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Breast cancer is the most common neoplasm among females. Estrogen receptor (ESR) signaling has a prominent impact in the pathogenesis of breast cancer. Among the transcription factors associated with ESR signaling, FOXM1, GATA3, FOXA1 and ESR1 have been suggested as a candidate in the pathogenesis of this neoplasm. In the current project, we have designed an  in silico  approach to find long non-coding RNAs (lncRNAs) that regulate these transcription factors. Then, we used clinical samples to carry out validation of our in silico findings. Our systems biology method led to the identification of  APTR ,  AC144450.1 ,  linc00663 ,  ZNF337.AS1 , and  RAMP2.AS1  lncRNAs. Subsequently, we assessed the expression of these genes in breast cancer tissues compared with the adjacent non-cancerous tissues (ANCTs). Expression of  GATA3  was significantly higher in breast cancer tissues compared with ANCTs (Ratio of mean expressions (RME) = 4.99, P value = 3.12E−04). Moreover, expression levels of  APTR ,  AC144450.1 , and  ZNF337.AS1  were elevated in breast cancer tissues compared with control tissues (RME = 2.27, P value = 5.40E−03; Ratio of mean expressions = 615.95, P value = 7.39E−19 and RME = 1.78, P value = 3.40E−02, respectively). On the other hand, the expression of  RAMP2.AS1  was lower in breast cancer tissues than controls (RME = 0.31, P value = 1.87E−03). Expression levels of  FOXA1 ,  ESR1 , and  FOXM1  and  linc00663  were not significantly different between the two sets of samples. Expression of  GATA3  was significantly associated with stage (P value = 4.77E−02). Moreover, expressions of  FOXA1  and  RAMP2.AS1  were associated with the mitotic rate (P values = 2.18E−02 and 1.77E−02, respectively). Finally, expressions of  FOXM1  and  ZNF337.AS1  were associated with breastfeeding duration (P values = 3.88E−02 and 4.33E−02, respectively). Based on the area under receiver operating characteristics curves,  AC144450.1  had the optimal diagnostic power in differentiating between cancerous and non-cancerous tissues (AUC = 0.95, Sensitivity = 0.90, Specificity = 0.96). The combination of expression levels of all genes slightly increased the diagnostic power (AUC = 0.96). While there were several significant pairwise correlations between expression levels of genes in non-tumoral tissues, the most robust correlation was identified between  linc00663  and  RAMP2.AS1  (r = 0.61, P value = 3.08E−8). In the breast cancer tissues, the strongest correlations were reported between  FOXM1 / ZNF337.AS1  and  FOXM1 / RAMP2.AS1  pairs (r = 0.51, P value = 4.79E−5 and r = 0.51, P value = 6.39E−5, respectively). The current investigation suggests future assessment of the functional role of  APTR ,  AC144450.1  and  ZNF337.AS1  in the development of breast neoplasms.

Expression Analysis of Long Non-Coding RNAs Related With FOXM1, GATA3, FOXA1 and ESR1 in Breast Tissues