Oncogenic Role of PLOD3 in Melanoma Progression via Wnt/β-catenin Signaling and Tumor Microenvironment Reprogramming

Melanoma is an aggressive malignancy, and treatment strategies remain limited for patients with advanced disease, highlighting the need for a better understanding of the driving mechanisms. This study aimed to identify genes associated with melanoma tumorigenesis, characterize their potential mechanisms, and explore the therapeutic relevance and druggability of selected candidates through experimental and computational approaches. Melanoma-related hub genes were screened by integrating weighted gene co-expression network analysis (WGCNA) with least absolute shrinkage and selection operator (LASSO) regression analysis. The biological functions of the candidate gene were validated using proliferation and migration assays in melanoma cells. RNA sequencing was applied to investigate the underlying molecular mechanism, whereas CIBERSORT and xCell analyses were used to investigate the relationship between PLOD3 and immune infiltration. Structure-based virtual screening was performed to explore candidate PLOD3-binding compounds. PLOD3, C4orf48, BUB1, and CD300LF were identified as a melanoma-related gene signature, among which PLOD3 exhibited the strongest association with melanoma progression and metastasis. PLOD3 was significantly upregulated in melanoma and positively correlated with epithelial-mesenchymal transition (EMT) signatures across multiple independent cohorts. Loss-of-function experiments revealed reduced proliferation, migration, and invasion of melanoma cells following PLOD3 depletion. PLOD3 expression was also associated with Wnt/β-catenin pathway activity, and treatment with a pharmacological Wnt/β-catenin activator partially restored the cellular phenotypes suppressed by PLOD3 silencing. Furthermore, elevated PLOD3 expression was associated with reduced CD8⁺ T-cell infiltration and an immunosuppressive tumor microenvironment. Structure-based virtual screening identified four candidate compounds-Rosamultin, Actein, Temsirolimus, and Punicalagin-with strong predicted binding affinity to the catalytic glycosyltransferase (GT) domain of PLOD3, supporting its target potential. PLOD3 functions as a critical driver of melanoma progression by promoting Wnt/β-catenin signaling and shaping an immunosuppressive tumor microenvironment. These findings identify PLOD3 as a promising therapeutic target and provide candidate compounds for further investigation in melanoma-targeted therapy.