Proteomic profiling identifies miR-423-5p as a modulator of oncogenic metabolism in HCC

Luce, A, Bocchetti, M, Cossu, AM, Tathode, MS, Boocock, DJ ORCID: https://orcid.org/0000-0002-7333-3549, Coveney, C ORCID: https://orcid.org/0000-0001-7047-6408, Romano, MP, De Iesu, MR, Simeone, I, Mele, L, Vitale, G, Sperlongano, R, Misso, G, Verderio, EAM ORCID: https://orcid.org/0000-0001-9153-8997, Zappavigna, S and Caraglia, M, 2025. Proteomic profiling identifies miR-423-5p as a modulator of oncogenic metabolism in HCC. Journal of Translational Medicine, 23: 1008. ISSN 1479-5876

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Abstract

Background: Hepatocellular carcinoma (HCC) remains a significant clinical challenge due to limited diagnostic and therapeutic options. Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), play key roles in cancer biology. Our previous findings showed that miR-423-5p enhances anti-cancer effects on HCC patients treated with sorafenib by promoting autophagy. Here, we investigated the molecular mechanisms underlying miR-423-5p function through a comprehensive proteomic approach.

Methods: We generated an HCC cell line stably overexpressing miR-423-5p via lentiviral transduction. Total proteins were extracted from SNU-387 cells, enzymatically digested into peptides, and subsequently analysed by liquid chromatography-tandem mass spectrometry (LC-MS/M). Raw spectral data were processed and quantified using MaxQuant. Differentially expressed proteins (DEPs) were defined based on fold-change (|log2FC| ≥ 1) and false discovery rate (FDR < 0.05). The full proteomic dataset is available via the ProteomeXchange repository (identifier: PXD064869). Functional enrichment analysis of DEPs were performed using DAVID and Reactome. To assess clinical relevance, predicted and validated miR-423-5p targets were integrated with The Cancer Genome Atlas (TCGA) Liver Hepatocellular Carcinoma (LIHC) dataset using GEPIA platform. Survival analyses were performed using the Kaplan–Meier method.

Results: Proteomic profiling identified 698 DEPs in miR-423-5p-overexpressing cells compared to controls with significant enrichment in metabolic pathways, related to purine/pyrimidine metabolism and gluconeogenesis. Integration with bioinformatic predictions and miRTarBase validation identified 43 DEPs as potential direct targets of miR-423-5p. Among these, seven proteins (ACACA, ANKRD52, DVL3, MCM5, MCM7, RRM2, SPNS1, and SRM) were significantly associated with patient prognosis in the TCGA-LIHC cohort. These targets were downregulated in miR-423-5p-overexpressing cells but upregulated in advanced-stage HCC tissues, suggesting a potential role for miR-423-5p in the regulation of HCC pathogenesis. Stage-specific expression analysis showed increased levels from stage I to III, followed by a decline at stage IV. Notably, we experimentally confirmed miR-423-5p-mediated suppression of MCM7, DVL3, IMPDH1, and SRM (SPEE), supporting their functional involvement in HCC progression.

Conclusion: Overall, our findings support a tumour-suppressive role for miR-423-5p in HCC, mediated by modulation of metabolic pathways and suppression of oncogenic proteins. These results suggest that miR-423-5p and its downstream effectors may serve as promising biomarkers and potential therapeutic targets in HCC.

Item Type:	Journal article
Publication Title:	Journal of Translational Medicine
Creators:	Luce, A., Bocchetti, M., Cossu, A.M., Tathode, M.S., Boocock, D.J., Coveney, C., Romano, M.P., De Iesu, M.R., Simeone, I., Mele, L., Vitale, G., Sperlongano, R., Misso, G., Verderio, E.A.M., Zappavigna, S. and Caraglia, M.
Publisher:	Springer Science and Business Media LLC
Date:	24 September 2025
Volume:	23
ISSN:	1479-5876
Identifiers:	Number Type 10.1186/s12967-025-07039-4 DOI 2504727 Other
Rights:	© The Author(s) 2025. This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creati​​ vecommons.org/licenses/by-nc-nd/4.0/.
Divisions:	Schools > School of Science and Technology
Record created by:	Laura Borcherds
Date Added:	26 Sep 2025 16:21
Last Modified:	26 Sep 2025 16:21
URI:	https://irep.ntu.ac.uk/id/eprint/54469

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