FANCB as a prognostic biomarker and therapeutic target in hepatocellular carcinoma with insights from pan-cancer analysis and experimental validation

FANCB, a Fanconi anemia protein, plays a role in DNA damage repair. However, its role in tumor immunity and prognosis prediction remains unclear. The expression data of FANCB in pan-cancer were extracted from public databases such as Cancer Genome Atlas (TCGA), Gene Expression Comprehensive Database (GEO), Genotype-Tissue Expression (GTEx), TIMER2.0, Cbiopportal, Xiantao Tool and UALCAN. Through comprehensive analysis, the association of FANCB with a variety of cancer-related factors was evaluated, including tumor survival prognosis, RNA/DNA methylation status, immune invasion level, immune checkpoint (ICP) indicators, tumor mutational burden (TMB), microsatellite instability (MSI), tumor microenvironment (TME) characteristics, and drug sensitivity. Specifically, in liver hepatocellular carcinoma (LIHC), we performed Cox regression analysis and functional enrichment analysis of related genes using the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Gene Set Enrichment Analysis (GSEA). In addition, the expression level of FANCB in LIHC was verified by immunohistochemistry (IHC). The potential anti-cancer effects of FANCB knockdown in hepatocellular carcinoma were revealed through molecular biology experiments such as Quantitative real-time PCR (qRT–PCR), western blot, and in vitro cell phenotyping experiments, including cell counting kit-8 (CCK-8) proliferation assays, colony formation assays, wound healing assays, and transwell assays, along with in vivo tumour formation assay. The study revealed that the expression level of FANCB was significantly up-regulated in a variety of tumor types, and the expression level of FANCB was significantly associated with the survival prognosis, TMB and MSI of patients. Further analysis showed that there was a significant correlation between FANCB expression and the number of five immune cell subsets, as well as stromal and immune scores, suggesting that FANCB may play an important role in the TME. In addition, we also found that there was a correlation between the half-inhibitory concentration (IC50) of anticancer drugs such as sorafenib and paclitaxel and the expression level of FANCB. Through functional enrichment analysis, we identified the association of FANCB with cell cycle regulation and the P53 signaling pathway in LIHC. Cox regression analysis showed that the expression level of FANCB was an independent prognostic factor for LIHC patients. Immunohistochemistry (IHC) results confirmed the high expression level of FANCB in LIHC. Cell phenotyping experiments showed that FANCB knockdown could significantly inhibit the proliferation, migration and invasion of Huh7 and SNU-449 hepatoma cells. In vivo tumour formation assay showed that downregulating FANCB expression could effectively inhibit the growth ability of LIHC cells in vivo. Our study found that FANCB plays a crucial role in tumor immune response, cancer treatment efficacy, and disease prognosis. This finding highlights the importance of FANCB as a potential therapeutic target for hepatocellular carcinoma and suggests that it may be an important prognostic biomarker.