CRISPR/Cas9-Derived Mutations Both Inhibit HIV-1 Replication and Accelerate Viral Escape

Wang, Zhen; Pan, Qinghua; Gendron, Patrick; Zhu, Weijun; Guo, Fei; Cen, Shan; Wainberg, Mark A.; Liang, Chen

doi:10.1016/j.celrep.2016.03.042

Cited by 222 publications

(215 citation statements)

References 38 publications

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“…Most indels within the target will likely create a resistance allele as well. Importantly, the driver itself is expected to produce its own resistance alleles when cleavage is repaired by end joining mechanisms such as nonhomologous end joining (NHEJ) or microhomology-mediated end joining, rather than homologous recombination, and such resistance alleles have already been observed in several experiments (Gantz and Bier 2015;Hammond et al 2016;Wang et al 2016).…”

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confidence: 99%

Evolution of Resistance Against CRISPR/Cas9 Gene Drive

2017

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CRISPR/Cas9 gene drive (CGD) promises to be a highly adaptable approach for spreading genetically engineered alleles throughout a species, even if those alleles impair reproductive success. CGD has been shown to be effective in laboratory crosses of insects, yet it remains unclear to what extent potential resistance mechanisms will affect the dynamics of this process in large natural populations. Here we develop a comprehensive population genetic framework for modeling CGD dynamics, which incorporates potential resistance mechanisms as well as random genetic drift. Using this framework, we calculate the probability that resistance against CGD evolves from standing genetic variation, de novo mutation of wild-type alleles, or cleavage repair by nonhomologous end joining (NHEJ)-a likely by-product of CGD itself. We show that resistance to standard CGD approaches should evolve almost inevitably in most natural populations, unless repair of CGD-induced cleavage via NHEJ can be effectively suppressed, or resistance costs are on par with those of the driver. The key factor determining the probability that resistance evolves is the overall rate at which resistance alleles arise at the population level by mutation or NHEJ. By contrast, the conversion efficiency of the driver, its fitness cost, and its introduction frequency have only minor impact. Our results shed light on strategies that could facilitate the engineering of drivers with lower resistance potential, and motivate the possibility to embrace resistance as a possible mechanism for controlling a CGD approach. This study highlights the need for careful modeling of the population dynamics of CGD prior to the actual release of a driver construct into the wild.KEYWORDS CRISPR/Cas9; gene drive; homing drive; mutagenic chain reaction; whole population replacement T HE prospect of driving genetically modified alleles to fixation in a population has enticed scientists for .40 years (Curtis 1968;Foster et al. 1972). Potential applications are broad and ambitious, including the eradication of vectorborne diseases such as malaria, dengue, and Zika (Burt 2003;Esvelt et al. 2014;Champer et al. 2016). For example, mosquitoes could be genetically altered such that they can no longer transmit Plasmodium parasites. If these altered alleles could then be spread in a wild population, we could effectively eradicate malaria in humans. Similarly, a gene drive could be used to reverse insecticide resistance in an agricultural pest, or to spread a deleterious allele in an invasive species to drive it toward extinction.While various strategies for implementing a gene drive have been discussed since the 1970s, all previously proposed mechanisms have faced significant obstacles. Ongoing efforts to transfer the Medea system from flour beetles to other insects have, thus far, fallen short (Chen et al. 2007;Akbari et al. 2014). Underdominance systems have also been developed (Altrock et al. 2010;Akbari et al. 2013;Reeves et al. 2014), but these are slow-spreading systems that requi...

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confidence: 99%

Evolution of Resistance Against CRISPR/Cas9 Gene Drive

2017

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“…One widely discussed approach is the use of gene editing to eliminate integrated virus(s) or virus receptors. When it comes to integrated viral genomes, a major problem with gene editing is that the editing process accelerates the generation of replication-competent viral escape mutants that are now resistant to Cas9/sgRNA, thereby greatly limiting its potential for HIV therapy (9). Because our approach is not genetic, viral escape would have to involve development of an alternative route for virus entry into cells that is unlikely and, if it happened, would be expected to be highly inefficient and selected against at the population level.…”

Section: Discussionmentioning

confidence: 99%

Immunochemical engineering of cell surfaces to generate virus resistance

Xie

Sok

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Modern immunochemical engineering allows the creation of cells that either secrete antibodies or incorporate them into various cellular compartments, including the plasma membrane. Because the receptors for most viruses are known, if one can achieve the proper stoichiometry and geometry, plasma membrane-associated antibodies to these receptors should block viral infection. In this report, we test this concept for two different viruses, human rhinovirus and HIV. Plasma membrane-tethered antibodies efficiently rendered cells permanently nonpermissive for infection by both these viruses. Membrane-bound antibodies were much more efficient than free antibody in preventing infection, likely because of the effective molarity of membrane bound antibodies. Such resistant cells may restore immune-competence to otherwise compromised HIV patients.

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“…While editing of T cells had shown promise for HIV resistance, two independent publications demonstrated NHEJ-mediated viral escape of Cas9/gRNA suppression [134, 135]. Sequencing of escaped viral mutants identified that the mutations clustered around the gRNA target cleavage site where indels are formed.…”

Section: Applicationsmentioning

confidence: 99%

Genome-Edited T Cell Therapies

Delhove

Qasim

2017

Curr Stem Cell Rep

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Purpose of ReviewAlternative approaches to conventional drug-based cancer treatments have seen T cell therapies deployed more widely over the last decade. This is largely due to their ability to target and kill specific cell types based on receptor recognition. Introduction of recombinant T cell receptors (TCRs) using viral vectors and HLA-independent T cell therapies using chimeric antigen receptors (CARs) are discussed. This article reviews the tools used for genome editing, with particular emphasis on the applications of site-specific DNA nuclease mediated editing for T cell therapies.Recent FindingsGenetic engineering of T cells using TCRs and CARs with redirected antigen-targeting specificity has resulted in clinical success of several immunotherapies. In conjunction, the application of genome editing technologies has resulted in the generation of HLA-independent universal T cells for allogeneic transplantation, improved T cell sustainability through knockout of the checkpoint inhibitor, programmed cell death protein-1 (PD-1), and has shown efficacy as an antiviral therapy through direct targeting of viral genomic sequences and entry receptors.SummaryThe combined use of engineered antigen-targeting moieties and innovative genome editing technologies have recently shown success in a small number of clinical trials targeting HIV and hematological malignancies and are now being incorporated into existing strategies for other immunotherapies.

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CRISPR/Cas9-Derived Mutations Both Inhibit HIV-1 Replication and Accelerate Viral Escape

Cited by 222 publications

References 38 publications

Evolution of Resistance Against CRISPR/Cas9 Gene Drive

Evolution of Resistance Against CRISPR/Cas9 Gene Drive

Immunochemical engineering of cell surfaces to generate virus resistance

Genome-Edited T Cell Therapies

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