Differential expression profile of mRNAs, lncRNAs, and circRNAs reveals potential molecular mechanism in breast cancer

Abstract

In recent years, breast cancer attracts more and more attention because of its high incidence. To explore the molecular functions and mechanisms, we performed RNA sequencing on the tumor tissues and their paired normal tissues from three breast cancer patients. By differential expression analysis, we found 3,764 differentially expressed mRNAs (DE mRNAs), 5,416 differentially expressed lncRNAs (DE lncRNAs) and 148 differentially expressed circRNAs (DE circRNAs). Enrichment analysis suggested that the DE lncRNAs and DE circRNAs were enriched in mitochondria and nucleus, which indicated that they may participate in the vital metabolism directly or indirectly, such as fatty acid metabolism. Subsequently, the protein-protein interaction (PPI) network was constructed and we got eight key proteins, of which the MMP9 (degree 5) draws our attention. Based on the 38 up-regulated circRNAs and 14 down-regulated circRNAs, we constructed competing endogenous RNA (ceRNA) networks, from which the has-miR-6794-5p has been identified to enriched in the up-regulated network and correlated with the circNFIX directly. At this point, we presented that the circNFIX and MMP9 may play a significant role by regulating fatty acid metabolism in breast cancer.

Circular RNAs in Breast Cancer: An Update

“…BC tissues RNA sequencing 70 circRNAs were upregulated and 78 circRNAs were downregulated. [48] BC tissues CircRNA microarray analysis 89 downregulated and 129 upregulated circRNAs were reported. [49] BC tissues CircRNA high-throughput sequencing 136 increased circRNAs were found.…”

“…Aberrant expression of circRNAs in BC has been reported in a significant quantity. Li et al performed RNA sequencing on BC tissues and matched normal tissues and discovered 148 differentially expressed (DE) circRNAs, of which 70 were upregulated and 78 were downregulated [48]. According to circRNA microarray analysis of six pairs of BC tissues and adjacent normal breast tissues, Li et al discovered 218 DE circRNAs, including 89 downregulated and 129 upregulated circRNAs [49].…”