ALS/FTD GWAS risk variant rs12973192 promotes severe cryptic splicing of the UNC13A transcript upon TDP-43 depletion

Tar DNA-binding protein 43 (TDP-43) is a primarily nuclear RNA-binding protein which is depleted from the nucleus and aggregated in the cytosol of neurons in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). TDP-43 represses the inclusion of aberrant cryptic exons which often lead to downregulation of the transcripts. By knocking down TDP-43 in human induced pluripotent stem cell (iPSC)-derived neurons, we uncover a novel cryptic exon in the presynaptic gene UNC13A. This cryptic exon leads to downregulation of UNC13Aon both the RNA and protein level after TDP-43 depletion. UNC13A crypticis in the same intron as two ALS/FTD GWAS risk associated SNPS, and throughmini-gene assays and isothermal titration calorimetry we show that one of these, rs12973192, causes increased inclusion of UNC13A cryptic exon by reducing the binding affinity of TDP-43. We propose that ALS/FTD risk SNP rs12973192 increases neuronal vulnerability to TDP-43 depletion by lowering binding affinity of TDP-43 and increasing inclusion of a cryptic exon that leads to the downregulation of critical presynaptic protein UNC13A.