Single-Cell RNA Sequencing Reveals the Role of Phosphorylation-Related Genes in Hepatocellular Carcinoma Stem Cells.

Fuwen Yao,Jing Deng,Yi’An Song,Changzheng Li,Zuhui Pu,Ying Lu,Lisha Mou,Qi Li,Kuifeng Tian,Yongqiang Zhan,Zijing Wu,Yong Ni,Jiao Chen,Binhua Chen,Jinjun Chen

doi:10.3389/fcell.2021.734287

Abstract

Abnormal activation of protein kinases and phosphatases is implicated in various tumorigenesis, including hepatocellular carcinoma (HCC). Advanced HCC patients are treated with systemic therapy, including tyrosine kinase inhibitors, which extend overall survival. Investigation of the underlying mechanism of protein kinase signaling will help to improve the efficacy of HCC therapy. Combining single-cell RNA sequencing data and TCGA RNA-seq data, we profiled the protein kinases, phosphatases, and other phosphorylation-related genes (PRGs) of HCC patients in this study. We found nine protein kinases and PRGs with high expression levels that were mainly detected in HCC cancer stem cells, including POLR2G, PPP2R1A, POLR2L, PRC1, ITBG1BP1, MARCKSL1, EZH2, DTYMK, and AURKA. Survival analysis with the TCGA dataset showed that these genes were associated with poor prognosis of HCC patients. Further correlation analysis showed that these genes were involved in cell cycle-related pathways that may contribute to the development of HCC. Among them, AURKA and EZH2 were identified as two hub genes by Ingenuity Pathway Analysis. Treatment with an AURKA inhibitor (alisertib) and an EZH2 inhibitor (gambogenic) inhibited HCC cell proliferation, migration, and invasion. We also found that both AURKA and EZH2 were highly expressed in TP53-mutant HCC samples. Our comprehensive analysis of PRGs contributes to illustrating the mechanisms underlying HCC progression and identifying potential therapeutic targets for future clinical trials.

Highlights

The most frequent type of primary liver cancer is hepatocellular carcinoma (HCC) (Budny et al, 2017; Khemlina et al, 2017)
To identify the key genes involved in the occurrence and progression of hepatocellular carcinoma (HCC) as well as prognosis, we conducted an in-depth analysis of public RNA-Seq data from the The Cancer Genome Atlas (TCGA) database of 369 HCC and 50 adjacent normal tissues
According to the results of differentially expressed gene (DEG) analysis, we identified 1,477 upregulated and 720 downregulated genes in HCC tissues compared with adjacent normal tissues (Supplementary Table S2)

Summary

Introduction

The most frequent type of primary liver cancer is hepatocellular carcinoma (HCC) (Budny et al, 2017; Khemlina et al, 2017). HCC commonly occurs in patients with chronic liver diseases such as hepatitis B and C infection (El-Serag, 2012). Treatments such as excision or transplantation may be successful in the early stages of HCC, but only a few therapeutic options are available when advanced HCC develops (Lencioni et al, 2014). The dysregulation of phosphorylation-dependent signaling pathways is a hallmark of oncogenesis (Bhatia et al, 2010; Berndt et al, 2013; Liu et al, 2018) This century, the first tyrosine kinase inhibitor (TKI) was approved as a potential precision therapy for HCC (da Fonseca et al, 2020). Interrogating the underlying molecular basis of abnormal expression of protein kinases, phosphatases, and other phosphorylation-related genes (PRGs) will help to improve the efficacy of HCC therapy

Methods

Results

Conclusion