Spatial transcriptomics reveals gene interactions and signaling pathway dynamics in rat embryos with anorectal
Chen-Yi Wang1, Mu-Yu Li1, Si-Ying Li1
1Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Sanhao Street No. 36, Shenyang, 110004, Liaoning, China.
Cell Biology and Toxicology
|May 20, 2024
Summary
Spatial transcriptomics reveals gene expression patterns in embryonic hindgut development, identifying key molecular differences in anorectal malformation (ARM). This study enhances understanding of ARM
Area of Science:
- Developmental Biology
- Genomics
- Bioinformatics
Background:
- Anorectal malformation (ARM) is a common congenital digestive anomaly.
- The embryonic cloaca's complex anatomy hinders traditional sequencing for location-specific data.
Purpose of the Study:
- To investigate spatial gene expression in the embryonic cloaca region during normal and ARM development.
- To identify molecular mechanisms underlying ARM using spatial transcriptomics and bioinformatics.
Main Methods:
- Spatial transcriptomics on embryonic rat hindgut sections (GD 14-16) from normal and ARM cases.
- Bioinformatics analyses including WGCNA, GSEA, PROGENy, and ceRNA network construction.
- Immunofluorescence staining to validate gene and protein expression.
Main Results:
- WGCNA identified gene modules associated with normal and ARM cloacal development.
- Downregulation of Pcsk9, Hmgb2, and Sod1 proteins observed in GD15 ARM hindgut.
- PROGENy predicted synergistic signaling pathway activities. A ceRNA network was constructed.
Conclusions:
- Spatial transcriptomics provides crucial location-specific gene expression data for ARM research.
- Bioinformatics analyses reveal molecular interactions and regulatory insights into ARM development.
- Findings guide future research on anorectal malformation etiology and gene regulation.
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