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. 2021 Aug 10:14:4369-4380.
doi: 10.2147/IJGM.S323868. eCollection 2021.

Investigation of Potential Molecular Biomarkers for Diagnosis and Prognosis of AFP-Negative HCC

Zijing Liu  1 , Youwei Pu  2 , Yixi Bao  2 , Song He  1
Affiliations

Investigation of Potential Molecular Biomarkers for Diagnosis and Prognosis of AFP-Negative HCC

Zijing Liu et al. Int J Gen Med. .

Abstract

Background: Alpha-fetoprotein (AFP) is the most important diagnostic and prognostic index of hepatocellular carcinoma (HCC). AFP-positive HCC can be easily diagnosed based on the serum AFP level and typical imaging features, but a number of HCC patients are negative (AFP < 20 ng/mL) for AFP. Therefore, it is necessary to develop novel diagnostic and prognostic biomarkers for AFP-negative HCC.

Methods: RNA data from TCGA and differential expression of lncRNAs, miRNAs, and mRNAs were downloaded to analyze the differential RNA expression patterns between AFP-negative HCC tissues and normal tissues. A lncRNA-miRNA-mRNA ceRNA regulatory network was constructed to elucidate the interaction mechanism of RNAs. Functional enrichment analysis of these DEmRNAs was performed to indirectly reveal the mechanism of action of lncRNAs. A PPI network was built using STRING, and the hub genes were identified with Cytoscape. The diagnostic value of hub genes was assessed with receiver operating characteristic (ROC) analysis. And the prognostic value of RNAs in the ceRNA was estimated with Kaplan-Meier curve analysis.

Results: A total of 131 lncRNAs, 185 miRNA, and 1309 mRNAs were found to be differentially expressed in AFP-negative HCC. A ceRNA network consisting of 12 lncRNA, 23 miRNA, and 74 mRNA was constructed. The top ten hub genes including EZH2, CCNB1, E2F1, PBK, CHAF1A, ESR1, RRM2, CCNE1, MCM4, and ATAD2 showed good diagnostic power under the ROC curve; and 2 lncRNAs (LINC00261, LINC00482), 3 miRNAs (hsa-miR-93, hsa-miR-221, hsa-miR-222), and 2 mRNAs (EGR2, LPCAT1) were found to be associated with the overall survival of AFP-negative patients.

Conclusion: This study could provide a novel insight into the molecular pathogenesis of AFP-negative HCC and reveal some candidate diagnostic and prognostic biomarkers for AFP-negative HCC.

Keywords: AFP-negative HCC; ceRNA network; diagnosis; prognosis.

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Conflict of interest statement

The authors declared no conflicts of interest for this work and no competing financial interests.

Figures

Figure 1
Figure 1
Volcano plots of differentially expressed lncRNA (A), miRNA (B) and mRNA (C) in AFP-negative HCC. Red dots indicate genes significantly upregulated and green indicates genes significantly downregulated.
Figure 2
Figure 2
Venn diagram analysis for the intersection set between differentially expressed mRNA in AFP-negative HCC and miRNA target genes.
Figure 3
Figure 3
The lncRNA-miRNA-mRNA ceRNA network in AFP-negative HCC. The diamond represents lncRNA, the square represents miRNA and the circle denotes mRNA. The red nodes indicate upregulated RNAs and the green nodes indicate downregulated RNAs.
Figure 4
Figure 4
The GO enrichment analysis of DEmRNAs in the ceRNA network of AFP-negative HCC.
Figure 5
Figure 5
The enriched KEGG pathway of DEmRNAs in the ceRNA network of AFP-negative HCC.
Figure 6
Figure 6
(A) A PPI network of DEmRNAs involved in the ceRNA network of AFP-negative HCC. Red nodes represent the upregulated DEmRNAs and green nodes represent the downregulated DEmRNAs. (B) The top ten highly interacted hub genes were recognized by cytoHubba.
Figure 7
Figure 7
The ROC curves of the top ten hub genes. The AUC of CCNB1, E2F1, RRM2, MCM4, EZH2, PBK, ATAD2, CCNE1, ESR1, and CHAF1A were 0.954, 0.949, 0.916, 0.848, 0.962, 0.929, 0.816, 0.873, 0.920, and 0.928, respectively.
Figure 8
Figure 8
Kaplan–Meier survival curves of lncRNAs (A and B), miRNA (C–E), mRNA (F and G) associated with overall survival in AFP-negative HCC.
See this image and copyright information in PMC

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