The therapeutic application of CRISPR/Cas9 technologies for HIV

Bibliography

• Palella FJJr, Delaney KM, Moorman AC, et al. Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection. HIV Outpatient Study Investigators. N Engl J Med 1998;338(13):853-60
   PubMed Web of Science ®Google Scholar
• DiGiusto DL, Krishnan A, Li L, et al. RNA-based gene therapy for HIV with lentiviral vector-modified CD34(+) cells in patients undergoing transplantation for AIDS-related lymphoma. Sci Transl Med 2010;2(36):36ra43
   PubMed Web of Science ®Google Scholar
• Chung J, Scherer LJ, Gu A, et al. Optimized lentiviral vectors for HIV gene therapy: multiplexed expression of small RNAs and inclusion of MGMT(P140K) drug resistance gene. Mol Ther 2014;22(5):952-63
   PubMed Web of Science ®Google Scholar
• Gaj T, Gersbach CA, Barbas CFIII. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 2013;31(7):397-405
   PubMed Web of Science ®Google Scholar
• Cai M, Yang Y. Targeted genome editing tools for disease modeling and gene therapy. Curr Gene Ther 2014;14(1):2-9
   PubMed Web of Science ®Google Scholar
• Mojica FJ, Diez-Villasenor C, Garcia-Martinez J, Almendros C. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 2009;155(Pt 3):733-40
   PubMed Web of Science ®Google Scholar
• Mojica FJ, Diez-Villasenor C, Garcia-Martinez J, Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 2005;60(2):174-82
   PubMed Web of Science ®Google Scholar
• Jinek M, Chylinski K, Fonfara I, et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012;337(6096):816-21
   PubMed Web of Science ®Google Scholar
• Cong L, Ran FA, Cox D, et al. Multiplex genome engineering using CRISPR/Cas systems. Science 2013;339(6121):819-23
   PubMed Web of Science ®Google Scholar
• Jinek M, East A, Cheng A, et al. RNA-programmed genome editing in human cells. Elife 2013;2:e00471
   PubMed Web of Science ®Google Scholar
• Mali P, Yang L, Esvelt KM, et al. RNA-guided human genome engineering via Cas9. Science 2013;339(6121):823-6
   PubMed Web of Science ®Google Scholar
• Gilbert LA, Larson MH, Morsut L, et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 2013;154(2):442-51
   PubMed Web of Science ®Google Scholar
• Qi LS, Larson MH, Gilbert LA, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 2013;152(5):1173-83
   PubMed Web of Science ®Google Scholar
• Maeder ML, Linder SJ, Cascio VM, et al. CRISPR RNA-guided activation of endogenous human genes. Nat Methods 2013;10(10):977-9
   PubMed Web of Science ®Google Scholar
• Perez-Pinera P, Kocak DD, Vockley CM, et al. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods 2013;10(10):973-6
   PubMed Web of Science ®Google Scholar
• Cheng AW, Wang H, Yang H, et al. Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Res 2013;23(10):1163-71
   PubMed Web of Science ®Google Scholar
• Hu J, Lei Y, Wong WK, et al. Direct activation of human and mouse Oct4 genes using engineered TALE and Cas9 transcription factors. Nucleic Acids Res 2014;42(7):4375-90
   PubMed Web of Science ®Google Scholar
• Siliciano JD, Kajdas J, Finzi D, et al. Long-term follow-up studies confirm the stability of the latent reservoir for HIV-1 in resting CD4+ T cells. Nat Med 2003;9(6):727-8
   PubMed Web of Science ®Google Scholar
• Sarkar I, Hauber I, Hauber J, Buchholz F. HIV-1 proviral DNA excision using an evolved recombinase. Science 2007;316(5833):1912-15
   PubMed Web of Science ®Google Scholar
• Buchholz F, Hauber J. In vitro evolution and analysis of HIV-1 LTR-specific recombinases. Methods 2011;53(1):102-9
   PubMed Web of Science ®Google Scholar
