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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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE167557 | GEO | 2024/02/23

REPOSITORIES: GEO

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Project description:Aims: Loss of nuclear TDP-43 characterises sporadic and most familial forms of amyotrophic lateral sclerosis (ALS). TDP-43 (encoded by TARDBP) has multiple roles in RNA processing. We aimed to determine whether 1) RNA splicing dysregulation is present in lower motor neurons in ALS and in a motor neuron-like cell model, and 2) TARDBP mutations (mtTARDBP) are associated with aberrant RNA splicing using patient-derived fibroblasts. Methods: Affymetrix exon arrays were used to study mRNA expression and splicing in lower motor neurons obtained by laser capture microdissection of autopsy tissue from individuals with sporadic ALS and TDP-43 proteinopathy. Findings were confirmed by qRT-PCR and in NSC34 motor neuronal cells following shRNA-mediated TDP-43 depletion. Exon arrays and immunohistochemistry were used to study mRNA splicing and TDP-43 expression in fibroblasts from patients with mtTARDBP-associated, sporadic and mutant SOD1-associated ALS. Results: We found altered expression of spliceosome components in motor neurons and widespread aberrations of mRNA splicing that specifically affected genes involved in ribonucleotide binding. This was confirmed in TDP-43 depleted NSC34 cells. Fibroblasts with mtTARDBP showed loss of nuclear TDP-43 protein and demonstrated similar changes in splicing and gene expression, that were not present in fibroblasts from patients with sporadic or SOD1-related ALS. Conclusion: Loss of nuclear TDP-43 is associated with RNA processing abnormalities in ALS motor neurons, patient-derived cells with mtTARDBP, and following artificial TDP-43 depletion, suggesting that splicing dysregulation directly contributes to disease pathogenesis. Key functional pathways affected include those central to RNA metabolism. RNA was extracted from fibroblasts grown from neurologically healthy controls (n=6) and 3 groups of patients with ALS: 1) sporadic cases (n=6); 2) cases due to mutations of SOD1 (n=4); 3) cases due to mutations of TARDBP (n=3). The three ALS groups were compared to the controls.

Project description:Aims: Loss of nuclear TDP-43 characterises sporadic and most familial forms of amyotrophic lateral sclerosis (ALS). TDP-43 (encoded by TARDBP) has multiple roles in RNA processing. We aimed to determine whether 1) RNA splicing dysregulation is present in lower motor neurons in ALS and in a motor neuron-like cell model, and 2) TARDBP mutations (mtTARDBP) are associated with aberrant RNA splicing using patient-derived fibroblasts. Methods: Affymetrix exon arrays were used to study mRNA expression and splicing in lower motor neurons obtained by laser capture microdissection of autopsy tissue from individuals with sporadic ALS and TDP-43 proteinopathy. Findings were confirmed by qRT-PCR and in NSC34 motor neuronal cells following shRNA-mediated TDP-43 depletion. Exon arrays and immunohistochemistry were used to study mRNA splicing and TDP-43 expression in fibroblasts from patients with mtTARDBP-associated, sporadic and mutant SOD1-associated ALS. Results: We found altered expression of spliceosome components in motor neurons and widespread aberrations of mRNA splicing that specifically affected genes involved in ribonucleotide binding. This was confirmed in TDP-43 depleted NSC34 cells. Fibroblasts with mtTARDBP showed loss of nuclear TDP-43 protein and demonstrated similar changes in splicing and gene expression, that were not present in fibroblasts from patients with sporadic or SOD1-related ALS. Conclusion: Loss of nuclear TDP-43 is associated with RNA processing abnormalities in ALS motor neurons, patient-derived cells with mtTARDBP, and following artificial TDP-43 depletion, suggesting that splicing dysregulation directly contributes to disease pathogenesis. Key functional pathways affected include those central to RNA metabolism. RNA was extracted from lower motor neurons obtained by laser capture microdissection from autopsy material from neurologically healthy controls (n=6) and cases of sporadic ALS (n=3) and ALS due to C9ORF72 mutations (n=3).

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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

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