基于组学数据分析的胃癌酸代谢异常分子机制研究与标志物确定
Investigation of Molecular Mechanisms and Biomarker Identification for Dysregulated Acid Metabolism in Gastric Cancer Based on Omics Data Analysis
摘要: 胃癌作为全球高发恶性肿瘤,其代谢重编程引起的酸代谢异常在肿瘤进展中具有重要作用,然而其具体分子机制及靶向干预策略仍有待深入探索。本研究结合TCGA和GTEx数据库的转录组数据,系统探究了胃癌细胞酸性代谢的分子调控机制及预后相关标志物。通过差异表达分析、WGCNA共表达网络构建、随机森林模型和生存分析,筛选出与酸性代谢特征及肿瘤微环境酸碱平衡的调控相关的103个差异表达基因(75个上调,28个下调),其中16个基因与胃癌细胞排酸功能显著相关。WGCNA分析揭示了green模块(模块核心基因包括LRRC8C)与胃癌TNM分期正相关。随机森林模型在胃癌诊断中表现出高灵敏度和特异性,其中LRRC8C基因的特征重要性位于其他基因前列。生存分析进一步鉴定了LRRC8C核心基因能够作为独立预后标志物,且该基因高表达与患者不良预后显著相关。本研究为胃癌的分子分型、预后评估及靶向治疗提供了新视角。
Abstract: Gastric cancer, a prevalent malignancy worldwide, is critically influenced by metabolic reprogramming-driven acid metabolism dysregulation during tumor progression. However, its specific molecular mechanisms and targeted intervention strategies remain underexplored. This study systematically investigated the molecular regulatory mechanisms of acidic metabolism and prognosis-related biomarkers in gastric cancer using transcriptomic data from the TCGA and GTEx databases. Through differential expression analysis, WGCNA co-expression network construction, random forest modeling, and survival analysis, 103 differentially expressed genes (75 upregulated and 28 downregulated) associated with acidic metabolic features and acid-base balance regulation in the tumor microenvironment were identified, including 16 genes significantly linked to acid extrusion in gastric cancer cells. WGCNA revealed the green module (core gene: LRRC8C) to be positively correlated with TNM staging. The random forest model demonstrated high sensitivity and specificity in gastric cancer diagnosis, with LRRC8C ranking high in feature importance. Survival analysis further identified LRRC8C as an independent prognostic biomarker, where its high expression was significantly associated with poor patient outcomes. This study provides novel insights into molecular subtyping, prognostic evaluation, and targeted therapy for gastric cancer.
文章引用:李宁. 基于组学数据分析的胃癌酸代谢异常分子机制研究与标志物确定[J]. 应用数学进展, 2025, 14(4): 331-341. https://doi.org/10.12677/aam.2025.144166

参考文献

[1] López, M.J., Carbajal, J., Alfaro, A.L., Saravia, L.G., Zanabria, D., Araujo, J.M., et al. (2023) Characteristics of Gastric Cancer around the World. Critical Reviews in Oncology/Hematology, 181, Article ID: 103841. [Google Scholar] [CrossRef] [PubMed]
[2] Liu, G. and Song, G. (2019) Regulation of Tumor Cell Glycometabolism and Tumor Therapy. Journal of Biomedical Engineering, 36, 691-695.
[3] El Hassouni, B., Granchi, C., Vallés-Martí, A., Supadmanaba, I.G.P., Bononi, G., Tuccinardi, T., et al. (2020) The Dichotomous Role of the Glycolytic Metabolism Pathway in Cancer Metastasis: Interplay with the Complex Tumor Microenvironment and Novel Therapeutic Strategies. Seminars in Cancer Biology, 60, 238-248. [Google Scholar] [CrossRef] [PubMed]
[4] Tufail, M., Jiang, C. and Li, N. (2024) Altered Metabolism in Cancer: Insights into Energy Pathways and Therapeutic Targets. Molecular Cancer, 23, Article No. 203. [Google Scholar] [CrossRef] [PubMed]
[5] Pavlova, N.N. and Thompson, C.B. (2016) The Emerging Hallmarks of Cancer Metabolism. Cell Metabolism, 23, 27-47. [Google Scholar] [CrossRef] [PubMed]
[6] DeBerardinis, R.J. and Chandel, N.S. (2016) Fundamentals of Cancer Metabolism. Science Advances, 2, e1600200. [Google Scholar] [CrossRef] [PubMed]
[7] Vander Heiden, M.G. and DeBerardinis, R.J. (2017) Understanding the Intersections between Metabolism and Cancer Biology. Cell, 168, 657-669. [Google Scholar] [CrossRef] [PubMed]
[8] Zhang, Y., Fang, N., You, J. and Zhou, Q. (2014) Advances in the Relationship between Tumor Cell Metabolism and Tumor Metastasis. Chinese Journal of Lung Cancer, 17, 812-818.
