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Spatial transcriptomic profiling to identify mesoderm progenitors with precision genomic screening and functional
Guanghui Liu1, Guanheng Yang1, Guijun Zhao1
1Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Cell Proliferation
|July 30, 2022
Summary
This study identifies 50 candidate mesoderm-specific genes crucial for development using advanced sequencing and bioinformatics. These findings offer new insights into mesoderm progenitor identification and function.
Area of Science:
- Developmental Biology
- Genomics
- Molecular Biology
Background:
- Mesoderm development is critical for forming diverse tissues and organs.
- Systematic identification of mesoderm-specific genes and markers remains a significant challenge in developmental biology.
- Understanding mesoderm development is key to regenerative medicine and disease research.
Purpose of the Study:
- To screen and identify novel candidate genes essential for mesoderm development.
- To elucidate the specific characteristics and markers of mesodermal cells.
- To validate the identified genes through functional assays.
Main Methods:
- Laser capture microdissection and microcellular RNA sequencing of cells from three germ layers.
- Bioinformatic analysis to identify mesoderm-specific differentially expressed genes (DEGs).
- Validation using real-time quantitative polymerase chain reaction, immunohistochemistry, ESCs-EBs differentiation, and colony-forming units (CFUs) assays.
Main Results:
- Identified 1962 differentially expressed mesoderm genes, with 50 selected as candidate mesoderm-specific DEGs.
- Gene Ontology (GO) analysis revealed these genes are involved in somite development, germ layer formation, segmentation, and pattern specification.
- Key genes (Cdh2, Cdh11, Jag1, T, Fn-1, Pcdh7) showed specific mesodermal expression; Pcdh7 demonstrated hematopoietic functions.
Conclusions:
- Spatial transcriptomic profiling combined with multi-method analysis successfully identified candidate mesoderm progenitors.
- The employed approach is efficient and reliable for screening and validating candidate genes.
- This methodology can be extended to diverse cellular systems for gene discovery in developmental processes.
