Table_3_Single-cell sequencing of the substantia nigra reveals microglial activation in a model of MPTP.XLSX

BackgroundN-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) is a neurotoxin widely used to induce PD models, but the effect of MPTP on the cells and genes of PD has not been fully elucidated.MethodsSingle-nucleus RNA sequencing was performed in the Substantia Nigra (SN) of MPTP mice. UMAP analysis was used for the dimensionality reduction visualization of the SN in the MPTP mice. Known marker genes highly expressed genes in each cluster were used to annotate most clusters. Specific Differentially Expressed Genes (DEGs) and PD risk genes analysis were used to find MPTP-associated cells. GO, KEGG, PPI network, GSEA and CellChat analysis were used to reveal cell type-specific functional alterations and disruption of cell-cell communication networks. Subset reconstruction and pseudotime analysis were used to reveal the activation status of the cells, and to find the transcription factors with trajectory characterized.ResultsInitially, we observed specific DEGs and PD risk genes enrichment in microglia. Next, We obtained the functional phenotype changes in microglia and found that IGF, AGRN and PTN pathways were reduced in MPTP mice. Finally, we analyzed the activation state of microglia and revealed a pro-inflammatory trajectory characterized by transcription factors Nfe2l2 and Runx1.ConclusionOur work revealed alterations in microglia function, signaling pathways and key genes in the SN of MPTP mice.

背景N-甲基-4-苯基-1,2,3,6-四氢吡啶（MPTP）作为一种广泛用于诱导帕金森病模型的神经毒素，其对帕金森病细胞和基因的影响尚未得到充分阐明。方法：对MPTP小鼠的黑质（SN）进行了单核RNA测序。利用UMAP分析对MPTP小鼠的黑质进行了降维可视化。通过使用每个簇中高表达的已知标记基因对大多数簇进行注释。利用特异性差异表达基因（DEGs）和帕金森病风险基因分析，寻找与MPTP相关的细胞。通过GO、KEGG、PPI网络、GSEA和CellChat分析，揭示了特定细胞类型的功能改变以及细胞间通讯网络的破坏。通过子集重建和伪时间分析，揭示了细胞的激活状态，并找到了具有轨迹特征的转录因子。结果：最初，我们观察到在微胶质细胞中存在特定的DEGs和帕金森病风险基因富集。随后，我们获得了微胶质细胞的功能表型变化，并发现MPTP小鼠中IGF、AGRN和PTN通路减少。最终，我们分析了微胶质细胞的激活状态，并揭示了由转录因子Nfe2l2和Runx1表征的促炎轨迹。结论：本研究揭示了MPTP小鼠黑质中微胶质细胞的功能、信号通路和关键基因的改变。