Pan-Cancer Identification of Prognostic-Associated Metabolic Pathways
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Data Collection
2.2. Collection of Metabolic Checkpoint Genes
2.3. Calculation of Metabolic Pathway Activity Scores
2.4. Multivariable Cox Regression Model
2.5. Statistical Analysis and Visualization
3. Results
3.1. Significant Correlation between the Pan-Cancer Survival and Metabolism Checkpoint Genes
3.2. Extensive Impact of the Activities of Metabolic Pathways on Cancer Prognosis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
- Elia, I.; Haigis, M.C. Metabolites and the tumour microenvironment: From cellular mechanisms to systemic metabolism. Nat. Metab. 2021, 3, 21–32. [Google Scholar] [CrossRef]
- Wang, R.N.; Green, D.R. Metabolic checkpoints in activated T cells. Nat. Immunol. 2012, 13, 907–915. [Google Scholar] [CrossRef]
- Liu, T.; Lin, Y.H.; Leng, W.; Jung, S.Y.; Zhang, H.; Deng, M.; Evans, D.; Li, Y.; Luo, K.; Qin, B.; et al. A divergent role of the SIRT1-TopBP1 axis in regulating metabolic checkpoint and DNA damage checkpoint. Mol. Cell 2014, 56, 681–695. [Google Scholar] [CrossRef] [Green Version]
- Geltink, R.I.K.; Kyle, R.L.; Pearce, E.L. Unraveling the Complex Interplay Between T Cell Metabolism and Function. Annu. Rev. Immunol. 2018, 36, 461–488. [Google Scholar] [CrossRef]
- McNamee, E.N.; Johnson, D.K.; Homann, D.; Clambey, E.T. Hypoxia and hypoxia-inducible factors as regulators of T cell development, differentiation, and function. Immunol. Res. 2013, 55, 58–70. [Google Scholar] [CrossRef]
- Reinfeld, B.I.; Madden, M.Z.; Wolf, M.M.; Chytil, A.; Bader, J.E.; Patterson, A.R.; Sugiura, A.; Cohen, A.S.; Ali, A.; Do, B.T.; et al. Cell-programmed nutrient partitioning in the tumour microenvironment. Nature 2021, 593, 282–288. [Google Scholar] [CrossRef]
- DeBerardinis, R.J.; Chandel, N.S. Fundamentals of cancer metabolism. Sci. Adv. 2016, 2. [Google Scholar] [CrossRef] [Green Version]
- Wang, R.N.; Dillon, C.P.; Shi, L.Z.; Milasta, S.; Carter, R.; Finkelstein, D.; McCormick, L.L.; Fitzgerald, P.; Chi, H.B.; Munger, J.; et al. The Transcription Factor Myc Controls Metabolic Reprogramming upon T Lymphocyte Activation. Immunity 2011, 35, 871–882. [Google Scholar] [CrossRef] [Green Version]
- Kishton, R.J.; Sukumar, M.; Restifo, N.P. Metabolic Regulation of T Cell Longevity and Function in Tumor Immunotherapy. Cell Metab. 2017, 26, 94–109. [Google Scholar] [CrossRef] [Green Version]
- Campbell, S.L.; Wellen, K.E. Metabolic Signaling to the Nucleus in Cancer. Mol. Cell 2018, 71, 398–408. [Google Scholar] [CrossRef] [Green Version]
- Goldman, M.J.; Craft, B.; Hastie, M.; Repecka, K.; McDade, F.; Kamath, A.; Banerjee, A.; Luo, Y.; Rogers, D.; Brooks, A.N.; et al. Visualizing and interpreting cancer genomics data via the Xena platform. Nat. Biotechnol. 2020, 38, 675–678. [Google Scholar] [CrossRef]
- Li, Y.; Tang, J.; Jiang, J.; Chen, Z. Metabolic checkpoints and novel approaches for immunotherapy against cancer. Int. J. Cancer 2022, 150, 195–207. [Google Scholar] [CrossRef] [PubMed]
- Kanehisa, M.; Furumichi, M.; Sato, Y.; Ishiguro-Watanabe, M.; Tanabe, M. KEGG: Integrating viruses and cellular organisms. Nucleic Acids Res. 2021, 49, D545–D551. [Google Scholar] [CrossRef] [PubMed]
- Hanzelmann, S.; Castelo, R.; Guinney, J. GSVA: Gene set variation analysis for microarray and RNA-seq data. BMC Bioinform. 2013, 14, 7. [Google Scholar] [CrossRef] [Green Version]
