Identification of lncRNAs via microarray analysis for predicting HER2-negative breast cancer response to neoadjuvant chemotherapy

Mortality is high in patients with locally advanced HER2-negative breast cancer, especially those with residual tumor after neoadjuvant chemotherapy (NAC). Tissue-specific long non-coding RNAs (lncRNAs) are responsible for specific breast cancer subtypes. To identify the lncRNAs involved in residual cancer tissues (RCTs) and to evaluate their potential for predicting HER2-negative breast cancer response to NAC, we used three paired tissues to compare differences in gene expression between RCTs and remittent tissues (RTs) after NAC in human HER2-negative breast cancer. Subsequently, we detected expression of the top ten up-regulated and down-regulated lncRNAs in 11 paired tissues via quantitative RT-PCR analysis. Finally, we explored the potential function of these dysregulated lncRNAs through bioinformatics analysis. Our results indicate that 1348 mRNAs and 183 lncRNAs were differentially expressed in RCTs compared with RTs, and the expression levels of four novel lncRNAs (DSCAM-AS1, LINC01508, lnc-MGST1-2 and lnc-BTG2-2) were in agreement with the microarray analysis results. Furthermore, we found that the expression level of LINC01508 was significantly related to poor prognosis, suggesting that LINC01508 is a potential biomarker for predicting breast cancer response to NAC, which might be helpful in exploring potential diagnostic factors and therapeutic targets for chemo-resistant HER2-negative breast cancer.