent the complete eradication of the virus by drug treatments.

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References

  1. http://aids.gov/federal-resources/policies/care-continuum, 2013.

  2. Baltimore D. Gene therapy. Intracellular immunization. Nature. 1988;335(6189):395–6.

    Article  CAS  PubMed  Google Scholar 

  3. Peterson CW, et al. Combinatorial anti-HIV gene therapy: using a multipronged approach to reach beyond HAART. Gene Ther. 2013;20(7):695–702.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Tebas P, Stein D, Tang WW, Frank I, Wang SQ, Lee G, et al. Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV. N Engl J Med. 2014;370:10.

    Article  CAS  Google Scholar 

  5. Sun J, et al. Human Ku70/80 protein blocks exonuclease 1-mediated DNA resection in the presence of human Mre11 or Mre11/Rad50 protein complex. J Biol Chem. 2012;287(7):4936–45.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Symington LS, Gautier J. Double-strand break end resection and repair pathway choice. Annu Rev Genet. 2011;45:247–71.

    Article  CAS  PubMed  Google Scholar 

  7. Chapman JR, Taylor MR, Boulton SJ. Playing the end game: DNA double-strand break repair pathway choice. Mol Cell. 2012;47(4):497–510.

    Article  CAS  PubMed  Google Scholar 

  8. Escribano-Diaz C, et al. A cell cycle-dependent regulatory circuit composed of 53BP1-RIF1 and BRCA1-CtIP controls DNA repair pathway choice. Mol Cell. 2013;49(5):872–83.

    Article  CAS  PubMed  Google Scholar 

  9. Heyer WD, Ehmsen KT, Liu J. Regulation of homologous recombination in eukaryotes. Annu Rev Genet. 2010;44:113–39.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Mohrin M, et al. Hematopoietic stem cell quiescence promotes error-prone DNA repair and mutagenesis. Cell Stem Cell. 2010;7(2):174–85.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Rossi DJ, et al. Hematopoietic stem cell quiescence attenuates DNA damage response and permits DNA damage accumulation during aging. Cell Cycle. 2007;6(19):2371–6.

    Article  CAS  PubMed  Google Scholar 

  12. Deng H, et al. Identification of a major co-receptor for primary isolates of HIV-1. Nature. 1996;381(6584):661–6.

    Article  CAS  PubMed  Google Scholar 

  13. Samson M, et al. Resistance to HIV-1 infection in Caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature. 1996;382(6593):722–5.

    Article  CAS  PubMed  Google Scholar 

  14. Novembre J, Galvani AP, Slatkin M. The geographic spread of the CCR5 Delta32 HIV-resistance allele. PLoS Biol. 2005;3(11), e339.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  15. Dean M, et al. Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study. Science. 1996;273(5283):1856–62.

    Article  CAS  PubMed  Google Scholar 

  16. Wood A, Armour D. The discovery of the CCR5 receptor antagonist, UK-427,857, a new agent for the treatment of HIV infection and AIDS. Prog Med Chem. 2005;43: 239–71.

    Article  CAS  PubMed  Google Scholar 

  17. Allers K, et al. Evidence for the cure of HIV infection by CCR5Delta32/Delta32 stem cell transplantation. Blood. 2011;117(10):2791–9.

    Article  CAS  PubMed  Google Scholar 

  18. Yukl SA, et al. Challenges in detecting HIV persistence during potentially curative interventions: a study of the Berlin patient. PLoS Pathog. 2013;9(5), e1003347.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Hutter G, et al. Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation. N Engl J Med. 2009;360(7):692–8.

    Article  PubMed  Google Scholar 

  20. Hutter G, Zaia JA. Allogeneic haematopoietic stem cell transplantation in patients with human immunodeficiency virus: the experiences of more than 25 years. Clin Exp Immunol. 2011;163(3):284–95.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Hayden EC. Hopes of HIV cure in ‘Boston patients’ dashed. Nature News 2013.

    Google Scholar 

  22. Ringpis GE, et al. Engineering HIV-1-resistant T-cells from short-hairpin RNA-expressing hematopoietic stem/progenitor cells in humanized BLT mice. PLoS One. 2012;7(12), e53492.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Lee MT, et al. Inhibition of human immunodeficiency virus type 1 replication in primary macrophages by using Tat- or CCR5-specific small interfering RNAs expressed from a lentivirus vector. J Virol. 2003;77(22):11964–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. ter Brake O, et al. Lentiviral vector design for multiple shRNA expression and durable HIV-1 inhibition. Mol Ther. 2008;16(3):557–64.

