Epithelial and mesenchymal compartments of the developing bladder and urethra display spatially distinct gene expression patterns.

The lower urinary tract is comprised of the bladder and urethra and develops from the cloaca, a transient endoderm-derived structure formed from the caudal hindgut. After cloacal septation to form the urogenital sinus and anorectal tract, the bladder gradually develops from the anterior portion of the urogenital sinus while the urethra elongates distally into the genital tubercle. The bladder is a target for regenerative and reconstructive therapies but engineering an impermeable bladder epithelial lining has proven challenging. Urethral epithelial function, including its role as an active immune barrier, is poorly studied and neglected in regenerative therapy. A deeper understanding of epithelial patterning of the urogenital sinus by the surrounding mesenchyme, also accounting for sex-specific differences, can inform regenerative therapies. In this study, we identified spatially distinct genes in the epithelial and mesenchymal compartments of the developing mouse bladder and urethra that could be potential drivers of patterning in the lower urinary tract. Our data revealed spatially restricted domains of transcription factor expression in the epithelium that corresponded with bladder or urethra-specific differentiation. Additionally, we identified the genes Wnt2, Klf4 and Pitx2 that localize to the mesenchyme of the developing bladder and could be potential drivers of bladder differentiation. Our data revealed an increase in the expression of several chemokine genes including Cx3cl1 and Cxcl14 in the developing urethral epithelium that correlated with an increase in epithelial-associated macrophages in the urethra. A survey of sex-specific differences in epithelial and mesenchymal compartments revealed several differentially expressed genes between the male and female urethra but few sex-specific differences in bladder. By comparing spatially distinct gene expression in the developing lower urinary tract, our study provides insights into the divergent differentiation trajectories of the fetal bladder and urethra that establish their adult functions.