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Deconvolving organogenesis in space and time via spatial transcriptomics in thick tissues
Soichiro Asami1, Chenshuo Yin1, Luis A Garza2
1Department of Biomedical Engineering, Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Biorxiv : the Preprint Server for Biology
|October 10, 2024
Summary
We developed a 3D spatial transcriptomic method to map hair follicle development, revealing early stem cell niche formation and molecular stages guiding organogenesis.
Area of Science:
- Developmental Biology
- Genomics
- Tissue Engineering
Background:
- Organ development relies on complex spatial and temporal cues.
- Characterizing the hair follicle, a mini-organ, is difficult due to its structure and asynchronous development.
Purpose of the Study:
- To develop a novel strategy for high-resolution spatial transcriptomics of developing hair follicles.
- To create a dynamic 3D atlas of hair follicle organogenesis.
- To define molecular stages and identify key developmental events.
Main Methods:
- Developed 3DEEP (3D tissue clearing and spatial transcriptomics).
- Analyzed 371 hair follicles from mouse skin at a single time point.
- Utilized molecular pseudotime to reconstruct developmental trajectories.
Main Results:
- Defined molecular stages of hair follicle organogenesis.
- Characterized the timing of structural emergence and signaling dynamics.
- Identified early establishment of hair follicle stem cells and niche stratification.
- Revealed morphogen shifts preceding structural changes.
Conclusions:
- 3DEEP enables 4D analysis of organogenesis with unprecedented depth.
- Early stem cell niche formation precedes hair bulb development.
- This approach provides a dynamic view of mini-organ development.
