Identification of differentially expressed genes and biological pathways in para-carcinoma tissues of HCC with different metastatic potentials

Abstract

Hepatocellular carcinoma (HCC) is a malignant tumor with extensive metastasis. Changes in the tumor microenvironment provide favorable conditions for tumor metastasis. However, the role of changes to the tumor microenvironment in HCC metastasis is yet to be elucidated. The Gene Expression Omnibus expression profile GSE5093 consists of 20 noncancerous tissues surrounding HCC tissues, including 9 metastasis-inclined microenvironment samples with detectable metastases and 11 metastasis-averse microenvironment samples without detectable metastases. The present study assessed 35 HCC samples to verify the results of chip analysis. In total, 712 upregulated and 459 downregulated genes were identified, with 1,033 nodes, 7,589 edges and 10 hub genes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the differentially expressed genes were significantly enriched in 'cell-cell adhesion', 'cell proliferation' and 'protein binding'. The top 10 hub genes were identified via a protein-protein interaction analysis. The 3 most significant modules were identified from the protein-protein network. Moreover, an association between hub genes and patient prognosis was identified. In conclusion, these candidate genes and pathways may help elucidate the mechanisms underlying HCC metastasis and identify more options for targeted therapy.

Keywords: differentially expressed genes; enrichment analysis; hepatocellular carcinoma; prognosis; protein-protein interaction; tumor microenvironment.

Figure 1.

Heat map of the top 100 differentially expressed genes in metastasis-inclined microenvironment and metastasis-averse microenvironment samples (50 upregulated and 50 downregulated genes). Red, upregulation; blue, downregulation.

Figure 2.

DEG protein-protein interaction network in metastasis-inclined microenvironment and metastasis-averse microenvironment. (A) The most significant interaction network of the upregulated DEGs interaction network. (B) Interaction network of the 317 downregulated DEGs interaction network. DEG, differentially expressed gene.

Figure 2.

DEG protein-protein interaction network in metastasis-inclined microenvironment and metastasis-averse microenvironment. (A) The most significant interaction network of the upregulated DEGs interaction network. (B) Interaction network of the 317 downregulated DEGs interaction network. DEG, differentially expressed gene.

Figure 3.

Top 10 hub genes were detected by reverse transcription-quantitative PCR. Expression of (A) CAD, (B) GART, (C) HSPA5, (D) NFKB1, (E) ACTB, (F) CDH1, (G) HSPA8, (H) PHLPP1, (I) PIK3GC and (J) STAT3 The data are presented as the mean ± standard deviation of 3 independent experiments. **P<0.01 MAM vs. MIM. CAD, carbamoyl-phosphate synthetase 2; GART, phosphoribosylglycinamide formyltransferase; HSPA5, heat shock protein family A member 5; NFκB1, nuclear factor κB subunit 1; ACTB, actin beta; CDH1, Cadherin 1; HSPA8, heat shock protein family A member 8; PHLPP1, PH domain and leucine rich repeat protein phosphatase 1; PIK3CG, phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit γ; STAT3, signal transducer and activator of transcription 3.

Figure 4.

Top 3 modules from the protein-protein interaction network determined by the molecular complex detection score. (A) Module 1 and (B) Module 2. Top 3 modules from the protein-protein interaction network determined by the molecular complex detection score. (C) Module 3.

Figure 4.

Top 3 modules from the protein-protein interaction network determined by the molecular complex detection score. (A) Module 1 and (B) Module 2. Top 3 modules from the protein-protein interaction network determined by the molecular complex detection score. (C) Module 3.

Figure 4.

Top 3 modules from the protein-protein interaction network determined by the molecular complex detection score. (A) Module 1 and (B) Module 2. Top 3 modules from the protein-protein interaction network determined by the molecular complex detection score. (C) Module 3.

Figure 5.

Prognostic value of hub genes in patients with HCC. Kaplan-Meier analysis of OS time un patients with HCC with high and low expression levels of: (A) CAD, (B) GART, (C) HSPA5, (D) NFκB1, (E) ACTB, (F) CDH1, (G) HSPA8, (H) PHLPP1, (I) PIK3CG and (J) STAT3. The red dotted line above the red curve and the red dotted line below represent the high (50%) and low cutoff (50%) on the survival curve. The blue dotted line above the blue curve and the blue dotted line below represent high (50%) and low cutoff (50%) on the survival curve. HCC, hepatocellular carcinoma; OS, overall survival; CAD, carbamoyl-phosphate synthetase 2; GART, phosphoribosylglycinamide formyltransferase; HSPA5, heat shock protein family A member 5; NFκB1, nuclear factor κB subunit 1; ACTB, actin beta; CDH1, cadherin 1; HSPA8, heat shock protein family A member 8; PHLPP1, PH domain and leucine rich repeat protein phosphatase 1; PIK3CG, phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit γ; STAT3, signal transducer and activator of transcription 3; HR, hazard ratio; TPM, transcripts per million.