[9] Damaghi, M., Wojtkowiak, J.W. and Gillies, R.J. (2013) Ph Sensing and Regulation in Cancer. Frontiers in Physiology, 4, Article 370. [Google Scholar] [CrossRef] [PubMed]
[10] Swietach, P., Vaughan-Jones, R.D., Harris, A.L. and Hulikova, A. (2014) The Chemistry, Physiology and Pathology of pH in Cancer. Philosophical Transactions of the Royal Society B: Biological Sciences, 369, Article ID: 20130099. [Google Scholar] [CrossRef] [PubMed]
[11] Supuran, C.T. (2008) Carbonic Anhydrases: Novel Therapeutic Applications for Inhibitors and Activators. Nature Reviews Drug Discovery, 7, 168-181. [Google Scholar] [CrossRef] [PubMed]
[12] Occhipinti, R. and Boron, W.F. (2019) Role of Carbonic Anhydrases and Inhibitors in Acid-Base Physiology: Insights from Mathematical Modeling. International Journal of Molecular Sciences, 20, Article 3841. [Google Scholar] [CrossRef] [PubMed]
[13] Lee, S., Boron, W.F. and Occhipinti, R. (2023) Potential Novel Role of Membrane-Associated Carbonic Anhydrases in the Kidney. International Journal of Molecular Sciences, 24, Article 4251. [Google Scholar] [CrossRef] [PubMed]
[14] Sheng, G., Gao, Y., Wu, H., Liu, Y. and Yang, Y. (2023) Functional Heterogeneity of MCT1 and MCT4 in Metabolic Reprogramming Affects Osteosarcoma Growth and Metastasis. Journal of Orthopaedic Surgery and Research, 18, Article No. 131. [Google Scholar] [CrossRef] [PubMed]
[15] Felmlee, M.A., Jones, R.S., Rodriguez-Cruz, V., Follman, K.E. and Morris, M.E. (2020) Monocarboxylate Transporters (SLC16): Function, Regulation, and Role in Health and Disease. Pharmacological Reviews, 72, 466-485. [Google Scholar] [CrossRef] [PubMed]
[16] Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., et al. (2015) Limma Powers Differential Expression Analyses for RNA-Sequencing and Microarray Studies. Nucleic Acids Research, 43, e47. [Google Scholar] [CrossRef] [PubMed]
[17] Liu, S., Wang, Z., Zhu, R., Wang, F., Cheng, Y. and Liu, Y. (2021) Three Differential Expression Analysis Methods for RNA Sequencing: Limma, EdgeR, DESeq2. Journal of Visualized Experiments, 175, e62528. [Google Scholar] [CrossRef
[18] Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., et al. (2005) Gene Set Enrichment Analysis: A Knowledge-Based Approach for Interpreting Genome-Wide Expression Profiles. Proceedings of the National Academy of Sciences, 102, 15545-15550. [Google Scholar] [CrossRef] [PubMed]
[19] Kanehisa, M., Furumichi, M., Sato, Y., Kawashima, M. and Ishiguro-Watanabe, M. (2022) KEGG for Taxonomy-Based Analysis of Pathways and Genomes. Nucleic Acids Research, 51, D587-D592. [Google Scholar] [CrossRef] [PubMed]
[20] Langfelder, P. and Horvath, S. (2008) WGCNA: An R Package for Weighted Correlation Network Analysis. BMC Bioinformatics, 9, Article No. 559. [Google Scholar] [CrossRef] [PubMed]
[21] Statnikov, A., Wang, L. and Aliferis, C.F. (2008) A Comprehensive Comparison of Random Forests and Support Vector Machines for Microarray-Based Cancer Classification. BMC Bioinformatics, 9, Article No. 319. [Google Scholar] [CrossRef] [PubMed]
[22] Wang, Q., Qiao, W., Zhang, H., Liu, B., Li, J., Zang, C., et al. (2022) Nomogram Established on Account of Lasso-Cox Regression for Predicting Recurrence in Patients with Early-Stage Hepatocellular Carcinoma. Frontiers in Immunology, 13, Article 1019638. [Google Scholar] [CrossRef] [PubMed]
