Constructing a Glioblastoma Prognostic Model Related to Fatty Acid Metabolism Using Machine Learning and Identifying F13A1 as a Potential Target
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data Acquisition
2.2. Classification of Molecular Subtypes
2.3. Analysis of the Immune Environment
2.4. Filtering of DEGs and Functional Analysis
2.5. Establishment and Validation of the Prognostic Signature
2.6. Differential Expression Analysis of F13A1
2.7. Immunity Analysis of F13A1
2.8. Functional Analysis of F13A1
2.9. Single-Cell Analysis
2.10. Statistical Analysis
3. Results
3.1. Identification of Key Genes Associated with FAM
3.1.1. Classification of Three Subtypes Based on FAM Genes
3.1.2. Analysis of the Immune Microenvironments of the Three Subtypes
3.1.3. Functional Analysis of Differential Genes
3.1.4. Obtaining of Key Genes
3.2. Establishment and Validation of the Prognostic Model
3.2.1. Machine Learning
3.2.2. RSF Analysis
3.3. Analysis of F13A1
3.3.1. Differential Expression Analysis of F13A1
3.3.2. Immunity Analysis of F13A1
3.3.3. Functional Analysis of F13A1
3.3.4. F13A1 Is Specifically Highly Expressed in Macrophages
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
References
- Dong, Z.; Cui, H. The Emerging Roles of RNA Modifications in Glioblastoma. Cancers 2020, 12, 736. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Rajesh, Y.; Pal, I.; Banik, P.; Chakraborty, S.; Borkar, S.A.; Dey, G.; Mukherjee, A.; Mandal, M. Insights into molecular therapy of glioma: Current challenges and next generation blueprint. Acta Pharmacol. Sin. 2017, 38, 591–613. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Sun, J.; Ma, Q.; Li, B.; Wang, C.; Mo, L.; Zhang, X.; Tang, F.; Wang, Q.; Yan, X.; Yao, X.; et al. RPN2 is targeted by miR-181c and mediates glioma progression and temozolomide sensitivity via the wnt/β-catenin signaling pathway. Cell Death Dis. 2020, 11, 890. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Jiang, T.; Mao, Y.; Ma, W.; Mao, Q.; You, Y.; Yang, X.; Jiang, C.; Kang, C.; Li, X.; Chen, L.; et al. CGCG clinical practice guidelines for the management of adult diffuse gliomas. Cancer Lett. 2016, 375, 263–273. [Google Scholar] [CrossRef] [PubMed]
- Luo, X.; Li, R.R.; Li, Y.Q.; Yu, H.P.; Yu, H.N.; Jiang, W.G.; Li, Y.N. Reducing VEGFB expression regulates the balance of glucose and lipid metabolism in mice via VEGFR1. Mol. Med. Rep. 2022, 26, 285. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Zhang, C.; Zhu, N.; Li, H.; Gong, Y.; Gu, J.; Shi, Y.; Liao, D.; Wang, W.; Dai, A.; Qin, L. New dawn for cancer cell death: Emerging role of lipid metabolism. Mol. Metab. 2022, 63, 101529. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Amiri, M.; Yousefnia, S.; Forootan, F.S.; Peymani, M.; Ghaedi, K.; Nasr Esfahani, M.H. Diverse roles of fatty acid binding proteins (FABPs) in development and pathogenesis of cancers. Gene 2018, 676, 171–183. [Google Scholar] [CrossRef] [PubMed]
- Santos, C.R.; Schulze, A. Lipid metabolism in cancer. FEBS J. 2012, 279, 2610–2623. [Google Scholar] [CrossRef] [PubMed]
- Feng, J.; Zhang, Q.; Zhou, Y.; Yu, S.; Hong, L.; Zhao, S.; Yang, J.; Wan, H.; Xu, G.; Zhang, Y.; et al. Integration of Proteomics and Metabolomics Revealed Metabolite-Protein Networks in ACTH-Secreting Pituitary Adenoma. Front. Endocrinol. 2018, 9, 678. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Wang, H.; Zhou, L. Random survival forest with space extensions for censored data. Artif. Intell. Med. 2017, 79, 52–61. [Google Scholar] [CrossRef] [PubMed]
