Comparison of cytosine base editors and development of the BEable-GPS database for targeting pathogenic SNVs

Abstract

A variety of base editors have been developed to achieve C-toT editing in different genomic contexts. Here, we compare a panel of five base editors on their C-toT editing efficiencies and product purity at commonly editable sites, including some human pathogenic C-toT mutations. We further profile the accessibilities of 20 base editors to all possible pathogenic mutations in silico. Finally, we build the BEable-GPS (Base Editable prediction of Global Pathogenic SNVs) database for users to select proper base editors to model or correct disease-related mutations. The in vivo comparison and in silico profiling catalog the availability of base editors and their broad applications in biomedical studies.

Single C-to-T substitution using engineered APOBEC3G-nCas9 base editors with minimum genome- and transcriptome-wide off-target effects

“…We estimated the scope of base-editable disease variants that could be corrected by using A3G-BEs. Among the total of 1515 pathogenic SNPs identified within the BEable-GPS (Base Editable prediction of Global Pathogenic-related SNVs) entries ( 12 ), 61% (929 of 1515) were found to lie within the C C or CN C sequence context preferred by A3G-BEs ( 18 ). We then identified 540 human pathogenic SNPs that could be precisely correctable by our A3G-BEs, occupying 36% of the total number (see data file S1).…”

“…However, in the most challenging case, when editable Cs are located consecutively within the activity window, especially in the case of C C dinucleotides when a bystander C is located right upstream of the target C, the existing CBEs nonselectively edit both of the Cs. Nearly 38% of the human pathogenic SNPs that are caused by T-to-C disease point mutations lie in the context of C C , followed by A C (29%), G C (21%), and T C (13%) (see data file S1) ( 1 , 12 ), necessitating the development of new CBEs that can precisely discriminate between the target and bystander Cs.…”

A Tale of Two Moieties: Rapidly Evolving CRISPR/Cas-Based Genome Editing

“…Distinct to convenient and efficient gene KO, the efficiency and product purity of precise editing by CRISPR/Cas has remained low [42], which hinders its application in therapeutics, such as correcting human genetic variants relevant to diseases. Considering that the majority of reported human pathogenetic variants are point mutations [48][49][50], new technologies are desired to achieve genome editing at single nucleotide resolution with high precision and efficiency. This dream came true in 2016, with the reports of efficient genome editing at single bases [16,51], originally referred to as base editors (BEs) and later as cytosine BE (CBE) more specifically.…”

“…Developing In Vitro Evolved Adenosine Deaminase Effector for A-to-G Base Editing Other than pathogenic T-to-C (or A-to-G) mutations that can be potentially corrected by CBEs, the majority of reported human pathogenic variants are G-to-A (or C-to-T) [48][49][50]. In this case, another type of genome editing technology was desired to reverse pathogenic G-to-A (or C-to-T) variants for treatment.…”

Prediction of synonymous corrections by the BE-FF computational tool expands the targeting scope of base editing

“…Moreover, such tools are not customized for base editing and thus, do not take under consideration BEs' activity window and amino acids (AA) sequence. Existing tools that are base editing oriented, do not match suitable BEs for specific SNVs (20), or lack the possibility to examine the translation outcome of the edited sequence (21). To magnify the potential of base editing in treating as many cases as possible, the utilization of multiple Cas varieties and the ability to translate DNA sequences and compare the editing outcome are needed.…”