Antiviral therapy of persistent viral infection using genome editing

Dampier, 2014, HIV excision utilizing CRISPR/Cas9 technology: Attacking the proviral quasispecies in reservoirs to achieve a cure, MOJ Immunol, 1 Price, 2015, Cas9-mediated targeting of viral RNA in eukaryotic cells, Proc Natl Acad Sci U S A, 112, 6164, 10.1073/pnas.1422340112 Yuen, 2015, CRISPR/Cas9-mediated genome editing of Epstein–Barr virus in human cells, J Gen Virol, 96, 626, 10.1099/jgv.0.000012 Noh, 2016, Targeted disruption of EBNA1 in EBV-infected cells attenuated cell growth, BMB Rep, 49, 226, 10.5483/BMBRep.2016.49.4.260 van Diemen, 2016, CRISPR/Cas9-mediated genome editing of herpesviruses limits productive and latent infections, PLoS Pathog, 12, e1005701, 10.1371/journal.ppat.1005701 Wollebo, 2015, CRISPR/Cas9 system as an agent for eliminating polyomavirus JC infection, PLoS ONE, 10, e0136046, 10.1371/journal.pone.0136046 Hu, 2014, Disruption of HPV16-E7 by CRISPR/Cas system induces apoptosis and growth inhibition in HPV16 positive human cervical cancer cells, Biomed Res Int, 2014, 612823, 10.1155/2014/612823 Hu, 2015, TALEN-mediated targeting of HPV oncogenes ameliorates HPV-related cervical malignancy, J Clin Invest, 125, 425, 10.1172/JCI78206 Ding, 2014, Zinc finger nucleases targeting the human papillomavirus E7 oncogene induce E7 disruption and a transformed phenotype in HPV16/18-positive cervical cancer cells, Clin Cancer Res, 20, 6495, 10.1158/1078-0432.CCR-14-0250 Kennedy, 2014, Inactivation of the human papillomavirus E6 or E7 gene in cervical carcinoma cells by using a bacterial CRISPR/Cas RNA-guided endonuclease, J Virol, 88, 11965, 10.1128/JVI.01879-14 Schiffer, 2012, Targeted DNA mutagenesis for the cure of chronic viral infections, J Virol, 86, 8920, 10.1128/JVI.00052-12 Ohno, 2015, Novel therapeutic approaches for hepatitis B virus covalently closed circular DNA, World J Gastroenterol, 21, 7084, 10.3748/wjg.v21.i23.7084 Kennedy, 2015, Bacterial CRISPR/Cas DNA endonucleases: a revolutionary technology that could dramatically impact viral research and treatment, Virology, 479–480, 213, 10.1016/j.virol.2015.02.024 Price, 2016, Harnessing the prokaryotic adaptive immune system as a eukaryotic antiviral defense, Trends Microbiol, 24, 294, 10.1016/j.tim.2016.01.005 Hütter, 2015, CCR5 targeted cell therapy for HIV and prevention of viral escape, Viruses, 7, 4186, 10.3390/v7082816 Wang, 2016, The clinical applications of genome editing in HIV, Blood, 127, 2546, 10.1182/blood-2016-01-678144 Gaj, 2013, ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering, Trends Biotechnol, 31, 397, 10.1016/j.tibtech.2013.04.004 Maeder, 2016, Genome-editing technologies for gene and cell therapy, Mol Ther, 24, 430, 10.1038/mt.2016.10 Maggio, 2015, Genome editing at the crossroads of delivery, specificity, and fidelity, Trends Biotechnol, 33, 280, 10.1016/j.tibtech.2015.02.011 Meinke, 2016, Cre recombinase and other tyrosine recombinases, Chem Rev, 10.1021/acs.chemrev.6b00077 Chevalier, 2001, Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility, Nucleic Acids Res, 29, 3757, 10.1093/nar/29.18.3757 Thyme, 2014, Reprogramming homing endonuclease specificity through computational design and directed evolution, Nucleic Acids Res, 42, 2564, 10.1093/nar/gkt1212 Joshi, 2011, Evolution of I-SceI homing endonucleases with increased DNA recognition site specificity, J Mol Biol, 405, 185, 10.1016/j.jmb.2010.10.029 Carroll, 2014, Genome engineering with targetable nucleases, Annu Rev Biochem, 83, 409, 10.1146/annurev-biochem-060713-035418 Kim, 2014, A guide to genome engineering with programmable nucleases, Nat Rev Genet, 15, 321, 10.1038/nrg3686 Ran, 2013, Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity, Cell, 154, 1380, 10.1016/j.cell.2013.08.021 Mali, 2013, CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering, Nat Biotechnol, 31, 833, 10.1038/nbt.2675 