TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A

Abstract

Variants of UNC13A, a critical gene for synapse function, increase the risk of amyotrophic lateral sclerosis and frontotemporal dementia1–3, two related neurodegenerative diseases defined by mislocalization of the RNA-binding protein TDP-434,5. Here we show that TDP-43 depletion induces robust inclusion of a cryptic exon in UNC13A, resulting in nonsense-mediated decay and loss of UNC13A protein. Two common intronic UNC13A polymorphisms strongly associated with amyotrophic lateral sclerosis and frontotemporal dementia risk overlap with TDP-43 binding sites. These polymorphisms potentiate cryptic exon inclusion, both in cultured cells and in brains and spinal cords from patients with these conditions. Our findings, which demonstrate a genetic link between loss of nuclear TDP-43 function and disease, reveal the mechanism by which UNC13A variants exacerbate the effects of decreased TDP-43 function. They further provide a promising therapeutic target for TDP-43 proteinopathies.

RNA targets of TDP-43: Which one is more important in neurodegeneration?

“…In studies to identify other key functional targets of TDP-43 that may directly contribute to disease pathogenesis, Ma et al [ 7 ] and Brown et al [ 8 ] identified novel cryptic exons regulated by TDP-43, including one in UNC13A (Fig. 1 ).…”

“…This dataset was obtained after separating TDP-43-positive and TDP-43-negative neuronal nuclei in ALS/FTD patient postmortem brains to identify transcriptomic changes caused by nuclear TDP-43 depletion. Similarly, Brown et al did an RNA-seq analysis of human neurons derived from induced pluripotent stem cells (iPSCs) after depletion of TDP-43 by CRISPR inhibition [ 8 ]. Among dozens of novel cryptic exons, both groups identified UNC13A as one of the most robust mis-spliced genes.…”

“…Among dozens of novel cryptic exons, both groups identified UNC13A as one of the most robust mis-spliced genes. Brown et al also detected a mis-splicing event in another UNC13 family member, UNC13B [ 8 ].…”

“…They found that TDP-43 depletion caused inclusion of the cryptic exon in the UNC13A transcript, confirming a role for TDP-43 in suppressing cryptic exons. This effect seems to be direct, as TDP-43 has a binding site within the intron containing the cryptic exon in UNC13A mRNA [ 7 , 8 ]. Moreover, they found that the UNC13A RNA containing the cryptic exon and a PTC is a degradation target of NMD, resulting in reduced levels of UNC13A mRNA and protein.…”

“…Moreover, they found that the UNC13A RNA containing the cryptic exon and a PTC is a degradation target of NMD, resulting in reduced levels of UNC13A mRNA and protein. This effect is distinct from that of aberrant STMN2 mRNA, which does not undergo NMD after cycloheximide treatment but is instead translated into a truncated STMN2 due to a predicted alternative polyA site in the cryptic exon [ 8 ].…”