📋 SUMMARY
Research published in Nature Communications (2025) developed Phospho-seq, a novel technology that simultaneously profiles 64 intracellular proteins alongside chromatin accessibility and gene expression in single cells. Using 3D Petri Dish® brain organoid cultures, the researchers revealed heterogeneous signaling states and lineage-specific WNT and MAPK/ERK signaling patterns within developing neural cell types.
Phospho-seq: Integrated Multi-Modal Profiling of Intracellular Protein Dynamics in Single Cells
Nature Communications · 2025 · Blair et al.
RESEARCH OVERVIEW
Phospho-seq represents a breakthrough in single-cell multi-omics, enabling simultaneous measurement of phosphoproteins, chromatin accessibility, and gene expression. The technology was validated on cell lines, iPSCs, and brain organoids grown in 3D Petri Dish® micro-molds, uncovering novel transcription factor-cis-regulatory element-gene associations including lineage-specific relationships in developing neural tissue.
🔑 Key Findings
- Simultaneously profiles 64 intracellular proteins with chromatin accessibility and transcriptomics at single-cell resolution
- Identified lineage-specific WNT and MAPK/ERK signaling patterns in brain organoids
- Revealed novel transcription factor regulatory relationships in developing neural tissue
- Demonstrated broad applicability across cell lines, iPSCs, and complex 3D organoid models
🧫 3D Petri Dish® Application
The 3D Petri Dish® micro-mold platform was used to generate uniform brain organoids for Phospho-seq validation.
- Spheroid Formation: 3D Petri Dish® enabled consistent organoid generation for multi-modal single-cell profiling
- Signaling Analysis: 3D organoid cultures revealed heterogeneous phosphoprotein states not detectable in 2D
- Technology Validation: The platform provided physiologically relevant 3D models to demonstrate Phospho-seq capabilities