    Article  PubMed  CAS  Google Scholar 

  25. Qin XF, et al. Inhibiting HIV-1 infection in human T cells by lentiviral-mediated delivery of small interfering RNA against CCR5. Proc Natl Acad Sci U S A. 2003;100(1):183–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. An DS, et al. Optimization and functional effects of stable short hairpin RNA expression in primary human lymphocytes via lentiviral vectors. Mol Ther. 2006;14(4):494–504.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Li MJ, et al. Inhibition of HIV-1 infection by lentiviral vectors expressing Pol III-promoted anti-HIV RNAs. Mol Ther. 2003;8(2):196–206.

    Article  CAS  PubMed  Google Scholar 

  28. Wu C, Dunbar CE. Stem cell gene therapy: the risks of insertional mutagenesis and approaches to minimize genotoxicity. Front Med. 2011;5(4):356–71.

    Article  PubMed  PubMed Central  Google Scholar 

  29. Didigu CA, et al. Simultaneous zinc-finger nuclease editing of the HIV coreceptors ccr5 and cxcr4 protects CD4+ T cells from HIV-1 infection. Blood. 2014;123(1):61–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Maier DA, et al. Efficient clinical scale gene modification via zinc finger nuclease-targeted disruption of the HIV co-receptor CCR5. Hum Gene Ther. 2013;24(3):245–58.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Perez EE, et al. Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases. Nat Biotechnol. 2008;26(7):808–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Lei Y, et al. Gene editing of human embryonic stem cells via an engineered baculoviral vector carrying zinc-finger nucleases. Mol Ther. 2011;19(5):942–50.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Li L, et al. Genomic editing of the HIV-1 coreceptor CCR5 in adult hematopoietic stem and progenitor cells using zinc finger nucleases. Mol Ther. 2013;21(6):1259–69.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Gaj T, et al. Targeted gene knockout by direct delivery of zinc-finger nuclease proteins. Nat Methods. 2012;9(8):805–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Holt N, et al. Human hematopoietic stem/progenitor cells modified by zinc-finger nucleases targeted to CCR5 control HIV-1 in vivo. Nat Biotechnol. 2010;28(8):839–47.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Kalos M, June CH. Adoptive T cell transfer for cancer immunotherapy in the era of synthetic biology. Immunity. 2013;39(1):49–60.

    Article  CAS  PubMed  Google Scholar 

  37. Scholler J, et al. Decade-long safety and function of retroviral-modified chimeric antigen receptor T cells. Sci Transl Med. 2012;4(132):132ra53.

    Article  PubMed  PubMed Central  Google Scholar 

  38. Mani M, et al. Design, engineering, and characterization of zinc finger nucleases. Biochem Biophys Res Commun. 2005;335(2):447–57.

    Article  CAS  PubMed  Google Scholar 

  39. Yi G, et al. CCR5 gene editing of resting CD4(+) T cells by transient ZFN expression from HIV envelope pseudotyped nonintegrating lentivirus confers HIV-1 resistance in humanized mice. Mol Ther Nucleic Acids. 2014;3, e198.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Shayakhmetov DM, et al. Efficient gene transfer into human CD34(+) cells by a retargeted adenovirus vector. J Virol. 2000;74(6):2567–83.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Chun TW, et al. Relationship between pre-existing viral reservoirs and the re-emergence of plasma viremia after discontinuation of highly active anti-retroviral therapy. Nat Med. 2000;6(7):757–61.

    Article  CAS  PubMed  Google Scholar 

  42. Hofer U, et al. Pre-clinical modeling of CCR5 knockout in human hematopoietic stem cells by zinc finger nucleases using humanized mice. J Infect Dis. 2013;208 Suppl 2:S160–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Lepus CM, et al. Comparison of human fetal liver, umbilical cord blood, and adult blood hematopoietic stem cell engraftment in NOD-scid/gammac−/−, Balb/c-Rag1−/−gammac−/−, and C.B-17-scid/bg immunodeficient mice. Hum Immunol. 2009;70(10):790–802.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Lapid K, et al. Egress and mobilization of hematopoietic stem and progenitor cells: a dynamic multi-facet process. Cambridge: Harvard Stem Cell Institute; 2008. StemBook [Internet].

