Whole-transcriptome sequencing with ceRNA regulation network construction and verification in glioblastoma

OBJECTIVES

To explore the key genes involved in the occurrence and development of glioblastoma (GBM) by analyzing whole-transcriptome sequencing and biologic data from GBM and normal cerebral cortex tissues and to search for important noncoding RNA (ncRNA) molecular markers based on the competitive endogenous RNA (ceRNA) network.

METHODS

Ten GBM and normal cerebral cortex tissues were collected for full transcriptome sequencing, screened for differentially expressed (DE) mRNAs, miRNAs, lncRNAs, and circRNAs, and subjected to bioinformatic analysis. We constructed a Protein-Protein Interaction (PPI) network and a circRNA/lncRNA-miRNA-mRNA regulatory network and identified them using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Finally, The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases were used to validate and conduct a survival analysis of the target genes.

RESULTS

A total of 5341 DEmRNAs, 259 DEmiRNAs, 3122 DElncRNAs, and 2135 DEcircRNAs were identified. Enrichment analysis showed that target genes regulated by DEmiRNA, DElncRNA, and DEcircRNA were closely related to chemical synaptic transmission and ion transmembrane transport. A PPI network analysis screened 10 hub genes that directly participate in tumor cell mitosis regulation. In addition, the ceRNA composite network showed that hsa-miR-296-5p and hsa-miR-874-5p were the central nodes of the network, and the reliability of relevant key molecules was successfully verified through RT-qPCR identification and the TCGA database. The CGGA database survival analysis produced 8 DEmRNAs closely related to GBM patient survival prognosis.

CONCLUSIONS

This study revealed the important regulatory functions and molecular mechanisms of ncRNA molecules and identified hsa-miR-296-5p and hsa-miR-874-5p as key molecules in the ceRNA network. They may play an important role in GBM pathogenesis, treatment, and prognosis.

Cloning and expression of UDP-glucose: flavonoid 3-O-glucosyltransferase gene in peach flowers

To elucidate the connection between flower coloration and the expression of genes associated with anthocyanin biosynthesis, a gene encoding UDP-glucose: flavonoid 3-O-glucosyltransferase (UFGT) was isolated, and the expression of the last four genes in the anthocyanin biosynthetic pathway during peach flower development was determined. The nucleotide sequence of the peach UFGT (GenBank accession No. JX149550) is highly similar to its homologs in other plants. Total anthocyanin content initially increased during peach flower development, and then decreased over time. Expression of the four anthocyanin biosynthesis genes increased until the full-bloom stage, and then decreased during late florescence. Expression of F3H, DFR, and UFGT increased dramatically at the full-bloom stage, coinciding with an increase in anthocyanin concentration. The UFGT gene may not be the only gene of the anthocyanin pathway to be differentially controlled in red peach flower tissues. Further studies are needed to genetically and physiologically characterize these genes and enzymes in peach flowers and to gain a better understanding of their functions and relationships with flower coloration.