An alternative cytoplasmic SFPQ isoform with divergent phase separation potential is upregulated in ALS

Splicing factor proline- and glutamine-rich (SFPQ) is an RNA-binding protein that broadly regulates RNA metabolism. Although its nuclear roles are well-studied, evidence of SFPQ’s cytoplasmic functionality is emerging. Altered expression and nuclear-to-cytoplasmic mislocalisation of SFPQ is a hallmark of amyotrophic lateral sclerosis (ALS), yet the mechanistic basis of this remains undetermined. We identified altered SFPQ splicing in ALS, increasing the expression of an alternative mRNA isoform lacking a nuclear localisation sequence, which we termed ‘altSFPQ’. We find that altSFPQ mRNA contributes to SFPQ autoregulation and is highly unstable yet exhibits context-specific translation with cytoplasm-predominant localisation. Notably, reduced canonical SFPQ coincides with increased altSFPQ transcript expression in familial and sporadic ALS models, providing a mechanistic basis for SFPQ nuclear-to-cytoplasmic mislocalisation in ALS patients. Finally, we observe that altSFPQ protein has reduced phase separation potential and differential protein binding compared to its canonical counterpart, providing insight into its mechanistic relevance to ALS.