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Integration of spatial and single-nucleus transcriptomics to map gene expression in the developing mouse kidney.

Christopher P Chaney1,2,3, Alexandria N Fusco1,3, Elyse D Grilli1,3

  • 1Department of Internal Medicine, Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

Development (Cambridge, England)
|November 26, 2025
PubMed
Summary

This study maps kidney cell gene expression, revealing new insights into kidney development and congenital defects. A new tool, KSTAT, helps visualize cell communication and gene activity in the developing kidney.

Keywords:
Cell communicationKidney developmentSingle-nucleus RNA sequencingSpatial transcriptomics

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Area of Science:

  • Developmental Biology
  • Genomics
  • Cell Biology

Background:

  • Kidney development involves complex cellular interactions, and defects can lead to kidney disease.
  • Understanding these mechanisms is crucial for addressing congenital kidney disorders.
  • RNA sequencing reveals cellular diversity, particularly in the kidney stroma, but cell relationships are unclear.

Purpose of the Study:

  • To create a comprehensive gene expression atlas of embryonic and postnatal kidneys.
  • To clarify the relationships between stromal, epithelial, and endothelial cells during kidney development.
  • To develop a tool for analyzing spatial transcriptomics in the kidney.

Main Methods:

  • Integrated single-nucleus and in situ RNA sequencing data from embryonic and postnatal kidneys.
  • Developed the Kidney Spatial Transcriptome Analysis Tool (KSTAT) for cell identification, communication prediction, and pathway mapping.
  • Analyzed gene expression patterns to understand cellular heterogeneity and interactions.

Main Results:

  • Generated a detailed gene expression atlas of the developing and mature kidney.
  • Uncovered significant heterogeneity within embryonic kidney pericytes.
  • KSTAT successfully enabled visualization of cell locations and predicted cell-cell communication pathways.

Conclusions:

  • The gene expression atlas provides a valuable resource for kidney development research.
  • The identified pericyte heterogeneity offers new avenues for studying kidney formation.
  • KSTAT is a powerful tool for advancing kidney developmental biology and disease research.