Base editing of trinucleotide repeats reduces somatic repeat expansions in Huntington disease and Friedreich ataxia patient cells and in mice
Trinucleotide repeat (TNR) diseases are neurological disorders that affect ~ 1 in 3,000 individuals worldwide and are caused by genomic expanded trinucleotide repeats that become unstable in somatic cells in a length-dependent manner. The most common pathogenic triplet base pair sequence, CAG/CTG, occurs in roughly one third of all known pathogenic TNR loci, including the HTT gene that causes Huntington disease (HD). The most prevalent hereditary ataxia in humans, Friedreich ataxia (FRDA), is caused by expansion of GAA repeats at the FXN locus. Currently there are no approved interventions that effectively halt progression of these diseases. We describe genome editing approaches that target pathogenic trinucleotide repeats to reduce the repetitiveness of these repeats in patient cells and in mice. We use cytosine and adenine base editing to introduce G:C-to-A:T interruptions at CAG repeats and A:T-to-G:C interruptions at GAA repeats, respectively, to reproduce naturally occurring, stable, non-pathogenic alleles that are found in the general population. AAV9 delivery of optimized base editors in the Htt.Q111 mouse model of HD and the YG8s mouse model of FRDA resulted in efficient repeat interruption in transduced tissues in vivo, and significantly reduced repeat expansions in the CNS. These findings establish for the first time that introducing interruptions in trinucleotide repeats of pathogenic length can reduce a key disease-associated neurological feature of these repeat tracts in animal models of two TNR diseases.