Transcription-based comparison of <i>Aggregatibacter actinomycetemcomitans</i> or <i>Porphyromonas gingivalis</i> -induced experimental periodontitis

Periodontitis is a chronic inflammatory disease caused by a dysregulated immune response against the subgingival dysbiotic biofilm. Among the Gram-negative bacteria detected in the infected periodontium, <i>Aggregatibacter actinomycetemcomitans</i> (<i>Aa</i>) and <i>Porphyromonas gingivalis</i> (<i>Pg</i>) are strongly associated with the most destructive forms of periodontitis. Given their phylogenetic divergence and distinct virulence potential, we performed a comparative transcriptomic analysis in a murine experimental periodontitis model induced by separate direct inoculations of <i>Aa</i> and <i>Pg</i>. After confirming periodontal destruction, a massive RNA sequencing (RNA-seq) was conducted on the palatal mucosa, which lines and forms part of the tissues affected by periodontitis. Our analysis identified 91 differentially expressed genes (DEGs) in response to <i>Aa</i> and 119 DEGs in response to <i>Pg</i>, with only 22 shared DEGs, 12 of which were associated with the humoral immune response. Comparative analysis revealed eight distinct co-expression modules, each exhibiting differential gene representation and expression patterns. Notably, Module 4, linked to the immune response, displayed a similar expression profile for both bacteria. Additionally, we constructed gene regulatory networks (GRNs) from transcriptomic data and identified a subnetwork comprising 8 clusters, 54 nodes, 17 transcription factors, and 53 regulatory interactions. Finally, the transcription factors <i>FOS</i>, <i>JUN</i>, <i>RELA</i>, <i>TP53</i>, <i>EGR1</i>, and <i>NFκB1</i> were identified as master regulators (MR-TFs) of inoculation-induced murine periodontitis and were conserved in human regulatory networks.IMPORTANCEPeriodontitis is the most common osteolytic disease in humans, significantly affecting oral health and worsening various systemic inflammatory conditions. Specific bacteria, such as <i>A. actinomycetemcomitans</i> and <i>P. gingivalis</i>, are frequently found in severe cases. This highlights the need to implement advanced methodologies to understand their underlying pathogenic mechanisms. We used massive RNA-seq to analyze, for the first time, the complete palatal mucosa of animals affected by, or not affected by, experimental periodontitis induced by the most virulent serotypes of both bacterial species. Our findings reveal that these bacteria explore distinct molecular pathways to induce disease. Despite their phylogenetic differences and distinctive virulence factors, <i>A. actinomycetemcomitans</i> and <i>P. gingivalis</i> activate common transcriptional regulators that promote periodontitis progression, suggesting conserved molecular mechanisms underlying periodontal destruction. These results provide valuable information for developing therapeutic strategies to modulate these regulatory nodes and improve treatment outcomes in periodontitis and other related inflammatory conditions.