Characterization of m⁶A-regulated targets and immune cells in dental caries: insights from multi-omics analysis

Dental caries is one of the most common oral diseases worldwide. N⁶-Methyladenosine (m⁶A), a type of RNA modification, plays an important role in various biological processes and cellular responses. This study aimed to investigate the causal relationship between specific genetic loci related to m⁶A and dental caries.

Caries-associated genetic loci and signaling pathways were explored by integrating publicly available single-nucleotide polymorphism (SNP) association data, m⁶A quantitative trait locus (m⁶A-QTL) data from genome-wide association studies (GWAS), and single-cell RNA sequencing data derived from the dental pulp of healthy individuals and patients with dental caries. Mendelian randomization (MR) was also used to explore the causal relationship between m⁶A-related genetic variants and dental caries.

Among 29,797 m⁶A-SNPs analyzed, four reached genome-wide significance (P < 5.0E-05), with rs3829225 showing the most significant association (P = 1.23E-06). The rs2259956 variant demonstrated significant cis-expression quantitative trait locus (cis-eQTL) effects on ABHD12 expression (z score = 19.072, P = 4.35E-81) and was predicted to enhance m⁶A modification (score change: 0.588 to 0.595). Single-cell RNA sequencing of 53,595 cells revealed that dendritic cells mainly existed in the carious pulp and showed the highest fold-change, with ABHD12 significantly upregulated in carious samples. Gene set enrichment analysis identified oxidative phosphorylation as the top enriched pathway (FDR < 0.05). Two-sample MR analysis (161,113 cases, 216,164 controls) revealed causal relationships between 15 immune cell traits and dental caries, with CD62L^-dendritic cells increasing dental caries risk (OR = 1.019, 95% CI 1.004-1.035, P = 1.6E-02) and plasmacytoid dendritic cells showing protective effects (OR = 0.978, 95% CI 0.965-0.991, P = 1.0E-03).

This study presents new evidence characterizing m⁶A-related SNPs in increasing dental caries susceptibility and provides a single-cell transcriptomic profiling of dental caries with insights into the relationship between dental caries and immune cells.