    Google Scholar 

  45. Cannon PM, et al. Electroporation of ZFN mRNA enables efficient CCR5 gene disruption in mobilized blood hematopoietic stem cells at clinical scale. Mol Ther. 2013;21:S71–2.

    Google Scholar 

  46. Miller JC, et al. A TALE nuclease architecture for efficient genome editing. Nat Biotechnol. 2011;29(2):143–8.

    Article  CAS  PubMed  Google Scholar 

  47. Llewellyn N, et al. Next generation TALENs mediate efficient disruption of the CCR5 gene in human HSCs. Mol Ther. 2013;21:S72.

    Google Scholar 

  48. Mussolino C, et al. A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity. Nucleic Acids Res. 2011;39(21):9283–93.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Mussolino C, et al. TALENs facilitate targeted genome editing in human cells with high specificity and low cytotoxicity. Nucleic Acids Res. 2014;42(10):6762–73.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Mock U, et al. mRNA transfection of a novel TAL effector nuclease (TALEN) facilitates efficient knockout of HIV co-receptor CCR5. Nucleic Acids Res. 2015;43(11):5560–71.

    Article  PubMed  PubMed Central  Google Scholar 

  51. Kim Y, Kweon J, Kim JS. TALENs and ZFNs are associated with different mutation signatures. Nat Methods. 2013;10(3):185.

    Article  CAS  PubMed  Google Scholar 

  52. Certo MT, et al. Coupling endonucleases with DNA end-processing enzymes to drive gene disruption. Nat Methods. 2012;9(10):973–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Cho SW, et al. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res. 2014;24(1):132–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Cradick TJ, et al. CRISPR/Cas9 systems targeting beta-globin and CCR5 genes have substantial off-target activity. Nucleic Acids Res. 2013;41(20):9584–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Mandal PK, et al. Efficient ablation of genes in human hematopoietic stem and effector cells using CRISPR/Cas9. Cell Stem Cell. 2014;15(5):643–52.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Li C, et al. Inhibition of HIV-1 infection of primary CD4+ T cells by gene editing of CCR5 using adenovirus-delivered CRISPR/Cas9. J Gen Virol. 2015;96(8):2381–93.

    Article  CAS  PubMed  Google Scholar 

  57. Wang W, et al. CCR5 gene disruption via lentiviral vectors expressing Cas9 and single guided RNA renders cells resistant to HIV-1 infection. PLoS One. 2014;9(12), e115987.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  58. Wilen CB, et al. Engineering HIV-resistant human CD4+ T cells with CXCR4-specific zinc-finger nucleases. PLoS Pathog. 2011;7(4), e1002020.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Yuan J, et al. Zinc-finger nuclease editing of human cxcr4 promotes HIV-1 CD4(+) T cell resistance and enrichment. Mol Ther. 2012;20(4):849–59.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. http://aidsinfo.nih.gov/guidelines/html/1/adult-and-adolescent-arv-guidelines/8/co-receptor-tropism-assays. Guidelines for the use of antiretroviral agents in HIV-1-infected adults and adolescents. 2013.

  61. Meyer L, et al. Early protective effect of CCR-5 delta 32 heterozygosity on HIV-1 disease progression: relationship with viral load. The SEROCO Study Group. AIDS. 1997;11(11):F73–8.

    Article  CAS  PubMed  Google Scholar 

  62. de Roda Husman AM, et al. Association between CCR5 genotype and the clinical course of HIV-1 infection. Ann Intern Med. 1997;127(10):882–90.

    Article  PubMed  Google Scholar 

  63. Meyer L, et al. CCR5 delta32 deletion and reduced risk of toxoplasmosis in persons infected with human immunodeficiency virus type 1. The SEROCO-HEMOCO-SEROGEST Study Groups. J Infect Dis. 1999;180(3):920–4.

    Article  CAS  PubMed  Google Scholar 

  64. Ioannidis JP, et al. Effects of CCR5-Delta, 32, CCR2–64I, and SDF-1 3′A alleles on HIV-1 disease progression: an international meta-analysis of individual-patient data. Ann Intern Med. 2001;135(9):782–95.

