Single cell spatial transcriptomics links Wnt signaling disruption to extracellular matrix development in a cleft...

Area of Science:

• Developmental Biology
• Genomics
• Molecular Biology

Background:

• Palatal clefts result from complex morphological disruptions, but the underlying signaling microenvironment alterations are not fully understood.
• Existing research lacks detailed molecular insights into the genomic basis of palatal cleft formation.

Purpose of the Study:

• To conduct the first single-cell spatial RNA sequencing study in a cleft palate model to uncover genomic perturbations.
• To identify key molecular targets for potential therapeutic interventions in human palatal clefts.

Main Methods:

• Utilized the Pax9-/- murine model exhibiting cleft palate defects at multiple developmental stages.
• Employed Visium HD for single-cell resolution spatially resolved transcriptomics with 2x2 μm spatial bins.
• Validated spatial gene expression using Xenium In Situ mRNA spatial profiling and RNAscope Multiplex assays.

Main Results:

• Functional enrichment analysis revealed palate cell-specific perturbations in Wnt signaling.
• Disrupted expression of extracellular matrix genes was observed in developing mesenchyme.
• The study generated a comprehensive dataset for understanding cleft palate etiology.

Conclusions:

• The findings provide a detailed molecular map of the signaling microenvironment in cleft palate development.
• Identified Wnt signaling and extracellular matrix gene dysregulation as key factors in palatal cleft formation.
• This research lays the groundwork for translational studies targeting effective therapies for human palatal clefts.