Exploration of the Core Pathways and Potential Targets of Luteolin Treatment on Late-Onset Depression Based on Cerebrospinal Fluid Proteomics
Abstract
:1. Introduction
2. Results
2.1. LUT Could Improve Depression-like Behaviors in LOD Rats
2.2. LUT Could Improve the Cognition of LOD Rats
2.3. Analysis of GSEA–KEGG Pathway in LOD Treatment with LUT
2.3.1. A General Description of CSF Proteomics Data
2.3.2. GSEA–Gene Ontology (GO) Annotation Analysis of LUT Treating LOD
2.3.3. Analysis of the Core GSEA–KEGG Pathways for LOD Treatment by LUT
2.3.4. HUB Gene Analysis of the Treatment of LOD by LUT through a Protein–Protein Interaction (PPI) Network
2.4. Analysis of Potential Targets for LUT Treatment on LOD Based on Axon Guidance Pathway
2.4.1. GSEA–KEGG Results of Axon Guidance Pathway Based on CSF Proteomics
2.4.2. Analysis of Potential Targets of LUT for LOD Based on Axon Guidance Pathway
2.4.3. Molecular Docking Results of LUT with Eight Potential Targets on the Axon Guidance Pathway
3. Discussion
4. Materials and Methods
4.1. Animals
4.2. Chronic Unpredictable Mild Stress (CUMS) Modeling
4.3. Behavioral Tests
4.3.1. Sucrose Preference Test (SPT)
4.3.2. Open Field Test (OFT)
4.3.3. Forced Swimming Test (FST)
4.3.4. Morris Water Maze Test (MWM)
4.4. CSF Sample Collection
4.5. CSF Proteomics Analysis
4.5.1. Analysis of CSF Proteomics with Data Independent Acquisition (DIA) Method
4.5.2. GSEA for GO Annotation and KEGG Pathway Enrichment
- The proteins were identified commonly by the CON and LOD groups, and the LUT and LOD groups were GO-annotated employing the GSEA method;
- The GSEA method was applied for KEGG pathway enrichment from the co-identified proteins of the CON and LOD groups and the LUT and LOD groups;
- The activity of the GSEA–KEGG pathways was determined based on the enrichment score, with less than zero indicating inhibition and greater than zero indicating activation. We screened the GSEA–KEGG pathway, which is co-regulated by LOD/CON and LUT/LOD with opposite activity states, as the key pathway for the LUT treatment of LOD.
4.5.3. Protein–Protein Interaction (PPI) Network Analysis
4.5.4. Molecular Docking Experiments
4.6. Network Pharmacology Analysis
4.6.1. Target Prediction of LUT
4.6.2. Target Genes for LOD
- We searched for depression-related targets using the GeneCards, DisGenet, OMIM, TTD, PharmGKB, and DrugBank databases, with the terms “depression” or “major depressive disorder” (hereafter collectively referred to as “Depression”) used as keywords. The targets generated from the GeneCards database were filtered with a relevance score ≥ 5. The targets acquired from the DisGeNET database were screened with a score ≥ 0.3.
- Aging-related targets were investigated in the GeneCards, DisGenet, OMIM, TTD, PharmGKB, and DrugBank databases based on the keywords “aging”, “senescence”, or “anti-aging” (hereafter collectively referred to as “Aging”). Targets derived from the GeneCards database were sorted by a relevance score ≥ 5. Targets obtained from the DisGeNET database were screened by a score ≥ 0.3.
- The target genes of “Depression” and “Aging” were merged to produce the target genes of LOD.
4.6.3. Network Pharmacology Analysis of the KEGG Pathway in LUT Treatment of LOD
4.7. Statistical Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
References
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Protein Name | Gene Name | Family | LOD/CON | LUT/LOD | ||
---|---|---|---|---|---|---|
Fold Change | p Value | Fold Change | p Value | |||
Ephrin-A5 | EFNA5 | Ephs/Ephrin | 0.57456 | 0.01075 | 1.85970 | 0.02264 |
EPH receptor B4 | EPHB4 | 0.56399 | 0.00026 | 1.54778 | 0.00798 | |
Eph receptor A4 | EPHA4 | 0.69904 | 0.01011 | 1.38487 | 0.01475 | |
Semaphorin 7A | SEMA7A | Semaphorins | 0.81877 | 0.01265 | 1.46891 | 0.00033 |
Netrin G1 | NTNG1 | Netrins | 0.74603 | 0.01773 | 1.37943 | 0.00113 |
Netrin receptor UNC5B | UNC5B | Other | 0.80701 | 0.02041 | 1.47754 | 0.03082 |
Neural cell adhesion molecule L1 | L1CAM | 0.78713 | 0.01719 | 1.28610 | 0.00572 | |
Netrin receptor DCC | DCC | 0.66085 | 0.02909 | 1.33989 | 0.01489 |
Compound | Target Name | Protein Name | ΔG (kJ·mol−1) | Target Name | Protein Name | ΔG (kJ·mol−1) |
---|---|---|---|---|---|---|
Luteolin | EPHB4 | EPH receptor B4 | −8.0970 | L1CAM | Neural cell adhesion molecule L1 | −6.9822 |
SEMA7A | Semaphorin 7A | −7.3077 | UNC5B | Netrin receptor UNC5B | −6.9678 | |
EPHA4 | Eph receptor A4 | −7.0616 | NTNG1 | Netrin G1 | −6.8523 | |
EFNA5 | Ephrin-A5 | −6.9858 | DCC | Netrin receptor DCC | −6.6671 |
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Liu, K.; Li, H.; Zeng, N.; Li, B.; Yao, G.; Wu, X.; Xu, H.; Yan, C.; Wu, L. Exploration of the Core Pathways and Potential Targets of Luteolin Treatment on Late-Onset Depression Based on Cerebrospinal Fluid Proteomics. Int. J. Mol. Sci. 2023, 24, 3485. https://doi.org/10.3390/ijms24043485
Liu K, Li H, Zeng N, Li B, Yao G, Wu X, Xu H, Yan C, Wu L. Exploration of the Core Pathways and Potential Targets of Luteolin Treatment on Late-Onset Depression Based on Cerebrospinal Fluid Proteomics. International Journal of Molecular Sciences. 2023; 24(4):3485. https://doi.org/10.3390/ijms24043485
Chicago/Turabian StyleLiu, Kaige, Huizhen Li, Ningxi Zeng, Bozhi Li, Gaolei Yao, Xiaofeng Wu, Hanfang Xu, Can Yan, and Lili Wu. 2023. "Exploration of the Core Pathways and Potential Targets of Luteolin Treatment on Late-Onset Depression Based on Cerebrospinal Fluid Proteomics" International Journal of Molecular Sciences 24, no. 4: 3485. https://doi.org/10.3390/ijms24043485
APA StyleLiu, K., Li, H., Zeng, N., Li, B., Yao, G., Wu, X., Xu, H., Yan, C., & Wu, L. (2023). Exploration of the Core Pathways and Potential Targets of Luteolin Treatment on Late-Onset Depression Based on Cerebrospinal Fluid Proteomics. International Journal of Molecular Sciences, 24(4), 3485. https://doi.org/10.3390/ijms24043485