• Mariyanna L, Priyadarshini P, Hofmann-Sieber H, et al. Excision of HIV-1 proviral DNA by recombinant cell permeable tre-recombinase. PLoS One 2012;7(2):e31576
   PubMedGoogle Scholar
• Hauber I, Hofmann-Sieber H, Chemnitz J, et al. Highly significant antiviral activity of HIV-1 LTR-specific tre-recombinase in humanized mice. PLoS Pathog 2013;9(9):e1003587
   PubMedGoogle Scholar
• Qu X, Wang P, Ding D, 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
   PubMed Web of Science ®Google Scholar
• Ebina H, Misawa N, Kanemura Y, Koyanagi Y. Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus. Sci Rep 2013;3:2510
   PubMed Web of Science ®Google Scholar
• Hu W, Kaminski R, Yang F, et al. RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection. Proc Natl Acad Sci USA 2014;111(31):11461-6
   PubMed Web of Science ®Google Scholar
• Liao HK, Gu Y, Diaz A, et al. Use of the CRISPR/Cas9 system as an intracellular defense against HIV-1 infection in human cells. Nat Commun 2015;6:6413
   PubMed Web of Science ®Google Scholar
• Shirakawa K, Chavez L, Hakre S, et al. Reactivation of latent HIV by histone deacetylase inhibitors. Trends Microbiol 2013;21(6):277-85
   PubMed Web of Science ®Google Scholar
• Archin NM, Liberty AL, Kashuba AD, et al. Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy. Nature 2012;487(7408):482-5
   PubMed Web of Science ®Google Scholar
• Ho Y-C, Shan L, Hosmane Nina N, et al. Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure. Cell 2013;155(3):540-51
   PubMed Web of Science ®Google Scholar
• Mali P, Aach J, Stranges PB, et al. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol 2013;31(9):833-8
   PubMed Web of Science ®Google Scholar
• Tanenbaum ME, Gilbert LA, Qi LS, et al. A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 2014;159(3):635-46
   PubMed Web of Science ®Google Scholar
• Konermann S, Brigham MD, Trevino AE, et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 2015;517(7536):583-8
   PubMed Web of Science ®Google Scholar
• Gilbert LA, Horlbeck MA, Adamson B, et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 2014;159(3):647-61
   PubMed Web of Science ®Google Scholar
• Cocchi F, DeVico AL, Garzino-Demo A, et al. Identification of RANTES, MIP-1 alpha, and MIP-1 beta as the major HIV-suppressive factors produced by CD8+ T cells. Science 1995;270(5243):1811-15
   PubMed Web of Science ®Google Scholar
• Nagasawa T, Hirota S, Tachibana K, et al. Defects of B-cell lymphopoiesis and bone-marrow myelopoiesis in mice lacking the CXC chemokine PBSF/SDF-1. Nature 1996;382(6592):635-8
   PubMed Web of Science ®Google Scholar
• Biti R, Ffrench R, Young J, et al. HIV-1 infection in an individual homozygous for the CCR5 deletion allele. Nat Med 1997;3(3):252-3
   PubMed Web of Science ®Google Scholar
• Samson M, Libert F, Doranz BJ, 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
   PubMed Web of Science ®Google Scholar
• Scarlatti G, Tresoldi E, Bjorndal A, et al. In vivo evolution of HIV-1 co-receptor usage and sensitivity to chemokine-mediated suppression. Nat Med 1997;3(11):1259-65
   PubMed Web of Science ®Google Scholar
• Allers K, Hutter G, Hofmann J, et al. Evidence for the cure of HIV infection by CCR5Delta32/Delta32 stem cell transplantation. Blood 2011;117(10):2791-9
   PubMed Web of Science ®Google Scholar
• Hutter G, Nowak D, Mossner M, et al. Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation. N Engl J Med 2009;360(7):692-8
   PubMed Web of Science ®Google Scholar
