Methylation levels in keratinocyte basal cells reflect donor age and associate with altered cellular proliferation pathways

AIMS: To determine if epigenomic and mRNA associations with donor age are present in basal keratinocytes in vitro. METHODS: Whole-genome methylation (EPIC array), RNAseq analysis, and in vitro cell growth assessments were performed on cultured keratinocytes (n = 9, 22-68 years), enriched for cells expressing the stem cell protein markers ITGB1 and EpCAM. RESULTS: Donor age associated with 1,244 differentially methylated positions (DMPs) (p < 0.01, >20% delta beta) and correlated with estimated ages from the Skin and Blood epigenetic clock (r = 0.83, p = 0.0018). The DMPs correlated with those in an in vivo epidermal dataset (r = 0.71, p < 0.0001). Donor age associated (p < 0.05) with 523 differentially expressed genes (DEGs), but the DEGs only weakly correlated with their changes in an in vivo epidermal dataset (r = 0.24, p < 0.0001). The "cell growth and proliferation" ontology term was significantly enriched in the methylation and expression datasets despite only 13 overlapping annotated genes. Decreased keratinocyte proliferation, increased differentiation and a reduced re-epithelialization ability were observed for an older versus a younger cell strain. CONCLUSION: Basal keratinocytes maintain in vivo age-associated epigenomic changes in vitro making them a good model for studying the impact of age-associated epigenomic changes on cellular function and behavior in vitro.