Changes of RNA expression in aging periodontal ligament cells

Aging is a major risk factor for periodontal disease and is associated with impaired tissue homeostasis and regenerative capacity. The periodontal ligament (PDL) plays a central role in periodontal integrity; however, the molecular mechanisms underlying PDL cell aging remain incompletely understood.

In this study, we established an in vitro passage-dependent cellular aging model using human periodontal ligament fibroblasts serially passaged from early to late stages. Transcriptomic changes associated with aging were analyzed using RNA sequencing, followed by principal component analysis, hierarchical clustering, pathway enrichment, and protein-protein interaction network analyses.

Global transcriptomic profiling revealed that PDL cell aging follows a non-linear and heterogeneous trajectory rather than a uniform progressive decline. Notably, passage 13 emerged as a distinct transitional stage. Genes with decreasing expression during aging were strongly enriched in biosynthetic and proliferative pathways, including DNA metabolism, rRNA processing, and cell cycle regulation. In contrast, genes with increasing expression showed limited functional convergence and were mainly associated with signaling, immune and cytokine responses, extracellular matrix remodeling, and stress adaptation. Post hoc analysis identified two passage-13-associated gene-expression patterns: 13deep, characterized by residual biosynthetic and proliferative programs, and 13peak, marked by enhanced regulatory, immune, and microenvironment-responsive signaling.

This study suggests that the passage 13 may represent a putative transition between biosynthetic decline and regulatory adaptation. Our findings provide a molecular framework for understanding age-related periodontal tissue degeneration and may inform future strategies for early intervention, prevention, and regeneration in periodontal disease associated with aging.