Genome editing-based HIV therapies

Trends in Biotechnology

Volumn 33, Issue 3, 2015, Pages 172-179

  Gu, Wan Gang ^a  

^a ZUNYI MEDICAL UNIVERSITY   (China)

Author keywords

AIDS; CCR5; Genome editing; HIV; Infusion

Indexed keywords

DRUG INFUSION; PATIENT TREATMENT;

AIDS; CCR5; CLINICAL TRIAL; HIV INFECTION; HIV THERAPY; LONG-TERM EVALUATION; POTENTIAL TARGETS; RESISTANT CELLS;

GENE THERAPY;

CD4 ANTIGEN; VIRUS DNA;

CCR5 GENE; CD4+ T LYMPHOCYTE; CXCR4 GENE; GENETIC ENGINEERING; GENOME EDITING; GENOTYPE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; NONHUMAN; PATIENT SAFETY; PRIORITY JOURNAL; PROVIRUS; RECEPTOR GENE; REVIEW; VIRUS RESISTANCE; ADVERSE EFFECTS; BIOLOGICAL THERAPY; GENE THERAPY; HIV INFECTIONS; PROCEDURES;

BIOLOGICAL THERAPY; GENETIC THERAPY; HIV INFECTIONS; HUMANS;

EID: 84924578713     PISSN: 01677799     EISSN: 18793096     Source Type: Journal    
DOI: 10.1016/j.tibtech.2014.12.006     Document Type: Review

References (82)

