Relevance of Cellular Homeostasis-Related Gene Expression Signatures in Distinct Molecular Subtypes of Breast Cancer
Abstract
:1. Background
2. Methods
2.1. Patient Population and Samples
2.2. Principal Component Analysis of Gene Expression Data
2.3. Differential Gene Expression Analysis
2.4. Gene Ontology (GO) and KEGG Pathway Enrichment Analysis
2.5. Protein–Protein Interaction (PPI) Network Analysis
3. Results
3.1. Study Population
3.2. Principal Component Analysis
3.3. Differentially Expressed Genes in MP Risk Categories and BP Molecular Subtypes
3.4. Pathways Differentially Modulated in MP and BP Subgroups
3.5. Protein–Protein Interaction Network Associated with Functional Enrichment Analysis of DEGs
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
References
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Variable | Mean ± SD [n (%)] |
---|---|
Age | 58.84 ± 13.04 |
BMI | 30.04 ± 7.34 |
Race | |
White | 799 (81.7) |
Black | 123 (12.6) |
Other * | 56 (5.7) |
Menopausal status | |
Post | 717 (73.3) |
Peri | 128 (13.1) |
Pre | 133 (13.6) |
ER status | |
Negative | 265 (27.1) |
Positive | 713 (72.9) |
PR status | |
Negative | 265 (27.1) |
Positive | 590 (60.5) |
HER2 status | |
Negative | 721 (73.7) |
Positive | 257 (26.3) |
Risk of recurrence | |
Ultralow | 76 (7.8) |
Low | 176 (18) |
High 1 | 315 (32.2) |
High 2 | 411 (42) |
Intrinsic molecular subtypes | |
Luminal A | 250 (25.6) |
Luminal B | 250 (25.6) |
HER2 | 228 (23.3) |
Basal | 250 (25.6) |
GO | Description | Count | % | −Log10(P) | −Log10(q) |
---|---|---|---|---|---|
GO:0000422 | autophagy of mitochondrion | 18 | 16.22 | 29.56 | 25.39 |
GO:0006749 | glutathione metabolic process | 17 | 15.32 | 28.03 | 24.15 |
GO:0062197 | cellular response to chemical stress | 24 | 21.62 | 25.58 | 22.19 |
GO:0019752 | carboxylic acid metabolic process | 30 | 27.03 | 21.57 | 18.47 |
GO:0043525 | positive regulation of neuron apoptotic process | 14 | 12.61 | 20.36 | 17.35 |
GO:0009410 | response to xenobiotic stimulus | 23 | 20.72 | 19.73 | 16.82 |
GO:0031667 | response to nutrient levels | 23 | 20.72 | 18.64 | 15.82 |
GO:1901699 | cellular response to nitrogen compound | 23 | 20.72 | 16.02 | 13.33 |
GO:0071216 | cellular response to biotic stimulus | 15 | 13.51 | 13.68 | 11.12 |
GO:0071214 | cellular response to abiotic stimulus | 15 | 13.51 | 12.09 | 9.69 |
GO:0097193 | intrinsic apoptotic signaling pathway | 12 | 10.81 | 12.04 | 9.66 |
GO:0006476 | protein deacetylation | 6 | 5.41 | 10.99 | 8.64 |
GO:2001233 | regulation of apoptotic signaling pathway | 15 | 13.51 | 10.73 | 8.4 |
GO:0050727 | regulation of inflammatory response | 15 | 13.51 | 10.3 | 8.01 |
GO:0034976 | response to endoplasmic reticulum stress | 12 | 10.81 | 10.29 | 8.01 |
GO:0010506 | regulation of autophagy | 14 | 12.61 | 10.24 | 7.97 |
GO:0030162 | regulation of proteolysis | 17 | 15.32 | 10.14 | 7.88 |
GO:0070848 | response to growth factor | 16 | 14.41 | 10.08 | 7.84 |
GO:2000377 | regulation of reactive oxygen species metabolic process | 10 | 9.01 | 9.69 | 7.47 |
GO:0048511 | rhythmic process | 12 | 10.81 | 9.49 | 7.28 |
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Singh, S.P.; Dhanasekara, C.S.; Melkus, M.W.; Bose, C.; Khan, S.Y.; Sardela de Miranda, F.; Mahecha, M.F.; Gukhool, P.J.; Tonk, S.S.; Jun, S.-R.; et al. Relevance of Cellular Homeostasis-Related Gene Expression Signatures in Distinct Molecular Subtypes of Breast Cancer. Biomedicines 2025, 13, 1058. https://doi.org/10.3390/biomedicines13051058
Singh SP, Dhanasekara CS, Melkus MW, Bose C, Khan SY, Sardela de Miranda F, Mahecha MF, Gukhool PJ, Tonk SS, Jun S-R, et al. Relevance of Cellular Homeostasis-Related Gene Expression Signatures in Distinct Molecular Subtypes of Breast Cancer. Biomedicines. 2025; 13(5):1058. https://doi.org/10.3390/biomedicines13051058
Chicago/Turabian StyleSingh, Sharda P., Chathurika S. Dhanasekara, Michael W. Melkus, Chhanda Bose, Sonia Y. Khan, Flavia Sardela de Miranda, Maria F. Mahecha, Prrishti J. Gukhool, Sahil S. Tonk, Se-Ran Jun, and et al. 2025. "Relevance of Cellular Homeostasis-Related Gene Expression Signatures in Distinct Molecular Subtypes of Breast Cancer" Biomedicines 13, no. 5: 1058. https://doi.org/10.3390/biomedicines13051058
APA StyleSingh, S. P., Dhanasekara, C. S., Melkus, M. W., Bose, C., Khan, S. Y., Sardela de Miranda, F., Mahecha, M. F., Gukhool, P. J., Tonk, S. S., Jun, S.-R., Uygun, S., & Layeequr Rahman, R. (2025). Relevance of Cellular Homeostasis-Related Gene Expression Signatures in Distinct Molecular Subtypes of Breast Cancer. Biomedicines, 13(5), 1058. https://doi.org/10.3390/biomedicines13051058