• Hutter G, Thiel E. Allogeneic transplantation of CCR5-deficient progenitor cells in a patient with HIV infection: an update after 3 years and the search for patient no. 2. AIDS 2011;25(2):273-4
   PubMed Web of Science ®Google Scholar
• Michael NL, Chang G, Louie LG, et al. The role of viral phenotype and CCR-5 gene defects in HIV-1 transmission and disease progression. Nat Med 1997;3(3):338-40
   PubMed Web of Science ®Google Scholar
• Zimmerman PA, Buckler-White A, Alkhatib G, et al. Inherited resistance to HIV-1 conferred by an inactivating mutation in CC chemokine receptor 5: studies in populations with contrasting clinical phenotypes, defined racial background, and quantified risk. Mol Med 1997;3(1):23-36
   PubMed Web of Science ®Google Scholar
• Perez EE, Wang J, Miller JC, 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
   PubMed Web of Science ®Google Scholar
• Holt N, Wang J, Kim K, 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
   PubMed Web of Science ®Google Scholar
• Schleifman EB, Bindra R, Leif J, et al. Targeted disruption of the CCR5 gene in human hematopoietic stem cells stimulated by peptide nucleic acids. Chem Biol 2011;18(9):1189-98
   PubMed Web of Science ®Google Scholar
• Tebas P, Stein D, Tang WW, et al. Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV. N Engl J Med 2014;370(10):901-10
   PubMed Web of Science ®Google Scholar
• Cho SW, Kim S, Kim JM, Kim JS. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol 2013;31(3):230-2
   PubMed Web of Science ®Google Scholar
• Ye L, Wang J, Beyer AI, 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 USA 2014;111(26):9591-6
   PubMed Web of Science ®Google Scholar
• Wang W, Ye C, Liu J, 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
   PubMed Web of Science ®Google Scholar
• Cho SW, Kim S, Kim Y, et al. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res 2014;24(1):132-41
   PubMed Web of Science ®Google Scholar
• Cradick TJ, Fine EJ, Antico CJ, Bao G. CRISPR/Cas9 systems targeting beta-globin and CCR5 genes have substantial off-target activity. Nucleic Acids Res 2013;41(20):9584-92
   PubMed Web of Science ®Google Scholar
• Monroe KM, Yang Z, Johnson JR, et al. IFI16 DNA sensor is required for death of lymphoid CD4 T cells abortively infected with HIV. Science 2014;343(6169):428-32
   PubMed Web of Science ®Google Scholar
• Truong L, Wood T, Henley J, et al. Autologous hematopoietic stem/progenitor cell (HSPC) therapy for monogenic blood disorders: scalable, cGMP-compliant process for generating highly efficient genome edited HSPC. Blood 2013;122(21):4213-13
   Google Scholar
• Mandal PK, Ferreira LM, Collins R, et al. Efficient ablation of genes in human hematopoietic stem and effector cells using CRISPR/Cas9. Cell Stem Cell 2014;15(5):643-52
   PubMed Web of Science ®Google Scholar
• Morris KV, Mattick JS. The rise of regulatory RNA. Nat Rev Genet 2014;15(6):423-37
   PubMed Web of Science ®Google Scholar
• Johnsson P, Ackley A, Vidarsdottir L, et al. A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells. Nat Struct Mol Biol 2013;20(4):440-6
   PubMed Web of Science ®Google Scholar
• Hawkins PG, Morris KV. Transcriptional regulation of Oct4 by a long non-coding RNA antisense to Oct4-pseudogene 5. Transcription 2010;1(3):165-75
   PubMedGoogle Scholar
• Yu W, Gius D, Onyango P, et al. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 2008;451(7175):202-6
   PubMed Web of Science ®Google Scholar
• Morris KV, Santoso S, Turner AM, et al. Bidirectional transcription directs both transcriptional gene activation and suppression in human cells. PLoS Genet 2008;4(11):e1000258
