Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 Nov 1:7:e8021.
doi: 10.7717/peerj.8021. eCollection 2019.

Identification of key genes and long non-coding RNA associated ceRNA networks in hepatocellular carcinoma

Jun Liu  1   2 , Wenli Li  3 , Jian Zhang  1 , Zhanzhong Ma  1 , Xiaoyan Wu  4 , Lirui Tang  2   5
Affiliations

Identification of key genes and long non-coding RNA associated ceRNA networks in hepatocellular carcinoma

Jun Liu et al. PeerJ. .

Abstract

Background: Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. Although multiple efforts have been made to understand the development of HCC, morbidity, and mortality rates remain high. In this study, we aimed to discover the mRNAs and long non-coding RNAs (lncRNAs) that contribute to the progression of HCC. We constructed a lncRNA-related competitive endogenous RNA (ceRNA) network to elucidate the molecular regulatory mechanism underlying HCC.

Methods: A microarray dataset (GSE54238) containing information about both mRNAs and lncRNAs was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and lncRNAs (DElncRNAs) in tumor tissues and non-cancerous tissues were identified using the limma package of the R software. The miRNAs that are targeted by DElncRNAs were predicted using miRcode, while the target mRNAs of miRNAs were retrieved from miRDB, miRTarBas, and TargetScan. Functional annotation and pathway enrichment of DEGs were performed using the EnrichNet website. We constructed a protein-protein interaction (PPI) network of DEGs using STRING, and identified the hub genes using Cytoscape. Survival analysis of the hub genes and DElncRNAs was performed using the gene expression profiling interactive analysis database. The expression of molecules with prognostic values was validated on the UALCAN database. The hepatic expression of hub genes was examined using the Human Protein Atlas. The hub genes and DElncRNAs with prognostic values as well as the predictive miRNAs were selected to construct the ceRNA networks.

Results: We found that 10 hub genes (KPNA2, MCM7, CKS2, KIF23, HMGB2, ZWINT, E2F1, MCM4, H2AFX, and EZH2) and four lncRNAs (FAM182B, SNHG6, SNHG1, and SNHG3) with prognostic values were overexpressed in the hepatic tumor samples. We also constructed a network containing 10 lncRNA-miRNA-mRNA pathways, which might be responsible for regulating the biological mechanisms underlying HCC.

Conclusion: We found that the 10 significantly overexpressed hub genes and four lncRNAs were negatively correlated with the prognosis of HCC. Further, we suggest that lncRNA SNHG1 and the SNHG3-related ceRNAs can be potential research targets for exploring the molecular mechanisms of HCC.

