TNF Signaling Pathway Is the Key Pathway Regulated by Disitamab Vedotin in Bladder Cancer Cells
Abstract
:1. Introduction
2. Materials and Methods
2.1. Acquisition of Transcriptome Sequencing Data
2.2. Identification of Differentially Expressed Genes (DEGs)
2.3. Gene Enrichment Analysis
2.4. Protein–Protein Interaction (PPI) Network Analysis and Identification of Hub Genes
2.5. Correlation Analysis of Hub Gene Expression
2.6. Identification of Signaling Pathways for Hub Genes
2.7. Cell Culture
2.8. Main Reagents and Instruments
2.9. Quantitative PCR (qPCR)
2.10. Statistics
3. Results
3.1. DEGs Regulated by Disitamab Vedotin in Bladder Cancer Cells
3.2. GO Function and KEGG Pathway Enrichment Analyses of DEGs
3.3. Identification of Hub Genes Through PPI Network Analysis
3.4. Correlation Analysis of the Expression Levels of Hub Gene
3.5. TNF Signaling Pathway as the Key Pathway Regulated by Disitamab Vedotin in Bladder Cancer Cells
3.6. TNF Signaling Pathway Genes Are Upregulated in Bladder Cancer Cells Treated with Disitamab Vedotin
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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Top 15 Upregulated DEGs * | ||||
Gene Symbol | Log2 (Fold Change) | Adjusted p-Value | t | B |
UBD | 8.974 | 0.010 | 14.425 | 3.185 |
LTB | 7.633 | 0.000 | 65.409 | 7.323 |
ERCC5 | 7.143 | 0.003 | 22.952 | 5.079 |
CXCL1 | 6.744 | 0.002 | 28.700 | 5.801 |
CXCL8 | 6.032 | 0.009 | 16.185 | 3.696 |
IL32 | 5.643 | 0.007 | 17.179 | 3.951 |
TNF | 5.549 | 0.001 | 38.924 | 6.560 |
CCL20 | 5.434 | 0.022 | 10.857 | 1.843 |
CXCL3 | 5.349 | 0.022 | 10.923 | 1.873 |
CSF2 | 5.087 | 0.038 | 8.334 | 0.535 |
LCN2 | 5.068 | 0.002 | 28.913 | 5.822 |
CXCL10 | 4.887 | 0.014 | 12.956 | 2.690 |
KLHDC7B | 4.725 | 0.009 | 15.411 | 3.481 |
SAA1 | 4.508 | 0.012 | 13.646 | 2.931 |
C3 | 4.334 | 0.005 | 21.047 | 4.763 |
Top 8 Downregulated DEGs | ||||
Gene Symbol | Log2 (Fold Change) | Adjusted p-Value | t | B |
HOTS | −2.451 | 0.022 | −10.652 | 1.750 |
FAM81A | −1.408 | 0.044 | −7.787 | 0.196 |
ZNF334 | −1.390 | 0.045 | −7.669 | 0.120 |
MEGF10 | −1.390 | 0.045 | −7.669 | 0.120 |
CLCA2 | −1.368 | 0.026 | −10.030 | 1.455 |
RGS16 | −1.327 | 0.034 | −8.814 | 0.814 |
GJA1 | −1.184 | 0.038 | −8.320 | 0.527 |
UGT2B28 | −1.000 | 0.002 | −28.944 | 5.826 |
Source | Term Name | FDR * | Count | Intersections |
---|---|---|---|---|
KEGG | IL-17 signaling pathway | <0.001 | 16 | CXCL1, CXCL8, TNF, CCL20, CXCL3, CSF2, LCN2, CXCL10, CCL2, TNFAIP3, S100A8, NFKBIA, IL1B, S100A9, IKBKE, MMP9 |
KEGG | TNF signaling pathway | <0.001 | 15 | CXCL1, TNF, CCL20, CXCL3, CSF2, CXCL10, CCL2, TNFAIP3, BIRC3, EDN1, ICAM1, NFKBIA, IL1B, CSF1, MMP9 |
KEGG | NF-kappa B signaling pathway | <0.001 | 14 | LTB, CXCL1, CXCL8, TNF, CXCL3, TNFAIP3, BIRC3, RELB, ICAM1, NFKB2, TNFSF14, NFKBIA, IL1B, PLAU |
