Differences in circRNA expression profiles between HER?2?positive breast cancer cells and normal mammary epithelial cells
10.3760/cma.j.issn.0253?3766.2019.05.003
- VernacularTitle:人表皮生长因子受体2亚型乳腺癌细胞与正常乳腺细胞环状RNA表达谱的差异分析
- Author:
Linhai LI
1
;
Bin XIAO
;
Muhetaer·Amier
;
Zhaohui SUN
Author Information
1. 解放军南部战区总医院检验科
- Keywords:
Breast neoplasms;
Human epidermal growth factor receptor?2;
Circular RNA;
Expression profile;
Microarray analysis
- From:
Chinese Journal of Oncology
2019;41(5):331-337
- CountryChina
- Language:Chinese
-
Abstract:
Objective To investigate the differential expression profiles of circular RNA (circRNA) in human epidermal growth factor receptor 2 ( HER?2) positive breast cancer cells and normal mammary epithelial cells, and to develop novel diagnostic and therapeutic markers for HER?2 positive breast cancer. Methods Total RNA were extracted from HER?2 positive breast cancer cell SK?BR?3 and normal mammary epithelial cell MCF10A. RNA quality was detected using NanoDrop ND?1000. Rnase R was applied to remove linear RNA and enrich circRNAs. After amplification and reverse transcription into fluorescent complementary RNA (cRNA) using random primer, the labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays. The raw data were extracted and the acquired array images were subjected to quantile normalization followed by heat map and volcano plot analysis. The expression of circRNAs with large fold change was verified by real?time quantitative polymerase chain reaction ( RT?qPCR). Finally, Gene Ontology ( GO) and Kyoto Encyclopedia of Genes and Genomes ( KEGG) enrichment analyses were performed in the differentially expressed circRNAs and circRNA?microRNA ( miRNA ) network was constructed. Results The total RNA extracted from SK?BR?3 and MCF10A had high integrity and quality. The expression profiles of circRNA in SK?BR?3 and MCF10A cells were significantly different shown by fluorescent expression signals. Compared with MCF10A cells, there were 6 584 up?regulated circRNAs and 6254 down?regulated circRNAs in SK?BR?3 cells. There were 348 circRNAs with |log2FC|≥2, of which 153 were up?regulated and 195 were down?regulated.Moreover, 8 circRNAs with |log2FC|＞5.Among them, 5 were up?regulated in SK?BR?3 cells, including hsa＿circRNA＿074595 (|log2FC|＝7.84), hsa＿circRNA＿074598 (| log2FC | ＝ 6.50 ), hsa＿circRNA＿085362 (| log2FC | ＝ 5.86 ), hsa＿circRNA＿101379 (|log2FC|＝5.71) and hsa＿circRNA＿406683 (|log2FC| ＝5.34); as well as 3 were down?regulated, including hsa＿circRNA＿021714 (|log2FC|＝5.46), hsa＿circRNA＿100777 (|log2FC|＝5.40), and hsa＿circRNA＿100796 (|log2FC|＝5.03). The expression levels of hsa＿circRNA＿074595, hsa＿circRNA＿074598 and hsa＿circRNA＿100777 were further validated by RT?qPCR in consistent with the results of microarray. GO analysis showed that differentially expressed circRNAs were significantly enriched in the biological process of heart development (P＜0.001), cellular component in the cell adhesion?related components ( P＜0.001), molecular function in protein serine／threonine kinase activity (P＜0.001). KEGG analysis revealed that differentially expressed circRNAs were significantly enriched in the PI3K?Akt signaling pathway. Conclusions The expression profile of circRNA in HER?2 positive breast cancer cells is significantly different from that in normal mammary epithelial cells. The differentially expressed circRNAs may be served as potential diagnostic or therapeutic targets for HER?2 positive breast cancer.
