Interaction between subventricular zone microglia and neural stem cells impacts the neurogenic response in a mouse model of cortical ischemic stroke

After a stroke, the neurogenic response from the subventricular zone (SVZ) to repair the brain is limited. Microglia, as an integral part of the distinctive SVZ microenvironment, control neural stem / precursor cell (NSPC) behavior. Here, we show that discrete stroke-associated SVZ microglial clusters negatively impact the innate neurogenic response, and we propose a repository of relevant microglia–NSPC ligand–receptor pairs. After photothrombosis, a mouse model of ischemic stroke, the altered SVZ niche environment leads to immediate activation of microglia in the niche and an abnormal neurogenic response, with cell-cycle arrest of neural stem cells and neuroblast cell death. Pharmacological restoration of the niche environment increases the SVZ-derived neurogenic repair and microglial depletion increases the formation and survival of newborn neuroblasts in the SVZ. Therefore, we propose that altered cross-communication between microglial subclusters and NSPCs regulates the extent of the innate neurogenic repair response in the SVZ after stroke. Overall design: Using a mouse model of cortical ischemic stroke (photothrombotic ischemia, PT), we performed single-cell RNA sequencing (scRNAseq) on neural stem progenitor cells (NSPCs) and microglia. Tamoxifen-treated Nestin-CreERT2:R26-yfp transgenic mice underwent PT after injection of photosensitive dye and light exposure. Subventricular zone (SVZ) compartments were microdissected from brains of control (Ctrl, no PT), 1 day post-PT (S1d), and 7 days post-PT (S7d) animals. SVZ tissue was digested enzymatically and dissociated mechanically, and GFP+ SVZ NSPCs and CD11b+CD45low microglia were FACS isolated before scRNAseq and library prep using the plate-based mCEL-Seq2 protocol. cDNA libraries were sequenced with Illumina HiSeq 3000. Reads were demultiplexed with bcl2fastq and aligned to the GRCm39 mouse reference genome.