Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer's Disease

While complex inflammatory-like alterations are observed around the amyloid plaques of Alzheimer disease (AD), little is known about the molecular changes and cellular interactions that characterize this response. We investigate here in an AD mouse model the transcriptional changes occurring in tissue domains of 100 um diameter around the amyloid plaques using spatial transcriptomics. We demonstrate early alterations in a gene co-expression network enriched for myelin and oligodendrocyte genes (OLIG), while a multicellular gene co- expression network of Plaque-Induced Genes (PIGs) involving the complement system, oxidative stress, lysosomes and inflammation is prominent in the later phase of the disease. We confirm the majority of the observed alterations at the cellular level using in situ sequencing on mouse and human brain sections. Genome-wide spatial transcriptomic analysis provides an unprecedented approach to untangle the dysregulated cellular network in the vicinity of pathogenic hallmarks of AD and other brain diseases. In situ 2D-RNAseq via Spatial Transcriptomics on coronal section of AppNL-G-F KI mice and C57Bl/6J mice at 3,6,12 and 18 months of age.尽管阿尔茨海默病（Alzheimer Disease, AD）的淀粉样斑块周围已观测到复杂的类炎症样改变，但目前学界对该反应所特有的分子变化与细胞互作机制仍知之甚少。本研究借助空间转录组学（Spatial Transcriptomics）技术，在阿尔茨海默病小鼠模型中，对淀粉样斑块周围100微米直径的组织区域内的转录组变化展开分析。研究发现，髓鞘与少突胶质细胞基因（OLIG）富集的基因共表达网络存在早期改变；而包含补体系统（complement system）、氧化应激（oxidative stress）、溶酶体（lysosomes）与炎症通路的斑块诱导基因（Plaque-Induced Genes, PIGs）多细胞基因共表达网络，则在疾病晚期阶段表现显著。本研究通过对小鼠与人类脑组织切片开展原位测序（in situ sequencing），在细胞层面验证了绝大多数观测到的转录改变。全基因组空间转录组学分析为厘清阿尔茨海默病及其他脑部疾病致病特征周边的失调细胞互作网络提供了前所未有的研究途径。本研究采用基于空间转录组学的原位二维RNA测序技术，对3、6、12及18月龄的AppNL-G-F敲入（KI，Knock-in）小鼠与C57BL/6J小鼠的冠状脑切片进行了检测。