Patient-derived HCC cells recapitulating the transcriptomic landscape of primary HCV-related liver cancer

Background The hepatocellular carcinoma is one of the leading causes of cancer-related mortality and is characterized by high heterogeneity and subsequently adaptation by developing resistance to current treatments. In this scenario the application of individualized models is crucial to understand the potential of approved therapies. Recently, we established a series of individual cell lines derived from patients who developed HCC on different entities, serving as a platform for individual approaches. In this study, we classified the LC4 cells derived from the center region of a HCC with underlying HIV-HCV co-infection, by using deep analysis on the pathway regulation level. Methods We employed DEG analysis, followed by pathway analysis to characterize the preservation level of the LC4 cells and the level of adoption. Next, we classify the model, by employing healthy donor samples, commonly used HCC cell lines and global RNAseq data sets. Results We showed that the LC4 cells reflect significant characteristics of the parental region, including the replication of the immuno-suppressive and the proliferative milieu. The LC4 cells exhibit a metabolic reprogramming characterized by the downregulation of drug-metabolizing CYP enzymes compared to healthy individuals, indicating a transition to alternate metabolic pathways. Moreover, we identified common Biomarkers in the parental tissue, global datasets and the LC4 cells. Conclusion We showed that the LC4 cell line is applicable as an individual model for pre-clinical testing of treatment regimens in HCC driven research.