Background: Basal cell carcinoma (BCC) is the most prevalent skin malignancy, with a growing global incidence attributed to increased UV exposure and an aging population. While early-stage BCC can be treated with Mohs surgery and photodynamic therapy, options for advanced cases are limited. Existing systemic therapies, including SMOOTHENED inhibitors that target the Hedgehog (HH)-signaling pathway in BCC, are associated with significant adverse effects, such as muscle spasms, hair loss, and teratogenicity. Additionally, the emergence of resistance to these inhibitors underscores the need for diversifying systemic treatment options. This study aims to deepen our understanding of HH-signaling pathway, with the goal of identifying FDA-approved drugs with favorable genetics profile to disrupt this pathway.

Methods: Expression levels of mRNA transcripts for six key genes involved in BCC pathogenesis—Gli1, Gli2, Gli3, Shh, Ptch1, Ptch2, and Smo—were acquired from 269 human neck skin tissues in the Gene Network 2.0 database. Pearson Correlation Matrix analysis revealed statistically significant correlations among these genes (p < 0.05). Signaling network analysis with NetworkAnalyst 3.0 identified key molecular pathways shared among these genes. Subsequently, a protein-protein interaction (PPI) network was constructed based on the six key genes using the IMEx Interactome database, and functional annotation analysis was conducted using KEGG, REACTOME, and Gene Ontology databases to identify associated biological processes, molecular functions, and cellular components. Lastly, a Protein-Drug Network analysis was performed using DrugBank 5.0 database to identify FDA-approved drugs capable of inhibiting protein components of the PPI network.

Results: Pearson correlation matrix analyses revealed significant positive correlations among Gli1, Gli2, Ptch1, and Ptch2 expressions. Notably, positive correlations were observed for Gli1-Gli2 (r = 0.651, p < 0.05), Ptch1-Ptch2 (r = 0.734, p < 0.01), and Gli1-Ptch1 (r = 0.528, p < 0.05). Signaling network analysis identified notable pathways, such as 'Chemokine signaling,' ‘RAS signaling,’ ‘Proteoglycans in cancer,’ and ‘Apelin signaling,’ latter of which has not been previously explored in the context of BCC pathogenesis. Subsequent PPI networks identified 198 proteins regulating various cancer-related pathways, specifically Histone Deacetylase 1 (HDAC1), AKT Serine/Threonine Kinase 2 (AKT2), Phosphatase and Tensin Homolog (PTEN) that are frequently dysregulated in cancerous cells. Subsequent functional annotation analysis identified ‘Positive regulation of transcription,’ ‘Chromatin binding,’ and ‘Nucleus’ as the primary associated biological process, molecular function, and cellular compartment. Finally, Protein-Drug analysis of the PPI network identified six FDA-approved drugs—Amitriptyline, Nintedanib, Pazopanib, Ponatinib, Regorafenib, and Sorafenib—that may disrupt the PPI network by targeting proteins involved in 'PI3K-AKT signaling pathway,’ 'RAS signaling pathway,' and 'Chemokine signaling pathway.'

Conclusion: This study provides deeper insights into the molecular components and signaling pathways in BCC pathogenesis. The significant correlations and identified pathways highlight interdependent regulation of Gli1, Gli2, Ptch1, and Ptch2 expressions. Identifying FDA-approved drugs that may disrupt HH-signaling pathways suggests potential therapeutic strategies to diversify treatment for advanced BCC. These findings support repurposing existing drugs to improve treatment options, warranting further research and clinical trials.