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E-MTAB-1925

ABSTRACT: Transcription profiling by array of post-mortem brain cortex from healthy control patients and amyotrophic lateral sclerosis (ALS) patients that carry an expanded GGGGCC repeat mutation in the chromosome 9 open reading frame 72 (C9ORF72) gene

PROVIDER: E-MTAB-1925 | ExpressionAtlas | 2025-01-23

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-MTAB-1925-analysis-methods.tsv	Tabular
	E-MTAB-1925-atlasExperimentSummary.Rdata	Rdata
	E-MTAB-1925-configuration.xml	Xml
	E-MTAB-1925-percentile-ranks.tsv	Tabular
	E-MTAB-1925.condensed-sdrf.tsv	Tabular

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Transcriptome profile of C9ORF72 ALS fibroblast

Project description:The purpose of this experiment was to compare the differences in transcript levels between RNA samples collected from fibroblasts from healthy control patients, amyotrophic lateral sclerosis (ALS) patients carrying an expanded GGGGCC repeat mutation in the chromosome 9 open reading frame 72 gene and ALS patients with a mutation in the SOD1 gene.

2013-10-29 | E-MTAB-1926 | biostudies-arrayexpress

Transcription profiling by array of post-mortem brain cortex from healthy control patients and amyotrophic lateral sclerosis patients that carry an expanded GGGGCC repeat mutation in the chromosome 9 open reading frame 72 (C9ORF72) gene

Project description:The purpose of this experiment was to compare differences in the transcript level between RNA samples collected from post-mortem motor cortex from healthy control patients and amyotrophic lateral sclerosis (ALS) patients that carry an expanded GGGGCC repeat mutation in the chromosome 9 open reading frame 72 (C9ORF72) gene.

2013-10-29 | E-MTAB-1925 | biostudies-arrayexpress

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Project description:The study design involves the proteomics characterization of primary skin fibroblast cell lines derived from skin biopsies from patients affected by either amyotrophic lateral sclerosis (ALS) or frontotemporal dementia (FTD). Patients enrolled were divided in three groups: 1) ALS patients carrying the C9ORF72 repeat expansion as main genetic mutation (c9orf72 pos; n=6), 2) sporadic ALS patients, carrying mutations other than the C9ORF72 repeat expansion (c9orf72 neg; n=8), 3) FTD patients carrying the C9ORF72 repeat expansion (FTD; n=2). Total protein extracts were obtained from primary skin fibroblasts cultures and trypsin digested. Shotgun proteomics by LC-MS/MS (two technical replicates per sample) and systems biology analyses were performed as follows

2021-11-02 | PXD023866 | Pride

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Project description:Amyotrophic lateral sclerosis (ALS), the most common form of motor neuron disease, is characterized by progressive muscle weakness and paralysis caused by degeneration of upper and lower motor neurons. A major breakthrough in understanding the genetics of ALS was the discovery of a GGGGCC hexanucleotide repeat expansion (HRE) within the non-coding region of chromosome 9 open reading frame 72 (C9orf72) as the most common mutation in both familial and sporadic forms of ALS [25, 80]. We report that C9orf72 loss of function and poly(GP) expression act together to induce motor neuron degeneration and paralysis. These synergistic properties of C9orf72 mutation affect autophagy, thus resulting in poly(GP) and p62 aggregation. In this context, poly(GP) accumulation occurs in motor neurons preferentially, along with swollen mitochondria, a typical signature of mitophagy defects. In motor neurons, accumulated abnormal mitochondria engage caspase cascade, ultimately giving rise to apoptotic cell death of motor neurons that results in paralysis

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Project description:Asses the transcriptome-wide changes associated with depletion of transcription elongation factor, SUPT4H1, in human fibroblasts. An expanded hexanucleotide repeat in C9orf72 is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (c9FTD/ALS). Therapeutics (e.g., antisense oligonucleotides) are being developed to target RNAs containing the expanded repeat sequence (GGGGCC); however, this approach is complicated by the presence of antisense strand transcription of expanded GGCCCC repeats. We found that targeting the transcription elongation factor, Spt4, selectively decreased production of both sense and antisense expanded transcripts, as well as their translated dipeptide repeat (DPR) products, and also mitigated degeneration in animal models. Inhibition of SUPT4H1, the human ortholog of Spt4, similarly decreased production of sense and antisense RNA foci as well as DPR proteins in c9ALS patient fibroblasts and neurons from patient-derived induced pluripotent stem cells, consistent with our finding that cerebellar DPR protein levels correlate with SUPT4H1 expression in c9FTD/ALS patients. Therapeutic targeting of a single factor to eliminate pathological features of c9FTD/ALS offers advantages over approaches that require targeting sense and antisense repeats separately.

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2024-07-16 | GSE224578 | GEO

Characterization of C9orf72 haplotypes to evaluate the effects of normal and pathological variations on its expression and splicing

Project description:Expansion of the hexanucleotide repeat (HR) in the first intron of the chromosome 9 open reading frame 72 (C9orf72) gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) in Caucasians. All C9orf72 ALS/FTD patients share a common risk (R) haplotype, but its single nucleotide polymorphism (SNP) signature has not been fully characterized. Here, we characterized the C9orf72 haplotypes in Europeans and created a detailed molecular map, including HR length, for each haplotype. By analyzing RNA-seq reads and sequencing chromatograms that overlap with heterozygous SNP sites, we identified allelic differences in C9orf72 expression in normal subjects and ALS patients. In cells from healthy individuals, upstream promoter transcript levels increased with increased HR length. Intron 1 levels were higher in one of the non-R haplotypes due to SNP variation, and in R haplotype with 10 or more HR units. In pathological HR expansion, we observed the highest levels of intron 1 that were accompanied by aberrantly spliced transcripts at cryptic donor sites downstream of the expanded HR. Intron 1 retention was associated with sequential intron 2 retention. The SNP signature of C9orf72 haplotypes described here enables allele-specific analysis of transcriptional products and may pave the way to allele-specific therapeutic strategies.

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