Base editing rescue of spinal muscular atrophy in cells and in mice

Arbab, Mandana; Matuszek, Żaneta; Kray, Kaitlyn M.; Du, Ailing; Newby, Gregory A.; Blatnik, Anton J.; Raguram, Aditya; Richter, Michelle F.; Zhao, Kevin T.; Levy, Jay M.; Shen, Max W.; Arnold, W. David; Wang, Dan; Xie, Jun; Gao, Guangping; Burghes, Arthur H.M.; Liu, David R.

doi:10.1126/science.adg6518

Cited by 61 publications

(31 citation statements)

References 164 publications

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“…We designed five tiled gRNAs for each variant allele that place the variant in positions shown to induce most efficient editing with ABE8e (Fig. 1e) 46 . Positive control gRNAs which ablate splice donor and acceptor consensus sites in six genes found to have significantly altered LDL-C uptake upon knockout 37 , and 100 non-targeting negative control gRNAs that tile 20 synthetic variants were included, for a total of 3,455 gRNAs.…”

Section: A Base Editing Reporter Profiles Endogenous Editing Outcomesmentioning

confidence: 99%

Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification

Ryu,

Barkal,

et al. 2023

Preprint

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CRISPR base editing screens are powerful tools for studying disease-associated variants at scale. However, the efficiency and precision of base editing perturbations vary, confounding the assessment of variant-induced phenotypic effects. Here, we provide an integrated pipeline that improves the estimation of variant impact in base editing screens. We perform high-throughput ABE8e-SpRY base editing screens with an integrated reporter construct to measure the editing efficiency and outcomes of each gRNA alongside their phenotypic consequences. We introduce BEAN, a Bayesian network that accounts for per-guide editing outcomes and target site chromatin accessibility to estimate variant impacts. We show this pipeline attains superior performance compared to existing tools in variant classification and effect size quantification. We use BEAN to pinpoint common variants that alter LDL uptake, implicating novel genes. Additionally, through saturation base editing ofLDLR, we enable accurate quantitative prediction of the effects of missense variants on LDL-C levels, which aligns with measurements in UK Biobank individuals, and identify structural mechanisms underlying variant pathogenicity. This work provides a widely applicable approach to improve the power of base editor screens for disease-associated variant characterization.

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Section: A Base Editing Reporter Profiles Endogenous Editing Outcomesmentioning

confidence: 99%

Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification

Ryu,

Barkal,

et al. 2023

Preprint

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“…Current therapies require repeated dosing and do not address the underlying SMN deficiency. The group used genome editing techniques to modify SMN2, a deficient copy of SMN1 with a specific mutation, to permanently restore SMN protein levels and alleviate SMA symptoms [47] . By delivering base editors using adeno‐associated virus (AAV9) vectors, they achieved significant conversion of the SMN2 mutation and observed improved motor function and increased lifespan in SMA mice.…”

Section: Engineering New‐to‐nature Activities and Enhancing The Thera...mentioning

confidence: 99%

Engineering of Therapeutic and Detoxifying Enzymes

Michailidou

2023

Angew Chem Int Ed

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Therapeutic enzymes present excellent opportunities for the treatment of human disease, modulation of metabolic pathways and system detoxification. However, current use of enzyme therapy in the clinic is limited as naturally occurring enzymes are seldom optimal for such applications and require substantial improvement by protein engineering. Engineering strategies such as design and directed evolution that have been successfully implemented for industrial biocatalysis can significantly advance the field of therapeutic enzymes, leading to biocatalysts with new‐to‐nature therapeutic activities, high selectivity, and suitability for medical applications. This minireview highlights case studies of how state‐of‐the‐art and emerging methods in protein engineering are explored for the generation of therapeutic enzymes and discusses gaps and future opportunities in the field of enzyme therapy.

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“…Although there are reports showing the potency of base editing in cell lines and in some cases in mice [8][9][10][11][12][13] , high levels of gene correction have yet to be demonstrated in tissues of humans (which was not certified by peer review) is the author/funder. All rights reserved.…”

Section: Introductionmentioning

confidence: 99%

High-efficiency base editing for Stargardt disease in mice, non-human primates, and human retina tissue

Muller

Sullivan

Schwarzer

et al. 2023

Preprint

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Stargardt disease is a currently untreatable, inherited neurodegenerative disease that leads to macular degeneration and blindness due to loss-of-function mutations in the ABCA4 gene. We have designed a dual adeno-associated viral vector split-intein adenine base-editing strategy to correct the most common mutation in ABCA4 (c.5882G>A, p.G1961E). We optimized ABCA4 base editing in human models, including retinal organoids, iPSC-derived retinal pigment epithelial cells (RPE), as well as adult human retinal- and RPE/choroid explants in vitro. The resulting gene therapy vectors achieved high levels of gene correction in mutation-carrying mice and in non-human primates, with an average editing of 37% of photoreceptors and 73% of RPE cells in vivo. The high editing rates in primates make way for precise and efficient gene editing in other neurodegenerative ocular diseases.

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Base editing rescue of spinal muscular atrophy in cells and in mice

Cited by 61 publications

References 164 publications

Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification

Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification

Engineering of Therapeutic and Detoxifying Enzymes

High-efficiency base editing for Stargardt disease in mice, non-human primates, and human retina tissue

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