Systems-level characterization of the molecular landscape of odontogenic keratocyst: insights from differential gene expression and pathway analysis

Abstract Background Odontogenic keratocysts (OKCs) are aggressive jaw cysts with a high recurrence rate and a molecular profile resembling neoplastic lesions. Understanding their genetic and signalling landscape may provide new insights into diagnostic and therapeutic strategies. Publicly available transcriptomic data (GSE38494; twelve OKC and six normal tissues) were analysed to identify key differentially expressed genes (DEGs) and dysregulated pathways contributing to OKC pathogenesis. Results A total of 277 DEGs were identified, comprising 245 upregulated and 32 downregulated genes. Upregulated genes such as PTCH1, SOX2, PDPN, MMP2, and SPARC indicated aberrant Hedgehog activation, epithelial proliferation, and extracellular matrix remodelling, while downregulation of CXCL12 and PTEN suggested altered immune signalling and PI3K/Akt dysregulation. Functional enrichment revealed significant involvement of the PI3K/Akt, Hedgehog, hypoxia-response, and extracellular matrix interaction pathways. Gene Ontology analysis further emphasized processes related to epithelial proliferation, inflammatory response, and tissue remodelling, underscoring the synergistic contribution of hypoxia, immune modulation, and growth-factor signalling to OKC progression. Conclusion Transcriptomic integration highlights Hedgehog and PI3K/Akt pathway activation as central molecular drivers of OKC, complemented by hypoxia-induced and immune-mediated mechanisms. Targeting these interconnected pathways may provide new therapeutic avenues for controlling the aggressive and recurrent nature of OKC.