- Fong, L.; Hotson, A.; Powderly, J.D.; Sznol, M.; Heist, R.S.; Choueiri, T.K.; George, S.; Hughes, B.G.M.; Hellmann, M.D.; Shepard, D.R.; et al. Adenosine 2A Receptor Blockade as an Immunotherapy for Treatment-Refractory Renal Cell Cancer. Cancer Discov. 2020, 10, 40–53. [Google Scholar] [CrossRef] [Green Version]
- Hsu, H.T.; Hsing, M.T.; Yeh, C.M.; Chen, C.J.; Yang, J.S.; Yeh, K.T. Decreased cytoplasmic X-box binding protein-1 expression is associated with poor prognosis and overall survival in patients with oral squamous cell carcinoma. Clin. Chim. Acta 2018, 479, 66–71. [Google Scholar] [CrossRef]
- Han, P.; Wu, S.; Li, L.; Li, D.; Zhao, J.; Zhang, H.; Wang, Y.; Zhong, X.; Zhang, Z.; Li, P.; et al. Epigenetic inactivation of ACAT1 promotes epithelial-mesenchymal transition of clear cell renal cell carcinoma. Genes. Genom. 2022, 44, 487–497. [Google Scholar] [CrossRef]
- Shao, J.; Shi, T.; Yu, H.; Ding, Y.; Li, L.; Wang, X.; Wang, X. Cytosolic GDH1 degradation restricts protein synthesis to sustain tumor cell survival following amino acid deprivation. EMBO J. 2021, 40, e107480. [Google Scholar] [CrossRef]
- Zhang, Z.; Wei, Y.Y.; Guo, Q.M.; Zhou, C.H.; Li, N.; Wu, J.F.; Li, Y.T.; Gao, W.W.; Li, H.L. Inflammation-Related Gene Signature: An Individualized Risk Prediction Model for Kidney Renal Clear Cell Carcinoma. J. Oncol. 2022, 2022, 2559258. [Google Scholar] [CrossRef]
- Hong, Y.; Lin, M.; Ou, D.; Huang, Z.; Shen, P. A novel ferroptosis-related 12-gene signature predicts clinical prognosis and reveals immune relevancy in clear cell renal cell carcinoma. BMC Cancer 2021, 21, 831. [Google Scholar] [CrossRef]
- Agrawal, K.; Chauhan, S.; Kumar, D. Expression analysis and regulation of GLI and its correlation with stemness and metabolic alteration in human brain tumor. 3 Biotech 2023, 13, 10. [Google Scholar] [CrossRef] [PubMed]
- Huang, Y.; Ouyang, F.; Yang, F.; Zhang, N.; Zhao, W.; Xu, H.; Yang, X. The expression of Hexokinase 2 and its hub genes are correlated with the prognosis in glioma. BMC Cancer 2022, 22, 900. [Google Scholar] [CrossRef] [PubMed]
- Rezen, T.; Rozman, D.; Kovacs, T.; Kovacs, P.; Sipos, A.; Bai, P.; Miko, E. The role of bile acids in carcinogenesis. Cell Mol. Life Sci. 2022, 79, 243. [Google Scholar] [CrossRef]
- Furukawa, J.; Tsuda, M.; Okada, K.; Kimura, T.; Piao, J.; Tanaka, S.; Shinohara, Y. Comprehensive Glycomics of a Multistep Human Brain Tumor Model Reveals Specific Glycosylation Patterns Related to Malignancy. PLoS ONE 2015, 10, e0128300. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Kudelka, M.R.; Ju, T.; Heimburg-Molinaro, J.; Cummings, R.D. Simple sugars to complex disease--mucin-type O-glycans in cancer. Adv. Cancer Res. 2015, 126, 53–135. [Google Scholar] [CrossRef] [PubMed]
- Liu, M.; Pan, Q.; Xiao, R.; Yu, Y.; Lu, W.; Wang, L. A cluster of metabolism-related genes predict prognosis and progression of clear cell renal cell carcinoma. Sci. Rep. 2020, 10, 12949. [Google Scholar] [CrossRef]
- Youssef, G.; Miller, J.J. Lower Grade Gliomas. Curr. Neurol. Neurosci. Rep. 2020, 20, 21. [Google Scholar] [CrossRef]
- Courtiol, P.; Maussion, C.; Moarii, M.; Pronier, E.; Pilcer, S.; Sefta, M.; Manceron, P.; Toldo, S.; Zaslavskiy, M.; Le Stang, N.; et al. Deep learning-based classification of mesothelioma improves prediction of patient outcome. Nat. Med. 2019, 25, 1519–1525. [Google Scholar] [CrossRef]
- Cekic, C.; Linden, J. Adenosine A2A receptors intrinsically regulate CD8+ T cells in the tumor microenvironment. Cancer Res. 2014, 74, 7239–7249. [Google Scholar] [CrossRef] [Green Version]
