Epigenetic patterns, accelerated biological aging, and enhanced epigenetic drift detected 6 months following COVID-19 infection: insights from a genome-wide DNA methylation study

Abstract

Background: The epigenetic status of patients 6-month post-COVID-19 infection remains largely unexplored. The existence of long-COVID, or post-acute sequelae of SARS-CoV-2 infection (PASC), suggests potential long-term changes. Long-COVID includes symptoms like fatigue, neurological issues, and organ-related problems, regardless of initial infection severity. The mechanisms behind long-COVID are unclear, but virus-induced epigenetic changes could play a role.

Methods and results: Our study explores the lasting epigenetic impacts of SARS-CoV-2 infection. We analyzed genome-wide DNA methylation patterns in an Italian cohort of 96 patients 6 months after COVID-19 exposure, comparing them to 191 healthy controls. We identified 42 CpG sites with significant methylation differences (FDR < 0.05), primarily within CpG islands and gene promoters. Dysregulated genes highlighted potential links to glutamate/glutamine metabolism, which may be relevant to PASC symptoms. Key genes with potential significance to COVID-19 infection and long-term effects include GLUD1, ATP1A3, and ARRB2. Furthermore, Horvath's epigenetic clock showed a slight but significant age acceleration in post-COVID-19 patients. We also observed a substantial increase in stochastic epigenetic mutations (SEMs) in the post-COVID-19 group, implying potential epigenetic drift. SEM analysis identified 790 affected genes, indicating dysregulation in pathways related to insulin resistance, VEGF signaling, apoptosis, hypoxia response, T-cell activation, and endothelin signaling.

Conclusions: Our study provides valuable insights into the epigenetic consequences of COVID-19. Results suggest possible associations with accelerated aging, epigenetic drift, and the disruption of critical biological pathways linked to insulin resistance, immune response, and vascular health. Understanding these epigenetic changes could be crucial for elucidating the complex mechanisms behind long-COVID and developing targeted therapeutic interventions.

Keywords: COVID-19; DNA methylation; EWAS; Epigenetic clock; Epigenetic drift; PASC; SARS-CoV-2; Stochastic epigenetic mutation.

Fig. 1

Scatter plots of principal component analysis (PCA). Scatter plot distribution of samples and the first two principal components at a sites, b genes, c promoters, and d CpG islands

Fig. 2

Circos plot visualizes the genomic distribution of differentially methylated sites throughout the human genome. The blue (hyper-methylated) and red (hypo-methylated) dots represent the genomic position of sites that have exceeded the statistical significance threshold (FDR < 0.05) and are spatially arranged according to the -log10 (unadjusted p-value). The solid red line indicates the FDR significance threshold, while the dashed red line represents the Bonferroni significance threshold. X and Y chromosomes are omitted from the analysis.

Fig. 3

Boxplots showing the distribution of age acceleration differences for different epigenetic clocks: A Horvath, B GrimAge, C Hannum, D PhenoAge, and E SkinBlood. The thick horizontal line in each box represents the median of the distribution, while the box itself represents the interquartile range (IQR). In the "ggplot" boxplot function, the whiskers extend to the data points located within 1.5 times the IQR from the box by default. Dots represent outliers (single values exceeding 1.5 IQRs). (F) Telomere length evaluation (DNAmTLadjAge)

Fig. 4

Boxplot showing the distribution of SEMs in Reference and post-COVID-19 groups. The thick horizontal line in the box represents the median of the distribution, while the box represents the interquartile range. By default, in the "ggplot" boxplot function, the whiskers extend to the data points located within 1.5 times the interquartile range (IQR) from the box. Dots represent outliers (single values exceeding 1.5 IQRs)

Fig. 5

Bar chart showing enrichment ratio of a KEGG and b PANTHER pathways