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Single-cell RNA sequencing analysis of iPSC-derived motor neurons from an ALS patient carrying ATXN2 intermediate repeat expansions and a healthy control

ABSTRACT: 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 an ALS patient carrying ATXN2 intermediate repeat expansions (ALS-G) are transcriptomically distinct from a healthy control(OH2.6). For that, we generated a single cell RNA sequencing dataset consisting of a total of 384 cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE224582 | GEO | 2024/07/16

REPOSITORIES: GEO

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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

Transcriptomic analysis of spinal cord microglial cells from NTg and ATXN2-Q33;TDP-43 adult mice

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. Our study shows that microglial cells might contribute to ALS-related pathology observed in mice carrying ATXN2 intermediate repeat expansions (Q33) in an ALS background (TDP-43). To investigate whether ATXN2-Q33;TDP-43 spinal cord microglia are transcriptomically different from non transgenic counterparts, we performed RNA sequencing of sorted microglial cells from knock-in (ATXN2-Q33;TDP-43) as well as non-transgenic (NTg) mice.

2024-07-16 | GSE224581 | GEO

Transcriptomic analysis of the spinal cords of knock-in adult mice carrying the ATXN2/TDP-43 human transgenes

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. To investigate gene expression changes and deregulated pathways caused by ataxin-2 intermediate repeat expansions in presence/absence of mutant TDP-43, we performed RNA sequencing of whole spinal cords from knock-in mice harboring ATXN2 and TDP-43 human transgenes as well as non-transgenic mice (NTg)

2024-07-16 | GSE224580 | GEO

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

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

| PRJNA934449 | ENA

Single-cell RNA sequencing analysis of iPSC-derived motor neurons from an ALS patient carrying ATXN2 intermediate repeat expansions and a healthy control

Project description:Single-cell RNA sequencing analysis of iPSC-derived motor neurons from an ALS patient carrying ATXN2 intermediate repeat expansions and a healthy control

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ATAXIN-2 Intermediate-length Polyglutamine Expansions Elicit ALS-associated Metabolic and Immune Phenotypes

Project description:ATAXIN-2 Intermediate-length Polyglutamine Expansions Elicit ALS-associated Metabolic and Immune Phenotypes

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Atxn2-Knock-Out mice show branched chain amino acids and fatty acids pathway alterations

Project description:Human Ataxin-2 (ATXN2) gene locus variants have been associated with obesity, diabetes mellitus type 1 and hypertension in genome-wide association studies, while mouse studies showed the knock-out of Atxn2 to lead to obesity, insulin resistance and dyslipidemia. Intriguingly, the deficiency of ATXN2 protein orthologues in yeast and flies rescues the neurodegeneration process triggered by TDP-43 and Ataxin-1 toxicity. To understand the molecular effects of ATXN2 deficiency by unbiased approaches, we quantified the global proteome and metabolome of Atxn2-knock-out mice with label-free mass spectrometry. In liver tissue, significant downregulations of the proteins ACADS, ALDH6A1, ALDH7A1, IVD, MCCC2, PCCA, OTC, together with bioinformatic enrichment of downregulated pathways for branched chain and other amino acid metabolism, fatty acids and citric acid cycle were observed. Statistical trends in the cerebellar proteome and in the metabolomic profiles supported these findings. They are in good agreement with recent claims that PBP1, the yeast orthologue of ATXN2, sequestrates the nutrient sensor TORC1 in periods of cell stress. Overall, ATXN2 appears to modulate nutrition and metabolism, and its activity changes are determinants of growth excess or cell atrophy.

2016-02-08 | PXD003155 | Pride

Genome-wide CRISPR screen reveals v-ATPase as a drug target to lower levels of ALS protein ataxin-2

Project description:ATXN2 has emerged as an exciting therapeutic target for neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and spinocerebellar ataxia type 2 (SCA2), as lowering its levels via genomic knockout or anti-sense oligonucleotide (ASO) treatment has been shown to mitigate disease phenotypes and led to a current clinical trial of ATXN2 ASOs for treatment of ALS in humans. To identify additional ways to lower ataxin‑2 protein levels, we performed a genome-wide fluorescence activated cell sorting (FACS)-based CRISPR screen in human cells and identified multiple components of the lysosomal vacuolar ATPase (v‑ATPase) as modifiers of ataxin‑2 levels. This dataset contains the RNA-sequencing data and CRISPR screen data used to support the conclusions from this study.