Keywords: Competitive endogenous RNAs; GEO database; Hepatocellular carcinoma; Molecular biological mechanisms; Prognostic values.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1. Identification of DElncRNAs and DEGs.
(A) Volcano plots of the gene expression profile data. The blue dots represent down-regulated genes and the orange dots represent up-regulated genes. (B) Heat map of lncRNAs in HCC samples compared with normal samples.
Figure 2
Figure 2. lncRNA-associated ceRNA network.
Red nodes represent the 11 DElncRNAs. Green nodes represent the 32 predictive miRNAs. Blue nodes represent the 126 predictive mRNAs.
Figure 3
Figure 3. GO and KEGG analysis of DEGs.
(A) Biological processes, (B) Cell components, (C) Molecular functions of GO analysis, (D) KEGG analysis.
Figure 4
Figure 4. PPI network of DEGs and hub genes.
(A) PPI network of DEGs. Blue nodes represent the interaction among DEGs. Only the 90 DEGs that interacting with other ones were demonstrated in the network. (B) A total of 10 Hub genes identified from the PPI network. From the red nodes to yellow ones, the connection degree of each molecule with others gradually decreases.
Figure 5
Figure 5. Overall survival analysis of the hub genes.
(A) MCM4. (B) MCM7. (C) ZWINT. (D) KPNA2. (E) CKS2. (F) KIF23. (G) E2F1. (H) HMGB2. (I) EZH2. (J) H2AFX. The overall survival of patients with highly expressed hub genes was significantly shorter than those with low expression.
Figure 6
Figure 6. Overall survival analysis of the DElncRNAs.
(A) FAM182B. (B) SNHG1. (C) SNHG3. (D) SNHG6. The overall survival of patients with highly expressed DElncRNAs was significantly shorter than those with low expression.
Figure 7
Figure 7. Validation of lncRNA expression in UALCAN database.
(A) FAM182B. (B) SNHG1. (C) SNHG3. (D) SNHG6. Based on UALCAN, all DElncRNAs were significantly overexpressed in HCC tissues compared with the normal ones.
Figure 8
Figure 8. Validation of hub genes expression in UALCAN database.
(A) MCM4. (B) MCM7. (C) ZWINT. (D) KPNA2. (E) CKS2. (F) KIF23. (G) E2F1. (H) HMGB2. (I) EZH2. (J) H2AFX. Based on UALCAN, all hub genes were significantly overexpressed in HCC tissues compared with the normal ones.
Figure 9
Figure 9. Validation of hepatic expression of hub genes in the Human Protein Atlas database.
Expression of (A) MCM4, (C) KIF23, (E) MCM7, (G) E2F1, (I) ZWINT, (K) HMGB2, (M) KPNA2, (O) EZH2, (Q) CKS2, (S) H2AFX in non-tumor tissues. Expression of (B) MCM4, (D) KIF23, (F) MCM7, (H) E2F1, (J) ZWINT, (L) HMGB2, (N) KPNA2, (P) EZH2, (R) CKS2, (T) H2AFX in tumor tissues. Proteins encoded by MCM4, MCM7, ZWINT, CKS2, E2FI, HMGB2, and EZH2 were expressed higher in tumor than in non-tumor tissues. KPNA2 were expressed moderately in both groups. KIF23 and H2AFX were highly expressed in both tumor and non-tumor tissues.
Figure 10
Figure 10. The lncRNA–miRNA–mRNA ceRNA network constructed from hub genes and DElncRNAs.
Red nodes represent lncRNAs. Green nodes represent miRNAs. Blue nodes represent hub genes. A total of 10 lncRNA–miRNA–mRNA pathways were reconstructed here.
Figure 11
Figure 11. Co-expression analysis of DElncRNAs from ceRNA network with related hub genes in HCC patients.
(A) lncRNA FAM182B with KIF23. (B) lncRNA FAM182B with MCM7. (C) lncRNA SNHG1 with E2F1. (D) lncRNA SNHG1 with EZH2. (E) lncRNA SNHG1 with HMGB2. (F) lncRNA SNHG1 with MCM4. (G) lncRNA SNHG3 with ZWINT. (H) lncRNA SNHG6 with CKS2. (I) lncRNA SNHG6 with H2AFX. (J) lncRNA SNHG6 with KPNA2. SNHG1 and SNHG3 were strongly correlatted with their hub genes. FAM182B and SNHG6 showed moderate correlation with corresponding hub genes.
See this image and copyright information in PMC

References

    1. Abbastabar M, Sarfi M, Golestani A, Khalili E. lncRNA involvement in hepatocellular carcinoma metastasis and prognosis. EXCLI Journal. 2018;17:900–913. doi: 10.17179/excli2018-1541. - DOI - PMC - PubMed
    1. An Y, Zhang Z, Shang Y, Jiang X, Dong J, Yu P, Nie Y, Zhao Q. miR-23b-3p regulates the chemoresistance of gastric cancer cells by targeting ATG12 and HMGB2. Cell Death & Disease. 2015;6(5):e1766. doi: 10.1038/cddis.2015.123. - DOI - PMC - PubMed
    1. Borel F, Konstantinova P, Jansen PLM. Diagnostic and therapeutic potential of miRNA signatures in patients with hepatocellular carcinoma. Journal of Hepatology. 2012;56(6):1371–1383. doi: 10.1016/j.jhep.2011.11.026. - DOI - PubMed
    1. Borji M, Nourbakhsh M, Shafiee SM, Owji AA, Abdolvahabi Z, Hesari Z, Ilbeigi D, Seiri P, Yousefi Z. Down-regulation of SIRT1 expression by mir-23b contributes to lipid accumulation in HepG2 cells. Biochemical Genetics. 2019;57(4):507–521. doi: 10.1007/s10528-019-09905-5. - DOI - PubMed
    1. Bugide S, Green MR, Wajapeyee N. Inhibition of enhancer of zeste homolog 2 (EZH2) induces natural killer cell-mediated eradication of hepatocellular carcinoma cells. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(15):E3509–E3518. doi: 10.1073/pnas.1802691115. - DOI - PMC - PubMed

LinkOut - more resources