IDENTIFICATION OF NEURONAL SUBTYPE-SPECIFIC SPLICE VARIANTS IN IPSC-DERIVED CELL MODELS OF ALS AND FTD

Amyotrophic lateral sclerosis (ALS) is characterised by the premature degeneration of upper and lower motor neurons. Many patients have cytoplasmic inclusions positive for the TDP-43 protein independent of the aetiology. TDP-43 is a nucleic acid-binding protein and is involved in gene regulation and the processing of RNA. Mutations in TARDBP, encoding TDP-43, can cause age-related TDP-43 aggregation and nuclear depletion, leading to pathogenic alternative mRNA splicing.

To discover neuron-specific TDP-43 targets, we used bulk RNA-sequencing to identify splice variants in our ioGlutamatergic and ioMotor Neurons carrying the heterozygous or homozygous M337V mutation in TARDBP. We used MAJIQ to compare the splice variants of TDP-43 WT/WT, TDP-43 M337V/WT and TDP-43 M337V/M337V neurons at different time points.

Comparative analysis of wild-type versus TDP-43 mutant cells revealed splice variants both unique to, and shared between, neuron subtypes. At day 30 of the culture, we identified multiple different splicing events when comparing wild-type to TDP-43 mutant cells. Previously reported splicing targets or ALS/FTD associated genes including SETD5, PRUNE2, CALD1 and DPP6, along with novel targets, were identified in this analysis.

Our data demonstrates that our iPSC-derived ALS/FTD cell models provide a platform to delineate TDP-43 function and identify cell specific target transcripts of TDP-43, and are valuable tools to study ALS/FTD and screen for drugs that can modulate the progression of these devastating diseases.