Spatial transcriptomics revealed the regulatory role of CCN1 to microglia distribution through region-specific cellular interactions.

During brain development, neural stem progenitor cells (NSPCs) and microglia interact within precise spatial niches; however, decoding mechanism is full of challenges using traditional analytical techniques. Here, we investigated the role of CCN1, a secreted protein enriched in NSPCs, using CNS-specific Ccn1 knockout mice. Through single cell RNA-seq analysis, we found that microglia were significantly reduced in the ventricular zone (VZ) at E17.5 and P2, with elevated expression of autophagy- and activation-related genes in Ccn1-CKO mice. Spatial transcriptomics at P2 further showed that Ccn1 deletion region-specific redistributes microglia and leads to increased microglial aggregation and activation in the rostral lateral septum (LSR), alongside reductions in the VZ. Mechanistically, Ccn1 deletion in NSCs led to region-specific dysregulation of the key signaling ligands, Csf1 and Il2. We found the elevated expression of Csf1 and Il2 specifically within the LSR region, which corresponded to the up-regulation of their respective receptors (Csf1r, Cd53) and downstream targets (Spp1, Ctsb) in LSR microglia, affecting microglial status. Our study reveals a region-specific NSC-microglia interaction regulated by Ccn1, offering a new paradigm for understanding multicellular dynamics in brain development.