LncRNA and mRNA interaction study based on transcriptome profiles reveals potential core genes in the pathogenesis of human glioblastoma multiforme

To study the expression profiles of lncRNA and mRNA in glioblastoma multiforme (GBM) and to find potential core genes in the pathogenesis of this high malignant disease. Agilent Microarray (Arrystar v2.0) was used to detect the expressions of 33,045 lncRNAs and 30,215 coding transcripts in 5 GBM and 5 normal brain samples. Differentially expressed lncRNAs and mRNAs were identified through Volcano Plot filtering. The expressions of six lncRNAs were further detected by qPCR to validate the results of microarray. The function of differential mRNA was determined by pathway and GO analysis, and the function of lncRNAs was studied by subgroup analysis and by their physical or functional relationships with corresponding mRNAs. A total of 815 lncRNAs and 738 mRNAs are found to be differentially expressed between the GBM and normal brain groups. With the expression of these differentially expressed genes, the two group samples could be clearly differentiated. The result of qPCR has showed a good consistency with the microarray, thus proving the accuracy of the microarray data. GO and Pathway analyses have proved that the functions of differentially expressed mRNAs in GBM related closely with many processes that important in the cancer pathogenesis. Core lncRNAs and mRNAs that may play important roles in the pathogenesis of GBM are revealed and listed according to various methods. The GBM shows an aberrant expression profile of lncRNA and mRNA. Potential core genes are revealed by the lncRNA and mRNA interaction study based on transcriptome profiles in GBM.