Restriction factors constitute a newly appreciated line of innate immune defense, blocking viral replication inside of infected cells. In contrast to these antiviral proteins, some cellular proteins, such as the CD4, CCR5, and CXCR4 cell surface receptors, facilitate HIV replication. We have used zinc finger nucleases (ZFNs) to insert a cocktail of anti-HIV restriction factors into the CCR5 locus in a T-cell reporter line, knocking out the CCR5 gene in the process. Mirroring the logic of highly active antiretroviral therapy, this strategy provides multiple parallel blocks to infection, dramatically limiting pathways for viral escape, without relying on random integration of transgenes into the genome. Because of the combination of blocks that this strategy creates, our modified T-cell lines are robustly resistant to both CCR5-tropic (R5-tropic) and CXCR4-tropic (X4-tropic) HIV-1. While zinc finger nuclease-mediated CCR5 disruption alone, which mimics the strategy being used in clinical trials, confers 16-fold protection against R5-tropic HIV, it has no effect against X4-tropic virus. Rhesus TRIM5α, chimeric human-rhesus TRIM5α, APOBEC3G D128K, or Rev M10 alone targeted to CCR5 confers significantly improved resistance to infection by both variants compared with CCR5 disruption alone. The combination of three factors targeted to CCR5 blocks infection at multiple stages, providing virtually complete protection against infection by R5-tropic and X4-tropic HIV.Molecular Therapy (2013); doi:10.1038/mt.2012.284.
"While we, and others, have observed that the ZFNs targeting CCR5 have some cellular toxicity, the effect on overall clonal dynamics was unknown and might be expected to be minimal . We performed the targeting experiment at nuclease concentrations shown to favor single allele targeting to minimize double-marking cells . After two pulses of ganciclovir to select against cells with off-target insertion of barcodes, GFP levels remained stable, suggesting that the majority of cells with off-target integrations had been eliminated. "
[Show abstract][Hide abstract] ABSTRACT: Background
Cell lines are often regarded as clonal, even though this simplifies what is known about mutagenesis, transformation and other processes that destabilize them over time. Monitoring these clonal dynamics is important for multiple areas of biomedical research, including stem cell and cancer biology. Tracking the contributions of individual cells to large populations, however, has been constrained by limitations in sensitivity and complexity.
We utilize cellular barcoding methods to simultaneously track the clonal contributions of tens of thousands of cells. We demonstrate that even with optimal culturing conditions, common cell lines including HeLa, K562 and HEK-293 T exhibit ongoing clonal dynamics. Starting a population with a single clone diminishes but does not eradicate this phenomenon. Next, we compare lentiviral and zinc-finger nuclease barcode insertion approaches, finding that the zinc-finger nuclease protocol surprisingly results in reduced clonal diversity. We also document the expected reduction in clonal complexity when cells are challenged with genotoxic stress. Finally, we demonstrate that xenografts maintain clonal diversity to a greater extent than in vitro culturing of the human non-small-cell lung cancer cell line HCC827.
We demonstrate the feasibility of tracking and quantifying the clonal dynamics of entire cell populations within multiple cultured cell lines. Our results suggest that cell heterogeneity should be considered in the design and interpretation of in vitro culture experiments. Aside from clonal cell lines, we propose that cellular barcoding could prove valuable in modeling the clonal behavior of heterogeneous cell populations over time, including tumor populations treated with chemotherapeutic agents.
"It is important to note that in this study stable modifications in K562 cells were measured for TALENs, RGENs, and ZFNs 14 days posttransfection. The absolute genome-editing frequencies reported here are thus somewhat different than published results for previously described nucleases where nuclease activity was measured at different time points, in different cell types, and with different nuclease levels (Mussolino et al., 2011; Perez et al., 2008; Voit et al., 2013). Nuclease-induced NHEJ is typically measured with high nuclease levels 3 days posttransfection to detect maximal NHEJ levels, but these modifications decrease over time due to toxicity (Doyon et al., 2010, 2011; Kim et al., 2009; Lombardo et al., 2007) (Figure S1). "
[Show abstract][Hide abstract] ABSTRACT: Targeted genome editing with engineered nucleases has transformed the ability to introduce precise sequence modifications at almost any site within the genome. A major obstacle to probing the efficiency and consequences of genome editing is that no existing method enables the frequency of different editing events to be simultaneously measured across a cell population at any endogenous genomic locus. We have developed a method for quantifying individual genome-editing outcomes at any site of interest with single-molecule real-time (SMRT) DNA sequencing. We show that this approach can be applied at various loci using multiple engineered nuclease platforms, including transcription-activator-like effector nucleases (TALENs), RNA-guided endonucleases (CRISPR/Cas9), and zinc finger nucleases (ZFNs), and in different cell lines to identify conditions and strategies in which the desired engineering outcome has occurred. This approach offers a technique for studying double-strand break repair, facilitates the evaluation of gene-editing technologies, and permits sensitive quantification of editing outcomes in almost every experimental system used.
"Of the R88-A3G mutants, R88-A3GD128K (R88-A3Gm) was the most resistant to Vif-induced degradation and exhibited most potent anti-HIV activity. Additionally, Voit et al. have shown that A3GD128K confers over 100-fold protection against HIV-1 infection, compared with the 3- to 64-fold protection provided by human–rhesus hybrid tripartite motif 5-α.21 Therefore, in the present study, R88-A3Gm was chosen as the candidate for anti-HIV gene therapy. "
[Show abstract][Hide abstract] ABSTRACT: Human immunodeficiency virus type 1 (HIV-1) drug resistance and the latent reservoir are the two major obstacles to effectively controlling and curing HIV-1 infection. Therefore, it is critical to develop therapeutic strategies specifically targeting these two obstacles. Recently, we described a novel anti-HIV approach based on a modified human intrinsic restriction factor, R88-APOBEC3G (R88-A3G). In this study, we further characterized the antiviral potential of R88-A3GD128K (R88-A3Gm) against drug-resistant strains of HIV-1 and viruses produced from latently infected cells. We delivered R88-A3Gm into target cells using a doxycycline (Dox)-inducible lentiviral vector and demonstrated that its expression and antiviral activity were highly regulated by Dox. In the presence of Dox, R88-A3Gm-transduced T cells were resistant to infection caused by wild-type and various drug-resistant strains of HIV-1. Moreover, when the R88-A3Gm-expressing vector was transduced into the HIV-1 latently infected ACH-2 cell line or human CD4(+) T cells, on activation by phorbol-12-myristate-13-acetate or phytohemaglutinin, R88-A3Gm was able to curtail the replication of progeny viruses. Altogether, these data clearly indicate that R88-A3Gm is a highly potent HIV-1 inhibitor, and R88-A3Gm-based anti-HIV gene therapy is capable of targeting both active and latent HIV-1-infected cells to prevent subsequent viral replication and dissemination.Molecular Therapy-Nucleic Acids (2014) 3, e151; doi:10.1038/mtna.2014.2; published online 4 March 2014.
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