Identification of a dysregulated CircRNA-associated gene signature for predicting prognosis, immune landscape, and drug candidates in bladder cancer

Chong Shen; Zhi Li; Yinglang Zhang; Zhe Zhang; Zhouliang Wu; La Da; Shaobo Yang; Zejin Wang; Yu Zhang; Yunkai Qie; Gangjian Zhao; Yuda Lin; Shiwang Huang; Mingli Zhou; Hailong Hu

doi:10.3389/fonc.2022.1018285

Identification of a dysregulated CircRNA-associated gene signature for predicting prognosis, immune landscape, and drug candidates in bladder cancer

Front Oncol. 2022 Oct 10:12:1018285. doi: 10.3389/fonc.2022.1018285. eCollection 2022.

Authors

Chong Shen^{1

2}, Zhi Li^{1

2}, Yinglang Zhang^{1

2}, Zhe Zhang^{1

2}, Zhouliang Wu^{1

2}, La Da^{1

2}, Shaobo Yang^{1

2}, Zejin Wang^{1

2}, Yu Zhang^{1

2}, Yunkai Qie^{1

2}, Gangjian Zhao^{1

2}, Yuda Lin^{1

2}, Shiwang Huang^{1

2}, Mingli Zhou³, Hailong Hu^{1

2}

Affiliations

¹ Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China.
² Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China.
³ Department of Neuromuscular Diseases, Third Hospital of Hebei Medical University, Shijiazhuang, China.

Abstract

Increasing evidences have demonstrated that circular RNA (circRNAs) plays a an essential regulatory role in initiation, progression and immunotherapy resistance of various cancers. However, circRNAs have rarely been studied in bladder cancer (BCa). The purpose of this research is to explore new circRNAs and their potential mechanisms in BCa. A novel ceRNA-regulated network, including 87 differentially expressed circRNAs (DE-circRNAs), 126 DE-miRNAs, and 217 DE-mRNAs was constructed to better understanding the biological processes using Cytoscape 3.7.1 based on our previously high-throughput circRNA sequencing and five GEO datasets. Subsequently, five randomly selected circRNAs (upregulated circ_0001681; downregulated circ_0000643, circ_0001798, circ_0006117 and circ_0067900) in 20 pairs of BCa and paracancerous tissues were confirmed using qRT-PCR. Functional analysis results determined that 772 GO functions and 32 KEGG pathways were enriched in the ceRNA network. Ten genes (PFKFB4, EDNRA, GSN, GAS1, PAPPA, DTL, TGFBI, PRSS8, RGS1 and TCF4) were selected for signature construction among the ceRNA network. The Human Protein Atlas (HPA) expression of these genes were consistent with the above sequencing data. Notably, the model was validated in multiple external datasets (GSE13507, GSE31684, GSE48075, IMvigor210 and GSE32894). The immune-infiltration was evaluated by 7 published algorithms (i.e., TIMER, CIBERSORT, CIBERSORT-ABS, QUANTISEQ, MCPCOUNTER, XCELL and EPIC). Next, Correlations between riskscore or risk groups and clinicopathological data, overall survival, recognized immunoregulatory cells or common chemotherapeutic agents of BCa patients were performed using wilcox rank test, chi-square test, cox regression and spearman's correlation analysis; and, these results are significant. According to R package "GSVA" and "clusterProfiler", the most significantly enriched HALLMARK and KEGG pathway was separately the 'Epithelial Mesenchymal Transition' and 'Ecm Receptor Interaction' in the high- vs. low-risk group. Additionally, the functional experiments in vitro also revealed that the overexpression of has_circ_0067900 significantly impaired the proliferation, migration, and invasion capacities of BCa cells. Collectively, the results of the current study provide a novel landscape of circRNA-associated ceRNA-regulated network in BCa. The ceRNA-associated gene model which was constructed presented a high predictive performance for the prognosis, immunotherapeutic responsiveness, and chemotherapeutic sensitivity of BCa. And, has_circ_0067900 was originally proposed as tumor suppressor for patients with BCa.

Keywords: CircRNA-related prognostic signature; bladder cancer; chemotherapy; immune infiltration; immunotherapy.