Competing endogenous RNA network analysis identifies critical genes among the different breast cancer subtypes

Abstract

Although competing endogenous RNAs (ceRNAs) have been implicated in many solid tumors, their roles in breast cancer subtypes are not well understood. We therefore generated a ceRNA network for each subtype based on the significance of both, positive co-expression and the shared miRNAs, in the corresponding subtype miRNA dys-regulatory network, which was constructed based on negative regulations between differentially expressed miRNAs and targets. All four subtype ceRNA networks exhibited scale-free architecture and showed that the common ceRNAs were at the core of the networks. Furthermore, the common ceRNA hubs had greater connectivity than the subtype-specific hubs. Functional analysis of the common subtype ceRNA hubs highlighted factors involved in proliferation, MAPK signaling pathways and tube morphogenesis. Subtype-specific ceRNA hubs highlighted unique subtype-specific pathways, like the estrogen response and inflammatory pathways in the luminal subtypes or the factors involved in the coagulation process that participates in the basal-like subtype. Ultimately, we identified 29 critical subtype-specific ceRNA hubs that characterized the different breast cancer subtypes. Our study thus provides new insight into the common and specific subtype ceRNA interactions that define the different categories of breast cancer and enhances our understanding of the pathology underlying the different breast cancer subtypes, which can have prognostic and therapeutic implications in the future.

Systematic analysis of lncRNA–miRNA–mRNA competing endogenous RNA network identifies four-lncRNA signature as a prognostic biomarker for breast cancer

“…In recent years, some studies have investigated the ceRNAs in BC. For instance, Chen et al [ 32 ] analyzed the BC ceRNA network on the basis of common miRNAs as well as co-expression, but did not consider miRNA expression. Another study also established a BC specific ceRNA network to investigate its underlying molecular mechanisms based on the PCC of miRNA–mRNA pairs [ 33 ].…”

WITHDRAWN: Endometrial epithelial cell apoptosis is inhibited via a ciR8073-miR181a-neurotensis pathway during embryo implantation

“…Several studies had shown that the ERK1/2 activation usually protected neurons from apoptosis, whereas prolonged activation of P38 and/or JNK often caused death [59]. Moreover, Chen reported that P27 expression level Figure 11: Proposed network of ciR8073-miR181a-NTS in the endometrium of dairy goats.…”

The landscape of DNA methylation-mediated regulation of long non-coding RNAs in breast cancer

“…Many studies have illustrated that lncRNAs often combined with the target miRNAs to regulate the expression of mRNAs [ 44 , 45 ]. To measure the potential tumorigenic role of lncRNAs through miR-mediated interaction in BRCA, we used DEGs and DELs to construct a background network and regarded the four groups mentioned above as seeds to mine four sub lncRNA-mRNA ceRNA networks: high-up network, high-down network, low-up network and low-down network (Table 2 and Figure 4 ).…”