Long noncoding RNAs (lncRNAs) are an emerging class of key regulatory RNAs that are greater than 200nt and do not code for protein. They appear to be critical for various biological processes including gene regulation. Increasing evidence has suggested that aberrantly expressed lncRNAs play a key role in the initiation and progression of breast cancer. In most studies of breast cancer, breast tumor tissue was compared to adjacent normal-appearing tissue to identify differentially expressed lncRNAs. However, expression of lncRNAs in normal breast tissue from healthy donors has rarely been studied, and the differences in expression of lncRNAs in breast tumor and normal breast tissue from healthy donors remain largely unknown. Using RNA-sequencing data generated from freshly-frozen breast tissue samples, we examined the expression of lncRNAs in 119 breast tumor, 47 adjacent normal-appearing breast tissue samples, and 23 normal breast tissue samples from healthy donors. Bowtie and RESM algorithms were used to align raw reads and quantify transcript abundance. Differential expression analyses were performed using edgeR software. We assessed the expression of a total of 7,844 mapped lncRNAs using normalized transcript counts. Unsupervised Principal Components Analysis (PCA) demonstrated that the lncRNA expression profile of adjacent normal-appearing tissue was different compared to normal breast tissue from healthy donors, and partially overlapped with the tumor. At various fold change thresholds, more differentially expressed lncRNAs can be detected when the tumor tissue is compared to normal tissue than to adjacent non-tumorous tissue. With a false discovery rate (FDR) < 0.05 and a fold change (FC) of more than ±2, we identified 107 differentially expressed lncRNAs for the tumor vs. normal breast tissue, 53 lncRNAs for tumor vs. adjacent normal-appearing tissue, and 20 lncRNAs for adjacent normal-appearing vs. normal breast tissue. In our analyses of tumor vs. adjacent normal-appearing tissue and tumor vs. normal tissue from healthy donors, we identified differentially expressed lncRNAs including HOTAIR, GAS5 and ANRIL/CDKN2B-AS1 that were previously implicated in breast cancer, with considerably higher fold changes in latter comparison. When using normal breast tissue from healthy donors as the baseline, we identified novel putative breast cancer-associated lncRNAs including EMX2OS, TERC, HOTAIRM1, and WT1-AS that are aberrantly expressed in breast tumor. These lncRNAs were not identifiable in a direct comparison of tumor and adjacent normal-appearing tissue. Our results suggest that adjacent normal-appearing tissue undergoes changes in lncRNAs expression similar to those observed in tumor tissue to some extent, and a number of new and potentially important lncRNAs can only be detected using normal tissue from healthy donors as an optimal baseline tissue.

Citation Format: Erin Wagner, Yunlong Liu, Bryan Schneider, Anna Maria Storniolo, Jiali Han, Chunyan He. Differences in expression of lncRNAs in breast tumor, adjacent normal-appearing breast tissue, and normal breast tissue from healthy donors. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3268. doi:10.1158/1538-7445.AM2014-3268