Hunner-type interstitial cystitis (HIC) is a chronic inflammatory bladder disorder characterized by persistent pelvic pain and severe lower urinary tract symptoms. Although histological studies suggest pancystitic inflammation, the cellular mechanisms underlying lesion formation and bladder-wide remodeling remain unclear. We hypothesized that disease-specific stromal populations orchestrate aberrant epithelial and immune responses in HIC. The aim of this study was to define the cellular landscape and intercellular communication networks in Hunner lesions, non-Hunner regions, and non-cystitis control bladder tissue using single-cell RNA sequencing (scRNA-seq).

Bladder biopsy samples were obtained from six patients with HIC (six Hunner lesions; three matched non-Hunner regions) and four non-cystitis controls. Single-cell suspensions were processed using the 10x Genomics platform and analyzed with Seurat and Harmony for clustering and batch correction (Figure 1a). Differential expression, Gene Ontology enrichment, and trajectory inference were performed to characterize lineage dynamics. Cell–cell communication was analyzed using CellChat to identify ligand–receptor interactions. A heterogeneity score based on transcriptomic closeness centrality was calculated to quantify lineage-specific diversity. Public scRNA-seq and bulk RNA-seq datasets were used for independent validation.

A total of 76,000 high-quality cells were analyzed and segregated into epithelial, stromal, immune, and endothelial compartments (Figure 1b). Immune cells were expanded in both Hunner and non-Hunner regions compared with controls, with marked increases in plasma cell subsets.
Stromal reclustering identified a previously unrecognized neuregulin-enriched fibroblast population (NRG_Fib), preferentially localized to Hunner lesions. Trajectory analysis demonstrated bifurcating differentiation of fibroblasts toward either NRG_Fib or myofibroblast states, with spatial predominance of NRG_Fib in Hunner lesions and myofibroblasts in non-Hunner regions.
Cell–cell interaction analysis revealed enhanced fibroblast-to-basal epithelial signaling in HIC, particularly via WNT and NRG pathways. NRG_Fib exhibited strong outgoing signals through WNT5A–FZD and NRG1–integrin receptor axes. Epithelial cells demonstrated increased transcriptional heterogeneity and differentiation toward inflammatory umbrella-cell states characterized by immunoglobulin-related gene expression.
Heterogeneity analysis showed decreased fibroblast diversity but increased epithelial and immune diversity in HIC, suggesting lineage-specific remodeling. Independent public dataset analysis confirmed enrichment of WNT signaling activity and reproducible detection of NRG-enriched fibroblasts in Hunner lesions.

These findings indicate that HIC represents a pan-bladder inflammatory condition characterized by disease-specific stromal remodeling rather than focal lesion-restricted pathology. The emergence of NRG_Fib and their amplified signaling toward basal epithelial cells suggest a fibroblast-centered mechanism driving epithelial injury and chronic inflammation. Reduced fibroblast heterogeneity alongside increased epithelial and immune diversity supports a model of convergent stromal activation with divergent epithelial and immune responses (Figure 2).

Single-cell transcriptomic profiling identifies a Hunner lesion–associated neuregulin-enriched fibroblast population and aberrant fibroblast–epithelial communication as central features of HIC. Fibroblast-driven WNT and NRG signaling networks may represent novel therapeutic targets in painful bladder syndrome/interstitial cystitis.

Continence 19S (2026) 102630
DOI: 10.1016/j.cont.2026.102630