BUB3: a novel prognostic biomarker and therapeutic target in hepatocellular carcinoma unveiled by pan-cancer analysis and experimental validation

Abstract

BUB3 is a core component of the spindle assembly checkpoint (SAC) that is indispensable for faithful chromosome segregation and mitotic progression. Although aberrant BUB3 expression has been reported in several malignancies, its comprehensive role in tumorigenesis, immune regulation, and therapeutic response across cancers remains poorly understood. This study aimed to systematically characterize the expression landscape, clinical significance, biological functions, and therapeutic relevance of BUB3 in a pan-cancer context. A comprehensive pan-cancer analysis integrating multiple public databases and bioinformatics platforms was performed to evaluate the expression pattern, diagnostic performance, prognostic value, genomic alterations, functional pathways immune infiltration characteristics, and drug sensitivity associated with BUB3. In addition, BUB3 expression in hepatocellular carcinoma (LIHC) was validated using RT-qPCR and Western blotting, and its biological functions were further investigated through in vitro experiments. BUB3 was significantly upregulated in most cancer types and exhibited strong diagnostic performance in several malignancies. Elevated BUB3 expression was associated with unfavorable clinical outcomes, especially in head and neck squamous cell carcinoma (HNSC), LIHC, and lung adenocarcinoma (LUAD). Genetic alterations in BUB3, predominantly mutations, were frequently observed in uterine corpus endometrial carcinoma (UCEC). Copy number variation (CNV) and tumor mutation burden (TMB) positively correlated with BUB3 expression in LUAD. Functional enrichment analyses suggested that BUB3-related genes are primarily involved in cell cycle regulation, proliferation, migration, and invasion pathways. Moreover, BUB3 expression was closely associated with immune cell infiltration patterns, while single-cell analyses demonstrated predominant BUB3 expression in immune populations, particularly T cells, indicating a potential role in remodeling the TIME. Importantly, elevated BUB3 expression was associated with reduced responsiveness to immunotherapy and decreased chemosensitivity, suggesting unfavorable therapeutic outcomes in patients with high BUB3 expression. Experimental validation further demonstrated increased BUB3 expression in LIHC tissues and cell lines. Functional assays revealed that BUB3 knockdown significantly inhibited colony formation, proliferation, migration, and invasion in HepG2 and Hep3B cells, supporting its oncogenic role in LIHC progression. Our findings demonstrate that BUB3 plays a critical role in tumor progression and immune regulation and possesses substantial diagnostic and prognostic value, highlighting its potential as both a biomarker for patient stratification and a promising therapeutic target across multiple cancer types.