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Epigenetic profiles of tissue informative CpGs inform ALS disease status and progression

ABSTRACT: Epigenetic profiles of tissue informative CpGs inform ALS disease status and progression

PROVIDER: PRJNA1327113 | ENA |

REPOSITORIES: ENA

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Epigenetic profiles of tissue informative CpGs inform ALS disease status and progression

Project description:Background: Cell-free DNA (cfDNA), derived from dying cells, has demonstrated utility across multiple clinical applications. However, its potential in neurodegenerative diseases remains underexplored, with most existing cfDNA technologies tailored to specific disease contexts like cancer or non-invasive prenatal screening. Methods: To address this gap, we developed a novel approach to characterize epigenetic cfDNA profiles by identifying key regions of DNA methylation that reveal the tissues origins undergoing apoptosis or necrosis. We evaluated this method in the largest cfDNA study of amyotrophic lateral sclerosis (ALS) and other neurological diseases (OND) to date, encompassing two independent cohorts (n=192) from Australia (UQ Ncases=48, Ncontrols=32, NOND=15) and the USA, (UCSF Ncases=50 , Ncontrols=45)).Results: Our approach accurately distinguished ALS patients from controls (UQ AUC=0.82, UCSF AUC=0.99) and from individuals with other neurological diseases (AUC=0.91). It also identified an asymptomatic carrier of a pathogenic C9orf72 variant, and strongly correlated with ALS disease progression measures (Pearson’s R=0.66, p=3.71×10⁻⁹). Conclusions: We identified DNA methylation signals from multiple tissue types in ALS cfDNA, highlighting diverse tissue involvement in ALS pathology. These findings promote epigenetic cfDNA analysis as a powerful tool for advancing our understanding of neurodegenerative disease.

2025-09-11 | GSE307705 | GEO

A novel six-CpGs signature predicts clinical outcome in glioblastomas

Project description:We aimed to identify a clinically useful biomarker using DNA methylation-based information to optimize the management of glioblastoma (GBM) patients. We identified a novel six-CpGs signature that predicts the clinical outcome in GBM. The methylation profiling of 79 GBM patients has been used as a validation cohort to demonstrate the performance and the robustness of the identified six-CpGs signature. The status of the âMGMTâ biomarker, traditionally used by clinicians to predict survival in GBM, is also indicated per sample.

2017-12-15 | E-MTAB-4969 | biostudies-arrayexpress

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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.

2023-02-10 | GSE223255 | GEO

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Project description:Sporadic ALS Australia

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Distinct circular DNA profile in hSOD1G93A ALS that intersects with ALS proteome changes

Project description:Numerous genes mutated in amyotrophic lateral sclerosis (ALS) share a role in DNA damage and repair, emphasizing genome disintegration in ALS. DNA instability and repair mechanisms segregate extrachromosomal circular DNAs (ec/eccDNAs) that can modulate gene expression somatically. Here, circulome profiling in a hSOD1G93A genotoxicity model of ALS revealed a 6-fold enrichment of small-size eccDNAs relative to controls. DifCir-based differential analysis identified 189 genes with patterned segregation of differentially produced per gene circles (DPpGCs) from ALS but not from control samples, implicating an inter-sample recurrence rate of at least 89% for the top 6 DPpGCs. Mass spectrometry-based ALS circulome-proteome cross-referencing revealed 31 corresponding differentially expressed proteins (DEPs), with 12 DPpGC-DEP pairs being itemized in ALS risk GWAS databases. DPpGC-DEP hotspots mainly convey neuron-specific functions counteracting ALS detriments. This is unanticipated evidence for non-random, profiled eccDNA accumulation in ALS neurodegeneration, involving putative interactions with their gene products as well as biomarker perspectives.

2023-09-20 | GSE214718 | GEO

hiPSC-derived motor neurons: sporadic ALS patients vs. controls

Project description:Differentiated motor neurons from hiPSC derived from peripheral nerve fibroblasts of sporadic ALS patients and evaluated the gene expression profile by means microarray-linked to specific analysis tools. Two-condition experiment, ALS patients motor neurons vs. controls. Biological replicates: 3 ALS replicates, 3 control replicates.

2015-04-25 | E-GEOD-68240 | biostudies-arrayexpress

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