IMR Press / JIN / Volume 22 / Issue 5 / DOI: 10.31083/j.jin2205128
Open Access Original Research
Single-Cell RNA-Seq Reveals Changes in Cell Subsets in the Cortical Microenvironment during Acute Phase of Ischemic Stroke Rats
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1 Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, 510280 Guangzhou, Guangdong, China
2 School of Rehabilitation Sciences, Southern Medical University, 528305 Foshan, Guangdong, China
3 Department of Oncology, First Affiliated Hospital of Gannan Medical University, 341000 Ganzhou, Jiangxi, China
4 Department of Rehabilitation, Affiliated Hospital of Jining Medical University, 272145 Jining, Shandong, China
*Correspondence: (Qing Zeng); (Guozhi Huang)
These authors contributed equally.
J. Integr. Neurosci. 2023, 22(5), 128;
Submitted: 21 December 2022 | Revised: 19 March 2023 | Accepted: 29 March 2023 | Published: 22 August 2023
Copyright: © 2023 The Author(s). Published by IMR Press.
This is an open access article under the CC BY 4.0 license.

Background: Ischemic stroke, the most common stroke type, has threatened human life and health. Currently, intravenous thrombolysis and endovascular thrombectomy are the mainstream treatment methods, but they may cause cerebral ischemia-reperfusion injury (CIRI), which aggravates brain injury. Consequently, it is worthwhile to start with a study of CIRI mechanism to identify better prevention and treatment methods. Applying single-cell RNA sequencing (scRNA-seq) technology to further understand the biological functions of various cell types in CIRI will facilitate the intervention of CIRI. Methods: This study aimed to establish a rat middle cerebral artery occlusion (MCAO) model to simulate cerebral ischemia-reperfusion, perform enzymatic hydrolysis, and suspend cerebral cortex tissue edema. Single-cell transcriptome sequencing was used, combined with cluster analysis, t-distributed stochastic neighbor embedding (t-SNE) visualization, and other bioinformatics methods to distinguish cell subgroups while using gene ontology (GO) function enrichment and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment to reveal the biological function of each cell subgroup. Results: We identified 21 brain clusters with cell type-specific gene expression patterns and cell subpopulations, as well as 42 marker genes representing different cell subpopulations. The number of cells in clusters 0–3 increased significantly in MCAO group compared to that in the sham group, and nine-cell subpopulations exhibited remarkable differences in the number of genes. Subsequently, GO and KEGG analyses were performed on the top 40 differentially expressed genes (DEGs) in the six cell subpopulations with significant differences. These results indicate that biological processes and signaling pathways are involved in different cell subpopulations. Conclusions: ScRNA-seq revealed the diversity of cell differentiation and the unique information of cell subpopulations in the cortex of rats with acute ischemic stroke, providing novel insight into the pathological process and drug discovery in stroke.

ischemic stroke
cerebral ischemia-reperfusion injury
single-cell RNA-seq
cellular heterogeneity
82072528/National Natural Science Foundation of China
81874032/National Natural Science Foundation of China
82002380/National Natural Science Foundation of China
DCMST-NHC-2019-AHT-01/National Health Commission project of China
Fig. 1.
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