    Article  CAS  PubMed  Google Scholar 

  65. Bevec D, et al. Inhibition of human immunodeficiency virus type 1 replication in human T cells by retroviral-mediated gene transfer of a dominant-negative Rev trans-activator. Proc Natl Acad Sci U S A. 1992;89(20):9870–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Bonyhadi ML, et al. RevM10-expressing T cells derived in vivo from transduced human hematopoietic stem-progenitor cells inhibit human immunodeficiency virus replication. J Virol. 1997;71(6):4707–16.

    CAS  PubMed  PubMed Central  Google Scholar 

  67. Stremlau M, et al. The cytoplasmic body component TRIM5alpha restricts HIV-1 infection in Old World monkeys. Nature. 2004;427(6977):848–53.

    Article  CAS  PubMed  Google Scholar 

  68. Sawyer SL, et al. Positive selection of primate TRIM5alpha identifies a critical species-specific retroviral restriction domain. Proc Natl Acad Sci U S A. 2005;102(8):2832–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Anderson J, Akkina R. Human immunodeficiency virus type 1 restriction by human-rhesus chimeric tripartite motif 5alpha (TRIM 5alpha) in CD34(+) cell-derived macrophages in vitro and in T cells in vivo in severe combined immunodeficient (SCID-hu) mice transplanted with human fetal tissue. Hum Gene Ther. 2008;19(3):217–28.

    Article  CAS  PubMed  Google Scholar 

  70. Schrofelbauer B, Chen D, Landau NR. A single amino acid of APOBEC3G controls its species-specific interaction with virion infectivity factor (Vif). Proc Natl Acad Sci U S A. 2004;101(11):3927–32.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  71. Xu H, et al. A single amino acid substitution in human APOBEC3G antiretroviral enzyme confers resistance to HIV-1 virion infectivity factor-induced depletion. Proc Natl Acad Sci U S A. 2004;101(15):5652–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Anderson J, et al. Safety and efficacy of a lentiviral vector containing three anti-HIV genes--CCR5 ribozyme, tat-rev siRNA, and TAR decoy--in SCID-hu mouse-derived T cells. Mol Ther. 2007;15(6):1182–8.

    CAS  PubMed  Google Scholar 

  73. Kumar P, et al. T cell-specific siRNA delivery suppresses HIV-1 infection in humanized mice. Cell. 2008;134(4):577–86.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. ter Brake O, et al. Evaluation of safety and efficacy of RNAi against HIV-1 in the human immune system (Rag-2(−/−)gammac(−/−)) mouse model. Gene Ther. 2009;16(1):148–53.

    Article  PubMed  CAS  Google Scholar 

  75. Novina CD, et al. siRNA-directed inhibition of HIV-1 infection. Nat Med. 2002;8(7):681–6.

    CAS  PubMed  Google Scholar 

  76. Kohn DB, et al. A clinical trial of retroviral-mediated transfer of a rev-responsive element decoy gene into CD34(+) cells from the bone marrow of human immunodeficiency virus-1-infected children. Blood. 1999;94(1):368–71.

    CAS  PubMed  Google Scholar 

  77. Humeau LM, et al. Efficient lentiviral vector-mediated control of HIV-1 replication in CD4 lymphocytes from diverse HIV+ infected patients grouped according to CD4 count and viral load. Mol Ther. 2004;9(6):902–13.

    Article  CAS  PubMed  Google Scholar 

  78. Michienzi A, et al. A nucleolar TAR decoy inhibitor of HIV-1 replication. Proc Natl Acad Sci U S A. 2002;99(22):14047–52.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Zahn RC, et al. Efficient entry inhibition of human and nonhuman primate immunodeficiency virus by cell surface-expressed gp41-derived peptides. Gene Ther. 2008;15(17):1210–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Voit RA, et al. Generation of an HIV resistant T-cell line by targeted “stacking” of restriction factors. Mol Ther. 2013;21(4):786–95.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Lombardo A, et al. Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery. Nat Biotechnol. 2007;25(11):1298–306.

    Article  CAS  PubMed  Google Scholar 

  82. Lombardo A, et al. Site-specific integration and tailoring of cassette design for sustainable gene transfer. Nat Methods. 2011;8(10):861–9.

    Article  CAS  PubMed  Google Scholar 

  83. Genovese P, et al. Targeted genome editing in human repopulating haematopoietic stem cells. Nature. 2014;510(7504):235–40.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Hoban MD, et al. Correction of the sickle cell disease mutation in human hematopoietic stem/progenitor cells. Blood. 2015;125(17):2597–604.

