Transcriptomic landscape of Gallbladder cancer reveals altered pathways related to cell cycle and Aurora kinase

Background Gallbladder cancer (GBC) is a rare but aggressive biliary tract malignancy. This study explores the transcriptomic profile of GBC to identify differentially expressed genes (DEGs) and dysregulated pathways involved in its pathogenesis. Methods RNA sequencing was performed on 13 GBC tumors and 6 matched controls. Functional enrichment analysis as well as WGCNA were used to identify dysregulated pathways, functionally relevant gene modules and hub genes. Key targets were validated in patient tissues and cell lines. Results A total of 621 DEGs were identified (247 upregulated, 374 downregulated). Gene set enrichment analysis revealed activation of E2F targets and G2/M checkpoint, with downregulation of bile acid metabolism and estrogen response pathways. A tumor grade-correlated WGCNA module was enriched in cell cycle genes. TPX2 emerged as a central hub gene. Inhibitors of aurora kinase, TPX2 dependent enzyme, significantly reduced proliferation, migration, and invasion in GBC cells. High-grade tumors confirmed elevated Aurora kinase expression. Conclusions This first transcriptomic analysis of GBC in South-East Asian Indians uncovers key drivers like TPX2 and Aurora kinases in disease progression. The study highlights cell cycle dysregulation and sex-linked signatures, offering insights for biomarker discovery and targeted therapies.