TDP-43 and other hnRNPs regulate cryptic exon inclusion of a key ALS/FTD risk gene, UNC13A

Abstract

A major function of TAR DNA-binding protein-43 (TDP-43) is to repress the inclusion of cryptic exons during RNA splicing. One of these cryptic exons is in UNC13A, a genetic risk factor for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The accumulation of cryptic UNC13A in disease is heightened by the presence of a risk haplotype located within the cryptic exon itself. Here, we revealed that TDP-43 extreme N-terminus is important to repress UNC13A cryptic exon inclusion. Further, we found hnRNP L, hnRNP A1, and hnRNP A2B1 bind UNC13A RNA and repress cryptic exon inclusion, independently of TDP-43. Finally, higher levels of hnRNP L protein associate with lower burden of UNC13A cryptic RNA in ALS/FTD brains. Our findings suggest that while TDP-43 is the main repressor of UNC13A cryptic exon inclusion, other hnRNPs contribute to its regulation and may potentially function as disease modifiers.

Induced pluripotent stem cells‐based disease modeling, drug screening, clinical trials, and reverse translational research for amyotrophic lateral sclerosis

“…This suggests the merit of ASO targeting STMN2 cryptic splicing for clinical application. TDP-43 also acts as a main repressor of the inclusion of UNC13A cryptic exons, which is a genetic risk factor for ALS and frontotemporal dementia (FTD) (Brown et al, 2022;Koike et al, 2023;Ma et al, 2022;Mehta et al, 2023). How the inclusion of UNC13A cryptic exons is involved in the pathogenesis of these ALS/FTD remains to be elucidated.…”

Elevated nuclear TDP-43 induces constitutive exon skipping

“…Loss of TDP-43 function has been linked to neurodegeneration via disruptions in the splicing repression of nonconserved cryptic exons (7,(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28). Indeed, compelling evidence from recent studies suggests that cryptic exons found in the genes STMN2 (16)(17)(18) and UNC13A (21,22) may contribute significantly to disease pathogenesis.…”

Single-nucleus multiomic atlas of frontal cortex in amyotrophic lateral sclerosis with a deep learning-based decoding of alternative polyadenylation mechanisms

“…Leveraging high depth 3'-end sequencing, we found a widespread switch towards distal polyadenylation (PA) site usage across ALS subtypes relative to controls. To explore this differential alternative PA (APA), we developed APA-Net, a deep neural network model that uses transcript sequence and expression levels of RNA-binding proteins (RBPs) to predict cell-type specific APA usage and RBP interactions likely to regulate APA across disease subtypes.The molecular underpinnings of cortical dysfunction associated with FTLD in ALS remain unclear but has been linked with changes in expression and/or subcellular localizations of various RNA binding proteins (RBPs), including TDP-43 7-10 , the most prevalent disease pathology in ALS/FTLD, as well as FUS 11 , SFPQ 12,13 , TIA1 14 , and heterogeneous ribonucleoproteins (HNRNPs) 15,16 . RBPs regulate diverse functions across cell types, including chromatin dynamics 10,[17][18][19] , transcription 7-10 , auto-regulation 20,21 , alternative splicing (AS) 8 , and alternative polyadenylation (APA) 20,[22][23][24][25] .…”

“…The molecular underpinnings of cortical dysfunction associated with FTLD in ALS remain unclear but has been linked with changes in expression and/or subcellular localizations of various RNA binding proteins (RBPs), including TDP-43 7-10 , the most prevalent disease pathology in ALS/FTLD, as well as FUS 11 , SFPQ 12,13 , TIA1 14 , and heterogeneous ribonucleoproteins (HNRNPs) 15,16 . RBPs regulate diverse functions across cell types, including chromatin dynamics 10,[17][18][19] , transcription 7-10 , auto-regulation 20,21 , alternative splicing (AS) 8 , and alternative polyadenylation (APA) 20,[22][23][24][25] .…”