KEGG | Cytokine-cytokine receptor interaction | <0.001 | 20 | LTB, CXCL1, CXCL8, IL32, TNF, CCL20, CXCL3, CSF2, CXCL10, CCL2, CCL22, IL7R, EBI3, CXCR4, IL23A, IL1A, TNFSF14, IL1B, BMP2, CSF1 |
KEGG | Viral protein interaction with cytokine and cytokine receptor | <0.001 | 11 | CXCL1, CXCL8, TNF, CCL20, CXCL3, CXCL10, CCL2, CCL22, CXCR4, TNFSF14, CSF1 |
KEGG | Lipid and atherosclerosis | <0.001 | 14 | CXCL1, CXCL8, TNF, CXCL3, CCL2, ICAM1, NFKBIA, NLRP3, IL1B, IRF7, IKBKE, NCF2, ABCG1, MMP9 |
KEGG | C-type lectin receptor signaling pathway | <0.001 | 10 | TNF, CCL22, RELB, IL23A, NFKB2, NFKBIA, NLRP3, IL1B, IRF9, IKBKE |
KEGG | Toll-like receptor signaling pathway | 0.001 | 8 | CXCL8, TNF, CXCL10, NFKBIA, IL1B, IRF9, IRF7, IKBKE |
KEGG | RIG-I-like receptor signaling pathway | 0.008 | 6 | CXCL8, TNF, CXCL10, NFKBIA, IRF7, IKBKE |
KEGG | Chemokine signaling pathway | 0.013 | 9 | CXCL1, CXCL8, CCL20, CXCL3, CXCL10, CCL2, CCL22, CXCR4, NFKBIA |
KEGG | Cytosolic DNA-sensing pathway | 0.018 | 6 | CXCL10, NFKBIA, NLRP3, IL1B, IRF7, IKBKE |
KEGG | Inflammatory bowel disease | 0.040 | 5 | TNF, IL23A, IL1A, IL1B, HLA-DQB1 |
Rank | Gene Symbol | Gene Description | Degree | Log2 (Fold Change) | Adjusted p-Value |
---|---|---|---|---|---|
1 | TNF | Tumor Necrosis Factor | 62 | 5.549 | 0.001 |
2 | IL1B | Interleukin 1 Beta | 60 | 1.752 | 0.005 |
3 | IL1A | Interleukin 1 Alpha | 58 | 2.094 | 0.027 |
4 | CXCL8 | C-X-C Motif Chemokine Ligand 8 | 58 | 6.032 | 0.009 |
5 | CXCL1 | C-X-C Motif Chemokine Ligand 1 | 54 | 6.744 | 0.002 |
6 | CCL2 | C-C Motif Chemokine Ligand 2 | 50 | 3.989 | 0.007 |
7 | MMP9 | Matrix Metallopeptidase 9 | 50 | 1.000 | 0.002 |
8 | ICAM1 | Intercellular Adhesion Molecule 1 | 50 | 2.580 | 0.009 |
9 | CXCL10 | C-X-C Motif Chemokine Ligand 10 | 50 | 4.887 | 0.014 |
10 | CCL20 | C-C Motif Chemokine Ligand 20 | 48 | 5.434 | 0.022 |
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Tang, X.; Liu, J.; Zhao, Q.; Cao, Y.; Yang, X.; Du, P.; Yang, Y. TNF Signaling Pathway Is the Key Pathway Regulated by Disitamab Vedotin in Bladder Cancer Cells. Curr. Issues Mol. Biol. 2025, 47, 369. https://doi.org/10.3390/cimb47050369
Tang X, Liu J, Zhao Q, Cao Y, Yang X, Du P, Yang Y. TNF Signaling Pathway Is the Key Pathway Regulated by Disitamab Vedotin in Bladder Cancer Cells. Current Issues in Molecular Biology. 2025; 47(5):369. https://doi.org/10.3390/cimb47050369
Chicago/Turabian StyleTang, Xingxing, Jia Liu, Qiang Zhao, Yudong Cao, Xiao Yang, Peng Du, and Yong Yang. 2025. "TNF Signaling Pathway Is the Key Pathway Regulated by Disitamab Vedotin in Bladder Cancer Cells" Current Issues in Molecular Biology 47, no. 5: 369. https://doi.org/10.3390/cimb47050369
APA StyleTang, X., Liu, J., Zhao, Q., Cao, Y., Yang, X., Du, P., & Yang, Y. (2025). TNF Signaling Pathway Is the Key Pathway Regulated by Disitamab Vedotin in Bladder Cancer Cells. Current Issues in Molecular Biology, 47(5), 369. https://doi.org/10.3390/cimb47050369