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Identification of Diagnostic Exosomal miRNAs and Pathogenic Regulatory Networks in Hepatocellular Carcinoma via mRNA Sequencing

ABSTRACT: Background/Objectives: Hepatocellular carcinoma (HCC) is the sixth most common malignancy worldwide and the third leading cause of cancer-related mortality. Prognosis is stage-dependent, but most patients are diagnosed at advanced stages when curative treatment is not feasible. Alpha-fetoprotein (AFP), the most widely used biomarker, has limited sensitivity and specificity for early detection. Serum-derived exosomal mi-croRNAs (miRNAs) are stable in circulation, tumor-specific, and actively involved in cancer biology, making them promising non-invasive biomarkers. This study aimed to identify, validate, and functionally characterize serum-derived exosomal miRNAs with diagnostic potential in HCC. Methods: Serum exosomes were isolated from 50 HCC pa-tients and 50 matched healthy controls, characterized by transmission electron micros-copy, nanoparticle tracking analysis, and CD9/CD63/CD81 flow cytometry. High-throughput small RNA sequencing of 3 HCC and 3 control samples identified dif-ferentially expressed miRNAs (DEMs). Target genes were predicted via multiple data-bases, integrated into STRING protein–protein interaction networks, and analyzed with cytoHubba. Gene Ontology (GO) and KEGG enrichment analyses were performed. Hub gene expression and survival relevance were evaluated using GEPIA2. Candidate miRNAs were validated by RT-qPCR, and diagnostic performance was assessed with receiver operating characteristic (ROC) analysis. Results: Seven DEMs were identified; FOXO1 and SRSF11 emerged as hub genes. hsa-miR-27a-3p targeted FOXO1, and hsa-miR-493-3p targeted SRSF11. RT-qPCR confirmed hsa-miR-27a-3p upregulation (P = 0.003) and hsa-miR-493-3p downregulation (P = 0.014) in HCC exosomes. ROC analysis showed high diagnostic accuracy for hsa-miR-493-3p (AUC = 0.840) and hsa-miR-27a-3p (AUC = 0.827), comparable to AFP (AUC = 0.828), with improved performance when combined. Conclusions: Serum-derived exosomal hsa-miR-27a-3p and hsa-miR-493-3p are promising non-invasive biomarkers for HCC, with diagnostic value comparable to AFP and mechanistic links to FOXO1 and SRSF11. Their integration into miRNA-based panels may improve early detection.

ORGANISM(S): Homo sapiens

PROVIDER: GSE306252 | GEO | 2026/01/21

REPOSITORIES: GEO

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Project description:In cancer management, early and accurate diagnosis of hepatocellular carcinoma (HCC) is important for enhancing survival rate of patients. Currently, serum alpha-fetoprotein (AFP) is the only one biomarker for detection of HCC. However, serum AFP is not satisfactory for diagnosis of HCC due to its low accuracy (about 60-70%). In this study, we collected 109 serum samples (discovery set) from healthy control (HC) and patients with chronic hepatitis B (CHB), liver cirrhosis (LC) and HCC, and analyzed them with custom lncRNA microarray. Profiling analysis shows 181 differentially expressed lncRNAs between HCs and patients with CHB, LC and HCC. Then a 48-lncRNA diagnostic signature was identified with 100% predictive accuracy for all subjects in the discovery set. This diagnostic signature was verified with a cross-validation analysis in the discovery set. To further corroborate the signature, we gathered another 66 serum samples (validation set) and also analyzed them with microarray. The result indicates that the same signature has similar diagnostic accuracy for HC (100%), CHB (73%), LC (88%) and HCC (95%), implying a reproducible diagnostic biomarker for HCC. Receiver operating characteristic (ROC) analysis exhibits that this signature has significantly higher diagnostic accuracy for HCC and non-cancerous subjects (area under curve [AUC]: 0.994) than AFP (AUC: 0.773) in the discovery set and this was also verified in the validation set (0.964 vs 0.792). More importantly, the signature detected small HCC (<3cm) with 100% (13/13) accuracy while AFP with only 61.5% (8/13). Altogether, this study demonstrates that the serum 48-lncRNA signature is not only a powerful and sensitive biomarker for diagnosis of HCC but also a potential biomarker for LC. ***************************************************************** Submitter declares these data are subject to patent number ZL 2016 1 0397094. *****************************************************************

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Identification of Diagnostic Exosomal miRNAs and Pathogenic Regulatory Networks in Hepatocellular Carcinoma via mRNA Sequencing

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