Comprehensive transcriptomic profiling of liver cancer identifies histone and PTEN are major regulators of scutellarein-induced anti-tumor activity

Worldwide, liver cancer is the most frequent fatal malignancy. The liver cancer prognosis is poor because patients frequently receive advanced-stage diagnoses. The current study aimed to establish the candidate pharmacological targets of scutellarein (SCU) and to identify its biological network. To identify the differentially expressed genes (DEG) between SCU-treated and SCU-untreated HCC HepG2 cells, RNA sequencing (RNA-seq) was carried out. A total of 463 genes were found to have differential expression, of which 288 showed up-regulation and 175 showed down-regulation in the group that had received SCU treatment. Gene ontology (GO) enrichment analysis of terms revealed they are mostly involved in the regulation of protein heterodimerization activity and nucleosomes. Interaction of protein and protein network analysis using Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) resulted in three crucial interacting hub targets namely, linker histone H1 (Histone H1) and PTPRC. Additionally, the crucial targets were validated by western blot analysis. Overall, we show that the use of RNA-seq data, with bioinformatics tools, can provide a valuable resource to identify the pharmacological targets that could have important biological roles in liver cancer.