J Cancer 2021; 12(3):740-753. doi:10.7150/jca.48245

Research Paper

Identification of Seven Cell Cycle-Related Genes with Unfavorable Prognosis and Construction of their TF-miRNA-mRNA regulatory network in Breast Cancer

Zhipeng Hong1,2,3*, Qinglan Wang1*, Chengye Hong1*, Meimei Liu1, Pengqin Qiu1, Rongrong Lin1, Xiaolan Lin1, Fangfang Chen1, Qiuhuang Li1, Lingling Liu1, Chuan Wang2,3✉, Debo Chen1✉

1. Department of Breast Surgery, Affiliated Quanzhou First Hospital of Fujian Medical University, Quanzhou, Fujian Province, 362000, P. R. China.
2. Department of Breast Surgery and General Surgery, The Affiliated Union Hospital of Fujian Medical University, Fuzhou, Fujian Province, 350001, P. R. China.
3. Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian Province, 350001, P.R. China.
*These authors contributed equally to this work.

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Citation:
Hong Z, Wang Q, Hong C, Liu M, Qiu P, Lin R, Lin X, Chen F, Li Q, Liu L, Wang C, Chen D. Identification of Seven Cell Cycle-Related Genes with Unfavorable Prognosis and Construction of their TF-miRNA-mRNA regulatory network in Breast Cancer. J Cancer 2021; 12(3):740-753. doi:10.7150/jca.48245. Available from https://www.jcancer.org/v12p0740.htm

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Abstract

Breast cancer (BC), with complex tumorigenesis and progression, remains the most common malignancy in women. We aimed to explore some novel and significant genes with unfavorable prognoses and potential pathways involved in BC initiation and progression via bioinformatics methods. BC tissue-specific microarray datasets of GSE42568, GSE45827 and GSE54002, which included a total of 651 BC tissues and 44 normal breast tissues, were obtained from the Gene Expression Omnibus (GEO) database, and 124 differentially expressed genes (DEGs) were identified between BC tissues and normal breast tissues via R software and an online Venn diagram tool. Database for Annotation, Visualization and Integration Discovery (DAVID) software showed that 65 upregulated DEGs were mainly enriched in the regulation of the cell cycle, and Search Tool for the Retrieval of Interacting Genes (STRING) software identified the 39 closest associated upregulated DEGs in protein-protein interactions (PPIs), which validated the high expression of genes in BC tissues by the Gene Expression Profiling Interactive Analysis (GEPIA) tool. In addition, 36 out of 39 BC patients showed significantly worse outcomes by Kaplan-Meier plotter (KM plotter), and an additional Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that seven genes (cyclin E2 (CCNE2), cyclin B1 (CCNB1), cyclin B2 (CCNB2), mitotic checkpoint serine/threonine kinase B (BUB1B), dual-specificity protein kinase (TTK), cell division cycle 20 (CDC20), and pituitary tumor transforming gene 1 (PTTG1)) were markedly enriched in the cell cycle pathway. Analysis of the clinicopathological characteristics of hub genes revealed that seven cell cycle-related genes (CCRGs) were significantly highly expressed in four BC subtypes (luminal A, luminal B, HER2-positive and triple-negative (TNBC)), and except for the CCNE2 gene, high expression levels were significantly associated with tumor pathological grade and stage and metastatic events of BC. Furthermore, genetic mutation analysis indicated that genetic alterations of CCRGs could also significantly affect BC patients' prognosis. A quantitative real-time polymerase chain reaction (qRT-PCR) assay found that the seven CCRGs were significantly differentially expressed in BC cell lines. Integration of published multilevel expression data and a bioinformatics computational approach were used to predict and construct a regulation mechanism: a transcription factor (TF)-microRNA (miRNA)-messenger RNA (mRNA) regulation network. The present work is the first to construct a regulatory network of TF-miRNA-mRNA in BC for CCRGs and provides new insights into the molecular mechanism of BC.

Keywords: bioinformatics analysis, microarray dataset, breast cancer, differentially expressed gene, cell cycle, TF-miRNA-mRNA