Hiom, 2010, Coping with DNA double strand breaks, DNA Repair (Amst), 9, 1256, 10.1016/j.dnarep.2010.09.018 Farinas, 2001, Directed enzyme evolution, Curr Opin Biotechnol, 12, 545, 10.1016/S0958-1669(01)00261-0 Buchholz, 2001, Alteration of Cre recombinase site specificity by substrate-linked protein evolution, Nat Biotechnol, 19, 1047, 10.1038/nbt1101-1047 Buchholz, 2011, In vitro evolution and analysis of HIV-1 LTR-specific recombinases, Methods, 53, 102, 10.1016/j.ymeth.2010.06.014 You, 2014, Update on hepatitis B virus infection, World J Gastroenterol, 20, 13293, 10.3748/wjg.v20.i37.13293 Cradick, 2010, Zinc-finger nucleases as a novel therapeutic strategy for targeting hepatitis B virus DNAs, Mol Ther, 18, 947, 10.1038/mt.2010.20 Weber, 2014, AAV-mediated delivery of zinc finger nucleases targeting hepatitis B virus inhibits active replication, PLoS ONE, 9, e97579, 10.1371/journal.pone.0097579 Chen, 2014, An efficient antiviral strategy for targeting hepatitis B virus genome using transcription activator-like effector nucleases, Mol Ther, 22, 303, 10.1038/mt.2013.212 Bloom, 2013, Inactivation of hepatitis B virus replication in cultured cells and in vivo with engineered transcription activator-like effector nucleases, Mol Ther, 21, 1889, 10.1038/mt.2013.170 Lin, 2014, The CRISPR/Cas9 system facilitates clearance of the intrahepatic HBV templates in vivo, Mol Ther Nucleic Acids, 3, e186, 10.1038/mtna.2014.38 Seeger, 2014, Targeting hepatitis B virus with CRISPR/Cas9, Mol Ther Nucleic Acids, 3, e216, 10.1038/mtna.2014.68 Kennedy, 2014, Suppression of hepatitis B virus DNA accumulation in chronically infected cells using a bacterial CRISPR/Cas RNA-guided DNA endonuclease, Virology, 476C, 196 Ramanan, 2015, CRISPR/Cas9 cleavage of viral DNA efficiently suppresses hepatitis B virus, Sci Rep, 5, 10833, 10.1038/srep10833 Wang, 2015, Dual gRNAs guided CRISPR/Cas9 system inhibits hepatitis B virus replication, World J Gastroenterol, 21, 9554, 10.3748/wjg.v21.i32.9554 Dong, 2015, Targeting hepatitis B virus cccDNA by CRISPR/Cas9 nuclease efficiently inhibits viral replication, Antiviral Res, 118, 110, 10.1016/j.antiviral.2015.03.015 Zhen, 2015, Harnessing the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated Cas9 system to disrupt the hepatitis B virus, Gene Ther, 22, 404, 10.1038/gt.2015.2 Liu, 2015, Inhibition of hepatitis B virus by the CRISPR/Cas9 system via targeting the conserved regions of the viral genome, J Gen Virol, 96, 2252, 10.1099/vir.0.000159 Zhu, 2016, CRISPR/Cas9 produces anti-hepatitis B virus effect in hepatoma cells and transgenic mouse, Virus Res, 217, 125, 10.1016/j.virusres.2016.04.003 Karimova, 2015, CRISPR/Cas9 nickase-mediated disruption of hepatitis B virus open reading frame S and X, Sci Rep, 5, 13734, 10.1038/srep13734 Sunbul, 2014, Hepatitis B virus genotypes: global distribution and clinical importance, World J Gastroenterol, 20, 5427, 10.3748/wjg.v20.i18.5427 Perez, 2008, Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases, Nat Biotechnol, 26, 808, 10.1038/nbt1410 Holt, 2010, Human hematopoietic stem/progenitor cells modified by zinc-finger nucleases targeted to CCR5 control HIV-1 in vivo, Nat Biotechnol, 28, 839, 10.1038/nbt.1663 Tebas, 2014, Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV, N Engl J Med, 370, 901, 10.1056/NEJMoa1300662 Pattanayak, 2011, Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection, Nat Methods, 8, 765, 10.1038/nmeth.1670 Gabriel, 2011, An unbiased genome-wide analysis of zinc-finger nuclease specificity, Nat Biotechnol, 29, 816, 10.1038/nbt.1948 Miller, 2011, A TALE nuclease architecture for efficient genome editing, Nat Biotechnol, 29, 143, 10.1038/nbt.1755 Mussolino, 2011, A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity, Nucleic Acids Res, 39, 9283, 10.1093/nar/gkr597 Mock, 2015, mRNA transfection of a novel TAL effector nuclease (TALEN) facilitates