Integration of Single-Cell and Bulk Transcriptome to Reveal an Endothelial Transition Signature Predicting Bladder Cancer Prognosis
Simple Summary
Abstract
1. Introduction
2. Methods
2.1. Data Collection
2.2. Identification of EC Subpopulations
2.3. Investigation of Endothelial Transition from Tip ECs to Capillary ECs
2.4. Exploring the Prognostic Significance of Endothelial Transition Signature
2.5. Cellular Communication Analysis
2.6. Construction of Prognostic Model Based on Endothelial Transition Signature
2.7. Characterisation of High-Risk Patients
2.8. Statistical Analysis and Plot
3. Results
3.1. Identification of EC Transitional Cluster Associated with Tumours
3.2. Identification of the Transition Signature from Tip Cells to Capillary Cells
3.3. Potential Prognostic Significance of Endothelial Transition Signature
3.4. Cellular Communication Pattern in Bladder Cancers
3.5. Construction and Evaluation of the Prognostic Prediction Model
3.6. Characterisation of the High-Risk Group in Terms of Tumour Progression and Cellular Infiltration
3.7. Characterisation of High-Risk Patients in Terms of Immunotherapy and Chemotherapy
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
ECs | Endothelial cells |
Enet | Elastic net |
GBM | Generalised boosted regression modelling |
GSEA | Gene set enrichment analysis |
GSVA | Gene set variation analysis |
IC50 | Half-maximal inhibitory concentration |
IHC | Immunohistochemistry |
IPS | Immunophenoscore |
MSI | Microsatellite instability |
PlsRcox | Partial least squares regression for Cox |
RSF | Random survival forest |
ScRNA-seq | Single-cell RNA sequencing |
SuperPC | Supervised principal components |
Survival-SVM | Survival support vector machine |
TC-ECs | Tip-to-capillary endothelial cells |
TIDE | Tumour Immune Dysfunction and Exclusion |
TMB | Tumour mutation burden |
TME | Tumour microenvironment |
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Cell Type | Marker Genes | |
---|---|---|
Tip endothelial cell | PGF | PXDN |
Venous endothelial cell | ACKR1 | SELP |
Capillary endothelial cell | CA4 | CD36 |
Arterial endothelial cell | FBLN5 | GJA5 |
Lymphatic endothelial cell | PROX1 | CCL21 |
Variable | HR | 95% CI | p |
---|---|---|---|
Risk score | 2.95 | 2.10–4.15 | 4.54 × 10−10 |
Stage | 1.70 | 1.11–2.59 | 1.49 × 10−2 |
Gender | 0.89 | 0.64–1.24 | 4.80 × 10−1 |
Age | 1.03 | 1.02–1.05 | 3.17 × 10−5 |
T stage | 1.69 | 1.23–2.33 | 1.13 × 10−3 |
Cigarettes per day | 1.01 | 0.97–1.06 | 6.27 × 10−1 |
M stage | 2.96 | 1.35–6.48 | 6.72 × 10−3 |
N stage | 1.54 | 1.16–2.03 | 2.59 × 10−3 |
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Yang, J.; Wu, W.; Tang, X. Integration of Single-Cell and Bulk Transcriptome to Reveal an Endothelial Transition Signature Predicting Bladder Cancer Prognosis. Biology 2025, 14, 486. https://doi.org/10.3390/biology14050486
Yang J, Wu W, Tang X. Integration of Single-Cell and Bulk Transcriptome to Reveal an Endothelial Transition Signature Predicting Bladder Cancer Prognosis. Biology. 2025; 14(5):486. https://doi.org/10.3390/biology14050486
Chicago/Turabian StyleYang, Jinyu, Wangxi Wu, and Xiaoli Tang. 2025. "Integration of Single-Cell and Bulk Transcriptome to Reveal an Endothelial Transition Signature Predicting Bladder Cancer Prognosis" Biology 14, no. 5: 486. https://doi.org/10.3390/biology14050486
APA StyleYang, J., Wu, W., & Tang, X. (2025). Integration of Single-Cell and Bulk Transcriptome to Reveal an Endothelial Transition Signature Predicting Bladder Cancer Prognosis. Biology, 14(5), 486. https://doi.org/10.3390/biology14050486