FUS ALS-causative mutations impact FUS autoregulation and the processing of RNA-binding proteins through intron retention

Abstract

Mutations in the RNA binding protein FUS cause amyotrophic lateral sclerosis (ALS), a devastating neurodegenerative disease in which the loss of motor neurons induces progressive weakness and death from respiratory failure, typically only 3-5 years after onset.FUS has been established to have a role in numerous aspects of RNA processing, including splicing. However, the impact of ALS-causative mutations on splicing has not been fully characterised, as most disease models have been based on FUS overexpression, which in itself alters its RNA processing functions. To overcome this, we and others have recently created knock-in models, and have generated high depth RNA-sequencing data on FUS mutants in parallel to FUS knockout. We combined three independent datasets with a joint modelling approach, allowing us to compare the mutation-induced changes to genuine loss of function. We find that FUS ALS-mutations induce a widespread loss of function on expression and splicing, with a preferential effect on RNA binding proteins. Mutant FUS induces intron retention changes through RNA binding, and we identify an intron retention event in FUS itself that is associated with its autoregulation. Altered FUS regulation has been linked to disease, and intriguingly, we find FUS autoregulation to be altered not only by FUS mutations, but also in other genetic forms of ALS, including those caused by TDP-43,

Intron retention is a robust marker of intertumoral heterogeneity in pancreatic ductal adenocarcinoma

“…Introns that are differentially retained in the FUS oncogene have been observed as recurrent events in cancers from many different tissues 25 , and FUS has been shown to affect proliferation of PDAC cells 83 . In particular, FUS mutations and deletions result in changes in gene expression and splicing changes, especially intron retention, affecting genes enriched in RNA-binding proteins 84 . SF3B1, a splicing factor and oncogene 31 , 70 , 71 , is consistently mutated in pancreatic cancer 85 .…”

The identification of protein and RNA interactors of the splicing factor Caper in the adult Drosophila nervous system

“…We find that Caper binds to its own mRNA. It is not unusual for RBPs and alternative splicing factors to engage in auto-regulation of their own mRNAs ( Dredge et al, 2005 ; Buratti and Baralle, 2012 ; Humphrey et al, 2019 ; Müller-Mcnicoll et al, 2019 ). It should be noted that caper has seven different spliceforms, five of which contain poison exons, exons that contain premature termination codons (PTCs) that either result in nonsense mediated decay or the translation of a truncated protein.…”

Low Level of Expression of C-Terminally Truncated Human FUS Causes Extensive Changes in the Spinal Cord Transcriptome of Asymptomatic Transgenic Mice

“…Therefore, it was not surprising that mRNA encoding proteins involved in RNA metabolism were barely represented in L-FUS DEGs in contrast to high representation of these mRNA in DEGs identified in studies of mouse lines expressing low levels of FUS variants with intact RNAbinding domains [38,40,43].…”

“…an inadequate functionality of deltaNLS FUS that remains nuclear in neurons of studied mice. Between identified DEGs, the most prominent changes common for knockout and knock-in, as well as specific for homozygous knock-in mice were upregulation for those that code for proteins involved in RNA metabolism and downregulation of those that code for proteins involved in synaptic transmission [43]. This is consistent with considerable changes of splicing pattern identified in these studies and the growing body of evidence that defects of synaptic transmission, particularly in the neuromuscular junctions, are very early events in the development of pathology in animal models and FUS-ALS.…”