biostudies-literatureJasmineNIDDK NIH HHSNational Institute of Diabetes and Digestive and Kidney DiseasesDBT/Wellcome Trust India AllianceWellcome TrustDepartment of Biotechnology, Ministry of Science and Technology, India1325-1340https://www.ebi.ac.uk/biostudies/studies/S-EPMC7618168biostudies-literatureUnknown18(6)Epithelial linings at mucosal sites act in concert with resident immune cells to direct host defense. The epithelial lining of the urethra is an understudied mucosal barrier with emerging roles in antimicrobial defense during urinary tract infections. Here, we present a comprehensive cellular atlas of the adult female mouse urethra, focusing on epithelial and resident immune cells. Single cell RNA-sequencing revealed two distinct macrophage populations compartmentalized within the epithelium and stroma. Epithelial-associated macrophages display a highly dendritic morphology and populate the urethral lining in increasing numbers over the course of development. Epithelial-associated macrophages express Cx3cr1, MHCII genes, Cd74 and Aif1/Iba-1, representing an activated macrophage type (Mac-AMucosal immunologySingle cell map of the adult female mouse urethra reveals epithelial and stromal macrophages with distinct functional identities.PMC7618168RC2 DK129994R01 DK135535IA/E/21/1/506274Rodrigues RSamtiya MJasmineAnushree ABinoy Joseph DLafin JTVezina CMMandal AStrand DWKavya TTfalseSingle cell map of the adult female mouse urethra reveals epithelial and stromal macrophages with distinct functional identities.Epithelial linings at mucosal sites act in concert with resident immune cells to direct host defense. The epithelial lining of the urethra is an understudied mucosal barrier with emerging roles in antimicrobial defense during urinary tract infections. Here, we present a comprehensive cellular atlas of the adult female mouse urethra, focusing on epithelial and resident immune cells. Single cell RNA-sequencing revealed two distinct macrophage populations compartmentalized within the epithelium and stroma. Epithelial-associated macrophages display a highly dendritic morphology and populate the urethral lining in increasing numbers over the course of development. Epithelial-associated macrophages express Cx3cr1, MHCII genes, Cd74 and Aif1/Iba-1, representing an activated macrophage type (Mac-A2025-01-01T00:00:00Z2025 Dec2026-06-15T06:10:09.186Z2026-06-15T03:08:55.923ZS-EPMC76181684090779110.1016/j.mucimm.2025.09.001