Recognition of c9orf72 Mutant RNA by Single-Stranded Silencing RNAs

Mutations within the chromosome 9 open reading frame 72 (c9orf72) gene are associated with both familial amyotrophic lateral sclerosis and frontotemporal dementia. The mutation leads to an expanded GGGGCC hexanucleotide repeat within the first intron of c9orf72 and an expanded CCCCGG repeat within a corresponding antisense transcript. Both the mutant intronic and antisense RNAs have been implicated in disease. We have previously reported that duplex RNAs complementary to the repeats can recognize disease-causing RNA and block detection of nuclear foci formed by the mutant transcripts. Here, we test the hypothesis that inhibition can also be achieved by single-stranded silencing RNAs (ss-siRNAs). ss-siRNAs are single-stranded antisense oligonucleotides (ASOs) that function through RNAi interference (RNAi) to silence gene expression. ss-siRNAs can block the expanded repeats within both intronic RNA and the antisense transcripts. Inhibition is more potent than by analogous duplex RNAs. Our data suggest that the potent effects on foci are caused by a combination of mechanisms including RNAi and direct binding of the ss-siRNA to the target transcripts. These findings reinforce the suggestion that ss-siRNAs combine the favorable properties of duplex RNA and single-stranded ASOs.