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Related Experiment Video

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Single-Cell Resolution Three-Dimensional Imaging of Intact Organoids
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Dissecting human organ development using spatial technologies.

Xiaoshan Zhang1, J Jeya Vandana1, Benjamin Greenspun2

  • 1Department of Surgery, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA; Center for Genomic Health, 1300 York Ave., New York, NY 10065, USA.

Developmental Cell
|July 8, 2026
PubMed
Summary
This summary is machine-generated.

Spatial technologies and stem cell-derived organoids are advancing human developmental biology. This review explores integrating these tools for mechanistic studies of organogenesis and developmental processes.

Keywords:
human developmentorganoidsspatial multiomicsspatial proteomicsspatial transcriptomicsstem cells

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Area of Science:

  • Developmental Biology
  • Regenerative Medicine
  • Genomics

Background:

  • Spatial technologies enable molecular profiling within intact tissue architecture, creating high-resolution atlases of embryonic and fetal organs.
  • These atlases reveal spatial and temporal organization of gene regulatory programs, cell-cell interactions, and tissue patterning during organogenesis.
  • Limited access to human developmental tissues and ethical constraints hinder experimental validation and mechanistic studies.

Purpose of the Study:

  • To review current spatial technologies and emerging organoid-based technologies for studying human development.
  • To discuss the integration of spatial profiling with organoids for systematic analysis of developmental processes.
  • To outline future directions for advancing mechanistic and predictive developmental biology.

Main Methods:

  • Spatial transcriptomics, epigenomics, proteomics, metabolomics, and multiomics for molecular profiling.
  • Stem cell-derived organoids as tractable models recapitulating developing organ features.
  • Integration of spatial profiling techniques with organoid models for controlled perturbation and longitudinal analysis.

Main Results:

  • Spatial technologies have generated high-resolution atlases of embryonic and fetal organs.
  • Organoids offer human-relevant models for studying lineage specification, niche signaling, and metabolic maturation.
  • Integration of spatial profiling and organoids enables sophisticated analysis of developmental biology.

Conclusions:

  • Integrating spatial multiomics with organoid models is a powerful approach for developmental biology research.
  • Future directions include leveraging machine learning and accessible data resources to advance mechanistic and predictive capabilities.
  • This integrated methodology holds significant promise for understanding human development and disease.