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Homo sapiens

ABSTRACT: Transcriptome sequencing of iPSC-derived motor neurons with TPD-43 knockdown

PROVIDER: PRJDB19918 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR631711_1.fastq.gz	Fastqsanger.gz
	DRR631711_2.fastq.gz	Fastqsanger.gz
	DRR631712_1.fastq.gz	Fastqsanger.gz
	DRR631712_2.fastq.gz	Fastqsanger.gz
	DRR631713_1.fastq.gz	Fastqsanger.gz

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Premature polyadenylation-mediated loss of stathmin-2 is a hallmark of TDP-43-dependent neurodegeneration

Project description:Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are associated with loss of nuclear TDP-43. Here we identify that TDP-43 regulates expression of the neuronal growth-associated factor stathmin-2. Lowered TDP-43 levels, which reduce its binding to sites within the first intron of stathmin-2 pre-mRNA, uncover a cryptic polyadenylation site whose utilization produces a truncated, non-functional mRNA. Reduced stathmin-2 expression is found in neurons trans-differentiated from patient fibroblasts expressing an ALS-causing TDP-43 mutation, in motor cortex and spinal motor neurons from sporadic ALS patients and familial ALS patients with expansion in C9orf72, and in induced pluripotent stem cell (iPSC)-derived motor neurons depleted of TDP-43. Remarkably, while reduction in TDP-43 is shown to inhibit axonal regeneration of iPSC-derived motor neurons, rescue of stathmin-2 expression restores axonal regenerative capacity. Thus, premature polyadenylation-mediated reduction in stathmin-2 is a hallmark of ALS/FTD that functionally links reduced nuclear TDP-43 function to enhanced neuronal vulnerability.

2019-01-01 | GSE122069 | GEO

Novel Kinesin Family 1A Variants Linked to Atypical Parkinsonism Elicit Altered Neuronal TDP-43 Interactions and Dendritic Atrophy

Project description:We used patient induced pluripotent stem cells (IPSC) derived neurons from a patient with two mutations in KIF1A to evaluate the quantitative changes to KIF1A protein interaction, relative to wild-type control IPSC-motor neurons, using an anti-KIF1A antibody during immunoprecipitation. Given the related findings and interests of the study, we also compared the quantitative changes to TDP-43 protein interaction, using an anti-TDP-43 antibody during immunoprecipitation.

2025-08-26 | PXD067234 | Pride

Ribo-seq of iPSC-derived neurons with TDP-43 knockdown

Project description:TDP-43 is a key splicing regulator. Here, we perform ribosome profiling on iPSC-derived neurons to examine how translation is affected by TDP-43 knockdown.

2022-02-28 | E-MTAB-10235 | biostudies-arrayexpress

iPSC derived motor neuron cultures from C9ORF72 carriers

Project description:Amyotrophic lateral sclerosis (ALS) is a severe neurodegenerative condition characterized by loss of motor neurons in the brain and spinal cord. Expansions of a hexanucleotide repeat (GGGGCC) in the noncoding region of the C9ORF72 gene are the most common cause of the familial form of ALS (C9-ALS), as well as frontotemporal lobar degeneration and other neurological diseases. How the repeat expansion causes disease remains unclear, with both loss of function (haploinsufficiency) and gain of function (either toxic RNA or protein products) proposed. We report a cellular model of C9-ALS with motor neurons differentiated from induced pluripotent stem cells (iPSCs) derived from ALS patients carrying the C9ORF72 repeat expansion. No significant loss of C9ORF72 expression was observed, and knockdown of the transcript was not toxic to cultured human motor neurons. Transcription of the repeat was increased, leading to accumulation of GGGGCC repeat–containing RNA foci selectively in C9-ALS iPSC-derived motor neurons. Repeat-containing RNA foci colocalized with hnRNPA1 and Pur-?, suggesting that they may be able to alter RNA metabolism. C9-ALS motor neurons showed altered expression of genes involved in membrane excitability including DPP6, and demonstrated a diminished capacity to fire continuous spikes upon depolarization compared to control motor neurons. Antisense oligonucleotides targeting the C9ORF72 transcript suppressed RNA foci formation and reversed gene expression alterations in C9-ALS motor neurons. These data show that patient-derived motor neurons can be used to delineate pathogenic events in ALS. Transcriptome profiling from iPSC derived motor neurons compared to controls

