{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T13:05:21Z","timestamp":1779368721604,"version":"3.53.0"},"reference-count":37,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T00:00:00Z","timestamp":1778803200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Key Basic Medical Discipline Project at the School Level of Xinjiang Second Medical College","award":["XKZ202502"],"award-info":[{"award-number":["XKZ202502"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Metabolic reprogramming is closely linked to tumor proliferation, invasion, and immune escape. Despite its central role in amino acid metabolism, the regulatory mechanisms of asparagine metabolism in hepatocellular carcinoma (HCC) progression remain poorly characterized. Rather than focusing on canonical metabolic genes, prognostic markers were identified from co-expression modules associated with asparagine metabolism signatures. Using the TCGA database and asparagine metabolism-related gene sets, a prognostic risk-scoring model was developed through differential expression analysis, univariate Cox regression, and the LASSO algorithm and externally validated with the GEO dataset (GSE14620). Survival analysis, ROC curve evaluation, nomogram construction, scRNA-seq, GSEA, and drug sensitivity analysis were performed to systematically delineate the molecular mechanisms by which asparagine metabolism drives HCC progression. A three-gene signature comprising BOP1, SAC3D1, and PDE2A effectively stratified patients into high- and low-risk groups. High-risk patients exhibited markedly poorer overall survival, enrichment in tumor proliferation-associated pathways, increased tumor purity, reduced immune cell infiltration, and a substantially higher TP53 mutation rate (38% vs. 13%). In contrast, the low-risk group showed enrichment in pathways linked to hepatoblastoma suppression and liver function, alongside improved predicted response to immunotherapy. Single-cell analysis identified NK cells and endothelial cells as central mediators of asparagine metabolism-driven HCC progression, with BOP1, SAC3D1, and PDE2A displaying dynamic expression patterns during differentiation. Furthermore, the high-risk group was predicted to be more sensitive to chemotherapeutics such as cyclophosphamide and 5-fluorouracil. These findings highlight a potential interplay between nitrogen metabolism and asparagine metabolism in HCC and suggest mechanisms by which these pathways may influence NK cell and endothelial cell function to promote disease progression. This study establishes a novel prognostic model and identifies potential chemotherapeutic vulnerabilities in high-risk patients, warranting further experimental and clinical validation.<\/jats:p>","DOI":"10.3390\/ijms27104425","type":"journal-article","created":{"date-parts":[[2026,5,18]],"date-time":"2026-05-18T14:40:31Z","timestamp":1779115231000},"page":"4425","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Prognostic Genes Linked to Asparagine Metabolism in Hepatocellular Carcinoma: Identification, Validation, and Regulatory Mechanisms Based on Transcriptome and Single-Cell RNA Sequencing"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-4716-3106","authenticated-orcid":false,"given":"Jianting","family":"Feng","sequence":"first","affiliation":[{"name":"School of Basic Medical Sciences, Xinjiang Second Medical College, Karamay 834000, China"},{"name":"College of Life Sciences, Shihezi University, Shihezi 832003, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaihua","family":"Wei","sequence":"additional","affiliation":[{"name":"School of Medicine, Shihezi University, Shihezi 832003, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nana","family":"Li","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences, Xinjiang Second Medical College, Karamay 834000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yinshi","family":"Li","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences, Xinjiang Second Medical College, Karamay 834000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fei","family":"Du","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences, Xinjiang Second Medical College, Karamay 834000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengjiao","family":"Lv","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences, Xinjiang Second Medical College, Karamay 834000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lifei","family":"Ma","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences, Xinjiang Second Medical College, Karamay 834000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suwen","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Shihezi University, Shihezi 832003, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuliang","family":"Niu","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences, Xinjiang Second Medical College, Karamay 834000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liang","family":"Feng","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences, Xinjiang Second Medical College, Karamay 834000, China"},{"name":"College of Life Sciences, Shihezi University, Shihezi 832003, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1007\/s13402-019-00487-3","article-title":"Multiple novel hepatocellular carcinoma signature genes are commonly controlled by the master pluripotency factor