Spatial transcriptomic profiling of the aging mouse brain [spatial scRNA-seq]

The mammalian brain can be divided into distinct structural and functional regions to perform a variety of diverse functions, but during normal aging, exactly how each region is affected, and the information interaction changes between different regions, remains largely unknown. To gain a better insight into these processes, here we generate a single-cell spatial transcriptomic (ST) atlas of young and old mice brains involving cerebrum, brain stem and fiber tracts regions. Based on the unbiased classification of spatial molecular atlas, 27 distinguished brain spatial domains were obtained, which are similar to known anatomical regions, but slightly different. Through differential expression analysis and gene set enrichment analysis (GSEA), we identified aging-related genes and pathways that vary in a coordinated or opposite manner across regions. Combined with single-cell transcriptomic data, we characterized the spatial distribution of cell types, identified an up-regulated gene Ifi27 across regions and cell types in VIS region. Through ligand-receptor interaction analysis, we identified all possible information interaction changes between regions with aging. In summary, we establish a brain spatial molecular atlas (accessible online at https:) to provide a rich resource of spatially differentially expressed genes and information interaction, which may help to understand aging and provide novel insights into the molecular mechanism of brain aging. 8 slices from young (2 months old) and old mice (28 months old) (strain C57BL/6J) were prepared according to Visium spatial protocols of tissue preparation guide (10x genomics). The brains were rapidly extracted from the cranial cavity, and immediately submerged in ice-cold artificial cerebrospinal fluid. The brains were then blotted to remove excess liquid. The brains were subsequently embedded in Optimal Cutting Temperature compound (OCT) and frozen in isopentane (2-methylbutane, Sigma) precooled with dry ice and liquid nitrogen. The brains were cut into 10-um sections.哺乳动物大脑可划分为不同的结构与功能区域，以执行多样的生物学功能。然而在正常衰老过程中，每个区域具体受到何种影响，以及不同区域间的信息交互如何变化，目前仍尚未明确。为更深入地解析这些过程，本研究构建了年轻与老年小鼠大脑的单细胞空间转录组（single-cell spatial transcriptomic, ST）图谱，涵盖端脑、脑干及纤维束区域。通过对空间分子图谱的无偏分类，我们获得了27个独特的大脑空间结构域，其与已知解剖区域高度相似，但存在细微差异。借助差异表达分析与基因集富集分析（Gene Set Enrichment Analysis, GSEA），我们鉴定出随衰老在不同区域呈现协同或拮抗表达变化的衰老相关基因与通路。结合单细胞转录组数据，我们解析了细胞类型的空间分布特征，并在VIS区域内鉴定出在多个区域与细胞类型中均上调的基因Ifi27。通过配体-受体相互作用分析，我们鉴定出衰老过程中区域间所有可能的信息交互变化。综上，我们构建了大脑空间分子图谱（可于https:在线获取），为空间差异表达基因与信息交互提供了丰富的研究资源，这将有助于理解衰老过程，并为大脑衰老的分子机制提供全新视角。 本研究按照10x Genomics公司的Visium空间组织制备指南流程，制备了8份脑组织切片：分别来自2月龄年轻小鼠与28月龄老年小鼠（品系为C57BL/6J）。具体实验步骤如下：从颅腔中快速取出脑组织后，立即将其浸没于预冷的人工脑脊液中；随后用吸水纸吸干脑组织表面多余液体；之后将脑组织包埋于冰冻切片最佳切割温度复合物（Optimal Cutting Temperature compound, OCT）中，并置于经干冰与液氮预冷的异戊烷（2-甲基丁烷，Sigma）内速冻；最终将包埋好的脑组织切成10微米厚度的切片。