USP15 Represses Hepatocellular Carcinoma Progression by Regulation of Pathways of Cell Proliferation and Cell Migration: A System Biology Analysis

SIMPLE SUMMARY: Expression levels of the protein USP15 correlated with slow proliferation and slow migration of HCC cells. In HCC patients, high expression of USP15 in tumor tissue was associated with significantly decreased risk for mortality and cancer relapse. Overexpression of USP15 led to reduced tumor growth in a mouse model. USP15 regulated indirectly tumor-related proteins through interactions mediated by other proteins. The functions “cell migration” and “cell proliferation” were significantly enriched in a network of pathway hierarchies that we found relevant for the regulatory role of USP15 in HCC. Six cluster of pathways described the link between experimental observed phenotypes and expression levels of USP15. ABSTRACT: Background: Hepatocellular carcinoma (HCC) leads to 600,000 people’s deaths every year. The protein ubiquitin carboxyl-terminal hydrolase 15 (USP15) is a ubiquitin-specific protease. The role of USP15 in HCC is still unclear. Method: We studied the function of USP15 in HCC from the viewpoint of systems biology and investigated possible implications using experimental methods, such as real-time polymerase chain reaction (qPCR), Western blotting, clustered regularly interspaced short palindromic repeats (CRISPR), and next-generation sequencing (NGS). We investigated tissues samples of 102 patients who underwent liver resection between January 2006 and December 2010 at the Sir Run Run Shaw Hospital (SRRSH). Tissue samples were immunochemically stained; a trained pathologist then scored the tissue by visual inspection, and we compared the survival data of two groups of patients by means of Kaplan–Meier curves. We applied assays for cell migration, cell growth, and wound healing. We studied tumor formation in a mouse model. Results: HCC patients (n = 26) with high expression of USP15 had a higher survival rate than patients (n = 76) with low expression. We confirmed a suppressive role of USP15 in HCC using in vitro and in vivo tests. Based on publicly available data, we constructed a PPI network in which 143 genes were related to USP15 (HCC genes). We combined the 143 HCC genes with results of an experimental investigation to identify 225 pathways that may be related simultaneously to USP15 and HCC (tumor pathways). We found the 225 pathways enriched in the functional groups of cell proliferation and cell migration. The 225 pathways determined six clusters of pathways in which terms such as signal transduction, cell cycle, gene expression, and DNA repair related the expression of USP15 to tumorigenesis. Conclusion: USP15 may suppress tumorigenesis of HCC by regulating pathway clusters of signal transduction for gene expression, cell cycle, and DNA repair. For the first time, the tumorigenesis of HCC is studied from the viewpoint of the pathway cluster.