Bio-diagnostic performances of microRNAs set related to DNA damage response pathway among hepatitis C virus-associated hepatocellular carcinoma patients

Abstract

Background: Up to date, a well-defined microRNAs (miRNAs) profile involved in hepatocellular carcinoma (HCC) pathogenesis remains indecisive. Thus, employing miRNAs for HCC diagnosis is demanded for early therapeutic interventions. We aimed to evaluate the usage of miRNAs set related to the SuperPath: miRNAs involved in DNA damage response pathway as effective biomarkers for HCV-related HCC diagnosis.

Results: The study enrolled 97 patients with HCV-related HCC, 84 with hepatitis C virus (HCV), 97 with liver cirrhosis (LC), and 84 healthy individuals. Serum miRNA-23a, miRNA-203, miRNA-100-5p, and miRNA-16 were quantified using qRT-PCR experiments, AFP and routine LFTs were estimated via standard techniques. Pathway enrichment analysis along with the construction of miRNAs regulatory network were performed. With respect to healthy individuals, miRNA-203, miRNA-100-5p, and miRNA-16 were significantly downregulated in HCC, HCV, and LC groups, while miRNA-23a showed significant upregulation (p < 0.001). miRNAs exhibited significant correlations with AFP, ALT, AST, and albumin. Also, elevated levels of miRNA-23a were recognized in patients with multiple focal lesions and/or lesion size > 5 cm. Additionally, the diagnostic performance of miRNA-23a expression level at a selected cut-off value of 3.99 overtakes AFP, while expressions of miR-203, miRNA-100-5p, and miRNA-16 represent poor diagnostic outcomes.

Conclusions: Keeping in mind the individual variability and high level of heterogeneity in HCC, our data revealed the diagnostic value of miRNA-23a expression in HCV-related HCC patients. Further extra in silico HCC-specific microRNAs sets are demanded in diagnosis.

Keywords: AFP; HCC,HCV-related HCC; In silico HCC-microRNAs; Serum biomarkers; miRNA-100-5p; miRNA-16; miRNA-203; miRNA-23a.

Fig. 1

ROC curve analysis for miRNA-23a , miRNA-203, miRNA-100-5p and miRNA-16 versus α-fetoprotein

Fig. 2

The Gene-disease relations of the studied miRNAs according to GeneAnalytics (https://geneanalytics.genecards.org)

Fig. 3

The main pathways related to the four studied miRNAs according to GeneAnalytics (https://geneanalytics.genecards.org)

Fig. 4

The gene ontology (GO) and pathways for the studied miRNAs. The biological processes and pathways from KEGG Reactome and WikiPathways according to g:Profiler (http://biit.cs.ut.ee/gprofiler/gost)

Fig. 5

MiRNAs-target gene network analysis. A The studied miRNAs and their target genes network, only the strong validated miRNAs targets were used. B–E The target/target pathway of miR-100, miR-23a, miR-16, and miR-203 respectively. F: miRNAs and their strong validated target gene network with filtering option of minimum two shared targets, representing that target/target pathway of hsa-miR-100 were IGF1R, MTOR and NCOR2; for hsa-miR-16, CDK6 , CCND2, NCOR2, MTOR, and IGF1R; for hsa-miR-203, CCND2, and CDK6, while hsa-miR-23a did not share any common target genes with other miRs according to miRTargetLink 2.0 (https://ccbcompute.cs.uni-saarland.de/mirtargetlink2)