Widespread intron retention impairs protein homeostasis in C9orf72 ALS brains
Abstract
The GGGGCC hexanucleotide expansion in C9orf72 (C9) is the most frequent known cause of Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD), yet a clear understanding of how C9 fits into the broader context of ALS/FTD pathology has remained lacking. The repetitive RNA derived from the C9 repeat is known to sequester hnRNP H, a splicing regulator, into insoluble aggregates, resulting in aberrant alternative splicing. Furthermore, hnRNP H insolubility and altered splicing of a robust set of targets have been observed to correlate in C9 and sporadic ALS/FTD patients alike, suggesting that changes along this axis are a core feature of disease pathogenesis. Here, we characterize previously uncategorized RNA splicing defects involving widespread intron retention affecting almost 2,000 transcripts in C9ALS/FTD brains exhibiting a high amount of sequestered, insoluble hnRNP H. These intron retention events appear not to alter overall expression levels of the affected transcripts, but rather the protein-coding regions. These retained introns affect transcripts in multiple cellular pathways predicted to be involved in C9 as well as sporadic ALS/FTD etiology, including the proteasomal and autophagy systems. The retained intron pre-mRNAs display a number of characteristics, including enrichment of hnRNP H-bound splicing enhancer motifs and a propensity for G-Q formation, linking the defective splicing directly to high amounts of sequestered hnRNP H. Together, our results reveal previously undetected splicing defects in high insoluble hnRNP H-associated C9ALS brains, suggesting a feedback between effective RNA-binding protein dosage and protein quality control in C9, and perhaps all, ALS/FTD.
- Received May 1, 2020.
- Accepted October 5, 2020.
- Published by Cold Spring Harbor Laboratory Press
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