FUS mutant human motoneurons transcriptome analysis reveals altered pathways and impairment of microRNA function

Mutations in the RNA-binding protein FUS have been genetically linked to Amyotrophic Lateral Sclerosis (ALS), a neurodegenerative disease caused by the death of motoneurons (MNs). FUS is a ubiquitous protein and the mechanisms leading to selective MN loss downstream of FUS mutations are still largely unknown. We report the first transcriptome analysis of human purified MNs, obtained from isogenic induced Pluripotent Stem Cells (iPSCs) with a FUS wild-type or mutant genetic background. Gene ontology analysis of differentially expressed genes identified significant enrichment of pathways previously associated to other neurological diseases and non-FUS ALS, suggesting a common pathological mechanism. We also found several microRNAs deregulated in FUS mutant MNs and focused on miR-375 and miR-125b. Notably, miR-125b is a neural-enriched microRNA with multiple functions in the nervous system and miR-375 had been previously associated to MN survival. We report that relevant targets of both microRNAs, including the neural RNA-binding protein ELAVL4 and apoptosis factors such as p53, are aberrantly increased in FUS mutant MNs. Characterization of FUS RNA targets in the cell type primarily affected by the disease contributes to the definition of the pathogenic mechanisms of FUS-linked ALS. Overall design: High-throughput sequencing of total RNA from human iPSC-derived motoneurons Hb9::GFP-positive (day12), 2 replicates; human iPSC-derived neural cells Hb9::GFP-negative (depleted of motoneurons, day12), 2 replicates; human iPSC-derived motoneurons FUS-WT (day12+7), 3 replicates; human iPSC-derived motoneurons FUS-P525L/P525L mutant (day 12+7), 3 replicates. High-throughput sequencing of small RNA from human iPSC-derived motoneurons FUS-WT (day12+7), 3 replicates; human iPSC-derived motoneurons FUS-P525L/P525L mutant (day 12+7), 3 replicates.