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

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

doi:10.3389/fcell.2021.734287

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

Front Cell Dev Biol. 2022 Jan 4:9:734287. doi: 10.3389/fcell.2021.734287. eCollection 2021.

Authors

Fuwen Yao^{1

2}, Yongqiang Zhan¹, Changzheng Li³, Ying Lu², Jiao Chen², Jing Deng², Zijing Wu², Qi Li², Yi'an Song², Binhua Chen¹, Jinjun Chen¹, Kuifeng Tian¹, Zuhui Pu⁴, Yong Ni¹, Lisha Mou^{1

2}

Affiliations

¹ Department of Hepatopancreatobiliary Surgery, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China.
² Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China.
³ Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou, China.
⁴ Imaging Department, Shenzhen Institute of Translational Medicine, Health Science Center, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.

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.

Keywords: AURKA; EZH2; TKI; cell cycle; hepatocellular carcinoma; protein kinases; single-cell RNA sequencing; tyrosine kinase inhibitors.

Grants and funding

This study was supported by Shenzhen Foundation of Science and Technology (grant number JCYJ20170817172116272), Sanming Project of Medicine in Shenzhen (SZSM201812079), and Shenzhen High-level Hospital Construction Fund (2019).