Individualized investigations of differentially expressed lncRNAs in breast cancer patients

Abstract

Objective To identify differential expression of long non-coding RNA (lncRNAs) in breast cancer patients individually. Methods LncRIndiv was used to detect differentially expressed lncRNAs in individual breast cancer patients. Hypergeometric test and log-rank test were used to identify subtype-specific lncRNAs and prognosis-related lncRNAs. Results The average precision for LncRIndiv was more than 96%. Totally, 181, 32, 15 and 72 lncRNAs were defined as basal-like, HER2-enriched, luminal A- and B- specific lncRNAs, respectively (False discovery rate<0.05, hypergeometric test). Breast cancer with down-regulation of ZNF582-AS1 showed poorer prognosis than patients without down-regulation of ZNF582-AS1 (TCGA, P=0.038; GSE42568, P=0.026, Log-rank test), which is a potential prognostic biomarker. Conclusion LncRIndiv show high precision in detection of individually differential expression of lncRNAs. The differentially expressed lncRNAs in individual breast cancer can be applied to detect subtype-specific lncRNAs and prognostic lncRNA. Key words: breast cancer; differential expression; lncRNA; individualized