Protein Quality Control Failure Enables Toxic Gain-of-Function by TDP43 C-Terminal Fragments

C-terminal fragments (CTFs) of TDP43 accumulate in neurodegenerative disease, but whether pathology arises from loss of normal TDP43 function or from toxic gain-of-function effects of the fragments remain unresolved. To address this, we examined two disease-associated fragments, TDP43 ²¹⁹ and TDP43 ²⁴⁷ , in cultured neurons and in vivo in the presence of intact endogenous TDP43, thereby isolating fragment-specific effects. TDP43 ²⁴⁷ formed prominent cytoplasmic inclusions in neurons, whereas TDP43 ²¹⁹ remained largely soluble, reflecting differences in their susceptibility to protein quality control pathways. Proteomic profiling revealed that proteins detected in soluble CTF fractions were enriched for RNA splicing and post-transcriptional regulatory processes, whereas proteins detected in insoluble CTF fractions were enriched for translation-associated and metabolic pathways. Notably, accumulation of aggregation-prone TDP43 ²⁴⁷ disrupted pre-mRNA splicing of STMN2 and UNC13A , inducing cryptic exon inclusion and resulting in loss of Stathmin-2 protein. In vivo expression of TDP43 ²⁴⁷ in the mouse motor cortex induced motor impairments despite the continued presence of endogenous TDP43. Together, these findings demonstrate that an elevated aggregate load of TDP43 CTFs can drive neuronal dysfunction through a toxic gain-of-function mechanism, linking impaired clearance to RNA-processing defects in the presence of intact full-length TDP43.