Single-cell Analysis Highlights Anti-apoptotic Subpopulation Promoting Malignant Progression and Predicting Prognosis in Bladder Cancer

Overview

Journal Cancer Inform

Publisher Sage Publications

Specialty Biomedical Engineering

Date 2025 Feb 28

PMID 40018511

Authors

Linhuan Chen

Yangyang Hao

Tianzhang Zhai

Fan Yang

Shuqiu Chen

Xue Lin

Jian Li

Affiliations

Soon will be listed here.

Abstract

Backgrounds: Bladder cancer (BLCA) has a high degree of intratumor heterogeneity, which significantly affects patient prognosis. We performed single-cell analysis of BLCA tumors and organoids to elucidate the underlying mechanisms.

Methods: Single-cell RNA sequencing (scRNA-seq) data of BLCA samples were analyzed using Seurat, harmony, and infercnv for quality control, batch correction, and identification of malignant epithelial cells. Gene set enrichment analysis (GSEA), cell trajectory analysis, cell cycle analysis, and single-cell regulatory network inference and clustering (SCENIC) analysis explored the functional heterogeneity between malignant epithelial cell subpopulations. Cellchat was used to infer intercellular communication patterns. Co-expression analysis identified co-expression modules of the anti-apoptotic subpopulation. A prognostic model was constructed using hub genes and Cox regression, and nomogram analysis was performed. The tumor immune dysfunction and exclusion (TIDE) algorithm was applied to predict immunotherapy response.

Results: Organoids recapitulated the cellular and mutational landscape of the parent tumor. BLCA progression was characterized by mesenchymal features, epithelial-mesenchymal transition (EMT), immune microenvironment remodeling, and metabolic reprograming. An anti-apoptotic tumor subpopulation was identified, characterized by aberrant gene expression, transcriptional instability, and a high mutational burden. Key regulators of this subpopulation included CEBPB, EGR1, ELF3, and EZH2. This subpopulation interacted with immune and stromal cells through signaling pathways such as FGF, CXCL, and VEGF to promote tumor progression. Myofibroblast cancer-associated fibroblasts (mCAFs) and inflammatory cancer-associated fibroblasts (iCAFs) differentially contributed to metastasis. Protein-protein interaction (PPI) network analysis identified functional modules related to apoptosis, proliferation, and metabolism in the anti-apoptotic subpopulation. A 5-gene risk model was developed to predict patient prognosis, which was significantly associated with immune checkpoint gene expression, suggesting potential implications for immunotherapy.

Conclusions: We identified a distinct anti-apoptotic tumor subpopulation as a key driver of tumor progression with prognostic significance, laying the foundation for the development of new therapeutic strategies to improve patient outcomes.

References

Chen Y, Zhu S, Liu T, Zhang S, Lu J, Fan W . Epithelial cells activate fibroblasts to promote esophageal cancer development. Cancer Cell. 2023; 41(5):903-918.e8. DOI: 10.1016/j.ccell.2023.03.001. View

Zheng H, Chen C, Luo Y, Yu M, He W, An M . Tumor-derived exosomal BCYRN1 activates WNT5A/VEGF-C/VEGFR3 feedforward loop to drive lymphatic metastasis of bladder cancer. Clin Transl Med. 2021; 11(7):e497. PMC: 8288020. DOI: 10.1002/ctm2.497. View

Dagogo-Jack I, Shaw A . Tumour heterogeneity and resistance to cancer therapies. Nat Rev Clin Oncol. 2017; 15(2):81-94. DOI: 10.1038/nrclinonc.2017.166. View

Steele T, Tsamouri M, Siddiqui S, Lucchesi C, Vasilatis D, Mooso B . Cisplatin-induced increase in heregulin 1 and its attenuation by the monoclonal ErbB3 antibody seribantumab in bladder cancer. Sci Rep. 2023; 13(1):9617. PMC: 10267166. DOI: 10.1038/s41598-023-36774-1. View

McElree I, Steinberg R, Mott S, ODonnell M, Packiam V . Comparison of Sequential Intravesical Gemcitabine and Docetaxel vs Bacillus Calmette-Guérin for the Treatment of Patients With High-Risk Non-Muscle-Invasive Bladder Cancer. JAMA Netw Open. 2023; 6(2):e230849. PMC: 9975907. DOI: 10.1001/jamanetworkopen.2023.0849. View

