Multi-omics analysis and experimental validation uncovers prognosis significance of IKBIP in patients with hepatocellular carcinoma: a multicenter cohort study

Abstract Background I Kappa B Kinase Interacting Protein (IKBIP) has been reported to promote tumor progression in diverse cancers. however, the role of IKBIP in hepatocellular carcinoma (HCC) has remained unclear. Methods Multi-omics analysis was performed using data from publicly databases, to systematically assess the expression patterns, prognostic value and immune landscape of IKBIP in HCC. The prognostic value of IKBIP was further verified using immunohistochemical (IHC) examination in two independent clinical cohorts. Furthermore, human HCC cell lines (Huh7, MHCC-97 H and HepG2) were knocked down for IKBIP using small-interfering RNA (siRNA), and cell proliferation, and migration ability were assessed. RNA-sequencing was performed on Huh7 cells with IKBIP knockdown to explore the effect of IKBIP in HCC cells. A nomogram was constructed by combining IKBIP expression and clinicopathological parameters to predict prognosis for individual patient. Functional enrichment analysis was performed to identify key pathways associated with IKBIP. Immune infiltration analyses were conducted to explore the relationship between IKBIP expression and immune microenvironment. Results The bioinformatics analyses indicated that IKBIP expression was significantly upregulated in tumor tissue and correlated with unfavorable prognosis. IHC experimental in both the Peking University Shenzhen Hospital (PKUSZ) and Shanghai Outdo cohorts demonstrated that IKBIP overexpression was associated with poorer survival. We found that IKBIP knockdown significantly inhibits HCC cell proliferation, colony formation, and migration in vitro. RNA-sequencing on IKBIP-knockdown Huh7 cells suggested that IKBIP played a role in promoting cell proliferation. The univariable and multivariable Cox analysis revealed that IKBIP expression was an independent factor for overall survival and diseases free survival. The nomogram by incorporating the IKBIP and clinicopathological features showed good performance in predicting prognosis. GSEA analysis revealed that IKBIP was associated with the cell cycle-related, epithelial-to-mesenchymal transition and angiogenesis pathways. We also found that IKBIP expression holds potential for predicting immunotherapeutic benefits. Conclusions The comprehensive multi-omics analysis and experimental findings demonstrate that IKBIP may be a biomarker with prognostic and functional significance in HCC.