Molecular mechanisms of pathogenesis in hepatocellular carcinoma revealed by RNA‑sequencing

Abstract

The present study aimed to explore the underlying molecular mechanisms of hepatocellular carcinoma (HCC). RNA‑sequencing profiles GSM629264 and GSM629265, from the GSE25599 data set, were downloaded from the Gene Expression Omnibus database and processed by quality evaluation. GSM629264 and GSM629265 were from HCC and adjacent non‑cancerous tissues, respectively. TopHat software was used for alignment analysis, followed by the detection of novel splicing sites. In addition, the Cufflinks software package was used to analyze gene expressions, and the Cuffdiff program was used to screen for differently expressed genes (DEGs) and differentially expressed splicing variants. Gene ontology functional enrichment and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses of DEGs were also performed. Transcription factors (TFs) and microRNAs (miRNAs) that regulate DEGs were identified, and a protein‑protein interaction (PPI) network was constructed. The hub node in the PPI network was obtained, and the TFs and miRNAs that regulated the hub node were further predicted. The quality of the sequencing data met the standards for analysis, and the clean reads were ~65%. Most sequencing reads mapped into coding sequence exons (CDS_exons), whereas other reads mapped into exon 3' untranslated regions (UTR_Exons), 5'UTR_Exons and Introns. Upregulated and downregulated DEGs between HCC and adjacent non‑cancerous tissues were screened. Genes of differentially expressed splicing variants were identified, including vesicle‑associated membrane protein 4, phosphatidylinositol glycan anchor biosynthesis class C, protein disulfide isomerase family A member 4 and growth arrest specific 5. Screened DEGs were enriched in the complement pathway. In the PPI network, ubiquitin C (UBC) was the hub node. UBC was predicted to be regulated by several TFs, including specificity protein 1 (SP1), FBJ murine osteosarcoma viral oncogene homolog (FOS), proto‑oncogene c‑JUN (JUN), FOS‑like antigen 2 (FOSL2) and SWI/SNF‑related, matrix‑associated, actin‑dependent regulator of chromatin, subfamily A, member 4 (SMARCA4), and several miRNAs, including miR‑30 and miR‑181. Results from the present study demonstrated that UBC, SP1, FOS, JUN, FOSL2, SMARCA4, miR‑30 and miR‑181 may participate in the development of HCC.

Figure 1.

Regulatory networks of miRNAs, TFs and target genes. (A) Predicted TF-target gene network. (B) Predicted miRNA-target gene network. The red nodes represent the miRNAs or TFs, and the blue nodes represent their target genes. A link represents an interaction between a TF or miRNA and its target gene, whereas the size of a node corresponds to the number of interactions that a TF or miRNA has. miRNA, microRNA; TF, transcription factor.

Figure 2.

Protein-protein interaction network with ubiquitin C as the hub node. In the network, a node represents a protein and a link represents each pairwise protein interaction. The red shaded nodes represent upregulated genes, and the blue shaded nodes represent downregulated genes. The size of a node corresponds to its degree (that is, the number of interactions one protein has). Green-framed nodes are those with a degree >50.

Figure 3.

Regulatory network of UBC. The UBC gene may be regulated by transcription factors, represented by the square nodes, and microRNAs, represented by the diamond nodes. Green square framed nodes were also identified as DEGs, with the red shaded nodes representing the upregulated DEGs, and the blue shaded nodes representing the downregulated DEGs. UBC, ubiquitin C; DEGs, differently expressed genes.