    Article  CAS  PubMed  Google Scholar 

  85. Wang J, Exline CM, et al. Highly efficient homology-driven genome editing in CD34+ hematopoietic stem/progenitor cells by combining zinc finger nuclease mRNA and AAV donor delivery. Nat Biotechnol. 2015;33(12):1256–1263.

    Google Scholar 

  86. Chu VT, et al. Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat Biotechnol. 2015;33(5):543–8.

    Article  CAS  PubMed  Google Scholar 

  87. Maruyama T, et al. Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat Biotechnol. 2015;33(5):538–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Ye L, et al. Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5Delta32 mutation confers resistance to HIV infection. Proc Natl Acad Sci U S A. 2014;111(26):9591–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Yao Y, et al. Generation of CD34+ cells from CCR5-disrupted human embryonic and induced pluripotent stem cells. Hum Gene Ther. 2012;23(2):238–42.

    Article  CAS  PubMed  Google Scholar 

  90. Chomont N, et al. HIV reservoir size and persistence are driven by T cell survival and homeostatic proliferation. Nat Med. 2009;15(8):893–900.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Chun TW, et al. Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection. Nature. 1997;387(6629):183–8.

    Article  CAS  PubMed  Google Scholar 

  92. Finzi D, et al. Latent infection of CD4+ T cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective combination therapy. Nat Med. 1999;5(5):512–7.

    Article  CAS  PubMed  Google Scholar 

  93. Sarkar I, et al. HIV-1 proviral DNA excision using an evolved recombinase. Science. 2007;316(5833):1912–5.

    Article  CAS  PubMed  Google Scholar 

  94. Qu X, et al. Zinc-finger-nucleases mediate specific and efficient excision of HIV-1 proviral DNA from infected and latently infected human T cells. Nucleic Acids Res. 2013;41(16):7771–82.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Hauber I, et al. Highly significant antiviral activity of HIV-1 LTR-specific tre-recombinase in humanized mice. PLoS Pathog. 2013;9(9), e1003587.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Ebina H, et al. Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus. Sci Rep. 2013;3:2510.

    Article  PubMed  PubMed Central  Google Scholar 

  97. Blackard JT, et al. Transmission of human immunodeficiency type 1 viruses with intersubtype recombinant long terminal repeat sequences. Virology. 1999;254(2):220–5.

    Article  CAS  PubMed  Google Scholar 

  98. Surendranath V, et al. SeLOX—a locus of recombination site search tool for the detection and directed evolution of site-specific recombination systems. Nucleic Acids Res. 2010;38(Web Server issue):W293–8.

    Google Scholar 

  99. Karpinski J, et al. Universal Tre (uTre) recombinase specifically targets the majority of HIV-1 isolates. J Int AIDS Soc. 2014;17(4 Suppl 3):19706.

    PubMed  PubMed Central  Google Scholar 

  100. Ebina H, et al. A high excision potential of TALENs for integrated DNA of HIV-based lentiviral vector. PLoS One. 2015;10(3), e0120047.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  101. Cong L, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339(6121):819–23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Zhu W, et al. The CRISPR/Cas9 system inactivates latent HIV-1 proviral DNA. Retrovirology. 2015;12:22.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  103. Liao HK, et al. Use of the CRISPR/Cas9 system as an intracellular defense against HIV-1 infection in human cells. Nat Commun. 2015;6.

    Google Scholar 

  104. Hu W, et al. RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection. Proc Natl Acad Sci U S A. 2014;111(31):11461–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Li H, et al. In vivo genome editing restores haemostasis in a mouse model of haemophilia. Nature. 2011;475(7355):217–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Joglekar AV, et al. Integrase-defective lentiviral vectors as a delivery platform for targeted modification of adenosine deaminase locus. Mol Ther. 2013;21(9):1705–17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Holkers M, et al. Differential integrity of TALE nuclease genes following adenoviral and lentiviral vector gene transfer into human cells. Nucleic Acids Res. 2013;41(5), e63.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Chen Z, et al. Receptor-mediated delivery of engineered nucleases for genome modification. Nucleic Acids Res. 2013;41(19), e182.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Mock U, et al. Novel lentiviral vectors with mutated reverse transcriptase for mRNA delivery of TALE nucleases. Sci Rep. 2014;4:6409.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Khatri N, et al. In vivo delivery aspects of miRNA, shRNA and siRNA. Crit Rev Ther Drug Carrier Syst. 2012;29(6):487–527.

