# TGF-β signaling and tumor microenvironment dynamics in bladder cancer progression post-BCG therapy: a longitudinal single-nucleus RNA-seq study

## TL;DR

This study uses single-nucleus RNA sequencing to explore how bladder cancer progresses after BCG therapy, identifying TGF-β signaling and specific cell interactions linked to treatment resistance.

## Contribution

The study reveals TGF-β signaling and specific TME subtypes as novel factors in bladder cancer progression post-BCG therapy.

## Key findings

- TGF-β signaling is enriched in bladder cancer progression post-BCG therapy.
- LAMP3+ dendritic cells and iCAF fibroblasts show unique progression-linked pseudotime trajectories.
- Ligand-receptor pairs like DSC2-DSG2 and ENG-BMPR2 are associated with poor clinical outcomes.

## Abstract

Although non-muscle-invasive bladder cancer (NMIBC) frequently recurs and progresses despite BCG therapy, cellular mechanisms behind this remain unclear. Understanding the dynamics within the tumor microenvironment (TME) and identifying pathways associated with BCG resistance are crucial for improving NMIBC treatment.

To elucidate transcriptional dynamics and key cellular interactions in the TME, we performed longitudinal single-nucleus RNA sequencing of 9 NMIBC cases with three pairs of treatment-naïve and disease progression samples. The resulting 58,037 nuclei were subject to cell type and subtyping annotations along with cell–cell interaction analyses.

Our analysis revealed marked interpatient heterogeneity in malignant cells, accompanied by copy number alterations associated with disease progression. TGF-β signaling emerged as a key pathway, showing gradual enrichment from pre-treatment to post-progression samples. Within the tumor microenvironment, we identified distinct subtypes including LAMP3 + dendritic cells and iCAF fibroblasts that followed unique pseudotime trajectories linked to progression. Cell–cell interaction analysis further highlighted critical ligand–receptor pairs such as DSC2–DSG2 and ENG–BMPR2, which were associated with poor clinical outcomes. These interactions may represent hypothesis-generating candidates that warrant further validation.

This study highlights key cellular and molecular mechanisms underlying bladder cancer progression Post-BCG treatment. Through single-nucleus RNA sequencing, we identified critical TME subtypes, TGF-β signaling involvement, and crucial ligand-receptor interactions such as DSC2-DSG2 and ENG-BMPR2, which may serve as preliminary biomarkers requiring confirmation in larger independent cohorts. These findings offer valuable insights into enhancement of treatment strategies and patient outcomes.

The online version contains supplementary material available at 10.1186/s12885-025-15079-8.