   PubMed Web of Science ®Google Scholar
• Landry S, Halin M, Lefort S, et al. Detection, characterization and regulation of antisense transcripts in HIV-1. Retrovirology 2007;4:71
   PubMed Web of Science ®Google Scholar
• Ludwig LB, Ambrus JLJr, Krawczyk KA, et al. Human Immunodeficiency Virus-Type 1 LTR DNA contains an intrinsic gene producing antisense RNA and protein products. Retrovirology 2006;3:80
   PubMedGoogle Scholar
• Kobayashi-Ishihara M, Yamagishi M, Hara T, et al. HIV-1-encoded antisense RNA suppresses viral replication for a prolonged period. Retrovirology 2012;9(1):38
   PubMedGoogle Scholar
• Saayman S, Ackley A, Turner AM, et al. An HIV-encoded antisense long noncoding RNA epigenetically regulates viral transcription. Mol Ther 2014;22(6):1164-75
   PubMed Web of Science ®Google Scholar
• Kirchhoff F, Greenough TC, Brettler DB, et al. Brief report: absence of intact nef sequences in a long-term survivor with nonprogressive HIV-1 infection. N Engl J Med 1995;332(4):228-32
   PubMed Web of Science ®Google Scholar
• Crowell TA, Gebo KA, Blankson JN, et al. Hospitalization rates and reasons among HIV elite controllers and persons with medically controlled HIV infection. J Infect Dis 2014. [ Epub ahead of print]
   PubMed Web of Science ®Google Scholar
• Wang X, Wang Y, Wu X, et al. Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors. Nat Biotechnol 2015;33(2):175-8
   PubMed Web of Science ®Google Scholar
• Fu Y, Sander JD, Reyon D, et al. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol 2014;32(3):279-84
   PubMed Web of Science ®Google Scholar
• Ran FA, Hsu PD, Lin CY, et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 2013;154(6):1380-9
   PubMed Web of Science ®Google Scholar
• Shen B, Zhang W, Zhang J, et al. Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects. Nat Methods 2014;11(4):399-402
   PubMed Web of Science ®Google Scholar
• Tsai SQ, Wyvekens N, Khayter C, et al. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat Biotechnol 2014;32(6):569-76
   PubMed Web of Science ®Google Scholar
• Sellmyer MA, Chen LC, Egeler EL, et al. Intracellular context affects levels of a chemically dependent destabilizing domain. PLoS One 2012;7(9):e43297
   PubMedGoogle Scholar
• Iwamoto M, Bjorklund T, Lundberg C, et al. A general chemical method to regulate protein stability in the mammalian central nervous system. Chem Biol 2010;17(9):981-8
   PubMed Web of Science ®Google Scholar
• Tai K, Quintino L, Isaksson C, et al. Destabilizing domains mediate reversible transgene expression in the brain. PLoS One 2012;7(9):e46269
   PubMedGoogle Scholar
• Spina CA, Anderson J, Archin NM, et al. An in-depth comparison of latent HIV-1 reactivation in multiple cell model systems and resting CD4+ T cells from aviremic patients. PLoS Pathog 2013;9(12):e1003834
   PubMed Web of Science ®Google Scholar
• Bullen CK, Laird GM, Durand CM, et al. New ex vivo approaches distinguish effective and ineffective single agents for reversing HIV-1 latency in vivo. Nat Med 2014;20(4):425-9
   PubMed Web of Science ®Google Scholar
• Sternberg SH, Redding S, Jinek M, et al. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 2014;507(7490):62-7
   PubMed Web of Science ®Google Scholar
• Anders C, Niewoehner O, Duerst A, Jinek M. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 2014;513(7519):569-73
   PubMed Web of Science ®Google Scholar
• Doudna JA, Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 2014;346(6213):1258096
   PubMed Web of Science ®Google Scholar