OCT4","volume":"43","author":"Ye","year":"2020","journal-title":"Cell. Oncol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1999","DOI":"10.1016\/j.cgh.2024.03.006","article-title":"The Global Epidemiology of Nonalcoholic Fatty Liver Disease and Nonalcoholic Steatohepatitis Among Patients With Type 2 Diabetes","volume":"22","author":"Younossi","year":"2024","journal-title":"Clin. Gastroenterol. Hepatol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1080\/17474124.2023.2206564","article-title":"Investigating the correlation between COVID-19 and the progression of chronic liver disease","volume":"17","author":"Philips","year":"2023","journal-title":"Expert Rev. Gastroenterol. Hepatol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1038\/s41575-022-00704-9","article-title":"Evolving therapeutic landscape of advanced hepatocellular carcinoma","volume":"20","author":"Yang","year":"2023","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1080\/15569527.2022.2034842","article-title":"Adverse cutaneous toxicities by PD-1\/PD-L1 immune checkpoint inhibitors: Pathogenesis, treatment, and surveillance","volume":"41","author":"Bhardwaj","year":"2022","journal-title":"Cutan. Ocul. Toxicol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"cr.25-0429","DOI":"10.70352\/scrj.cr.25-0429","article-title":"Hepatocellular Carcinoma Confined to the Bile Duct without Hepatic Mass or Jaundice: A Case Report","volume":"11","author":"Aoki","year":"2025","journal-title":"Surg. Case Rep."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1186\/s12967-024-05917-x","article-title":"Napabucasin-loaded PLGA nanoparticles trigger anti-HCC immune responses by metabolic reprogramming of tumor-associated macrophages","volume":"22","author":"Song","year":"2024","journal-title":"J. Transl. Med."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1111\/cas.15272","article-title":"E2F1-mediated AUF1 upregulation promotes HCC development and enhances drug resistance via stabilization of AKR1B10","volume":"113","author":"Zhang","year":"2022","journal-title":"Cancer Sci."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"558","DOI":"10.1016\/j.apsb.2021.09.019","article-title":"Metabolic dysregulation and emerging therapeutical targets for hepatocellular carcinoma","volume":"12","author":"Du","year":"2022","journal-title":"Acta Pharm. Sin. B"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Bai, J., Tang, R., Zhou, K., Chang, J., Wang, H., Zhang, Q., Shi, J., and Sun, C. (2022). An asparagine metabolism-based classification reveals the metabolic and immune heterogeneity of hepatocellular carcinoma. BMC Med. Genom., 15.","DOI":"10.1186\/s12920-022-01380-z"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"115013","DOI":"10.1016\/j.intimp.2025.115013","article-title":"The role of tumor-associated endothelial cells in malignant progression and immune evasion of liver cancer","volume":"161","author":"Pu","year":"2025","journal-title":"Int. Immunopharmacol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1016\/j.jhep.2022.03.015","article-title":"Unique molecular characteristics of NAFLD-associated liver cancer accentuate \u03b2-catenin\/TNFRSF19-mediated immune evasion","volume":"77","author":"Wong","year":"2022","journal-title":"J. Hepatol."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Jian, H., Xu, Q., Wang, X., Liu, Y., Miao, S., Li, Y., Mou, T., Dong, X., and Zou, X. (2022). Amino Acid and Fatty Acid Metabolism Disorders Trigger Oxidative Stress and Inflammatory Response in Excessive Dietary Valine-Induced NAFLD of Laying Hens. Front. Nutr., 9.","DOI":"10.3389\/fnut.2022.849767"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1186\/s12967-022-03416-5","article-title":"VCP interaction with HMGB1 promotes hepatocellular carcinoma progression by activating the PI3K\/AKT\/mTOR pathway","volume":"20","author":"Pu","year":"2022","journal-title":"J. Transl. Med."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2372","DOI":"10.1158\/0008-5472.CAN-22-3561","article-title":"PTTG1 Reprograms Asparagine Metabolism to Promote Hepatocellular Carcinoma Progression","volume":"83","author":"Zhou","year":"2023","journal-title":"Cancer Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"103813","DOI":"10.1016\/j.redox.2025.103813","article-title":"Asparagine synthetase modulates glutaminase inhibitor sensitivity through metabolic reprogramming and serves as a prognostic biomarker in hepatocellular carcinoma","volume":"86","author":"Gao","year":"2025","journal-title":"Redox Biol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/s41419-023-06110-6","article-title":"Stromal cells in the tumor microenvironment: Accomplices of tumor progression?","volume":"14","author":"Zhao","year":"2023","journal-title":"Cell Death Dis."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"eadg3840","DOI":"10.1126\/scitranslmed.adg3840","article-title":"The extracellular matrix as hallmark of cancer and metastasis: From biomechanics to therapeutic targets","volume":"16","author":"Sleeboom","year":"2024","journal-title":"Sci. Transl. Med."