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Cell-free DNA Methylation Patterns in Aging and Their Association with Inflamm-aging

ABSTRACT: Cell-free DNA Methylation Patterns in Aging and Their Association with Inflamm-aging

PROVIDER: PRJNA1080627 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28106254_1.fastq.gz	Fastqsanger.gz
	SRR28106254_2.fastq.gz	Fastqsanger.gz
	SRR28106255_1.fastq.gz	Fastqsanger.gz
	SRR28106255_2.fastq.gz	Fastqsanger.gz
	SRR28106256_1.fastq.gz	Fastqsanger.gz

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Cell-free DNA Methylation Patterns in Aging and Their Association with Inflamm-aging

Project description:Background: Liquid biopsies analyzing cell-free DNA methylation in plasma offer a non-invasive diagnostic for diseases, with aging biomarker potential underexplored. Methods: Utilizing enzymatic methyl-seq (EM-seq), this study assessed cfDNA methylation patterns in aging with blood from 35 healthy individuals. Results: It found aging signatures, including higher cfDNA levels and variations in fragment sizes, plus over 2 million age-related differentially methylated CpG sites. A biological age predictive model based on 41 CpG sites showed a strong correlation with chronological age, verified by two datasets. Age-specific epigenetic shifts linked to inflammation were revealed through differentially methylated regions profiling and Olink proteomics. Conclusion: These findings indicate cfDNA methylation as a potential biomarker for aging, and it might exacerbate immunoinflammatory reactivity in older individuals.

2024-05-23 | GSE259312 | GEO

DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association

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DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association

Project description:This study evaluate the methylation profile of 84 clinically sporadic pancreatic neuroendocrine tumors (PanNETs) with associated clinical and genomic information. We identified three subgroups of PanNETs, termed T1, T2 and T3, with distinct patterns of methylation. The T1 subgroup was enriched for functional tumors and ATRX, DAXX and MEN1 wild-type genotypes. The T2 subgroup contained tumors with mutations in ATRX, DAXX and MEN1 and recurrent patterns of chromosomal losses in half of the genome with no association between regions with recurrent LOH and methylation levels. T2 tumors were larger and had lower methylation in the MGMT gene body, which showed positive correlation with gene expression. The T3 subgroup harboured mutations in MEN1 with recurrent LOH of chromosome 11, was enriched for grade G1 tumors and showed histological parameters associated with better prognosis. Our results suggest a role for methylation in both driving tumorigenesis and potentially stratifying prognosis in PanNETs. These set of normal adjacent pancreata was compared to ICGC pancreatic neuroendocrine tumour methylation. We identified CpG sites located in promoter regions with low levels of methylation (beta value <0.3) in all normal adjacent pancreata and from those selected the most variable probes with a standard deviation >0.20 of DNA methylation levels across all tumors to identify sub-groups.

2021-02-16 | GSE149395 | GEO

Epigenome-wide association of liver methylation patterns and complex metabolic traits in mice

Project description:Heritable epigenetic factors can contribute to complex disease etiology. In this study we examine, on a global scale, the contribution of DNA methylation to complex traits that are precursors to heart disease, diabetes and osteoporosis. We profiled DNA methylation patterns in the liver using bisulfite sequencing in 90 mouse inbred strains, genome-wide expression levels, proteomics, metabolomics and sixty-eight clinical traits, and performed epigenome-wide association studies (EWAS). We found associations with numerous clinical traits including bone mineral density, plasma cholesterol, insulin resistance, gene expression, protein and metabolite levels. A large proportion of associations were unique to EWAS and were not identified using GWAS. Methylation levels were regulated by genetics largely in cis, but we also found evidence of trans regulation, and we demonstrate that genetic variation in the methionine synthase reductase gene Mtrr affects methylation of hundreds of CpGs throughout the genome. Our results indicate that natural variation in methylation levels contributes to the etiology of complex clinical traits. Reduced representation bisulfite sequencing in mouse strains using liver genomic DNA

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Project description:A cell-free pipeline for recreating methylation patterns radically enhances DNA transformation in bacteria

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Reduced DNA methylation patterning and transcriptional connectivity define human skin aging

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