Integrated Protein–Protein Interaction and Weighted Gene Co-expression Network Analysis Uncover Three Key Genes in Hepatoblastoma

Linlin Tian,Tong Chen,Jiaju Lu,Peifang Qin,Jianguo Yan,Sentai Ding,Yuting Zhang,Yali Zhou

doi:10.3389/fcell.2021.631982

Abstract

Hepatoblastoma (HB) is the most common liver tumor in the pediatric population, with typically poor outcomes for advanced-stage or chemotherapy-refractory HB patients. The objective of this study was to identify genes involved in HB pathogenesis via microarray analysis and subsequent experimental validation. We identified 856 differentially expressed genes (DEGs) between HB and normal liver tissue based on two publicly available microarray datasets (GSE131329 and GSE75271) after data merging and batch effect correction. Protein–protein interaction (PPI) analysis and weighted gene co-expression network analysis (WGCNA) were conducted to explore HB-related critical modules and hub genes. Subsequently, Gene Ontology (GO) analysis was used to reveal critical biological functions in the initiation and progression of HB. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that genes involved in cell cycle phase transition and the PI3K/AKT signaling were associated with HB. The intersection of hub genes identified by both PPI and WGCNA analyses revealed five potential candidate genes. Based on receiver operating characteristic (ROC) curve analysis and reports in the literature, we selected CCNA2, CDK1, and CDC20 as key genes of interest to validate experimentally. CCNA2, CDK1, or CDC20 small interfering RNA (siRNA) knockdown inhibited aggressive biological properties of both HepG2 and HuH-6 cell lines in vitro. In conclusion, we identified CCNA2, CDK1, and CDC20 as new potential therapeutic biomarkers for HB, providing novel insights into important and viable targets in future HB treatment.

Highlights

Hepatoblastoma (HB) is caused by aberrant proliferation and/or differentiation of hepatic progenitor cell and represents a rare tumor that accounts for most of liver tumors in infants and children (Allan et al, 2013)
The results of our study showed that differentially expressed genes (DEGs) between HB and normal liver tissue samples were primarily associated with PI3K-AKT signaling, cell cycle, and FoxO signaling
Forty DEGs were associated with PI3K-AKT signaling, indicating that these genes may be critical for HB growth

Summary

Introduction

Hepatoblastoma (HB) is caused by aberrant proliferation and/or differentiation of hepatic progenitor cell and represents a rare tumor that accounts for most of liver tumors in infants and children (Allan et al, 2013). The majority of HB patients are diagnosed before 3 years of age, with a median age at diagnosis of 18 months (Spector and Birch, 2012). HB accounts for several cases per million per year in the pediatric population (Tulla et al, 2015). Combined modality therapy, including complete surgical resection and adjuvant cisplatin-based chemotherapy, has significantly improved the prognosis for HB. The prognosis of patients with advanced-stage or chemotherapy-refractory HB remains poor, with a 3-year event-free survival of less than 50% (Perilongo et al, 2004; Hiyama, 2014).

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