Single cell approached deine forebrain neural stem cell niches and identify microglial ligands that enhance precursor-mediated remyelination (Xenium)

Here we used single cell RNA-sequencing and single cell spatial transcriptomics to characterize the forebrain neural stem cell (NSC) niche under homeostatic and injury conditions. We define the dorsal and lateral ventricular-subventricular zones (V-SVZ) as two distinct neighborhoods, and show that following white matter injury, dorsal NSCs are locally activated to make oligodendrocytes for remyelination. This activation is coincident with a robust increase in transcriptionally-distinct microglia in the dorsal V-SVZ niche. We modeled ligand-receptor interactions within this changing niche and identified two remyelination-associated microglial ligands, IGF1 and OSM, that promote precursor proliferation and oligodendrogenesis in culture. Infusion of either ligand into the lateral ventricles also enhanced oligodendrogenesis, even in the lateral V-SVZ, where NSCs normally make neuroblasts. These data support a model where gliogenesis versus neurogenesis is determined by the local NSC neighborhood and where injury-induced niche alterations promote NSC activation, local oligodendrogenesis, and likely contribute to myelin repair. Multiplexed in situ hybridization-based spatial transcriptomics using the 10X genomics Xenium platform was used to analyze coronal adult (P100) CD-1 mouse forebrain sections containing the V-SVZ and corpus callosum, with a probeset that included marker genes for relevant cell types, ligands and receptors. We analyzed a region of interest that included the V-SVZ and corpus callosum from four different brains from mice which had been exposed to either a control or cuprizone-rapamycin (cup-rap) protocol (2 control, and 2 cup-rap). Replicates are indicated at the end of each sample name (i.e. Adult_Control_Forebrain_Xenium_Biol1, Adult_CupRap_Forebrain_Xenium_Biol1 ). Multiplexed in situ hybridization-based spatial transcriptomics using the 10X genomics Xenium platform was used to analyze coronal adult (P100) CD-1 mouse forebrain sections containing the V-SVZ and corpus callosum, with a probeset that included marker genes for relevant cell types, ligands and receptors. We analyzed a region of interest that included the V-SVZ and corpus callosum from four different brains from mice which had been exposed to either a control or cuprizone-rapamycin (cup-rap) protocol and were given no recovery after treatment cessation. Replicates are indicated at the end of each sample name (i.e. Adult_Control_NoRecovery_Xenium_Biol1, Adult_CupRap_NoRecovery_Xenium_Biol1 ). We also collected tissue from adult CD1 mice which were fitted with osmotic minipumps to infused ligands into the right lateral ventricle. Animals were then either infused with 0.1% BSA-PBS (control) or 204ng OSM in 0.1% BSA-PBS for 7 days, with a delivery rate of 0.5ul per hour.