Identification of differentially expressed lncRNAs and mRNAs in luminal-B breast cancer by RNA-sequencing

BMC Cancer

Ying Yi¹  Xue Luo¹  Xiang-Mei Jiang²  Jian-Fei E²  Cheng-Liang Yuan²  Ning Zou²  Wei Wei²  Nai-Dan Zhang²  Ying-Ying Liu³ 

[1] Department of Breast Surgery, People’s Hospital of Deyang City;Department of Clinical Laboratory, People’s Hospital of Deyang City;Department of Science and Education, People’s Hospital of Deyang City;

关键词: Luminal-B breast cancer;    mRNA;    Long non-coding RNA (lncRNA);    RNA-sequencing;   

DOI  :  10.1186/s12885-019-6395-5

来源: DOAJ

【 摘 要 】

Abstract Background Luminal B cancers show much worse outcomes compared to luminal A. This present study aims to screen key lncRNAs and mRNAs correlated with luminal-B breast cancer. Methods Luminal-B breast cancer tissue samples and adjacent tissue samples were obtained from 4 patients with luminal-B breast cancer. To obtain differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) between luminal-B breast cancer tumor tissues and adjacent tissues, RNA-sequencing and bioinformatics analysis were performed. Functional annotation of DEmRNAs and protein-protein interaction networks (PPI) construction were performed. DEmRNAs transcribed within a 100 kb window up- or down-stream of DElncRNAs were searched, which were defined as cis nearby-targeted DEmRNAs of DElncRNAs. DElncRNA-DEmRNA co-expression networks were performed. The mRNA and lncRNA expression profiles were downloaded from The Cancer Genome Atlas (TCGA) database to validate the expression patterns of selected DEmRNAs and DElncRNAs. Results A total of 1178 DEmRNAs and 273 DElncRNAs between luminal-B breast cancer tumor tissues and adjacent tissues were obtained. Hematopoietic cell lineage, Cytokine-cytokine receptor interaction, Cell adhesion molecules (CAMs) and Primary immunodeficiency were significantly enriched KEGG pathways in luminal-B breast cancer. FN1, EGFR, JAK3, TUBB3 and PTPRC were five hub proteins of the PPI networks. A total of 99 DElncRNAs-nearby-targeted DEmRNA pairs and 1878 DElncRNA-DEmRNA co-expression pairs were obtained. Gene expression results validated in TCGA database were consistent with our RNA-sequencing results, generally. Conclusion This study determined key genes and lncRNAs involved in luminal-B breast cancer, which expected to present a new avenue for the diagnosis and treatment of luminal-B breast cancer.

【 授权许可】

Unknown