- Miska, J.; Chandel, N.S. Targeting fatty acid metabolism in glioblastoma. J. Clin. Investig. 2023, 133, e163448. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Chinnaiyan, P.; Kensicki, E.; Bloom, G.; Prabhu, A.; Sarcar, B.; Kahali, S.; Eschrich, S.; Qu, X.; Forsyth, P.; Gillies, R. The metabolomic signature of malignant glioma reflects accelerated anabolic metabolism. Cancer Res. 2012, 72, 5878–5888. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Martin, D.D.; Robbins, M.E.; Spector, A.A.; Wen, B.C.; Hussey, D.H. The fatty acid composition of human gliomas differs from that found in nonmalignant brain tissue. Lipids 1996, 31, 1283–1288. [Google Scholar] [CrossRef] [PubMed]
- Dubinski, D.; Wölfer, J.; Hasselblatt, M.; Schneider-Hohendorf, T.; Bogdahn, U.; Stummer, W.; Wiendl, H.; Grauer, O.M. CD4+ T effector memory cell dysfunction is associated with the accumulation of granulocytic myeloid-derived suppressor cells in glioblastoma patients. Neuro Oncol. 2016, 18, 807–818. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Kourou, K.; Exarchos, T.P.; Exarchos, K.P.; Karamouzis, M.V.; Fotiadis, D.I. Machine learning applications in cancer prognosis and prediction. Comput. Struct. Biotechnol. J. 2014, 13, 8–17. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Wang, Z.; Chen, G.; Yuan, D.; Wu, P.; Guo, J.; Lu, Y.; Wang, Z. Caveolin-1 promotes glioma proliferation and metastasis by enhancing EMT via mediating PAI-1 activation and its correlation with immune infiltrates. Heliyon 2024, 10, e24464. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Roy, A.; Coum, A.; Marinescu, V.D.; Põlajeva, J.; Smits, A.; Nelander, S.; Uhrbom, L.; Westermark, B.; Forsberg-Nilsson, K.; Pontén, F.; et al. Glioma-derived plasminogen activator inhibitor-1 (PAI-1) regulates the recruitment of LRP1 positive mast cells. Oncotarget 2015, 6, 23647–23661. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Zhang, S.; Cao, G.; Shen, S.; Wu, Y.; Tan, X.; Jiang, X. CAF-derived miR-642a-3p supports migration, invasion, and EMT of hepatocellular carcinoma cells by targeting SERPINE1. PeerJ 2024, 12, e18428. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Wang, B.; Liu, W.; Song, B.; Li, Y.; Wang, Y.; Tan, B. Targeting LINC00665/miR-199b-5p/SERPINE1 axis to inhibit trastuzumab resistance and tumorigenesis of gastric cancer via PI3K/AKt pathway. Noncoding RNA Res. 2024, 10, 153–162. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Doelker, T.; Gallwas, J.; Gründker, C. Suppressing Expression of SERPINE1/PAI1 Through Activation of GPER1 Reduces Progression of Vulvar Carcinoma. Cancer Genom. Proteom. 2024, 21, 566–579. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Robins, J.E.; Capehart, A.A. Matrix remodeling associated 5 expression in trunk and limb during avian development. Int. J. Dev. Biol. 2018, 62, 335–340. [Google Scholar] [CrossRef] [PubMed]
- Fedele, M.; Cerchia, L.; Pegoraro, S.; Sgarra, R.; Manfioletti, G. Proneural-Mesenchymal Transition: Phenotypic Plasticity to Acquire Multitherapy Resistance in Glioblastoma. Int. J. Mol. Sci. 2019, 20, 2746. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Rahane, C.S.; Kutzner, A.; Heese, K. A cancer tissue-specific FAM72 expression profile defines a novel glioblastoma multiform (GBM) gene-mutation signature. J. Neurooncol. 2019, 141, 57–70. [Google Scholar] [CrossRef] [PubMed]
- Han, X.; Zhou, H.; Ge, X.; Hou, L.; Li, H.; Zhang, D.; Wang, Y.; Xue, X. Identification of an Immune signature assisted prognosis, and immunotherapy prediction for IDH wildtype glioblastoma. J. Cancer 2024, 15, 6452–6467. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Nie, L.; Huang, L.; Zhu, Q.; Yao, Q.; Wu, Y.; Zhao, L.; Yu, L.; Fu, F. HIF-1α Activates Hypoxia-Induced MXRA5 Expression in the Progression of Ovarian Cancer. J. Environ. Pathol. Toxicol. Oncol. 2025, 44, 47–55. [Google Scholar] [CrossRef] [PubMed]
