ATXN2 Knockout Mitigates TDP-43–Induced Transcriptomic Dysregulation in ALS Motor Neurons

Amyotrophic lateral sclerosis (ALS) is a devastating progressive neurodegenerative disorder characterized by the loss of motor neurons in the brain and spinal cord. TDP-43 proteinopathy is a hallmark of nearly all ALS cases. This study reanalyzed transcriptome RNA-seq dataset GSE261875 and characterized transcriptomic changes induced by nuclear overexpression of wild-type TDP-43 (wTDP) and cytoplasmic mislocalization of TDP-43 (cTDP) in human iPSC-derived motor neurons, and ascertained the effects of CRISPR-mediated ATXN2 knockout (AKO) on these cells. PCA plots revealed distinct clusters of wTDP, cTDP and Neg CTRL. DEG analysis between wTDP and Neg CTRL yielded 3,222 up- and 3,302 down-regulated DEGs, while that between cTDP and Neg CTRL identified 2,828 up- and 2,949 down-regulated DEGs. Shared DEGs (964 up, 820 down) between wTDP and cTDP were enriched for ALS-relevant pathways. Further, PCA plots revealed distinct clusters of wTDP-AKO, cTDPAKO, wTDP, and cTDP. ATXN2 knockout reversed many TDP-43–induced changes, including 2,794 upand 2,956 down-regulated DEGs between wTDP-AKO and wTDP groups, and 3,024 up- and 2,838 downregulated DEGs between cTDP-AKO and cTDP groups. Integration of shared DEGs between the two TDP-43–induced and ATXN2-reversed groups defined a core signature list comprising 125 pathogenic and 222 protective genes that may be potential biomarkers to ALS pathogenesis and its attenuation. The identification of both pathogenic and protective gene signatures provides novel molecular insights into ALS pathogenesis and highlights ATXN2 as a promising therapeutic target. These findings not only refine candidate biomarker panels for ALS but also open new ways for targeted therapy.