2022-10-18 | GSE189417 | GEO

C9orf72 Intermediate Repeats are Associated with Corticobasal Degeneration, Increased C9orf72 Expression and Disruption of Autophagy

Project description:Microsatellite repeat expansion disease loci can exhibit pleiotropic clinical and biological effects depending on repeat length. Large expansions in C9orf72 (100s-1000s of units) are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). However, whether intermediate expansions also contribute to neurodegenerative disease is not well understood. Several studies have identified intermediate repeats in Parkinson’s disease patients, but the association was not found in autopsy confirmed cases. We hypothesized that intermediate C9orf72 repeats are a genetic risk factor for corticobasal degeneration (CBD), a neurodegenerative disease that can be clinically similar to Parkinson’s but has distinct tau protein pathology. Indeed, intermediate C9orf72 repeats were significantly enriched in autopsy-proven CBD (n=354 cases, odds ratio=3.59, p-value=0.00024). While large C9orf72 repeat expansions are known to decrease C9orf72 expression, intermediate C9orf72 repeats result in increased C9orf72 expression in human brain tissue and CRISPR/cas9 knockin iPSC derived neural progenitor cells. In contrast to cases of FTD/ALS with large C9orf72 expansions, CBD with intermediate C9orf72 repeats was not associated with pathologic RNA foci or dipeptide repeat protein aggregates. Knock-in cells with intermediate repeats exhibit numerous changes in gene expression pathways relating to vesicle trafficking and autophagy. Additionally, overexpression of C9orf72 without the repeat expansion leads to defects in autophagy under nutrient starvation conditions. These results raise the possibility that therapeutic strategies to reduce C9orf72 expression may be beneficial for the treatment of CBD.

2019-09-17 | GSE133323 | GEO

Structured and disordered regions of Ataxin-2 contribute differently to the specificity and efficiency of mRNP granule formation

Project description:Ataxin-2 (ATXN2) is a gene implicated in spinocerebellar ataxia type II (SCA2), amyotrophic lateral sclerosis (ALS) and Parkinsonism. The encoded protein is a therapeutic target for ALS and related conditions. ATXN2 (or Atx2 in insects) functions in translational regulation, mRNA stability, and in the assembly of mRNP-granules, a process mediated by intrinsically disordered regions (IDRs). Previous work has shown that the LSm (Like-Sm) domain of Atx2, which mediates translational activation of some target mRNAs, antagonizes mRNP-granule assembly. Here we advance these findings through a series of experiments on Drosophila and human Ataxin-2 proteins. Results of Targets of RNA-Binding Proteins Identified by Editing (TRIBE) experiments indicate that a polyA-binding protein (PABP) interacting, PAM2 motif of Ataxin-2 may be a major determinant of the mRNA content of Ataxin-2 mRNP granules. Co-localization and co-immunoprecipitation analyses show that structured interactions between Ataxin-2 and PABP additionally help determine protein components of Ataxin-2-associated mRNP granules and contribute to Ataxin-2’s association with stress granules. Finally, in vivo experiments in Drosophila indicate that while the Atx2-LSm domain protects against neurodegeneration, structured PAM2- and unstructured IDR- interactions both promote degeneration. Taken together the data: (a) lead to a proposal for how Ataxin-2 interactions are remodelled during different stages of translational control; (b) show how structured and non-structured interactions of Ataxin-2 contribute differently to the specificity and efficiency of RNP granule condensation; and (c) demonstrate that the Ataxin-2 protein contains multiple activities that may respectively prevent or promote neurodegeneration.

2024-04-22 | GSE196739 | GEO

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