- Newton, H.S.; Chimote, A.A.; Arnold, M.J.; Wise-Draper, T.M.; Conforti, L. Targeted knockdown of the adenosine A(2A) receptor by lipid NPs rescues the chemotaxis of head and neck cancer memory T cells. Mol. Ther. Methods Clin. Dev. 2021, 21, 133–143. [Google Scholar] [CrossRef]
- Jiang, D.; Niwa, M.; Koong, A.C. Targeting the IRE1alpha-XBP1 branch of the unfolded protein response in human diseases. Semin. Cancer Biol. 2015, 33, 48–56. [Google Scholar] [CrossRef] [Green Version]
- Zhao, Y.; Zhang, W.; Huo, M.; Wang, P.; Liu, X.; Wang, Y.; Li, Y.; Zhou, Z.; Xu, N.; Zhu, H. XBP1 regulates the protumoral function of tumor-associated macrophages in human colorectal cancer. Signal Transduct. Target. Ther. 2021, 6, 357. [Google Scholar] [CrossRef]
- Pavlova, N.N.; Thompson, C.B. The Emerging Hallmarks of Cancer Metabolism. Cell Metab. 2016, 23, 27–47. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Vander Heiden, M.G.; Cantley, L.C.; Thompson, C.B. Understanding the Warburg effect: The metabolic requirements of cell proliferation. Science 2009, 324, 1029–1033. [Google Scholar] [CrossRef] [Green Version]
- Jacobs, S.R.; Herman, C.E.; Maciver, N.J.; Wofford, J.A.; Wieman, H.L.; Hammen, J.J.; Rathmell, J.C. Glucose uptake is limiting in T cell activation and requires CD28-mediated Akt-dependent and independent pathways. J. Immunol. 2008, 180, 4476–4486. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Konno, A.; Hoshino, Y.; Terashima, S.; Motoki, R.; Kawaguchi, T. Carbohydrate expression profile of colorectal cancer cells is relevant to metastatic pattern and prognosis. Clin. Exp. Metastasis 2002, 19, 61–70. [Google Scholar] [CrossRef] [PubMed]
- Park, J.H.; Pyun, W.Y.; Park, H.W. Cancer Metabolism: Phenotype, Signaling and Therapeutic Targets. Cells 2020, 9, 2308. [Google Scholar] [CrossRef]
- Guo, R.; Chen, Y.; Borgard, H.; Jijiwa, M.; Nasu, M.; He, M.; Deng, Y. The Function and Mechanism of Lipid Molecules and Their Roles in The Diagnosis and Prognosis of Breast Cancer. Molecules 2020, 25, 4864. [Google Scholar] [CrossRef]
- Choi, S.; Yoo, Y.J.; Kim, H.; Lee, H.; Chung, H.; Nam, M.H.; Moon, J.Y.; Lee, H.S.; Yoon, S.; Kim, W.Y. Clinical and biochemical relevance of monounsaturated fatty acid metabolism targeting strategy for cancer stem cell elimination in colon cancer. Biochem. Biophys. Res. Commun. 2019, 519, 100–105. [Google Scholar] [CrossRef]
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. |
© 2023 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
Chen, W.; Chen, X.; Zhao, Z.; Li, M.; Dong, S.; Hu, S.; Li, X.; Feng, M.; Chen, K.; Zhong, S.; et al. Pan-Cancer Identification of Prognostic-Associated Metabolic Pathways. Biology 2023, 12, 1129. https://doi.org/10.3390/biology12081129
Chen W, Chen X, Zhao Z, Li M, Dong S, Hu S, Li X, Feng M, Chen K, Zhong S, et al. Pan-Cancer Identification of Prognostic-Associated Metabolic Pathways. Biology. 2023; 12(8):1129. https://doi.org/10.3390/biology12081129
Chicago/Turabian StyleChen, Wenbo, Xin Chen, Zhenyu Zhao, Menglu Li, Shuang Dong, Sheng Hu, Xiaoyu Li, Mingqian Feng, Ke Chen, Shan Zhong, and et al. 2023. "Pan-Cancer Identification of Prognostic-Associated Metabolic Pathways" Biology 12, no. 8: 1129. https://doi.org/10.3390/biology12081129
APA StyleChen, W., Chen, X., Zhao, Z., Li, M., Dong, S., Hu, S., Li, X., Feng, M., Chen, K., Zhong, S., & He, C. (2023). Pan-Cancer Identification of Prognostic-Associated Metabolic Pathways. Biology, 12(8), 1129. https://doi.org/10.3390/biology12081129