Identification of Crucial lncRNAs for Luminal A Breast Cancer through RNA Sequencing

Abstract

Background. The growing body of evidence indicates aberrant expression of long noncoding RNAs (lncRNAs) in breast cancer. Nevertheless, a few studies have focused on identifying key lncRNAs for patients with luminal A breast cancer. In our study, we tried to find key lncRNAs and mRNAs in luminal A breast cancer. Methods. RNA sequencing was performed to identify differentially expressed mRNAs (DEmRNAs) and differentially expressed lncRNAs (DElncRNAs) in luminal A breast cancer. The protein-protein interaction (PPI), DElncRNA-DEmRNA coexpression, DElncRNA-nearby DEmRNA interaction networks, and functional annotation were performed to uncover the function of DEmRNAs. Online databases were used to validate the RNA sequencing result. The diagnostic value of candidate mRNAs was evaluated by receiver operating characteristic (ROC) curve analysis. Results. A total number of 1451 DEmRNAs and 272 DElncRNAs were identified. Several hub proteins were identified in the PPI network, including TUBB3, HIST2H3C, MCM2, MYOC, NEK2, LIPE, FN1, FOXJ1, S100A7, and DLK1. In the DElncRNA-DEmRNA coexpression, some hub lncRNAs were identified, including AP001528.2, LINC00968, LINC02202, TRHDE-AS1, LINC01140, AL354707.1, AC097534.1, MIR222HG, and AL662844.4. The mRNA expression result of TFF1, COL10A1, LEP, PLIN1, PGM5-AS1, and TRHDE-AD1 in the GSE98793 was consistent with the RNA sequencing result. The protein expression results of TUBB3, MCM2, MYOC, FN1, S100A7, and TFF1 were consistent with the mRNA expression result COL10A1, LEP, PLIN1, PGM5-AS1, and TRHDE-AD1 were capable of discriminating luminal A breast cancer and normal controls. Four lncRNA-nearby and coexpressed mRNA pairs of HOXC-AS3-HOXC10, AC020907.2-FXYD1, AC026461.1-MT1X, and AC132217.1-IGF2 were identified. AMPK (involved LIPE and LEP) and PPAR (involved PLIN1) were two significantly enriched pathways in luminal A breast cancer. Conclusion. This study could be helpful in unraveling the pathogenesis and providing novel therapeutic strategies for luminal A breast cancer.

Transcriptomics analysis of long non-coding RNAs in smooth muscle cells from patients with peripheral artery disease and diabetes mellitus

“…Consequently, whether these lncRNAs also affect SMCs has not yet been investigated. MIR222HG was also described in association with cancer 36 , 37 but also with macrophage polarisation 38 . In this context, it is to be noted that SMCs can adopt various phenotypes, including also that of macrophages or foam cells 39 .…”

Transcriptomics analysis of long non-coding RNAs in smooth muscle cells from patients with peripheral artery disease and diabetes mellitus

“…Consequently, whether these lncRNAs also affect SMCs has not yet been investigated. MIR222HG was also described in association with cancer 34,35 but also with macrophage polarisation 36 . In this context, it is to be noted that SMCs can adopt various phenotypes, including also that of macrophages or foam cells 37 .…”

An insight into the potential role of LINC00968 in luminal breast cancer: Case-control study and bioinformatics analysis

“…Extensive studies have reported that the majority of lncRNAs are abnormally expressed in tumor tissues, and each lncRNA exerts its function through different mechanisms in cancers [ 18 ]. According to the previous studies, LINC00968 was upregulated in osteosarcoma and lung squamous cell carcinoma and was downregulated in BC [ 14 , 16 , 17 , 19 ]. Also, this lncRNA combined with MIAT and LIN01140 lncRNAs can be used as potential diagnostic biomarkers for BC [ 16 ].…”

“…One study has indicated the downregulation of LINC00968 in plasma of patients with BC and GEO datasets [ 16 ]. Another study has reported that LINC00968 is downregulated in luminal A BC [ 17 ]. The potential role of LINC00968 in luminal A and B subtypes of BC remains unexplored.…”