1. Centers for Disease Control and Prevention HIV surveillance - United States, 1981-2008. MMWR Morb. Mortal. Wkly. Rep. 2011, 60:689-693.
2. Gu W.G., et al. Anti-HIV drug development through computational methods. AAPS J. 2014, 16:674-680.
3. Gilden D. When HAART is not enough. GMHC Treat. Issues 1996, 10:1-6.
4. Hutter G., et al. Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation. N. Engl. J. Med. 2009, 360:692-698.
5. Allers K., et al. Evidence for the cure of HIV infection by CCR5Delta32/Delta32 stem cell transplantation. Blood 2010, 117:2791-2799.
6. Burke B.P., et al. CCR5 as a natural and modulated target for inhibition of HIV. Viruses 2014, 6:54-68.
7. Wyman C., Kanaar R. DNA double-strand break repair: all's well that ends well. Annu. Rev. Genet. 2006, 40:363-383.
8. Osborn M.J., et al. TALEN-based gene correction for epidermolysis bullosa. Mol. Ther. 2013, 21:1151-1159.
9. Li T., Yang B. TAL effector nuclease (TALEN) engineering. Methods Mol. Biol. 2013, 978:63-72.
10. Bedell V.M., et al. In vivo genome editing using a high-efficiency TALEN system. Nature 2012, 491:114-118.
11. Berdien B., et al. TALEN-mediated editing of endogenous T-cell receptors facilitates efficient reprogramming of T lymphocytes by lentiviral gene transfer. Gene Ther. 2014, 21:539-548.
12. Ding Q., et al. A TALEN genome-editing system for generating human stem cell-based disease models. Cell Stem Cell 2014, 12:238-251.
13. Katsuyama T., et al. An efficient strategy for TALEN-mediated genome engineering in Drosophila. Nucleic Acids Res. 2013, 41:e163.
14. Heigwer F., et al. E-TALEN: a web tool to design TALENs for genome engineering. Nucleic Acids Res. 2013, 41:e190.
15. Anguela X.M., et al. Robust ZFN-mediated genome editing in adult hemophilic mice. Blood 2013, 122:3283-3287.
16. Gupta A., et al. An optimized two-finger archive for ZFN-mediated gene targeting. Nat. Methods 2012, 9:588-590.
17. Mattis A.N., Willenbring H. A ZFN/piggyBac step closer to autologous liver cell therapy. Hepatology 2012, 55:2033-2035.
18. Manjunath N., et al. Newer gene editing technologies toward HIV gene therapy. Viruses 2013, 5:2748-2766.
19. Gaj T., et al. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 2013, 31:397-405.
20. 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:e63.
21. Montague T.G., et al. CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res. 2014, 42:W401-W407.
22. Shao Y., et al. CRISPR/Cas-mediated genome editing in the rat via direct injection of one-cell embryos. Nat. Protoc. 2014, 9:2493-2512.
23. Gilbert L.A., et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 2014, 159:647-661.
24. Owens B. Zinc-finger nucleases make the cut in HIV. Nat. Rev. Drug Discov. 2014, 13:321-322.
25. Rossetti M., et al. HIV-derived vectors for gene therapy targeting dendritic cells. Adv. Exp. Med. Biol. 2012, 762:239-261.
26. Merkert S., et al. Efficient ZFN-based gene inactivation in transgenic human iPS cells as a model for gene editing in patient-specific cells. J. Stem Cells Regen. Med. 2010, 6:118.
27. van Lunzen J., et al. Transfer of autologous gene-modified T cells in HIV-infected patients with advanced immunodeficiency and drug-resistant virus. Mol. Ther. 2007, 15:1024-1033.
28. Voit R.A., et al. Generation of an HIV resistant T-cell line by targeted 'stacking' of restriction factors. Mol. Ther. 2013, 21:786-795.
29. Kiem H.P., et al. Hematopoietic-stem-cell-based gene therapy for HIV disease. Cell Stem Cell 2012, 10:137-147.
30. Chan E., et al. Gene therapy strategies to exploit TRIM derived restriction factors against HIV-1. Viruses 2014, 6:243-263.
31. + T cells in human immunodeficiency virus-infected subjects. Blood 2000, 96:785-793.
32. Walker R.E., et al. Long-term in vivo survival of receptor-modified syngeneic T cells in patients with human immunodeficiency virus infection. Blood 2000, 96:467-474.
33. Deeks S.G., et al. A phase II randomized study of HIV-specific T-cell gene therapy in subjects with undetectable plasma viremia on combination antiretroviral therapy. Mol. Ther. 2002, 5:788-797.
34. Zhang J., et al. Why CCR5 is chosen as the target for stem cell gene therapy for HIV infection?. J. Nanosci. Nanotechnol. 2012, 12:2045-2048.
35. Nkenfou C.N., et al. Distribution of CCR5-Delta32, CCR5 promoter 59029 A/G, CCR2-64I and SDF1-3'A genetic polymorphisms in HIV-1 infected and uninfected patients in the west region of Cameroon. BMC Res. Notes 2013, 6:288.
36. + T cells by genome editing using zinc-finger nucleases. Nat. Biotechnol. 2008, 26:808-816.
37. Wang J., et al. Targeted gene addition to a predetermined site in the human genome using a ZFN-based nicking enzyme. Genome Res. 2014, 22:1316-1326.
38. + cells from CCR5-disrupted human embryonic and induced pluripotent stem cells. Hum. Gene Ther. 2011, 23:238-242.
39. 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, 28:839-847.
40. 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, 21:1259-1269.
41. Badia R., et al. Gene editing using a zinc-finger nuclease mimicking the CCR5Delta32 mutation induces resistance to CCR5-using HIV-1. J. Antimicrob. Chemother. 2014, 69:1755-1759.
42. Tebas P., et al. Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV. N. Engl. J. Med. 2014, 370:901-910.
