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Epigenetics of Yakutia and Central Russia regions

ABSTRACT: Lobachevsky University DNAm dataset. Whole blood DNA Methylation (EPIC) profiles from healthy samples from two regions: central Russia (131 samples) and Yakutia (114 samples) obtained in the Laboratory of System Medicine for Healthy Aging, Lobachevsky State University of Nizhny Novgorod, Russia Dataset contains DNAm data from 245 healthy control samples from two regions: central Russia (131) and Yakutia (114). The following characteristics are available for all samples: sex, age, region. Healthy participants in the central Russia region were recruited in 2019–2022. Yakutian participants we recruited in 2022. All measurements were performed at the Laboratory of System Medicine for Healthy Aging, Lobachevsky State University of Nizhny Novgorod, Russia.

ORGANISM(S): Homo sapiens

PROVIDER: GSE234461 | GEO | 2023/12/14

REPOSITORIES: GEO

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Project description:Background: Patients with paediatric-onset systemic lupus erythematosus (SLE) often present with more severe clinical courses than adult-onset patients. Although genome-wide DNA methylation (DNAm) profiling has been performed in adult-onset SLE patients, parallel data on paediatric-onset SLE are not available. Therefore, we undertook a genome-wide DNAm study in paediatric-onset SLE patients across multiple blood cell lineages. Methods: The DNAm profiles of four purified immune cell lineages were compared in 16 Chinese patients with paediatric-onset SLE and 13 healthy controls using the Illumina HumanMethylationEPIC BeadChip. The DNAm dataset consisted of 145 samples, including data from CD4+ T cells, CD8+ T cells, B cells, neutrophils and whole blood. Results: Genome-wide DNAm analysis revealed considerable variation in DNAm levels across samples, and as expected, clustering occurred by cell type rather than disease status. Comparison of DNAm in whole blood and within each independent cell lineage identified a consistent pattern of loss of DNAm at 21 CpG sites overlapping 15 genes, which represented a robust, disease-specific DNAm signature for paediatric-onset SLE in our cohort. This DNAm signature shows considerable overlap with that identified in our adult-onset SLE patient cohort, predominantly showing a loss of DNAm and enrichment in genes involved in type I interferon signalling in SLE, regardless of the age of onset. In addition, cell lineage-specific changes, involving both loss and gain of DNAm, were observed in both novel genes and genes with well-described roles in SLE pathogenesis. Conclusion: The SLE-specific DNAm signature has the potential to develop into a diagnostic biomarker for SLE, which is particularly important for paediatric-onset patients, as diagnosing SLE in children can be challenging. This study also highlights the importance of studying DNAm changes in different immune cell lineages rather than only whole blood, since cell type-specific DNAm changes facilitated the elucidation of the cell type-specific molecular pathophysiology of SLE.

Dataset Information

Epigenetics of Yakutia and Central Russia regions

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