Integrated single-cell and spatial transcriptomics reveal stromal–immune–vascular crosstalk in patients with interstitial cystitis/bladder pain syndrome

Abstract Interstitial cystitis/bladder pain syndrome (IC/BPS) is characterized by complex cellular heterogeneity and inflammatory dysfunction in the bladder. However, the molecular pathogenesis of IC/BPS remains poorly understood, and few studies have provided comprehensive analyses. To elucidate the mechanisms underlying disease pathology, we performed integrated single-cell and spatial transcriptomic analyses of human bladder tissue. Comprehensive single-cell multiomics analyses have identified disease-specific alterations across multiple cell types. T helper 17 cells were significantly expanded in Hunner lesions and activated autoimmune and pro-inflammatory signaling pathways, suggesting a critical role in disease progression. Endothelial cells (ECs) shift from homeostatic (EC2) to pro-angiogenic inflammatory phenotypes (EC3), contributing to vascular remodeling. In the monocyte–macrophage lineage, we identified macrophage 2 cells with pro-angiogenic features that engaged in vascular endothelial growth factor-mediated and tumor necrosis factor-mediated interactions that promoted pathological angiogenesis. Smooth muscle cells (SMCs) display notable phenotypic plasticity, transitioning from a contractile to a synthetic state in IC/BPS tissues. Additionally, spatial transcriptomic analysis revealed upregulation of the EDN1–EDNRA/EDNRB signaling axis, suggesting a role for SMCs in bladder hypercontractility. Fibroblasts have emerged as key mediators of nociceptive signaling, with specific subpopulations enriched in neurotrophin-related pathways (for example, NTF3–NTRK2/NTRK3 and NGF–SORT1) and showing active crosstalk with SMCs, potentially contributing to the development of chronic pain. Collectively, these findings delineate a complex stromal–immune–vascular network underlying the pathological remodeling and pain characteristics of IC/BPS. Our study identified novel cellular players and intercellular signaling pathways that may be promising targets for therapeutic interventions.