Developing novel Type 1 CRISPR tools for gene editing therapy

ABSTRACT/PROJECT SUMMARY Gene editing therapy using the Nobel Prize award-winning CRISPR-Cas9 technology promises a permanent cure for thousands of human diseases. Up to date, CRISPR tools have enabled dozens of FDA-approved clinical trials to tackle single-gene disorders (e.g., sickle cell disease), infectious (e.g., HIV) and complex diseases (e.g., cancer). Yet to realize CRISPR’s full therapeutic potential, many issues remain to be addressed. Most of the current gene editing work uses Cas9, the RNA-guided nuclease of Type II CRISPR. Cas9 nuclease tools suffer from several drawbacks, including low efficacy in precise gene modification mediated by human cells’ intrinsic homology-directed repair pathway, and serious safety concerns caused by the toxic DNA double-strand breaks (DSBs) formed at on- and off- target sites. The non-DSB-reliant base editors (BEs) offer a path towards safer, highly-efficiency, and precise single nucleotide editing using DNA deaminase fused to catalytically impaired Cas9. But their targeting scope is limited by two factors, the NGG PAM required by Cas9 to be present next to the target site, and the inflexible editing window position. Here we propose to leverage another major branch of native CRISPR, the Type I (T1) systems, to broaden the targeting scope for gene editing therapy. In 2019, we pioneered T1 CRISPR-mediated genome engineering in human cells. Our ensuing study expanded the T1 toolbox by harnessing the most compact groups of Type I editors with diverse PAM preferences and guide orthogonality. We also found that a hidden gene product of the T1 machinery, Cas11, must be expressed from its own eukaryotic translation initiation element to enable robust editing by compact T1 gene editors. Built on these lines of prior work, we propose to establish novel T1 CRISPR tools and apply them to correct disease-causing mutations. Successful completion of Phase I work will set a solid foundation for Phase II, where we plan to evaluate the efficacy and safety of T1 CRISPR gene therapy strategies in preclinical cell and animal models.