Generalizing genome editing for rare disease-causing variants

Johns Hopkins University, Baltimore MD

Investigators

Abstract

PROJECT SUMMARY The latest generations of base editing and prime editing tools can efficiently install genetic variants and correct those associated with disease. However, it is still not practical to treat most patients with rare or unique disease-causing genetic variants because the cost and effort required to optimize an editing strategy and bring it to the clinic is prohibitive. Existing editing therapeutics approved or in clinical trials are all applicable to treat either a common disease-associated allele or a large set of potential disease-associated alleles. For example, the recently approved Casgevy genome editing treatment can be used to cure patients with nearly any beta-thalassemia or sickle cell disease genotype, including rare and common variants. For most types of rare genetic disease, no known genome edit could treat multiple disease-associated alleles. This proposal describes methods to establish generalizable editing strategies that would each be broadly applicable to treat hundreds of rare disease-causing genetic variants, helping to bring the benefits of genome editing to the patients who need them. Two classes of generalizable therapeutics are proposed here. One will address rare loss- of-function alleles such as haploinsufficiencies, recessive hypomorphic alleles, and diseases where expression of a paralogous gene could provide the lacking function. The other class of therapeutics will address rare gain-of-function alleles by allele-specific knockout. These conceptual strategies will be studied in the context of Marfan’s Syndrome, vascular Ehlers Danlos Syndrome, adrenoleukodystrophy, and Charcot-Marie-Tooth Disease. Success would motivate adapting the same development platforms to a plethora of other forms of rare genetic disease. In addition, this proposal aims to establish safer and more effective delivery of genome editors by adeno-associated viral (AAV) vectors, which would be best suited to access the target tissues to correct the above disorders. While AAV delivery of genome editors has proven to be effective in a range of mouse models of genetic disease, it has not been deployed in the clinic due to concerns of continued off-target editing and immunogenicity of the editor. This proposal will overcome the limitations that prevent adapting base editor and prime editor tools to drug- inducible vectors. By establishing potent and drug inducible genome editing AAVs, it will be possible to avoid sustained off-target editing and immunogenicity once the therapeutic editing is achieved.