Estrogen receptor-positive (ER+) and ER-negative (ER-) subtypes of
breast cancer have distinct clinical outcomes because they respond differentially to endocrine
therapies. We aimed to comprehensively analyze differentially expressed
microRNA (
miRNAs), long non-coding RNAs (lncRNAs) and mRNAs in different ER subtypes as well as to identify prognosis-related RNAs. The expression levels of
miRNAs, lncRNAs, and mRNAs between
breast cancer and normal samples were compared using data from The
Cancer Genome Atlas database. Differentially expressed
miRNAs, lncRNAs and mRNAs between ER+ and ER- samples were also screened. An ER subtype-related
miRNA-
lncRNA-
mRNA network was constructed. lncRNAs and mRNAs in this network were further subjected to an analysis of their associations with patient prognosis. Sets of differentially expressed
miRNAs, lncRNAs, and
miRNAs between
breast cancer and normal samples were identified among which 14
miRNAs, 78 lncRNAs, and 475 mRNAs were differentially expressed between ER subtypes. Relationships between these RNAs were analyzed. The resultant ER subtype-related
miRNA-
lncRNA-
mRNA network consisted of 14 nodes, among which LINC0092 and chromosome 2 open reading frame 71 (C2orf71) were correlated with better prognosis of
breast cancer. LINC0092 was co-expressed with SFRP1 and RGMA and regulated by hsa-miR-449a and hsa-miR-452-5p. C2orf71 was co-expressed with LINC00511 and regulated by hsa-miR-184. Cross-talk among differentially expressed
miRNAs, lncRNAs, and
miRNAs may be an important feature in ER+ and ER- subtypes of
breast cancer. LINC0092 and C2orf71, two of these cross-talking RNAs, may serve as novel prognostic predictor of
breast cancer because of their close associations with prognosis.