In Silico Analysis of Non-Conventional Oxidative Stress-Related Enzymes and Their Potential Relationship with Carcinogenesis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data Mining and Processing
2.2. Protein–Protein Interaction (PPI) Network and Hub Gene Identification
2.3. Differential Gene Expression Analysis
2.4. Differential Protein Expression Analysis
2.5. Genomic Alterations
3. Results
3.1. Identification and Enrichment of Genes Associated with Oxidative Stress
3.2. Protein–Protein Interaction (PPI) Network and Hub Gene Identification
- -
- ALOX5, encoding 5-lipoxygenase (5-LO);
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- CYBB, a component of the microbicidal oxidase system in phagocytes;
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- DUOX1, encoding a dual-function oxidase;
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- Several cytochrome P450 genes, such as CYP1A1, CYP1A2, and CYP1B1;
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- Protein tyrosine kinase genes, including EGFR, JAK2, PDGFRA, PDGFRB, and SRC;
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- Various isoforms of glutathione peroxidase: GPX2, GPX3, GPX4, GPX5, GPX6, GPX7, and GPX8;
- -
- Genes involved in glutathione metabolism, such as GSR, GSS, GSTO1, GSTO2, GSTP1, MGST1, MGST2, and MGST3;
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- PLCG2, a phospholipase tyrosine kinase;
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- PRDX6, a classic antioxidant enzyme;
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- ROS-generating enzymes NOX1, NOX3, NOX4, and NOX5;
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- Mitochondrial respiratory complex genes, including MT-CO1, MT-CO2, MT-ND1, MT-ND2, MT-ND3, MT-ND4, MT-ND5, MT-ND6, NDUFS1, NDUFS2, NDUFS3, and NDUFS8.
3.3. Enrichment Pathway Analysis
3.4. Deregulated OSRE in Cancer Samples
3.5. Upstream Regulators of OSRE Genes
3.6. Protein Expression of OSRE
4. Discussion
5. Conclusions
6. Limitations
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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GO | GO ID | GO Description | FDR |
---|---|---|---|
BP | GO:0034599 | Response to oxidative stress | 2.14−184 |
BP | GO:0062197 | Cellular response to chemical stress | 1.33−98 |
BP | GO:1901700 | Metabolic process | 7.11−82 |
BP | GO:0000302 | Response to reactive oxygen species | 8.51−80 |
BP | GO:0010035 | Response to oxygen-containing compound | 1.12−73 |
MF | GO:0016491 | Catalytic activity | 2.67−153 |
MF | GO:0016209 | Oxidoreductase activity | 2.54−88 |
MF | GO:0003824 | Antioxidant activity | 3.52−50 |
MF | GO:0004601 | Small molecule binding | 1.96−47 |
MF | GO:0019899 | Peroxidase activity | 9.80−41 |
CC | GO:0005739 | Mitochondrion | 1.65−46 |
CC | GO:0005737 | Cytoplasm | 1.76−32 |
CC | GO:0043227 | Membrane-bound organelle | 1.20−25 |
CC | GO:0005740 | Mitochondrial envelope | 7.96−18 |
CC | GO:0031967 | Oxidoreductase complex | 1.07−15 |
Term | p Value | Odds Ratio | Combined Score |
---|---|---|---|
Hepatoma HepG2 | 2.98 × 10−8 | 13.38 | 231.97 |
Prostate LNCaP | 3.73 × 10−7 | 10.07 | 149.14 |
Lung A-549 | 1.45 × 10−4 | 11.24 | 99.36 |
Colon RKO | 0.001 | 7.11 | 48.54 |
Breast MDA-MB | 0.004 | 6.36 | 33.84 |
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Seiva, F.R.F.; Agneis, M.L.G.; de Almeida, M.R.; Caputo, W.L.; de Souza, M.C.; das Neves, K.A.; Oliveira, É.N.; Justulin, L.A., Jr.; Chuffa, L.G.d.A. In Silico Analysis of Non-Conventional Oxidative Stress-Related Enzymes and Their Potential Relationship with Carcinogenesis. Antioxidants 2024, 13, 1279. https://doi.org/10.3390/antiox13111279
Seiva FRF, Agneis MLG, de Almeida MR, Caputo WL, de Souza MC, das Neves KA, Oliveira ÉN, Justulin LA Jr., Chuffa LGdA. In Silico Analysis of Non-Conventional Oxidative Stress-Related Enzymes and Their Potential Relationship with Carcinogenesis. Antioxidants. 2024; 13(11):1279. https://doi.org/10.3390/antiox13111279
Chicago/Turabian StyleSeiva, Fábio Rodrigues Ferreira, Maria Luisa Gonçalves Agneis, Matheus Ribas de Almeida, Wesley Ladeira Caputo, Milena Cremer de Souza, Karoliny Alves das Neves, Érika Novais Oliveira, Luis Antônio Justulin, Jr., and Luiz Gustavo de Almeida Chuffa. 2024. "In Silico Analysis of Non-Conventional Oxidative Stress-Related Enzymes and Their Potential Relationship with Carcinogenesis" Antioxidants 13, no. 11: 1279. https://doi.org/10.3390/antiox13111279
APA StyleSeiva, F. R. F., Agneis, M. L. G., de Almeida, M. R., Caputo, W. L., de Souza, M. C., das Neves, K. A., Oliveira, É. N., Justulin, L. A., Jr., & Chuffa, L. G. d. A. (2024). In Silico Analysis of Non-Conventional Oxidative Stress-Related Enzymes and Their Potential Relationship with Carcinogenesis. Antioxidants, 13(11), 1279. https://doi.org/10.3390/antiox13111279