[23] Engebretsen, S. and Bohlin, J. (2019) Statistical Predictions with Glmnet. Clinical Epigenetics, 11, Article No. 123. [Google Scholar] [CrossRef] [PubMed]
[24] Rich, J.T., Neely, J.G., Paniello, R.C., Voelker, C.C.J., Nussenbaum, B. and Wang, E.W. (2010) A Practical Guide to Understanding Kaplan‐Meier Curves. OtolaryngologyHead and Neck Surgery, 143, 331-336. [Google Scholar] [CrossRef] [PubMed]
[25] Peng, Y., Wang, Y., Zhou, C., Mei, W. and Zeng, C. (2022) PI3K/Akt/mTOR Pathway and Its Role in Cancer Therapeutics: Are We Making Headway? Frontiers in Oncology, 12, Article 819128. [Google Scholar] [CrossRef] [PubMed]
[26] Kroemer, G. and Pouyssegur, J. (2008) Tumor Cell Metabolism: Cancer’s Achilles’ Heel. Cancer Cell, 13, 472-482. [Google Scholar] [CrossRef] [PubMed]
[27] Hanahan, D. and Weinberg, R.A. (2011) Hallmarks of Cancer: The Next Generation. Cell, 144, 646-674. [Google Scholar] [CrossRef] [PubMed]
[28] Xu, H., Ghishan, F.K. and Kiela, P.R. (2018) SLC9 Gene Family: Function, Expression, and Regulation. Comprehensive Physiology, 8, 555-583.
[29] Bernardazzi, C., Sheikh, I.A., Xu, H. and Ghishan, F.K. (2022) The Physiological Function and Potential Role of the Ubiquitous Na+/H+ Exchanger Isoform 8 (NHE8): An Overview Data. International Journal of Molecular Sciences, 23, Article 10857. [Google Scholar] [CrossRef] [PubMed]
[30] Laubitz, D., Gurney, M.A., Midura-Kiela, M., Clutter, C., Besselsen, D.G., Chen, H., et al. (2022) Decreased NHE3 Expression in Colon Cancer Is Associated with DNA Damage, Increased Inflammation and Tumor Growth. Scientific Reports, 12, Article No. 14725. [Google Scholar] [CrossRef] [PubMed]
[31] Ueno, Y., Ozaki, S., Umakoshi, A., Yano, H., Choudhury, M.E., Abe, N., et al. (2019) Chloride Intracellular Channel Protein 2 in Cancer and Non-Cancer Human Tissues: Relationship with Tight Junctions. Tissue Barriers, 7, Article ID: 1593775. [Google Scholar] [CrossRef] [PubMed]
[32] Kostritskaia, Y., Klüssendorf, M., Pan, Y.E., Hassani Nia, F., Kostova, S. and Stauber, T. (2023) Physiological Functions of the Volume-Regulated Anion Channel VRAC/LRRC8 and the Proton-Activated Chloride Channel ASOR/TMEM206. In: Fahlke, C., Ed., Anion Channels and Transporters, Springer, 181-218. [Google Scholar] [CrossRef] [PubMed]
[33] Lu, P., Ding, Q., Li, X., Ji, X., Li, L., Fan, Y., et al. (2019) SWELL1 Promotes Cell Growth and Metastasis of Hepatocellular Carcinoma in Vitro and in Vivo. EBioMedicine, 48, 100-116. [Google Scholar] [CrossRef] [PubMed]
[34] Guang, D., Xiaofei, Z., Yu, M., Hui, N., Min, S. and Xiaonan, S. (2024) Pomiferin Targeting SLC9A9 Based on Histone Acetylation Modification Pattern Is a Potential Therapeutical Option for Gastric Cancer with High Malignancy. Biochemical Pharmacology, 226, Article ID: 116333. [Google Scholar] [CrossRef] [PubMed]
[35] Liu, T., Li, Y., Wang, D., Stauber, T. and Zhao, J. (2023) Trends in Volume-Regulated Anion Channel (VRAC) Research: Visualization and Bibliometric Analysis from 2014 to 2022. Frontiers in Pharmacology, 14, Article 1234885. [Google Scholar] [CrossRef] [PubMed]