Stage-Specific Proteomic Profiles in Dental Caries

This study investigated the proteomic landscape of sound and carious coronal dentin to uncover the molecular signatures of host response, including tissue degradation, inflammation, and repair, across progressive stages of caries lesions. Dentin from deidentified human molars, grouped into 6 clusters of 3 teeth each, was pulverized to obtain ~1 g of tissue per cluster (<i>n</i> = 6). G1 and G2 protein extracts were obtained using guanidine before and after demineralization. Extracts from sound (S), distinct dentin caries (DDC), and extensive dentin caries (EDC) lesions were digested with trypsin and analyzed by label-free relative quantification via liquid chromatography-tandem mass spectrometry (LC-MS/MS). Spectral data were matched against the UniProt <i>Homo sapiens</i> database using Mascot and Sequest HT in Proteome Discoverer. Statistical analysis using the <i>limma</i> package identified differentially expressed (DE) proteins (false discovery rate-adjusted <i>P</i> < 0.05), and ingenuity pathway analysis revealed key pathways, regulators, and networks. A total of 320 proteins were identified, with differential expression observed in 80 for EDC × S, 16 for EDC × DDC, and only 3 for DDC × S. In the G2 × G1 comparison, 200 proteins exhibited differential recovery in at least 1 of the extracts. Proteins such as S100A8, S100A12, DEFA1, SERPINB1, MPO, and PRTN3 were upregulated in EDC compared with DDC and S. TIMP3, MMP20, DMP1, and other collagen and matrix-associated proteins showed higher coverage in G2 than in G1, revealing extract-specific profiles. Functional analysis highlighted enrichment in immune and inflammatory pathways, with strong activation of neutrophil degranulation, antimicrobial peptides, neutrophil extracellular trap signaling, and macrophage alternative activation in carious tissues. In conclusion, this study reveals stage-specific proteomic signatures in caries, reflecting a dynamic interplay between microbial-induced degradation and host-driven defense and repair. These findings offer new molecular insights into caries pathophysiology and may inform future diagnostic and therapeutic strategies.