Differential expression reveals inflammatory response and oxidative stress genes in dentin caries

Objective

This study employs RNA-Seq to investigate differentially expressed genes involved in extracellular matrix (ECM) degradation, focusing on collagenases (MMP-2 and MMP-9) and their inhibitors (TIMP-1 and TIMP-2).

Design

Total RNA from caries and caries-free teeth was extracted from pulp, predentin, and dentin. Samples were sequenced using Illumina® technology. Quality validation was done with FASTQC, and low-quality bases were removed using TRIMMOMATIC. Reads were aligned using SALMON against the human transcriptome (CHR38), followed by quantification using Transcripts Per Million. Differential gene expression analysis was conducted using DESeq2 (FDR < 0.05, |log2FC| ≥ 1). Functional enrichment analyses employed Gene Ontology and KEGG databases.

Results

Sequencing produced 16–37 million reads per sample, with an average alignment rate of 88.08 %. A total of 334 differentially expressed genes (DEGs) were identified: 195 upregulated and 139 downregulated. Upregulated genes included SAA1 (log2FC = 2.3, p-adj = 0.001) and ORM1 (log2FC = 2.0, p-adj = 0.002), associated with inflammation. MMP-9 was significantly downregulated (log2FC = −1.8, p-adj = 0.003), while MMP-2 showed higher expression in decayed tissues. TIMP-1 expression increased in decayed dentin; TIMP-2 was upregulated in both decayed and caries-free dentin. Protein interaction analysis identified EGFR and metallothioneins as key acute-phase proteins.

Conclusions

This study reveals the role of inflammatory and oxidative stress-related genes in dentin caries and shows disruption in the ECM degradation-repair balance. Increased MMP-2 and TIMP-1 expression suggests a compensatory response. MMP activity may serve as a therapeutic target to enhance tissue resilience and slow caries progression.