TDP-43 overexpression induces cellular dysfunction and ALS-associated transcriptional changes

Transactive response DNA-binding protein (TDP-43) plays a key pathological role in several neurodegenerative diseases, particularly amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Despite the well-established role of TDP-43 in neurodegenerative disorders, it remains a complex area of study as it is unclear whether nuclear loss-of-function, cytoplasmic gain-of-function, or both drive pathogenesis. TDP-43 overexpression models are advantageous tools when developing drug candidates targeted at TDP-43, however, existing models often lack comprehensive RNA-seq data benchmarked against patient datasets. Given the value of TDP-43 overexpression as a model of ALS-related pathology, we have developed a stable, inducible system in a HEK293-derived cell line, offering a practical and scalable platform to investigate TDP-43 dysregulation. Utilizing this system, we found that TDP-43 overexpression reflected key features associated with ALS pathology, causing cytotoxicity, nucleocytoplasmic mislocalization, and extensive transcriptomic changes. Furthermore, comparative RNA-seq analysis between this model and ALS patient-derived data revealed substantial overlaps, where 64% of the differentially expressed genes in the TDP-43 overexpression cell line were also found to be altered in ALS patient tissue, supporting the disease relevance of the model. Genes of interest identified in the analysis included NUP85 , SREBF2 , VAMP5 , WDR41 , CDC23 , DKC1 , and PTS . This stable, inducible TDP-43 overexpression model and its associated transcriptomic dataset provide a versatile platform for ALS and other TDP-43 proteinopathy research, enabling the investigation of molecular drivers of TDP-43 dysfunction, the identification of potential disease-relevant pharmacological targets, and the evaluation of therapeutic candidates aimed at mitigating TDP-43 driven cytotoxicity or restoring normal TDP-43 localization.