- Deng, H.; Wen, C.; Jiang, S.; Yu, Y.; Zhao, J.; Zhang, B. Single-cell analysis reveals one cancer-associated fibroblasts subtype linked to metastasis in breast cancer: MXRA5 as a potential novel marker for prognosis. Am. J. Cancer Res. 2024, 14, 526–544. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Mitsueda, R.; Toda, H.; Shinden, Y.; Fukuda, K.; Yasudome, R.; Kato, M.; Kikkawa, N.; Ohtsuka, T.; Nakajo, A.; Seki, N. Oncogenic Targets Regulated by Tumor-Suppressive miR-30c-1-3p and miR-30c-2-3p: TRIP13 Facilitates Cancer Cell Aggressiveness in Breast Cancer. Cancers 2023, 15, 4189. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Wang, D.; He, M.Q.; Fan, D.Q. RARRES1 is a novel immune-related biomarker in GBM. Am. J. Transl. Res. 2019, 11, 5655–5663. [Google Scholar] [PubMed] [PubMed Central]
- Lan, Y.L.; Nie, T.; Zou, S. Identification of the prognostic and immunological roles of aquaporin 4: A potential target for survival and immunotherapy in glioma patients. Front. Cell. Neurosci. 2022, 16, 1061428. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Roy, A.; Ramalinga, M.; Kim, O.J.; Chijioke, J.; Lynch, S.; Byers, S.; Kumar, D. Multiple roles of RARRES1 in prostate cancer: Autophagy induction and angiogenesis inhibition. PLoS ONE 2017, 12, e0180344. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Coyle, K.M.; Murphy, J.P.; Vidovic, D.; Vaghar-Kashani, A.; Dean, C.A.; Sultan, M.; Clements, D.; Wallace, M.; Thomas, M.L.; Hundert, A.; et al. Breast cancer subtype dictates DNA methylation and ALDH1A3-mediated expression of tumor suppressor RARRES1. Oncotarget 2016, 7, 44096–44112. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Geng, X.; Chi, K.; Liu, C.; Fu, Z.; Wang, X.; Meng, L.; Wang, H.; Cai, G.; Chen, X.; Hong, Q. Interaction of RARRES1 with ICAM1 modulates macrophages to suppress the progression of kidney renal clear cell carcinoma. Front. Immunol. 2022, 13, 982045. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Byrnes, J.R.; Duval, C.; Wang, Y.; Hansen, C.E.; Ahn, B.; Mooberry, M.J.; Clark, M.A.; Johnsen, J.M.; Lord, S.T.; Lam, W.A.; et al. Factor XIIIa-dependent retention of red blood cells in clots is mediated by fibrin α-chain crosslinking. Blood 2015, 126, 1940–1948. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Ercan, H.; Mauracher, L.M.; Grilz, E.; Hell, L.; Hellinger, R.; Schmid, J.A.; Moik, F.; Ay, C.; Pabinger, I.; Zellner, M. Alterations of the Platelet Proteome in Lung Cancer: Accelerated F13A1 and ER Processing as New Actors in Hypercoagulability. Cancers 2021, 13, 2260. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Palumbo, J.S.; Barney, K.A.; Blevins, E.A.; Shaw, M.A.; Mishra, A.; Flick, M.J.; Kombrinck, K.W.; Talmage, K.E.; Souri, M.; Ichinose, A.; et al. Factor XIII transglutaminase supports hematogenous tumor cell metastasis through a mechanism dependent on natural killer cell function. J. Thromb. Haemost. 2008, 6, 812–819. [Google Scholar] [CrossRef] [PubMed]
- Porrello, A.; Leslie, P.L.; Harrison, E.B.; Gorentla, B.K.; Kattula, S.; Ghosh, S.K.; Azam, S.H.; Holtzhausen, A.; Chao, Y.L.; Hayward, M.C.; et al. Factor XIIIA-expressing inflammatory monocytes promote lung squamous cancer through fibrin cross-linking. Nat. Commun. 2018, 9, 1988. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Lee, S.H.; Suh, I.B.; Lee, E.J.; Hur, G.Y.; Lee, S.Y.; Lee, S.Y.; Shin, C.; Shim, J.J.; In, K.H.; Kang, K.H.; et al. Relationships of coagulation factor XIII activity with cell-type and stage of non-small cell lung cancer. Yonsei Med. J. 2013, 54, 1394–1399. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Raval, J.S.; Berg, A.N.; Djokic, M.; Roth, C.G.; Rollins-Raval, M.A. Factor XIII Subunit A Immunohistochemical Expression is Associated With Inferior Outcomes in Acute Promyelocytic Leukemia. Appl. Immunohistochem. Mol. Morphol. 2018, 26, 202–205. [Google Scholar] [CrossRef] [PubMed]