43. ClinicalTrials.gov (2014) Phase 1 dose escalation study of autologous T-cells genetically modified at the CCR5 gene by zinc finger nucleases in HIV-infected patients. Published online June 4, 2014. http://clinicaltrials.gov/ct2/show/NCT01044654/.
44. ClinicalTrials.gov (2014) Dose escalation study of cyclophosphamide in HIV-infected subjects on HAART receiving SB-728-T. Published online August 22, 2014. http://clinicaltrials.gov/ct2/show/NCT01543152.
45. California Stem Cell Agency (2013) Zinc finger nuclease-based stem cell therapy for AIDS. http://www.cirm.ca.gov/our-progress/awards/ziinc-finger-nuclease-based-stem-cell-therapy-aids.
46. Mussolino C., et al. A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity. Nucleic Acids Res. 2011, 39:9283-9293.
47. Cho S.W., et al. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat. Biotechnol. 2013, 31:230-232.
48. 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, 111:9591-9596.
49. + T cells with CXCR4-specific zinc-finger nucleases. PLoS Pathog. 2011, 7:e1002020.
50. + T cell resistance and enrichment. Mol. Ther. 2012, 20:849-859.
51. Wayengera M. Proviral HIV-genome-wide and pol-gene specific zinc finger nucleases: usability for targeted HIV gene therapy. Theor. Biol. Med. Model. 2011, 8:26.
52. Das K.T.S., Segal D. Engineered zinc finger nucleases to inactivate the HIV genome. Proceedings of the 19th HIV International Conference 2014, http://pag.aids2012.org/Abstracts.aspx?AID=5906.
53. 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, 41:7771-7782.
54. Ebina H., et al. Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus. Sci. Rep. 2013, 3:2510.
55. 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, 111:11461-11466.
56. Tanaka A., et al. A novel therapeutic molecule against HTLV-1 infection targeting provirus. Leukemia 2013, 27:1621-1627.
57. Wayengera M. Identity of zinc finger nucleases with specificity to herpes simplex virus type II genomic DNA: novel HSV-2 vaccine/therapy precursors. Theor. Biol. Med. Model. 2011, 8:23.
58. Cradick T.J., et al. Zinc-finger nucleases as a novel therapeutic strategy for targeting hepatitis B virus DNAs. Mol. Ther. 2010, 18:947-954.
59. Demeulemeester J., et al. LEDGINs, non-catalytic site inhibitors of HIV-1 integrase: a patent review (2006-2014). Expert Opin. Ther. Pat. 2014, 24:609-632.
60. Christ F., Debyser Z. The LEDGF/p75 integrase interaction, a novel target for anti-HIV therapy. Virology 2012, 435:102-109.
61. Fadel H.J., et al. TALEN knockout of the PSIP1 gene in human cells: analyses of HIV-1 replication and allosteric integrase inhibitor mechanism. J. Virol. 2014, 88:9704-9717.
62. Zhou T., et al. The mitochondrial translocator protein, TSPO, inhibits HIV-1 envelope glycoprotein biosynthesis via the endoplasmic reticulum-associated protein degradation pathway. J. Virol. 2014, 88:3474-3484.
63. Didigu C., Doms R. Gene therapy targeting HIV entry. Viruses 2014, 6:1395-1409.
64. Trounson A., et al. Clinical trials for stem cell therapies. BMC Med. 2011, 9:52.
65. Lutz S.E., et al. Stem cell-based therapies for multiple sclerosis: recent advances in animal models and human clinical trials. Regen. Med. 2014, 9:129-132.
66. Gabriel R., et al. An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat. Biotechnol. 2011, 29:816-823.
67. Pattanayak V., et al. Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Nat. Methods 2011, 8:765-770.
68. Veres A., et al. Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. Cell Stem Cell 2014, 15:27-30.
69. Hruscha A., et al. Efficient CRISPR/Cas9 genome editing with low off-target effects in zebrafish. Development 2013, 140:4982-4987.
70. Cradick T.J., et al. ZFN-site searches genomes for zinc finger nuclease target sites and off-target sites. BMC Bioinformatics 2011, 12:152.
71. Lin Y., et al. CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Res. 2014, 42:7473-7485.
72. Shen B., et al. Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects. Nat. Methods 2014, 11:399-402.
73. Grau J., et al. TALENoffer: genome-wide TALEN off-target prediction. Bioinformatics 2013, 29:2931-2932.
74. Xiao A., et al. CasOT: a genome-wide Cas9/gRNA off-target searching tool. Bioinformatics 2014, Published online January 21, 2014. http://dx.doi.org/10.1093/bioinformatics/btt764.
75. Pattanayak V., et al. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat. Biotechnol. 2013, 31:839-843.
76. Loftin L.M., et al. R5X4 HIV-1 coreceptor use in primary target cells: implications for coreceptor entry blocking strategies. J. Transl. Med. 2011, 9(Suppl. 1):S3.
77. Naif H.M. Pathogenesis of HIV Infection. Infect. Dis. Rep. 2014, 5:e6.
78. Sundquist W.I., Krausslich H.G. HIV-1 assembly, budding, and maturation. Cold Spring Harb. Perspect. Med. 2012, 2:a006924.
79. Kassler K., Sticht H. Molecular mechanism of HIV-1 gp120 mutations that reduce CD4 binding affinity. J. Biomol. Struct. Dyn. 2013, 32:52-64.
80. Di Primio C., et al. Single-cell imaging of HIV-1 provirus (SCIP). Proc. Natl. Acad. Sci. U.S.A. 2013, 110:5636-5641.
81. Maiuri P., et al. Real-time imaging of the HIV-1 transcription cycle in single living cells. Methods 2010, 53:62-67.
82. Hadi K., et al. A mutagenesis approach for the study of the structure-function relationship of human immunodeficiency virus type 1 (HIV-1) Vpr. Genetic Manipulation of DNA and Protein - Examples from Current Research 2013, InTech, Chapter 10. http://dx.doi.org/10.5772/45824, D. Figurski (Ed.).