Non-coding RNA in C9orf72-related amyotrophic lateral sclerosis and frontotemporal dementia: A perfect storm of dysfunction

Abstract

A hexanucleotide repeat expansion in the first intron/promoter region of C9orf72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Both sense and antisense transcripts exist at the C9orf72 locus but the function of the antisense lncRNA is unknown. RNA toxicity of the transcribed repeat expansion has been implicated in the pathogenesis of C9orf72-related ALS/FTD, not only through direct sequestration of important RNA binding proteins but also indirectly through non-ATG dependent translation into dipeptide repeats. Formation of RNA/DNA hybrid R-loops may also play a key role in the pathogenesis of this condition and this mechanism could provide a link between the repeat expansion, DNA damage, repeat instability and deficiency of RNA binding proteins. Non-coding C9orf72 antisense transcripts could also act to epigenetically regulate gene expression at the locus. The potential effects of such non-coding RNAs should be considered in the design of antisense oligonucleotide therapeutics for C9orf72-related ALS/FTD. Furthermore, the mechanisms of RNA dysregulation exemplified by C9orf72-related disease may help illustrate more broadly how a "perfect storm" of dysfunction occurs in ALS/FTD and how targeting these factors could lead to corrective or preventative therapies.

Keywords: ALS; Amyotrophic lateral sclerosis; C9orf72; FTD; Frontotemporal dementia; Non-coding RNA.

Fig. 1

Transcripts of C9orf72. A. Human C9orf72 has three annotated RefSeq transcripts but at least two additional transcripts utilising an alternative first exon 1c have also been described (transcripts 4 and 5), as have natural antisense transcripts (NATs) [46].

Fig. 2

The region upstream of the C9orf72 locus. A. A degree of sequence conservation is present among mammals upstream of C9orf72. B. The mouse C9orf72 orthologue locus (3110043O21Rik) also exhibits a NAT (Gm12367). C. miRBase analysis of the kilobase of sequence immediately upstream of C9orf72 exon 1a reveals a putative miR-511-5p binding site. D. The stem-loop structure of miR-511 (image from miRbase).

Fig. 3

Potential non-coding RNA effects in C9orf72-related ALS/FTD. Bidirectional transcription across the (GGGGCC)_n repeat expansion may lead to aberrant R-loop formation, predisposing the exposed DNA strands to damage, which in turn can lead to repeat instability through aberrant DNA repair. Bidirectional transcription may also lead to transcriptional interference between sense and antisense transcripts. Polymerase stalling may generate abortive transcripts and in the sense direction these can form G-quadruplex-containing RNA foci, which sequester RNA binding proteins such as SRSF1, Pur-α and hnRNP-H, leading to splicing dysregulation. Concurrently, repeat-containing transcripts undergo repeat-associated non-ATG dependent translation, forming dipeptide repeats that impact upon cellular stress at multiple levels such as through impaired nucleocytoplasmic transport and ubiquitin-proteasome function and through nucleolar stress. The natural antisense transcript of C9orf72 may induce downregulation through the RNAi pathway and may also potentially bind miRNAs relevant to neuronal function. Epigenetic modifiers such as the repressive PRC2 complex may be recruited to the locus, leading to histone trimethylation, chromatin compaction and DNA methylation.