The use of base editing technology to characterize single nucleotide variants

McDaniel, Sophia; Komor, Alexis C.; Goren, Alon

doi:10.1016/j.csbj.2022.03.031

Cited by 6 publications

(2 citation statements)

References 103 publications

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“…Large-scale variant screens have also been made possible through the direct application of Cas9-Base Editors (Cas9-BEs), which modify DNA sequences through highly efficient chemical reactions (21, 22). This involves the tethering of a deaminase domain selective for cytidines (cytidine base editors, CBEs) or adenines (adenine base editors, ABEs) to a nickase or catalytically-dead Cas9 (Cas9n or dCas9) along with recruitment to a locus of interest using a standard single guide RNA (sgRNA).…”

Section: Introductionmentioning

confidence: 99%

Accelerated drug resistant variant discovery with an enhanced, scalable mutagenic base editor platform

Dorighi,

Zhu,

Fortin

et al. 2023

Preprint

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Personalized cancer therapeutics bring directed treatment options to patients based on the genetic signatures of their tumors. Unfortunately, tumor genomes are remarkably adaptable, and acquired resistance to these drugs through genetic means is an all-too-frequent occurrence. Identifying mutations that promote resistance within drug-treated patient populations can be cost, resource, and time intensive. Accordingly, base editing, enabled by Cas9-deaminase domain fusions, has emerged as a promising approach for rapid, large-scale resistance variant screening in situ. We adapted and optimized a conditional activation-induced cytidine deaminase (AID)-dCas9 system, which demonstrated greater heterogeneity of edits with an expanded footprint compared to the most commonly utilized cytosine base editor, BE4. When combined with a custom sgRNA library, we were able to identify both individual and complex, compound variants in EGFR and BRAF that confer resistance to established EGFR inhibitors. This system and the developed analytical pipeline provide a simple, highly-scalable platform for cis or trans drug-modifying variant discovery and for uncovering unique insights into protein structure-function relationships.

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Section: Introductionmentioning

confidence: 99%

Accelerated drug resistant variant discovery with an enhanced, scalable mutagenic base editor platform

Dorighi,

Zhu,

Fortin

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…However, the design of gRNAs for base editors is complicated, and several specific criteria are carefully considered [24] , including the preferred editing window, bystander effect, potential codon change, and off-target effect. Thus a convenient tool for the rapid design of gRNAs for base editors is required and currently, there are a few programs available [37] .…”

Section: Introductionmentioning

confidence: 99%