Genome-wide profiling of salivary promoter-region DNA methylation in periodontitis: the Tromsø Study.

BACKGROUND

Methylation of DNA is an epigenetic reversible process that regulates gene expression. Aberrant promoter methylation is associated with chronic inflammation; however, the genome-wide DNA promoter methylation signature in periodontitis remains unexplored.

METHODS

The present study is an epigenome-wide association study (EWAS) aimed at investigating salivary DNA methylation patterns within gene promoter regions in individuals with Stage III/IV periodontitis compared to healthy controls. Cases (all available individuals with Stage III/IV and probing pocket depths (PPD) > 5 mm, n = 50, 48% women) were participants in an oral health examination (40–54-year-old subsample, n = 1668) of the population-based seventh survey of the Tromsø Study, conducted from 2015 to 2016. Periodontally healthy controls with similar age and sex to the cases (n = 50, 58% women) were randomly selected from the same subsample. We used the Illumina DNA methylation BeadChip technology, targeting ~ 935 K unique methylation sites. The R package RnBeads was used to study the difference in methylation. Separate lists of all significantly (comb.p.adj.fdr < 0.05) hypomethylated (hypoMPs, n = 3411) and hypermethylated (hyperMPs, n = 3437) promoters in participants with periodontitis relative to controls were used as inputs for enrichment analysis (g:Profiler) and network visualization (Cystoscape).

RESULTS

Gene ontology terms enriched among the hypoMPs included DNA biosynthesis, cell cycle/checkpoint, nuclear chromosome, endoplasmic reticulum, regulation of inflammatory response and leucocyte activation, cell adhesion, TRIF-dependent Toll-like receptor signaling, tyrosine phosphorylation of STAT proteins, regulation of PI3K/Akt, collagen extracellular matrix, and mucopolysaccharide metabolic process. HyperMPs were enriched in mRNA catabolism, mitochondrial electron transport, intrinsic apoptotic signaling, B-lymphocyte differentiation, actin cytoskeleton, regulation of extracellular matrix organization, epithelial-mesenchymal transition, ubiquitination, wound healing, acylglycerol metabolism, and serine/threonine signaling. NF-κB, GMEB-1, and IRF-8 were enriched in hypoMPs; ZFP85, ELF-5, and HNF4-alpha in hyperMPs.

CONCLUSIONS

We identified a differential DNA promoter methylation signature in participants with Stage III/IV periodontitis in middle adulthood. Our study highlights biological pathways involved in inflammation, immune response, tissue destruction, and repair that may be epigenetically dysregulated.