efficient knockout of HIV co-receptor CCR5, Nucleic Acids Res, 43, 5560, 10.1093/nar/gkv469 Gray, 2006, Genetic and functional analysis of R5X4 human immunodeficiency virus type 1 envelope glycoproteins derived from two individuals homozygous for the CCR5delta32 allele, J Virol, 80, 3684, 10.1128/JVI.80.7.3684-3691.2006 Henrich, 2015, Viremic control and viral coreceptor usage in two HIV-1-infected persons homozygous for CCR5 Delta32, AIDS, 29, 867, 10.1097/QAD.0000000000000629 Westby, 2006, Emergence of CXCR4-using human immunodeficiency virus type 1 (HIV-1) variants in a minority of HIV-1-infected patients following treatment with the CCR5 antagonist maraviroc is from a pretreatment CXCR4-using virus reservoir, J Virol, 80, 4909, 10.1128/JVI.80.10.4909-4920.2006 Kordelas, 2014, Shift of HIV tropism in stem-cell transplantation with CCR5 Delta32 mutation, N Engl J Med, 371, 880, 10.1056/NEJMc1405805 Kohn, 2016, Ethical and regulatory aspects of genome editing, Blood, 127, 2553, 10.1182/blood-2016-01-678136 Sarkar, 2007, HIV-1 proviral DNA excision using an evolved recombinase, Science, 316, 1912, 10.1126/science.1141453 Hauber, 2013, Highly significant antiviral activity of HIV-1 LTR-specific Tre-recombinase in humanized mice, PLoS Pathog, 9, e1003587, 10.1371/journal.ppat.1003587 Karpinski, 2016, Directed evolution of a recombinase that excises the provirus of most HIV-1 primary isolates with high specificity, Nat Biotechnol, 34, 401, 10.1038/nbt.3467 Qu, 2013, Zinc-finger-nucleases mediate specific and efficient excision of HIV-1 proviral DNA from infected and latently infected human T cells, Nucleic Acids Res, 41, 7771, 10.1093/nar/gkt571 Qu, 2014, Zinc finger nuclease: a new approach for excising HIV-1 proviral DNA from infected human T cells, Mol Biol Rep, 41, 5819, 10.1007/s11033-014-3456-3 Ebina, 2015, A high excision potential of TALENs for integrated DNA of HIV-based lentiviral vector, PLOS ONE, 10, e0120047, 10.1371/journal.pone.0120047 De Silva Feelixge, 2016, Detection of treatment-resistant infectious HIV after genome-directed antiviral endonuclease therapy, Antiviral Res, 126, 90, 10.1016/j.antiviral.2015.12.007 Ebina, 2013, Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus, Sci Rep, 3, 2510, 10.1038/srep02510 Hu, 2014, RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection, Proc Natl Acad Sci USA, 111, 11461, 10.1073/pnas.1405186111 Liao, 2015, Use of the CRISPR/Cas9 system as an intracellular defense against HIV-1 infection in human cells, Nat Commun, 6, 6413, 10.1038/ncomms7413 Zhu, 2015, The CRISPR/Cas9 system inactivates latent HIV-1 proviral DNA, Retrovirology, 12, 22, 10.1186/s12977-015-0150-z Kaminski, 2016, Elimination of HIV-1 genomes from human T-lymphoid cells by CRISPR/Cas9 gene editing, Sci Rep, 6, 22555, 10.1038/srep22555 Kaminski, 2016, Excision of HIV-1 DNA by gene editing: a proof-of-concept in vivo study, Gene Ther, 23, 690, 10.1038/gt.2016.41 Wang, 2016, CRISPR-Cas9 can inhibit HIV-1 replication but NHEJ repair facilitates virus escape, Mol Ther, 24, 522, 10.1038/mt.2016.24 Wang, 2016, CRISPR/Cas9-Derived mutations both inhibit HIV-1 replication and accelerate viral escape, Cell Rep, 15, 481, 10.1016/j.celrep.2016.03.042 Ueda, 2016, Anti-HIV-1 potency of the CRISPR/Cas9 system insufficient to fully inhibit viral replication, Microbiol Immunol, 60, 483, 10.1111/1348-0421.12395 Yoder, 2016, Host double strand break repair generates HIV-1 strains resistant to CRISPR/Cas9, Sci Rep, 6, 29530, 10.1038/srep29530 Liang, 2016, CRISPR/Cas9: a double-edged sword when used to combat HIV infection, Retrovirology, 13, 37, 10.1186/s12977-016-0270-0 Aguirre, 2016, Genomic copy number dictates a gene-independent cell response to CRISPR/Cas9 targeting, Cancer Discov, 6, 914, 10.1158/2159-8290.CD-16-0154 Chen, 2016, Engineered viruses as genome editing devices, Mol Ther, 24, 447, 10.1038/mt.2015.164