Transcriptome sequencing reveals aberrant alternative splicing in Huntington's disease

Abstract

Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by a CAG expansion in the gene-encoding Huntingtin (HTT). Transcriptome dysregulation is a major feature of HD pathogenesis, as revealed by a large body of work on gene expression profiling of tissues from human HD patients and mouse models. These studies were primarily focused on transcriptional changes affecting steady-state overall gene expression levels using microarray based approaches. A major missing component, however, has been the study of transcriptome changes at the post-transcriptional level, such as alternative splicing. Alternative splicing is a critical mechanism for expanding regulatory and functional diversity from a limited number of genes, and is particularly complex in the mammalian brain. Here we carried out a deep RNA-seq analysis of the BA4 (Brodmann area 4) motor cortex from seven human HD brains and seven controls to systematically discover aberrant alternative splicing events and characterize potential associated splicing factors in HD. We identified 593 differential alternative splicing events between HD and control brains. Using two expanded panels with a total of 108 BA4 tissues from patients and controls, we identified four splicing factors exhibiting significantly altered expression levels in HD patient brains. Moreover, follow-up molecular analyses of one splicing factor PTBP1 revealed its impact on disease-associated splicing patterns in HD. Collectively, our data provide genomic evidence for widespread splicing dysregulation in HD brains, and suggest the role of aberrant alternative splicing in the pathogenesis of HD.

Small interfering RNAs based on huntingtin trinucleotide repeats are highly toxic to cancer cells

“…These results suggest that established tumors respond to the siCAG/CUG treatment. This was confirmed in another experiment in which 10 6 HeyA8 cells were injected and mice were first treated 3 times a week and then switched to daily treatment 19 days after tumor cell injection (data not shown).…”

“…Another mechanism by which CAG/CUG TNRs could be toxic at the RNA level is by interfering with cellular splicing. This has been shown for CUG in DM1 [9] and CAG in HD [10].…”

“…Another mechanism by which CAG/CUG TNRs could be toxic at the RNA level is by interfering with cellular splicing. This has been shown for CUG in DM1 [9] and CAG in HD [10].Mounting evidence suggests the CAG TNR expansions are toxic at the RNA level. It was shown in Drosophila that the toxicity of the CAG repeat disease gene spinocerebellar ataxia type 3 (SCA3) protein ataxin-3, is in large part caused by the trinucleotide repeat RNA and not the polyQ protein [11].…”

Quantitative Proteomic Analysis Reveals Similarities between Huntington’s Disease (HD) and Huntington’s Disease-Like 2 (HDL2) Human Brains

“…Table S5 lists around 200 proteins that changed in abundances in our study and in at least one of the three transcriptomics 44,55,56 or two proteomics studies, 26,27 or have been identified as Htt interactors in one out of two previous Htt interaction studies. 21,57 The most comparable to our work is the gene profiling study by Hodges and coworkers 44 performed on several human brain regions, including cortex.…”

“…Out of these 25 genes, we found 11 corresponding proteins that changed concordantly. In addition, the most recent RNA-seq study, performed on comparable human brain region, 56 includes 224 differentially expressed genes in HD versus controls. 56 The common genes between the above and our study are also included in Table S5.…”