GSE167557
Transcriptome profiling (RNA-seq) to identify aberrant splicing events in induced pluripotent stem cells derived from an ALS patient harboring a TDP-43(M337V) mutation
Mutations in the TDP-43 gene (also called TARDBP), which encodes transactive response DNA-binding protein 43 (TDP-43), have been found in 1–5% of sporadic and familial cases of the devastating adult-onset neurodegenerative disorder amyotrophic lateral sclerosis (ALS). TDP-43 is a predominantly nuclear RNA/DNA-binding protein that has diverse roles in RNA processing, but in diseased motor neurons it is depleted from the nucleus and sequestered into cytoplasmic protein aggregates that are a hallmark of the disease. How the loss of the RNA/DNA-binding activity of TDP-43 contributes to ALS pathogenesis is largely unknown. Using a large-scale RNAi screening approach, we recently identified TDP-43 as a gene required for maintaining genomic stability. We showed that induced pluripotent stem cells (iPSCs) and neurons derived from ALS patients harboring TDP-43 mutations are defective in two major pathways for repair of DNA double-strand breaks, non-homologous end joining and homologous recombination. Accordingly, TDP-43-mutant ALS iPSCs and neurons display increased DNA damage, which we also observed in brain tissues from ALS mice harboring a knock-in ALS-linked Tdp-43 mutation and from human ALS patients. To gain insight into the mechanistic basis by which ALS-associated TDP-43 mutants result in increased DNA damage, we performed transcriptome profiling (RNA-seq) in TDP-43-mutant ALS iPSCs, and found aberrant alternative pre-mRNA splicing of a number of genes involved in DNA repair. Our results suggest a role for TDP-43 in DNA repair and reveal a previously unknown mechanism that likely contributes to the pathogenesis of ALS harboring TDP-43 mutations. Overall design: Paired-end RNA-seq to compare splicing events in TDP-43 (WT) and TDP-43(M337V) ALS iPSCs