Acute ischemia induces spatially and transcriptionally distinct microglial subclusters

作者：Huiya Li, Pinyi Liu, Bing Zhang, Zengqiang Yuan, Mengdi Guo, Xinxin Zou, Yi Qian, Shiji Deng, Liwen Zhu, Xiang Cao, Tao Tao, Shengnan Xia, Xinyu Bao, Yun Xu · 发表于：Genome Medicine · 年份：2023 · DOI：10.1186/s13073-023-01257-5 · 被引用次数：117 · 研究领域：Neuroinflammation and Neurodegeneration Mechanisms、Single-cell and spatial transcriptomics、Neurogenesis and neuroplasticity mechanisms

BACKGROUND: Damage in the ischemic core and penumbra after stroke affects patient prognosis. Microglia immediately respond to ischemic insult and initiate immune inflammation, playing an important role in the cellular injury after stroke. However, the microglial heterogeneity and the mechanisms involved remain unclear. METHODS: We first performed single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics (ST) on middle cerebral artery occlusion (MCAO) mice from three time points to determine stroke-associated microglial subclusters and their spatial distributions. Furthermore, the expression of microglial subcluster-specific marker genes and the localization of different microglial subclusters were verified on MCAO mice through RNAscope and immunofluorescence. Gene set variation analysis (GSVA) was performed to reveal functional characteristics of microglia sub-clusters. Additionally, ingenuity pathway analysis (IPA) was used to explore upstream regulators of microglial subclusters, which was confirmed by immunofluorescence, RT-qPCR, shRNA-mediated knockdown, and targeted metabolomics. Finally, the infarct size, neurological deficits, and neuronal apoptosis were evaluated in MCAO mice after manipulation of specific microglial subcluster. RESULTS: We discovered stroke-associated microglial subclusters in the brains of MCAO mice. We also identified novel marker genes of these microglial subclusters and defined these cells as ischemic core-associated (ICAM) and ischemic ...