2013-11-07 | E-GEOD-52202 | biostudies-arrayexpress

5010e6d3-946d-422c-b44c-d9f580de3813 - samples

Project description:eCLIP of TDP-43 from iPSC-derived motor neurons in 2 control lines. Per line input and IP samples and analysis including bigWig files and peak files.

| EGAD00001008426 | EGA

Transcriptomic analysis of iPSC-derived motor neurons from ALS patients carrying ATXN2 intermediate repeat expansions and healthy controls

Project description:Intermediate-length repeat expansions in ATAXIN-2 (ATXN2) are a strong genetic risk factor for amyotrophic lateral sclerosis (ALS). At the molecular level, ATXN2 intermediate expansions enhance TDP-43 toxicity and pathology. However, whether this triggers ALS pathogenesis at the cellular and functional level remains unknown. Here, we developed a human iPSC-derived model to investigate whether motor neurons derived from ALS patients carrying ATXN2 intermediate repeat expansions are transcriptomically distinct from healthy controls. For that, we performed RNA sequencing of motor neurons derived from 5 ATXN2-ALS iPSC lines and 5 healthy controls (HC).

2024-07-16 | GSE224578 | GEO

HDAC6 inhibition restores TDP-43 pathology and axonal transport defects in human motor neurons with TARDBP mutations

Project description:TDP-43 is the major component of pathological inclusions in most ALS patients and in up to 50% of patients with frontotemporal dementia (FTD). Heterozygous missense mutations in TARDBP, the gene encoding TDP-43, are one of the common causes of familial ALS. In this study, we investigate TDP-43 protein behavior in induced pluripotent stem cell (iPSC)-derived motor neurons from three ALS patients with different TARDBP mutations and three healthy controls. TARDPB mutations induce several TDP-43 changes in spinal motor neurons, including cytoplasmic mislocalization and accumulation of insoluble TDP-43, C-terminal fragments and phospho-TDP-43. By generating iPSC lines with allele-specific tagging of TDP-43, we find that mutant TDP-43 initiates the observed disease phenotypes and has an altered interactome as indicated by mass spectrometry-based proteomics. Our findings also indicate that TDP-43 proteinopathy results in a defect in mitochondrial transport. Lastly, proteomics analyses also show that pharmacological inhibition of histone deacetylase 6 (HDAC6) restores the observed TDP-43 pathologies and the axonal mitochondrial motility, suggesting that HDAC6 inhibition may be an interesting therapeutic target for neurodegenerative disorders linked to TDP-43 pathology.

2021-03-15 | PXD023852 | Pride

d782907f-c292-4a6b-ae9e-5d56eac78ef9 - samples

Project description:Gene expression from human iPSC derived motor neurons.

| EGAD00001005216 | EGA

Gene expression from human iPSC derived motor neurons.

Project description:Gene expression from human iPSC derived motor neurons.

| EGAS00001003785 | EGA

Homo sapiens bulk RNA-seq for iMGLs and iMGL-motor neuron co-cultures with cGAS inhibitor

Project description:This study investigates the role of cGAS signaling in amyotrophic lateral sclerosis using human microglial-like cells (iMGLs) and iMGL-motor neuron co-cultures. Bulk RNA sequencing was performed to assess transcriptional and RNA splicing changes associated with TDP-43 pathology and their modulation by pharmacological cGAS inhibition.

2026-02-16 | GSE319347 | GEO

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