Development of CRISPR-Cas Editing Tools for Therapeutic Genome Editing

Abstract

The discovery and development of clustered, regularly interspaced, short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) systems have revolutionized targeted genomic medicine. In my thesis, we discuss our efforts to improve and optimize various CRISPR-Cas systems for therapeutic genome editing applications. In part one, we propose that aberrant splice site disruption could be a simple and efficient strategy for treating some mutations associated with β-thalassemia. Specifically, we show that disruption of common mutant alleles in the HBB gene by Cas9 and Cas12a results in restoration of normal β-globin splicing, functional expression of HBB, and improved quality of erythroid maturation in edited β-thalassemia patient CD34+ hematopoietic stem and progenitor cells. In part two, we demonstrate that optimization of the nuclear localization signal (NLS) sequence framework is an effective method to improve the mutagenesis frequencies of Cas12a nuclease. In particular, the 3xNLS-NLP-cMyc-cMyc framework improves genome editing in mammalian and primary cells, relative to previous Cas12a NLS frameworks. We show that our NLS optimization approach can be applied to various Cas12a orthologs resulting in high editing activity without sacrificing the high intrinsic specificity of Cas12a nucleases. Furthermore, we demonstrate that NLS-optimized enAspCas12a can efficiently disrupt the ATF4-binding motif at the +55 enhancer of BCL11A, which may serve as an alternative therapeutic strategy for β-hemoglobinopathies. In part three, we develop and characterize fusion enhanced base editor (feBE) systems, which are fusions of base editors to our Cas9-programmable DNA binding domain (pDBD) and Cas9-Cas9 platforms. We report that our feBEs are more active than previously described base editor platforms at canonical and noncanonical PAMs. Furthermore, we show that feBEs can selectively edit a therapeutically relevant target site, CCR5, with minimal editing at a highly homologous off-target site. Taken together, my thesis research aimed to engineer CRISPR-Cas tools to improve their efficiency and specificity for therapeutic genome editing applications.