- Lehrer, S.; Dembitzer, F.R.; Rheinstein, P.H.; Rosenzweig, K.E. In primary glioblastoma fewer tumor copy number segments of the F13A1 gene are associated with poorer survival. Thromb. Res. 2018, 167, 12–14. [Google Scholar] [CrossRef] [PubMed]
- Zhang, Y.; Geng, X.; Xu, J.; Li, Q.; Hao, L.; Zeng, Z.; Xiao, M.; Song, J.; Liu, F.; Fang, C.; et al. Identification and characterization of N6-methyladenosine modification of circRNAs in glioblastoma. J. Cell. Mol. Med. 2021, 25, 7204–7217. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Lin, H.; Patel, S.; Affleck, V.S.; Wilson, I.; Turnbull, D.M.; Joshi, A.R.; Maxwell, R.; Stoll, E.A. Fatty acid oxidation is required for the respiration and proliferation of malignant glioma cells. Neuro Oncol. 2017, 19, 43–54. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Naukkarinen, J.; Surakka, I.; Pietiläinen, K.H.; Rissanen, A.; Salomaa, V.; Ripatti, S.; Yki-Järvinen, H.; van Duijn, C.M.; Wichmann, H.E.; Kaprio, J.; et al. Use of genome-wide expression data to mine the “Gray Zone” of GWA studies leads to novel candidate obesity genes. PLoS Genet. 2010, 6, e1000976. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Kaartinen, M.T.; Arora, M.; Heinonen, S.; Rissanen, A.; Kaprio, J.; Pietiläinen, K.H. Transglutaminases and Obesity in Humans: Association of F13A1 to Adipocyte Hypertrophy and Adipose Tissue Immune Response. Int. J. Mol. Sci. 2020, 21, 8289. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Elsherbiny, M.E.; Emara, M.; Godbout, R. Interaction of brain fatty acid-binding protein with the polyunsaturated fatty acid environment as a potential determinant of poor prognosis in malignant glioma. Prog. Lipid Res. 2013, 52, 562–570. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Suganami, T.; Nishida, J.; Ogawa, Y. A paracrine loop between adipocytes and macrophages aggravates inflammatory changes: Role of free fatty acids and tumor necrosis factor alpha. Arterioscler. Thromb. Vasc. Biol. 2005, 25, 2062–2068. [Google Scholar] [CrossRef] [PubMed]
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2025 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Liu, Y.; Deng, H.; Song, P.; Zhang, M. Constructing a Glioblastoma Prognostic Model Related to Fatty Acid Metabolism Using Machine Learning and Identifying F13A1 as a Potential Target. Biomedicines 2025, 13, 256. https://doi.org/10.3390/biomedicines13020256
Liu Y, Deng H, Song P, Zhang M. Constructing a Glioblastoma Prognostic Model Related to Fatty Acid Metabolism Using Machine Learning and Identifying F13A1 as a Potential Target. Biomedicines. 2025; 13(2):256. https://doi.org/10.3390/biomedicines13020256
Chicago/Turabian StyleLiu, Yushu, Hui Deng, Ping Song, and Mengxian Zhang. 2025. "Constructing a Glioblastoma Prognostic Model Related to Fatty Acid Metabolism Using Machine Learning and Identifying F13A1 as a Potential Target" Biomedicines 13, no. 2: 256. https://doi.org/10.3390/biomedicines13020256
APA StyleLiu, Y., Deng, H., Song, P., & Zhang, M. (2025). Constructing a Glioblastoma Prognostic Model Related to Fatty Acid Metabolism Using Machine Learning and Identifying F13A1 as a Potential Target. Biomedicines, 13(2), 256. https://doi.org/10.3390/biomedicines13020256