{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T12:45:20Z","timestamp":1785415520661,"version":"3.56.0"},"reference-count":42,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T00:00:00Z","timestamp":1778112000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The researchers would like to thank the Deanship of Graduate Studies and Scientific Research at Qassim University for financial support (QU-APC-2026).","award":["QU-APC-2026"],"award-info":[{"award-number":["QU-APC-2026"]}]},{"award":["QU-APC-2026"],"award-info":[{"award-number":["QU-APC-2026"]}],"id":[{"id":"https:\/\/ror.org\/01wsfe280","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality worldwide, underscoring the need for robust molecular biomarkers to improve prognosis and therapeutic strategies. Although advances have been made in imaging, surgery, as well as systemic therapies, the prognosis of HCC remains poor due to late detection, high recurrence, and molecular heterogeneity, underscoring the significance of identifying robust prognostic biomarkers and therapeutic targets. mRNA-sequencing data from the TCGA-HCC cohort were examined to recognize differentially expressed genes (DEGs) between tumor and normal tissues. Weighted gene co-expression network analysis (WGCNA) was applied to uncover key gene modules and hub genes. Protein\u2013protein interaction network (PPIN) construction and modular analysis further refined candidate genes. Univariate overall survival (OS) analysis identified five genes (TTK, CENPA, NUF2, KIF2C, and CDCA8) whose elevated expression significantly correlated with poor patient survival. Pathway enrichment analysis exhibited a strong association with mitotic checkpoint and kinetochore signaling pathways. Mutational profiling demonstrated frequent genomic alterations, particularly in NUF2, whereas immune infiltration analysis demonstrated significant correlations between NUF2 expression and multiple immune cell populations. In this study, we employed an integrative transcriptomic and systems biology approach to recognize prognostically relevant hub genes in HCC. Collectively, this finding highlights the critical genes that may serve as prognostic biomarkers and potential therapeutic targets in HCC.<\/jats:p>","DOI":"10.3390\/ijms27104164","type":"journal-article","created":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T12:15:07Z","timestamp":1778156107000},"page":"4164","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Uncovering Prognostic Biomarkers Underlying Hepatocellular Carcinoma Through Integrative Multi-Omics and a Network-Based Approach"],"prefix":"10.3390","volume":"27","author":[{"given":"Arshad Husain","family":"Rahmani","sequence":"first","affiliation":[{"name":"Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9685-7388","authenticated-orcid":false,"given":"Anam","family":"Beg","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tarique","family":"Sarwar","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6030-4493","authenticated-orcid":false,"given":"Amjad Ali","family":"Khan","sequence":"additional","affiliation":[{"name":"Department of Basic Health Sciences, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,7]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"159","DOI":"10.22270\/jddt.v15i5.7123","article-title":"Hepatocellular Carcinoma: A Comprehensive Review of Pathophysiology, Risk Factors, Diagnosis and Treatment Strategies","volume":"15","author":"Dafe","year":"2025","journal-title":"J. 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