A new study has mapped human urogenital development in its native spatial context, revealing how neighboring organs coordinate their development through cellular communication and molecular signaling during embryogenesis.

The study, published in Science, was led by GUO Jingtao and WANG Xiaoyan at the Institute of Zoology of the Chinese Academy of Sciences, in collaboration with researchers from Peking University Third Hospital and the Women and Children's Hospital, Qingdao University.

The urinary and reproductive systems share embryonic origins and develop in close physical proximity. During the fourth to fifth weeks, the intermediate mesoderm forms the mesonephros, adrenal primordium, and gonadal primordium. Single-cell studies have clarified cell types and developmental trajectories within individual organs. However, tissue dissociation removes the spatial relationships needed to study communication across organ boundaries.

To investigate the coordinated development of the human urogenital system within its native spatial context, the researchers combined high-resolution spatial transcriptomics with single-cell multi-omics, tissue protein imaging, and human embryonic stem cell models to analyze male and female human embryos at Carnegie stages 15, 19, and 23. These stages span gonadal specification and sex differentiation.

Stereo-seq profiling and spatially informed clustering resolved major gonadal, adrenal cortical, renal, mesenchymal, and neural populations. The analysis further classified the dataset into 33 cell types.

Developmental trajectories suggest that renal lineages diverge relatively early, while adrenal cortical and gonadal somatic lineages remain more closely related.

Early gonadal development

At Carnegie stage 15 (CS15), spatial cell-communication analysis showed that the gonadal primordium receives WNT, BMP, and NCAM signals from nearby tissues including the mesonephros and adrenal primordium. Guided by the spatial data, the team treated human embryonic stem cell-derived intermediate mesoderm with BMP7, NCAM1, and CHIR99021. The three-factor combination increased early gonadal marker expression and shifted the transcriptome toward an in vivo early gonadal state. These results suggest that neighboring tissues can help shape early gonadal fate.

As development progresses, the gonads remain spatially adjacent to the mesonephros. In the region where the rete testis or rete ovarii forms, the team identified PAX8-expressing rete cells. Spatial and transcriptomic analyses showed that these cells were more similar to mesonephric mesenchyme than to early gonadal somatic cells. This points to a close developmental relationship between rete cells and the mesonephros.

To investigate this relationship, the researchers integrated pseudotime analysis, single-nucleus RNA sequencing, chromatin accessibility profiling, spatial mapping, and immunofluorescence. They identified cells with features of both rete cells and gonadal supporting cells.

Together with previous mouse Pax8 lineage-tracing data, the results suggest a possible noncanonical contribution from mesonephros-associated rete cells to a subset of gonadal supporting cells. Computational perturbation and in vitro PAX8 knockdown also suggested that PAX8 helps maintain rete cell identity. It may therefore restrain the transition toward a supporting-cell state.

Coordinated steroidogenic programs

The study also revealed coordinated steroidogenic programs across the adrenal gland and gonad. Researchers identified three transcriptionally distinct steroidogenic populations during the first trimester. These include fetal Leydig cells in the male gonad and two adrenal fetal-zone states, FZ_state I and FZ_state II.

FZ_state I showed a stronger de novo cholesterol-synthesis program marked by SREBF2. FZ_state II expressed the lipoprotein receptors SCARB1 and LDLR, together with cortisol-synthesis genes. These findings suggest that FZ_state II preferentially utilizes circulating lipoprotein particles as a source of cholesterol and possesses the capacity for cortisol synthesis.

During sex differentiation, cortisol reduces androgen levels through negative-feedback regulation, thereby protecting normal female development. In contrast to female gonadal steroidogenic cells, which do not emerge until puberty, male gonadal steroidogenic cells differentiate after CS19 during embryogenesis and express androgen biosynthetic genes, thereby supporting normal male sex differentiation. These complementary programs link the steroidogenic functions of the adrenal glands and gonads to sex differentiation.

Together, the findings describe human urogenital development as a coordinated multi-organ process at the levels of chemical signaling, cellular communication, and hormonal coordination. This spatial framework may help researchers study how disrupted coordination contributes to congenital anomalies and differences of sex development.

The researchers also created an interactive platform for exploring the spatial transcriptomic and single-cell multi-omic datasets.

The study was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences, the National Key Research and Development Program of China, and the National Natural Science Foundation of China.

Using spatial transcriptomics and single-cell multi-omics, researchers analyzed Carnegie stages 15–23 human embryos, mapping the urogenital system's native spatial context to reveal its coordinated codevelopment. (Image by GUO Jingtao)