Spatial Characterization of Cell Type Proximity in the Developing Mouse Brain

Overview

We studied how maternal immune activation reshapes the spatial organization of brain cells during development using large scale MERFISH spatial transcriptomics data covering over 148,000 cells.

Key findings

• Under immune activation, microglia showed a 68.85% increase in proximity to migratory excitatory neurons, while oligodendrocyte precursor cells exhibited a 97% increase, revealing coordinated immune and glial remodeling in the developing brain
• Region specific analysis further uncovered targeted microglial enrichment and oligodendrocyte precursor depletion across multiple brain regions

Key highlights

• Engineered an occurrence matrix to quantify pairwise cell-type proximities and regional enrichments.
• Developed a scalable framework for quantifying spatial cell-cell interactions in complex tissues.
• Identified significant proximity shifts in glial and neuroimmune cell pairs associated with inflammation.