Engineering Novel Precision Genome Editing Tools

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PROJECT SUMMARY/ABSTRACT Half of the known human genetic variations that contribute to disease are due to single nucleotide polymorphisms (SNPs). Thus, there is a pressing need to develop precision genome editing tools that are able to correct these SNPs with high efficiency and accuracy. Current CRISPR-Cas based precision genome editing tools, such as DNA base editors and prime editors, were designed to perform targeted single nucleotide changes without introducing double stranded breaks and relying on the homology-directed repair pathway. However, these tools have several drawbacks observed in cells, such as off-target DNA and RNA editing, low efficiency, and unintended editing of nucleotides within the neighborhood of the target nucleotide (bystander editing) leading to undesired genomic changes. Moreover, DNA base editors are able to perform only transitions (interchanging purines (AG) or pyrimidines (CT)) but not transversions (interchanging pyrimidines for purines and vice versa). These shortcomings reduce the targeting capabilities of current precision genome editing tools and are the key limitations of using them as therapeutic agents. Building on our recent work that explains the molecular basis of the DNA base editors’ drawbacks, we propose four innovative strategies to design precision genome editing approaches that address the limitations of current genome editing tools and expand their targeting scope. Three of the four strategies will yield base editors with dual programmability. Besides the programable nuclease (Cas9) that guides base editors to the sequence of interest, these novel base editors will additionally have easily programmable catalytic modules that will allow selecting only one nucleotide for editing. This dual programmability will eliminate the bystander editing and make these DNA base editors exceptionally accurate. Two out of four designs will yield DNA base editors able to perform transversions (interchanging pyrimidines for purines (CG and TG)) and to correct additional ~25% of pathogenic SNPs inaccessible by current base editors. Moreover, one of the two transversion base editors will possess dual programmability, hence will be exceptionally accurate. Overall, the four strategies proposed here will yield the next generation precision genome editing tools that, besides the direct therapeutic corrections of SNPs’ in vivo, will also allow interrogating the association between multiple SNPs, gene expression and diseases (neurodegenerative diseases or various types of cancers). Thus, these DNA editing tools will pave the way for investigating the molecular mechanisms of multiple genetic disorders and enable us to develop new therapeutic strategies.