Spatial Mapping of Mouse Brain Aging through Indexed Sequencing

Here, we have developed a novel methodology called IRIS (Imaging Reconstruction using Indexed Sequencing) that enables cost-effective spatial transcriptomics profiling without relying on optical imaging. Through neighborhood interaction-based reconstruction, IRIS allows extensive analysis of large tissue sections and many replicates with adjustable mapping resolution at only a fraction of the cost of other commercial platforms. With the IRIS platform, we reconstructed a large area spatial area with two whole mouse brain coronal sections. Moreover, we also created a spatially resolved transcriptome atlas of the mouse brain and identified aging-associated changes in gene expression and spatial organization across various brain cell types. Further analysis of cell-cell interaction changes identified aging-associated foci in white matter regions enriched with inflammatory subtypes of microglia and oligodendrocytes. Overall, the IRIS methodology cost-effective and ease-of-use approach makes it broadly applicable to the studies of spatial gene expression changes in various systems. Utilizing the IRIS platform, we conducted a comprehensive spatial analysis of molecular profiles and spatial arrangements of cell types in mouse brains. To study the aging-associated transcriptome changes, here we collected brain tissues from adult (4-month) and the aged (23-month) wild-type C57BL/6 mice, with three replicates per age group.本研究开发了一种名为IRIS（基于索引测序的成像重建，Imaging Reconstruction using Indexed Sequencing）的新型方法，可在无需依赖光学成像的前提下，实现兼具成本效益的空间转录组谱分析。通过基于邻域相互作用的重建流程，IRIS可对大尺寸组织切片及大量生物学重复样本开展全面分析，且可调节空间映射分辨率，所需成本仅为其他商用平台的一小部分。依托IRIS平台，本研究完成了两块完整小鼠大脑冠状切片的大区域空间重建。此外，本研究还构建了小鼠大脑的空间分辨转录组图谱，并鉴定出不同脑细胞类型中与衰老相关的基因表达及空间组织模式变化。进一步对细胞间相互作用变化的分析，在富集小胶质细胞与少突胶质细胞炎症亚型的白质区域中鉴定出了衰老相关病灶。综上，IRIS方法兼具成本效益与易用性，可广泛应用于多种生物系统的空间基因表达变化研究。依托IRIS平台，本研究对小鼠大脑的分子谱及细胞类型空间排布开展了全面的空间分析。为研究与衰老相关的转录组变化，本研究收集了成年（4月龄）与老年（23月龄）野生型C57BL/6小鼠的脑组织样本，每个年龄组设置3次生物学重复。