Selective targeting of mutant <i>huntingtin</i> intron 1 improves rescue provided by antisense oligonucleotides in Huntington’s disease mice

Huntington's disease (HD) arises from the toxic gain of function caused by a CAG expansion in the coding region of the <i>huntingtin</i> (<i>HTT</i>) gene. HD is increasingly appreciated to emerge from multiple pathogenic processes, including somatic instability in mutant <i>HTT</i>'s (<i>mHTT</i>) CAG repeat tract, which leads to diverse deleterious consequences. These include the alternative processing of <i>HTT</i> pre-mRNA to generate the <i>HTT1a</i> transcript that encodes the very toxic mHTT isoform referred to as HTT1a. We set out to compare the efficacy and safety of allele-selective lowering of mHTT with those of non-allele-selective lowering using antisense oligonucleotides (ASOs) in heterozygous <i>Htt^Q111</i> (Q111) mice. We developed a mutant-specific ASO (MutASO) targeting <i>Htt</i> intron 1 that selectively reduced mutant full-length HTT, as well as HTT1a, in the brains of Q111 mice. Compared with the rescue provided by a panallele-targeting ASO (PanASO) that lowers wild-type HTT and full-length mHTT (sparing HTT1a), the MutASO essentially eliminated aggregate formation and provided marked protection from transcriptional dysregulation in HD knockin mice. Thus, by targeting the ASO to the region upstream of the cryptic polyadenylation sites required to generate the <i>HTT1a</i> transcript, our allele-selective MutASO potently reduced HTT1a transcript and protein levels. Our findings suggest that HTT1a may have a disproportionate impact on aggregate formation and transcriptional dysregulation and that lowering the levels of HTT1a could provide benefit when designing HTT-lowering-based therapeutic strategies for HD.