MicroRNA-related transcription factor regulatory networks in human colorectal cancer

Abstract

Objective Colorectal cancer (CRC) is an extremely common gastrointestinal malignancy. The present study aimed to identify microRNAs (miRNAs) and transcription factors (TFs) associated with tumor development. MethodsThree miRNA profile datasets were integrated and analyzed to elucidate the potential key candidate miRNAs in CRC. The starBase database was used to identify the potential targets of common differentially expressed miRNAs (DEMs). Transcriptional Regulatory Element Database and Transcriptional Regulatory Relationships Unraveled by Sentence-based Text databases were used to identify cancer-related TFs and the TF-regulated target genes. Functional and pathway enrichment analyses were performed using the Database for Annotation, Visualization and Integration Discovery (DAVID) database, and the miRNA-TF-gene networks were constructed by Cytoscape. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to detect the expression of genes and miRNAs. Results In total, 14 DEMs were found in CRC. By bioinformatics analysis, 5 DEMs (miR-145, miR-497, miR-30a, miR-31, and miR-20a) and 8 TFs (ELK4 (ETS-family transcription factor), myeloblastosis proto-oncogene like (MYBL)1, MYBL2, CEBPA, PPARA, PPARD, PPARG, and endothelial PAS domain protein (EPAS1)) appeared to be associated with CRC and were therefore used to construct miRNA-TF-gene networks. From the networks, we found that miR-20a might play the most important role as an miRNA in the networks. By qRT-PCR, we demonstrated that miR-20a was significantly upregulated in CRC tissues. We also performed qRTPCR to identify the expression of miR-20a-related TFs (PPARA, PPARD, PPARG, EPAS1). Three of them, PPARA, PPARG, and EPAS1, were downregulated in CRC tissues, with statistically significant differences, while the downregulation of PPARD in CRC tissues was not significantly different. Pathway enrichment analyses indicated that the phosphoinositide 3-kinase (PI3K)-Akt signaling pathway was the most significantly enriched pathway. Two main elements of the PI3K-Akt signaling pathway, phosphatase and tensin homolog deleted on chromosome 10 and B-cell lymphoma 2-associated agonist of cell death, were demonstrated to be downregulated in CRC. ConclusionThe present study identified hub miRNAs and miRNA-related TF regulatory networks in CRC, which might be potential targets for the diagnosis and treatment of CRC. Abbreviations: BAD = B-cell lymphoma 2-associated agonist of cell death, BP = biological process, CC = cellular component, CEBPA = CCAAT/enhancer binding protein A, CRC = colorectal cancer, DAVID = Database for Annotation, Visualization and Integration Discovery, DEM = differentially expressed miRNA, GEO = Gene Expression Omnibus, GO = Gene Ontology, HIF = hypoxia-inducible factor, KEGG = Kyoto Encyclopedia of Genes and Genomes, logFC = log fold change, MF = molecular function, miRNA = microRNA, mRNA = messenger RNA, NCBI = National Center for Biotechnology Information, NFI = nuclear factor I, PANT = paired adjacent normal tissues, PI3K = phosphoinositide 3-kinase, PPAR = peroxisome proliferator-activated receptor, PTEN = phosphatase and tensin homolog deleted on chromosome 10, qRT-PCR = quantitative reverse transcription polymerase chain reaction, STAT = signal transducer and activator of transcription, TCGA = The Cancer Genome Atlas, TF = transcription factor, TRED = Transcriptional Regulatory Element Database, TRRUST = Transcriptional Regulatory Relationships Unraveled by Sentence-based Text, VEGF = vascular endothelial growth factor.