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1773","DOI":"10.1002\/hep.32740","article-title":"The liver cancer immune microenvironment: Therapeutic implications for hepatocellular carcinoma","volume":"77","author":"Donne","year":"2023","journal-title":"Hepatology"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1172","DOI":"10.1016\/j.jhep.2023.06.022","article-title":"The XOR-IDH3\u03b1 axis controls macrophage polarization in hepatocellular carcinoma","volume":"79","author":"Lu","year":"2023","journal-title":"J. Hepatol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"4741","DOI":"10.1111\/bph.16342","article-title":"Innovative pharmacotherapy for hepatic metabolic and chronic inflammatory diseases in China","volume":"182","author":"Zhang","year":"2025","journal-title":"Br. J. Pharmacol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1016\/j.jhep.2022.10.011","article-title":"Treatment of HCC with claudin-1-specific antibodies suppresses carcinogenic signaling and reprograms the tumor microenvironment","volume":"78","author":"Roehlen","year":"2023","journal-title":"J. Hepatol."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Bhat, N., and Mani, A. (2023). Dysregulation of Lipid and Glucose Metabolism in Nonalcoholic Fatty Liver Disease. Nutrients, 15.","DOI":"10.3390\/nu15102323"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Chakravarthy, A., Pasini, E., Zhao, X., To, J., Shen, S.Y.R., Fischer, S., Ghanekar, A., Vogel, A., Grant, R.C., and Knox, J. (2025). Evolutionary dynamics of recurrent hepatocellular carcinoma under divergent immune selection pressures. Front. Oncol., 15.","DOI":"10.3389\/fonc.2025.1537087"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1186\/s12935-022-02643-6","article-title":"Noncoding RNA-mediated molecular bases of chemotherapy resistance in hepatocellular carcinoma","volume":"22","author":"He","year":"2022","journal-title":"Cancer Cell Int."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/s13045-023-01453-1","article-title":"Amino acid metabolism in immune cells: Essential regulators of the effector functions, and promising opportunities to enhance cancer immunotherapy","volume":"16","author":"Yang","year":"2023","journal-title":"J. Hematol. Oncol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"55110","DOI":"10.18632\/oncotarget.10399","article-title":"Carboxyl-terminal truncated HBx contributes to invasion and metastasis via deregulating metastasis suppressors in hepatocellular carcinoma","volume":"7","author":"Li","year":"2016","journal-title":"Oncotarget"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1080\/19768354.2022.2134206","article-title":"LncRNA SNHG6 promotes glycolysis reprogramming in hepatocellular carcinoma by stabilizing the BOP1 protein","volume":"26","author":"Chen","year":"2022","journal-title":"Anim. Cells Syst."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"15608","DOI":"10.1038\/s41598-018-34129-9","article-title":"SAC3D1: A novel prognostic marker in hepatocellular carcinoma","volume":"8","author":"Han","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.2147\/JHC.S413935","article-title":"A Novel Gene Pair CSTF2\/DPE2A Impacts Prognosis and Cell Cycle of Hepatocellular Carcinoma","volume":"10","author":"Huang","year":"2023","journal-title":"J. Hepatocell. Carcinoma"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Chen, L., Zhou, J., Zhao, Z., Zhu, Y., Xing, J., An, J., and Guo, X. (2022). Low Expression of Phosphodiesterase 2 (PDE2A) Promotes the Progression by Regulating Mitochondrial Morphology and ATP Content and Predicts Poor Prognosis in Hepatocellular Carcinoma. Cells, 12.","DOI":"10.3390\/cells12010068"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Marin, J.J.G., Reviejo, M., Soto, M., Lozano, E., Asensio, M., Ortiz-Rivero, S., Berasain, C., Avila, M.A., and Herraez, E. (2021). Impact of Alternative Splicing Variants on Liver Cancer Biology. Cancers, 14.","DOI":"10.3390\/cancers14010018"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"4910","DOI":"10.1182\/bloodadvances.2025017079","article-title":"Dietary tryptophan augments cancer-associated venous thrombogenicity mitigated by indoleamine 2,3-dioxygenase 1 inhibition","volume":"9","author":"Lotfollahzadeh","year":"2025","journal-title":"Blood Adv."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"8509","DOI":"10.1002\/jcp.27782","article-title":"CD8(+) cytotoxic T lymphocytes in cancer immunotherapy: A review","volume":"234","author":"Farhood","year":"2019","journal-title":"J. Cell. Physiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1007\/978-3-030-49270-0_4","article-title":"NK Cells in the Tumor Microenvironment","volume":"1273","author":"Guillerey","year":"2020","journal-title":"Adv. Exp. Med. Biol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1007\/s10238-024-01490-1","article-title":"The crossroad between tumor and endothelial cells","volume":"24","author":"Ribatti","year":"2024","journal-title":"Clin. Exp. Med."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"eadv2293","DOI":"10.1126\/scitranslmed.adv2293","article-title":"Metabolism-programming mRNA-lipid nanoparticles remodel the immune microenvironment to improve immunotherapy against MAFLD","volume":"17","author":"Yu","year":"2025","journal-title":"Sci. Transl. Med."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/10\/4425\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T12:08:34Z","timestamp":1779365314000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/10\/4425"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,15]]},"references-count":37,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2026,5]]}},"alternative-id":["ijms27104425"],"URL":"https:\/\/doi.org\/10.3390\/ijms27104425","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,15]]}}}