Achieng, M. A. | Search bioRxiv

bioRxiv2025

Axial Nephron Fate Switching Demonstrates a Plastic System Tunable on Demand

The human nephron is a highly patterned tubular structure. It develops specialized cells that regulate bodily fluid homeostasis, blood pressure, and urine secretion throughout life. Approximately 1 million nephrons form in each kidney during embryonic and fetal development, but how they develop is poorly understood. Here we interrogate axial patterning mechanisms in the human nephron using an iPSC-derived kidney organoid system that generates hundreds of developmentally synchronized nephrons, and we compare it to in vivo human kidney development using single cell and spatial transcriptomic approaches. We show that human nephron patterning is controlled by integrated WNT/BMP/FGF signaling. Imposing a WNTON/BMPOFF state established a distal nephron identity that matures into thick ascending loop of Henle cells by endogenously activating FGF. Simultaneous suppression of FGF signaling switches cells back to a proximal cell-state, a transformation that is in itself dependent on BMP signal transduction. Our system highlights plasticity in axial nephron patterning, delineates the roles of WNT, FGF, and BMP mediated mechanisms controlling nephron patterning, and paves the way for generating nephron cells on demand.

developmental biology↗

bioRxiv2025

Comparative analysis of Xenopus mesonephric transcriptomics: Conservation of the developmental lineage of nephron stages

The vertebrate kidney develops through three sequential forms: the pronephros, mesonephros, and metanephros. These three forms are composed of segmented nephrons that mediate fluid filtration and solute homeostasis. In aquatic egg-laying vertebrates such as Xenopus laevis, the mesonephros serves as the final functional renal organ, whereas in mammals it is a transient embryonic structure that precedes metanephric development. Despite its central developmental and evolutionary significance, the cellular and transcriptional organization of the mesonephric kidney remains poorly defined at single-cell resolution. Here, we mapped the cellular and transcriptional landscape of the Xenopus laevis mesonephros from NF stages 46-53 to define its composition and analyze its relationship to other kidney types. By integrating single-cell RNA sequencing with in situ hybridization, immunostaining, and functional uptake assays, we identify mesonephric nephron segments, progenitor populations, and the progressive transition from mesenchymal precursors to differentiated epithelial tubules. Transcriptomic profiling of 14,411 cells reveals conserved nephron segment identities and shared differentiation programs revealed conserved nephron segment identities and a clear transition from mesenchymal progenitors to epithelialized tubules. Comparative analyses with published Xenopus pronephric and mammalian metanephric datasets identified strong transcriptional conservation between Xenopus mesonephric and mammalian metanephric nephrons. Functional assays confirmed the timing of filtrate uptake, marking the onset of renal function during metamorphosis. Together, these findings provide the first comprehensive single-cell map of Xenopus mesonephric development, demonstrating that the mechanisms of nephron patterning and differentiation are conserved across vertebrate kidney forms. This work establishes the Xenopus mesonephros as a robust model for studying vertebrate kidney development and evolutionary transitions among nephron types.

developmental biology↗