Molecular Signatures of Peripheral and Central Dental Pulp Subpopulations in Response to Streptococcus mutans : A Bulk RNA ‐Seq Analysis

ABSTRACT Aim The dental pulp is an immunologically active tissue that responds dynamically to cariogenic challenge. Peripheral pulp cells adjacent to dentine encounter bacterial stimuli earlier than cells located in the central pulp. To investigate signalling and immune interactions, this study profiled the transcriptomes of dentine‐adherent cells (DACs) and central dental pulp cells (DPCs) cocultured with Streptococcus mutans . Methodology Primary cultures of both DACs and DPCs were obtained from healthy third molars of three female and three male donors aged 13–16. Cells were cocultured with viable S. mutans (2 × 10 8 CFU/mL) for 6 h ( n = 6). Controls included γ‐inactivated bacteria and unexposed cells. RNA libraries (Illumina Stranded mRNA Prep) were sequenced on a NextSeq2000. Bioinformatic analysis included differential gene expression (DESeq2), gene set enrichment analysis (GSEA), and protein–protein interaction (PPI) network construction. Batch effects were corrected, and significantly regulated genes (|log 2 FC| > 1.5, p adj < 0.05) were identified. Validation of DEGs was performed via reverse transcription quantitative polymerase chain reaction (RT‐qPCR). Results RNA‐Seq revealed a dynamic shift in the transcriptome of DACs and DPCs stimulated with S. mutans , while cells exposed to γ‐inactivated or no bacteria did not. Although DACs and DPCs shared common DEGs (33 up, 8 down), several regulations were exclusive to DACs (22 up, 9 down) and DPCs (9 up, 25 down), highlighting a donor‐independent functional specificity of the pulp subpopulations. Functional enrichment analysis revealed a strong and comparable activation of hypoxia‐related pathways in both DPCs and DACs. However, DACs additionally showed enrichment in extracellular matrix organisation and cytokine signalling, while DPCs were characterised by intracellular stress responses and protein folding pathways. Additionally, protein–protein interaction analysis identified IL‐6 as a key hub in DACs, while ANGPTL4 was central in DPCs. Conclusion Following exposure to S. mutans , mechanically isolated DACs and DPCs displayed distinct transcriptomic profiles, indicating functional heterogeneity in the pulpal immune response. DACs engaged immunomodulatory pathways, while DPCs were marked by cellular stress responses, suggesting divergent contributions to tissue defence and homeostasis.