Vanlandewijck M, He L, Mae M, Andrae J, Ando K, Del Gaudio F . A molecular atlas of cell types and zonation in the brain vasculature. Nature. 2018; 554(7693):475-480. DOI: 10.1038/nature25739. View

Apte R, Chen D, Ferrara N . VEGF in Signaling and Disease: Beyond Discovery and Development. Cell. 2019; 176(6):1248-1264. PMC: 6410740. DOI: 10.1016/j.cell.2019.01.021. View

Gu X, Jiang Y, Xue W, Song C, Wang Y, Liu Y . SPNS2 promotes the malignancy of colorectal cancer cells via regulating Akt and ERK pathway. Clin Exp Pharmacol Physiol. 2019; 46(9):861-871. DOI: 10.1111/1440-1681.13124. View

McGranahan N, Swanton C . Clonal Heterogeneity and Tumor Evolution: Past, Present, and the Future. Cell. 2017; 168(4):613-628. DOI: 10.1016/j.cell.2017.01.018. View

10.

Liao J, Yu Z, Chen Y, Bao M, Zou C, Zhang H . Single-cell RNA sequencing of human kidney. Sci Data. 2020; 7(1):4. PMC: 6940381. DOI: 10.1038/s41597-019-0351-8. View

11.

Ou Y, Wang S, Li D, Chu B, Gu W . Activation of SAT1 engages polyamine metabolism with p53-mediated ferroptotic responses. Proc Natl Acad Sci U S A. 2016; 113(44):E6806-E6812. PMC: 5098629. DOI: 10.1073/pnas.1607152113. View

12.

Nicolson G . Tumor cell instability, diversification, and progression to the metastatic phenotype: from oncogene to oncofetal expression. Cancer Res. 1987; 47(6):1473-87. View

13.

Li X, Wang J . Mechanical tumor microenvironment and transduction: cytoskeleton mediates cancer cell invasion and metastasis. Int J Biol Sci. 2020; 16(12):2014-2028. PMC: 7294938. DOI: 10.7150/ijbs.44943. View

14.

Han Y, Wang D, Peng L, Huang T, He X, Wang J . Single-cell sequencing: a promising approach for uncovering the mechanisms of tumor metastasis. J Hematol Oncol. 2022; 15(1):59. PMC: 9096771. DOI: 10.1186/s13045-022-01280-w. View

15.

Xiao Y, Wang Z, Gu M, Wei P, Wang X, Li W . Cancer-associated fibroblasts: heterogeneity and their role in the tumor immune response. Clin Exp Med. 2024; 24(1):126. PMC: 11169017. DOI: 10.1007/s10238-024-01375-3. View

16.

Ohlund D, Elyada E, Tuveson D . Fibroblast heterogeneity in the cancer wound. J Exp Med. 2014; 211(8):1503-23. PMC: 4113948. DOI: 10.1084/jem.20140692. View

17.

Gajewski T, Meng Y, Harlin H . Immune suppression in the tumor microenvironment. J Immunother. 2006; 29(3):233-40. DOI: 10.1097/01.cji.0000199193.29048.56. View

18.

Goel S, Duda D, Xu L, Munn L, Boucher Y, Fukumura D . Normalization of the vasculature for treatment of cancer and other diseases. Physiol Rev. 2011; 91(3):1071-121. PMC: 3258432. DOI: 10.1152/physrev.00038.2010. View

19.

Song Z, Gao P, Zhong X, Li M, Wang M, Song X . Identification of Five Hub Genes Based on Single-Cell RNA Sequencing Data and Network Pharmacology in Patients With Acute Myocardial Infarction. Front Public Health. 2022; 10:894129. PMC: 9219909. DOI: 10.3389/fpubh.2022.894129. View

20.

Makar A, Boraman A, Mosen P, Simpson J, Marques J, Michelberger T . The V-ATPase complex component RNAseK is required for lysosomal hydrolase delivery and autophagosome degradation. Nat Commun. 2024; 15(1):7743. PMC: 11374810. DOI: 10.1038/s41467-024-52049-3. View