Transcriptome analysis of the course of ischemic stroke from acute to chronic phase in mice [2]

We conducted an examination of alterations in gene expression in the ischemic brain of mice at 3 and 14 days after cerebral infarction, in comparison to the control and sham operation groups at single nucleus-transcriptomic levels. By cell type annotation, we obtained neurons (glutamatergic and GABAergic), fibroblast-like cells, astrocytes, oligodendrocyte progenitor cells (OPCs), oligodendrocytes, microglia, endothelial cells, and pericytes. We observed survival signals in neurons in addition to extensive inflammatory changes and neuronal death signals. A massive change was observed on day3, showing the loss of glutamatergic neuron and the increase of endothelial cells. This tendency was slightly recovered towards day14. Our findings revealed elevated expression of autophagy and cAMP signaling in surviving neurons within the penumbra region. Overall design: Mouse cerebral infarcts were produced in a model of distal middle cerebral artery occlusion (dMCAO). The mice were divided into four groups: 3 days post-stroke, 14 days post-stroke, the control group, and the sham surgery group. Each brains brain tissue is mechanically dissociated, and cell membranes are lysed using enzymatic treatment and detergents to isolate and purify the nuclei. After confirming the quality of the nuclei, a library is prepared, and single nucleus RNA sequencing is performed.