Comprehensive Analysis Of Micro-RNAs And Messenger RNAs Associated With Prognosis In Triple-Negative Breast Cancer

Background and purposesTriple-negative breast cancer is a subtype of malignant breast tumor with poor prognosis,which tends to occur in young women.It is often characterized by high pathologically histological grade,strong invasiveness,and prones to recurrence and metastasis.More and more studies have shown that microRNA(miRNA)and messenger RNA(mRNA)play an important regulatory role in the occurrence and development of various somatic tumors including breast cancer,but the mechanism of action between these two types of RNA has not yet been clarified.The purpose of this study is to use the public breast cancer data downloaded from the TCGA website,through a series of bioinformatics analysis,to obtain the potential miRNA biomarkers and targets associated with the prognosis of triple-negative breast cancer,and to figure out the effects of miRNA and mRNA,in preparation for further exploring the molecular mechanism of germination and development in breast cancer.Materials and methodsSequencing samples of miRNAs and mRNAs from TNBC patients(level 3)were acquired from the Cancer Genome Atlas(TCGA)website.After the pretreatment of raw data,the differential expression of miRNAs(DEMs)and mRNAs(DEGs)between tumor and normal breast tissue was compared by using the Bioconductor software package.The DEMs were screened for meaningful prognostic-related miRNAs by performing survival R package and Kaplan-Meier curves.Two miRNA data analysis tools,miRDB,and miRTarBase were used to comprehensively predict target genes for miRNAs associated with TNBC.Subsequently,molecular function and pathway enrichment analysis were performed on the overlapping portions of target genes and DEGs,and then significantly differentially expressed genes were selected for conducting a miRNA-mRNA regulatory network and for further topological analysis to obtain key genes related to tumor prognosis.Finally,survival statistical analysis was performed in the key genes which had been identified as mentioned at the first beginning,for the purpose to verify key prognostic genes.ResultResults 1:There were 156 DEMs,of which 88 were up-regulated and 68 were down-regulated.There were 4828 DEGs,of which 2264 were up-regulated and 2564 were down-regulated.Results 2:According to the online Kaplan-Meier plotter analysis,there were 10 DEMs related to prognosis,of which 6 were up-regulated,and these miRNA are hsa-miR-33a,hsa-miR-934,hsa-miR-200c,hsa-miR-203a,hsa-miR-579 and hsa-miR-147b;there are four down-regulated DEMs,and they are hsa-let-7c,hsa-miR-383,hsa-miR-495,and hsa-miR-4732.Results 3:The cross-analysis of miRNA target gene prediction and DEGs revealed that there were 879 overlapping genes.The GO annotation results of these overlapping genes showed that the main biological process enrichment included:regulation of neuron differentiation,cellular response to growth factor stimulus,regulation of system process,etc.The main cellular component enrichment included:synaptic membrane,ion channel complex,receptor complex,etc.The main molecular function enrichment included:RNA polymerase Ⅱ regulatory region sequence-specific DNA binding,glycosaminoglycan binding,substrate-specific channel activity,etc.The results of KEGG pathway analysis showed that the main enrichment pathways included:pathways in cancer,neuroactive ligand-receptor interaction,cGMP-PKG signaling pathway,and so on.Results 4:Construction and regulation of the PPI network of miRNA-mRNA helped to find that there were 17 genes with high connectivity,including IGF2,JUN,VEGFA,IGF1,BDNF,BRCA1,CDKN2A,CCNA2,DNMT1,EZH2,FGF2,NTRK2,ALB,PIK3R1,ESR1,FN1,and NCAM1,and subsequent Kaplan-Meier survival analysis revealed that the key genes significantly associated with the prognosis of TNBC were VEGFA,FN1,and BRCA1.Conclusion1.The numbers of DEMs and DEGs determined by the final analysis were 156 and 4828,respectively.And it can be seen from the result that the number of up-and down-regulated miRNAs and mRNAs was basically balanced.2.There were a total of 10 DEMs related to tumor survival,and 3 miRNAs had not been reported in related breast cancer research,which were considered as new indicators to judge the prognosis of TNBC.3.There were 879 overlapping genes that were mainly involved in the construction of basic components such as the plasma membrane,ion channels,as well as receptor complexes.They also participated in the regulation of multiple complex tumor-related signaling pathways,like peptides and microRNAs.4.The results of the protein-protein interaction network showed that a total of 17 genes played an important role in the occurrence and development of TNBC,and these genes were IGF2,JUN,VEGFA,IGF1,BDNF,BRCA1,CDKN2A,CCNA2,DNMT1,EZH2,FGF2,NTRK2,ALB,PIK3R1,ESR1,FN1,NCAM1.And the subsequent survival analysis results also indicated that three genes,VEGFA,FN1 and BRCA1,were crucial for the prognosis in TNBC.These key genes were directly or indirectly involved in the carcinogenesis and metastasis of TNBC,so it is reasonable to assume that they might be effective targets in searching for potential drug therapy.