Single-Cell Transcriptomic Profiling of Bladder Cancer - Expert Commentary

Single-cell RNA sequencing is advancing our understanding of the contributions of different cells in the tumor microenvironment to clinical phenotypes. A recent report by Luo et al. used single-cell RNA-sequencing to characterize the molecular and cellular differences between bladder cancer and Cystitis glandularis (CG), a pre-malignant chronic inflammatory condition. The transcriptomes of 26,792 cells that were profiled and then clustered into 17 cell populations using known markers for annotation include immune cell, stromal cell, and epithelial cell compartments.

Enrichment analysis revealed that CG epithelial cells exhibited upregulation in immune and inflammatory pathways genes. To determine changes that may reflect the progression from low-grade to high-grade bladder cancer, the authors then compared cells from patients with LG and HG bladder cancer and found 278 genes that showed significant differential expression levels. The authors validated some of this data by analyzing gene expression (qPCR) in bladder cancer cell lines. The expression of inhibitory genes that could prevent cell invasion and increase autophagy was upregulated in LG bladder cancer compared to HG bladder cancer cell lines.

Next, Luo et al. examined the role of the tumor microenvironment (TME) in tumor progression. Stromal cells (endothelial cells and fibroblasts) appeared to be enriched in the HG bladder cancer relapse. All bladder cancer cells showed a higher proportion of macrophages than the CG cells, which showed a higher proportion of T cells. In the sample from the patient with recurrence, the number of T cells and macrophages dropped after recurrence while the number of stromal cells was higher, reflecting potential immunosuppression. These findings were also validated using immunohistochemistry. Immunosuppressive macrophages were particularly enriched in HG bladder cancer cells. Endothelial cells and fibroblasts were also particularly enriched in HG relapse.

This report shows the feasibility of single-cell RNA sequencing of bladder cancers and supports the utility of this technique for profiling the tumor microenvironment. Due to the small sample size, these findings should be considered hypothesis-generating.

Written by: Bishoy M. Faltas, MD, Director of Bladder Cancer Research, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York City, New York


  1. Luo, Y., Tao, T., Tao, R., Huang, G., & Wu, S. (2022). Single-Cell Transcriptome Comparison of Bladder Cancer Reveals Its Ecosystem. Frontiers in oncology, 12, 818147.

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