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ATAC-Seq analysis of the chromatin accessibilities in C9HRE ALS/FTD patient cells

ABSTRACT: ATAC-Seq analysis of the chromatin accessibilities in C9HRE ALS/FTD patient cells

PROVIDER: PRJNA925663 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23125373_1.fastq.gz	Fastqsanger.gz
	SRR23125373_2.fastq.gz	Fastqsanger.gz
	SRR23125374_1.fastq.gz	Fastqsanger.gz
	SRR23125374_2.fastq.gz	Fastqsanger.gz
	SRR23125375_1.fastq.gz	Fastqsanger.gz

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Chromatin accessibilities in C9HRE ALS/FTD patient cells

Project description:Chromatin accessibilities in C9HRE ALS/FTD patient cells

| PRJNA925486 | ENA

ATAC-Seq analysis of the chromatin accessibilities in C9HRE ALS/FTD patient cells

Project description:ATAC-seq was utilized to profile the chromatin status in ALS/FTD patient cells carrying the hexanuleotide repeat expansion in C9orf72.

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Profiling the genomic binding of DAXX in C9HRE ALS/FTD patient cells

Project description:Using ChIP-seq to profile the genomic binding of DAXX in control and C9HRE ALS/FTD patient B lymphocytes.

2023-02-10 | GSE223401 | GEO

Disruption of nuclear speckle integrity dysregulates RNA splicing in C9ORF72-FTD/ALS

Project description:Dysregulation of RNA processing contributes to neurodegenerative diseases, especially amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Expansion of an intronic (GGGGCC)n repeat within the C9ORF72 gene is the most common cause of both FTD and ALS (C9-FTD/ALS), characterized with aberrant repeat RNA foci in the nucleus and noncanonical translation-produced dipeptide repeat (DPR) protein inclusions in the cytoplasm. Here we elucidate that the (GGGGCC)n repeat RNA co-localizes with nuclear speckles and alters their phase separation properties and granule dynamics. Moreover, the essential nuclear speckle scaffold protein SRRM2 is sequestered into the poly-GR cytoplasmic inclusions in C9-FTD/ALS mouse model and patient postmortem tissues, exacerbating the nuclear speckle dysfunction. Impaired nuclear speckle integrity induces global exon-skipping and intron retention in human iPSC-derived neurons. Similar alternative splicing changes can be found in patient postmortem tissues. This work identified novel molecular mechanism of global RNA splicing defects by impaired nuclear speckle function in C9-FTD/ALS and revealed novel potential biomarkers or therapeutic targets.

2024-08-23 | GSE248404 | GEO

Neuronal polyunsaturated fatty acids are protective in FTD/ALS

Project description:We report a conserved transcriptomic signature of reduced fatty acid and lipid metabolism gene expression in human post-mortem ALS spinal cord and a Drosophila model of the most common genetic cause of FTD/ALS, a repeat expansion in C9orf72. To investigate lipid alterations, we performed lipidomics on C9FTD/ALS iPSC-neurons and post-mortem FTLD brain tissue. This revealed a common and specific reduction in phospholipid species containing polyunsaturated fatty acids (PUFAs). To determine whether this PUFA deficit contributes to neurodegeneration, we fed C9FTD/ALS flies PUFAs, which yielded a modest increase in survival. However, increasing PUFA levels specifically in neurons of the C9orf72 flies, by overexpressing fatty acid desaturase enzymes, led to a substantial extension of lifespan. Neuronal overexpression of fatty acid desaturases also suppressed stressor induced neuronal death in C9FTD/ALS patient iPSC-neurons. These data implicate neuronal fatty acid saturation in the pathogenesis of FTD/ALS and suggest that interventions to increase PUFA levels specifically within neurons will be beneficial.

2024-11-15 | GSE255099 | GEO

Single cell RNA-sequencing of long-term human control and C9ORF72 ALS/FTD patient-specific iPSC-derived cortical organoid slice cultures

Project description:Single cell RNA sequencing data was collected from 150 day old human cortical organoid slice cultures grown at the air-liquid interface (ALI-COs) from control and ALS/FTD patient-specific induced pluripotent stem cell (iPSC) lines harbouring the C9ORF72 hexanucleotide repeat expansion mutation. Data collection included ALI-COs derived from the following iPSC lines: WTSli042-B (WTS42b) and A18945 (EpiC) for healthy controls, CS30iALS-C9nxx (CS30) and CS29iALS-C9nxx (CS29) for ALS/FTD, and CS29iALS-C9n1.ISOxx (ISO29), a mutation-corrected isogenic line. A total of 148,223 cells were processed over two batches.

2021-10-21 | GSE180122 | GEO

N6-methyladenosine regulates RNA metabolism and neurodegeneration in C9ORF72-ALS/FTD [seq_polyA_RNA-decay]

Project description:N6-methyladenosine (m6A) is the most prevalent internal mRNA modification and regulates RNA metabolism. Repeat expansion in C9ORF72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). Here, we showed that m6A is downregulated in C9ORF72-ALS/FTD patient-derived iPSC-differentiated neurons and postmortem brain tissues. The global m6A hypomethylation leads to transcriptome-wide mRNA stabilization and upregulated gene expression, especially ones involved in synaptic activity and neuronal functions. The m6A modification in the C9ORF72 intron sequence preceding the expanded repeats enhances RNA degradation via the nuclear reader YTHDC1. The m6A reduction leads to increased accumulation of repeat RNA and poly-dipeptides. Moreover, the antisense RNA can also be regulated by m6A. Elevating m6A level significantly reduces both sense and antisense repeat RNA and poly-dipeptides, rescues global mRNA homeostasis, and improves survival of C9ORF72-ALS/FTD patient neurons.

2023-06-09 | GSE203579 | GEO

N6-methyladenosine regulates RNA metabolism and neurodegeneration in C9ORF72-ALS/FTD [seq_polyA_RNA-RIP]

2023-06-09 | GSE203578 | GEO

N6-methyladenosine regulates RNA metabolism and neurodegeneration in C9ORF72-ALS/FTD [seq_total_RNA-MeRIP]

2023-06-09 | GSE203580 | GEO

A high-fidelity CRISPR-Cas13 system improves abnormalities associated with C9ORF72-linked ALS/FTD

Project description:An abnormal expansion of a G4C2 hexanucleotide repeat in the C9ORF72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), two debilitating neurodegenerative disorders driven in part by gain-of-function mechanisms involving transcribed forms of the repeat expansion. By utilizing a Cas13 variant with reduced collateral effects, we developed a high-fidelity RNA-targeting CRISPR-based system for C9ORF72-linked ALS/FTD. When delivered to the brain of a transgenic rodent model, this Cas13-based platform curbed the expression of the G4C2 repeat-containing RNA without affecting normal C9ORF72 levels, which in turn decreased the formation of RNA foci, reduced the production of a dipeptide repeat protein, and reversed transcriptional deficits. This high-fidelity system possessed improved transcriptome-wide specificity compared to its native form and mediated targeting in motor neuron-like cells derived from a patient with ALS. These results lay the foundation for the implementation of RNA-targeting CRISPR technologies for C9ORF72-linked ALS/FTD.

2024-11-28 | GSE250633 | GEO

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