Analysis of the miRNA-mRNA-lncRNA networks in ER+ and ER- XXXX cell lines.

@entity1 @entity1782 @entity34947 @entity10014 @entity2931 @entity5 @entity0 @entity22075 @entity20591 @entity5933 @entity73296 @entity3 @entity20478 @entity8332
UNASSIGNED: Recently, rapid advances in bioinformatics analysis have expanded our understanding of the transcriptome to a genome-wide level. miRNA-mRNA-lncRNA interactions have been shown to play critical regulatory role in @entity5 biology. In this study, we discussed the use of an integrated systematic approach to explore new facets of the @entity2931 receptor (ER)-regulated transcriptome. The identification of RNAs that are related to the expression status of the ER may be useful in clinical therapy and prognosis. We used a network modelling strategy. First, microarray expression profiling of mRNA, lncRNA and miRNA was performed in MCF-7 (ER-positive) and MDA-MB-231 cells (ER- negative). A co-expression network was then built using co-expression relationships of the differentially expressed mRNAs and lncRNAs. Finally, the selected miRNA-mRNA network was added to the network. The key miRNA-mRNA-lncRNA interaction can be inferred from the network. The mRNA and non-coding RNA expression profiles of the cells with different ER phenotypes were distinct. Among the aberrantly expressed miRNAs, the expression levels of @entity34947 -3p, miR-19b-3p and miR-130a-3p were much lower in the MCF-7 cells, whereas that of @entity20478 -3p was much higher. In a cluster of @entity10014 , the expression levels of six of seven miRNAs were lower in the MCF-7 cells, in addition to @entity22075 in the @entity20591 -363 cluster. However, the levels of all the miRNAs in the @entity20591 -25 cluster were higher in the MCF-7 cells. In the co-expression networking, @entity5933 and @entity73296 gene which is involved in the immune response and @entity3 , respectively, had a stronger correlation with ER. Among the aberrantly expressed lncRNAs, lncRNA- @entity8332 was highly expressed in the MCF-7 cells. A statistical analysis revealed that there was a co-expression relationship between @entity1782 and lncRNA- @entity8332 . In addition, @entity34947 and lncRNA- @entity8332 are both located on the @entity1 chromosome 13q. We speculate that @entity34947 might be co-expressed with lncRNA- @entity8332 to co-regulate the expression of @entity1782 , which influences the occurrence and development of @entity0 cells with different levels of ER expression. Our findings reveal that the status of ER is mainly due to the differences in the mRNA and ncRNA profile between the @entity0 cell lines, and highlight the importance of studying the miRNA-mRNA-lncRNA interactions to completely illustrate the intricate transcriptome.
