Bioinformatic Evidence Suggesting a Dopaminergic-Related Molecular Association Between GenX Exposure and Major Depressive Disorder
Abstract
1. Introduction
2. Materials and Methods
2.1. Acquisition of MDD, Dopamine, and GenX-Related Genes
2.2. Hub Gene Screening Based on Machine Learning
2.3. Diagnostic Performance Evaluation of Hub Genes
2.4. Genome-Wide Visualization and Functional Enrichment of Hub Genes
2.5. Immune Infiltration Correlation Analysis of Hub Genes
2.6. GeneMANIA-Based Functional Association and Biological Clustering of Hub Genes
2.7. Molecular Docking and Molecular Dynamics Simulation
3. Results
3.1. Intersection of MDD, Dopamine and GenX-Related Genes
3.2. Identification of Hub Gene Screening Based on Machine Learning
3.3. Diagnostic Performance and Associated Features of Hub Genes
3.4. Genome-Wide Visualization and Functional Enrichment of Hub Genes
3.5. Analysis of Hub Gene Correlation with Immune Infiltration
3.6. GeneMANIA Functional Association and Biological Function Clustering of Hub Genes
3.7. Molecular Docking and Molecular Dynamics Simulations
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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| Module | Input Genes (n) | Balancing Method | Selected Features |
|---|---|---|---|
| LASSO | 12 | None | 8 |
| SVM-RFE (MinError) | 12 | None | 6 |
| SVM-RFE (One-SE) | 12 | None | 6 |
| SVM-RFE (Balanced) | 12 | None | 10 |
| Gene Symbol | logFC (in MDD) | Adjusted p-Value | Functional Notes |
|---|---|---|---|
| JAK2 | 0.294 | 9.40 × 10−3 | Non-receptor tyrosine kinase; crucial in cytokine signaling and inflammatory responses, which are implicated in MDD pathophysiology. |
| PHGDH | −0.332 | 4.89 × 10−2 | Key enzyme in serine biosynthesis; links metabolic reprogramming to neuronal function and survival. |
| NT5E (CD73) | −0.747 | 9.19 × 10−3 | Ecto-5′-nucleotidase; regulates purinergic signaling, extracellular adenosine levels, and has roles in immune suppression and neuroinflammation. |
| UCP2 | −0.343 | 4.55 × 10−3 | Mitochondrial uncoupling protein; regulates energy metabolism, reactive oxygen species (ROS) production, and is neuroprotective. |
| MFHAS1 | −0.273 | 1.62 × 10−2 | Involved in innate immune response and regulation of TLR4 signaling; potential link to neuroinflammation. |
| HSPB1 | −0.275 | 2.45 × 10−2 | Heat shock protein; functions as a molecular chaperone, protects against oxidative and proteotoxic stress. |
| AKR1B1 | −0.278 | 4.62 × 10−3 | Aldo-keto reductase; involved in glucose metabolism, oxidative stress response, and synthesis of inflammatory mediators. |
| TP53 | −0.336 | 8.17 × 10−4 | Tumor protein p53; a master regulator of cell cycle, DNA repair, and apoptosis in response to cellular stress. |
| F5 | 0.478 | 1.88 × 10−2 | Coagulation Factor V; a central player in the coagulation cascade, linking hemostasis to inflammatory processes. |
| DPP4 | −0.445 | 1.37 × 10−2 | Dipeptidyl peptidase−4; cleaves neuroactive peptides including GLP−1, and functions as a T-cell activation antigen. |
| LCK | −0.295 | 1.11 × 10−2 | Lymphocyte-specific protein tyrosine kinase; essential for T-cell receptor signaling and adaptive immune activation. |
| ETS1 | −0.344 | 1.35 × 10−2 | Transcription factor; regulates differentiation and function of immune cells, including T and B lymphocytes. |
| JAK2 | 0.294 | 9.40 × 10−3 | Non-receptor tyrosine kinase; crucial in cytokine signaling and inflammatory responses, which are implicated in MDD pathophysiology. |
| PHGDH | −0.332 | 4.89 × 10−2 | Key enzyme in serine biosynthesis; links metabolic reprogramming to neuronal function and survival. |
| NT5E (CD73) | −0.747 | 9.19 × 10−3 | Ecto-5′-nucleotidase; regulates purinergic signaling, extracellular adenosine levels, and has roles in immune suppression and neuroinflammation. |
| MFHAS1 | −0.273 | 1.62 × 10−2 | Involved in innate immune response and regulation of TLR4 signaling; potential link to neuroinflammation. |
| Targets of GenX | Alphafold ID/PDB ID | Binding Energy (kcal/mol) |
|---|---|---|
| AKR1B1 | 1US0 | −8.2 |
| F5 | 8TN9 | −7.3 |
| TP53 | 2X0U | −5.8 |
| UCP2 | P55851 | −6.4 |
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Huang, X.; Wang, Y.; Zheng, Y.; Wang, W.; Lu, Y. Bioinformatic Evidence Suggesting a Dopaminergic-Related Molecular Association Between GenX Exposure and Major Depressive Disorder. Toxics 2025, 13, 1046. https://doi.org/10.3390/toxics13121046
Huang X, Wang Y, Zheng Y, Wang W, Lu Y. Bioinformatic Evidence Suggesting a Dopaminergic-Related Molecular Association Between GenX Exposure and Major Depressive Disorder. Toxics. 2025; 13(12):1046. https://doi.org/10.3390/toxics13121046
Chicago/Turabian StyleHuang, Xiangyuan, Yanyun Wang, Yuqing Zheng, Weiguang Wang, and Ying Lu. 2025. "Bioinformatic Evidence Suggesting a Dopaminergic-Related Molecular Association Between GenX Exposure and Major Depressive Disorder" Toxics 13, no. 12: 1046. https://doi.org/10.3390/toxics13121046
APA StyleHuang, X., Wang, Y., Zheng, Y., Wang, W., & Lu, Y. (2025). Bioinformatic Evidence Suggesting a Dopaminergic-Related Molecular Association Between GenX Exposure and Major Depressive Disorder. Toxics, 13(12), 1046. https://doi.org/10.3390/toxics13121046