    Article  CAS  PubMed  Google Scholar 

  111. Morizono K, et al. Lentiviral vector retargeting to P-glycoprotein on metastatic melanoma through intravenous injection. Nat Med. 2005;11(3):346–52.

    Article  CAS  PubMed  Google Scholar 

  112. Lin AH, et al. Receptor-specific targeting mediated by the coexpression of a targeted murine leukemia virus envelope protein and a binding-defective influenza hemagglutinin protein. Hum Gene Ther. 2001;12(4):323–32.

    Article  CAS  PubMed  Google Scholar 

  113. Frecha C, et al. A novel lentiviral vector targets gene transfer into human hematopoietic stem cells in marrow from patients with bone marrow failure syndrome and in vivo in humanized mice. Blood. 2012;119(5):1139–50.

    Article  CAS  PubMed  Google Scholar 

  114. Anliker B, et al. Specific gene transfer to neurons, endothelial cells and hematopoietic progenitors with lentiviral vectors. Nat Methods. 2010;7(11):929–35.

    Article  CAS  PubMed  Google Scholar 

  115. Paraskevakou G, et al. Epidermal growth factor receptor (EGFR)-retargeted measles virus strains effectively target EGFR- or EGFRvIII expressing gliomas. Mol Ther. 2007;15(4):677–86.

    CAS  PubMed  Google Scholar 

  116. Kneissl S, et al. Measles virus glycoprotein-based lentiviral targeting vectors that avoid neutralizing antibodies. PLoS One. 2012;7(10), e46667.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Kneissl S, et al. CD19 and CD20 targeted vectors induce minimal activation of resting B lymphocytes. PLoS One. 2013;8(11), e79047.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Alwin S, et al. Custom zinc-finger nucleases for use in human cells. Mol Ther. 2005;12(4):610–7.

    Article  CAS  PubMed  Google Scholar 

  119. Kim HJ, et al. Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly. Genome Res. 2009;19(7):1279–88.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Koo T, Lee J, Kim JS. Measuring and reducing off-target activities of programmable nucleases including CRISPR-Cas9. Mol Cells. 2015;38(6):475–81.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Hendel A, et al. Quantifying on- and off-target genome editing. Trends Biotechnol. 2015;33(2):132–40.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Pattanayak V, et al. Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Nat Methods. 2011;8(9):765–70.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Gabriel R, et al. An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat Biotechnol. 2011;29(9):816–23.

    Article  CAS  PubMed  Google Scholar 

  124. Chiarle R, et al. Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells. Cell. 2011;147(1):107–19.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Frock RL, et al. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat Biotechnol. 2015;33(2):179–86.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Tsai SQ, et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol. 2015;33(2):187–97.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Crosetto N, et al. Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nat Methods. 2013;10(4):361–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Ran FA, et al. In vivo genome editing using Staphylococcus aureus Cas9. Nature. 2015;520(7546):186–98.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Kim D, et al. Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nat Methods. 2015;12(3):237–43, 1 p following 243.

    Article  CAS  PubMed  Google Scholar 

  130. Doyon Y, et al. Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures. Nat Methods. 2011;8(1):74–9.

    Article  CAS  PubMed  Google Scholar 

  131. Tsai SQ, et al. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat Biotechnol. 2014;32(6):569–76.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We gratefully acknowledge the expertise of our collaborators at Sangamo BioSciences, including Michael Holmes, Jianbin Wang and Philip Gregory, and thank Liz Wolffe for her help compiling Table 1. This work was supported by the James B. Pendleton Charitable Trust, NIH grants HL073104, AI110149 and HL129902, and the California HIV/AIDS Research Program grant ID12-USC-245.

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Correspondence to Paula M. Cannon Ph.D. .

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© 2016 American Society of Gene and Cell Therapy

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Llewellyn, G.N., Exline, C.M., Holt, N., Cannon, P.M. (2016). Using Engineered Nucleases to Create HIV-Resistant Cells. In: Cathomen, T., Hirsch, M., Porteus, M. (eds) Genome Editing. Advances in Experimental Medicine and Biology(). Springer, New York, NY. https://doi.org/10.1007/978-1-4939-3509-3_10

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