GSE162943
Characterization of C9orf72 haplotypes to evaluate the effects of normal and pathological variations on its expression and splicing
Expansion of the hexanucleotide repeat (HR) in the first intron of the chromosome 9 open reading frame 72 (C9orf72) gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) in Caucasians. All C9orf72 ALS/FTD patients share a common risk (R) haplotype, but its single nucleotide polymorphism (SNP) signature has not been fully characterized. Here, we characterized the C9orf72 haplotypes in Europeans and created a detailed molecular map, including HR length, for each haplotype. By analyzing RNA-seq reads and sequencing chromatograms that overlap with heterozygous SNP sites, we identified allelic differences in C9orf72 expression in normal subjects and ALS patients. In cells from healthy individuals, upstream promoter transcript levels increased with increased HR length. Intron 1 levels were higher in one of the non-R haplotypes due to SNP variation, and in R haplotype with 10 or more HR units. In pathological HR expansion, we observed the highest levels of intron 1 that were accompanied by aberrantly spliced transcripts at cryptic donor sites downstream of the expanded HR. Intron 1 retention was associated with sequential intron 2 retention. The SNP signature of C9orf72 haplotypes described here enables allele-specific analysis of transcriptional products and may pave the way to allele-specific therapeutic strategies. Overall design: Expression profiling by high throughput sequencing of human primary fibroblasts and iPSCs of control and C9orf72-ALS patients. Three C9orf72-ALS primary fibroblasts samples were compared to two control samples. Three samples from each condition were taken for iPSCs.