217 shared genes in DEGs related to human age.

ObjectiveTo guide animal experiments, we investigated the similarities and differences between humans and mice in aging and Alzheimer’s disease (AD) at the single-nucleus RNA sequencing (snRNA-seq) or single-cell RNA sequencing (scRNA-seq) level.MethodsMicroglia cells were extracted from dataset GSE198323 of human post-mortem hippocampus. The distributions and proportions of microglia subpopulation cell numbers related to AD or age were compared. This comparison was done between GSE198323 for humans and GSE127892 for mice, respectively. The Seurat R package and harmony R package were used for data analysis and batch effect correction. Differentially expressed genes (DEGs) were identified by FindMarkers function with MAST test. Comparative analyses were conducted on shared genes in DEGs associated with age and AD. The analyses were done between human and mouse using various bioinformatics techniques. The analysis of genes in DEGs related to age was conducted. Similarly, the analysis of genes in DEGs related to AD was performed. Cross-species analyses were conducted using orthologous genes. Comparative analyses of pseudotime between humans and mice were performed using Monocle2.Results(1) Similarities: The proportion of microglial subpopulation Cell_APOE/Apoe shows consistent trends, whether in AD or normal control (NC) groups in both humans and mice. The proportion of Cell_CX3CR1/Cx3cr1, representing homeostatic microglia, remains stable with age in NC groups across species. Tuberculosis and Fc gamma R-mediated phagocytosis pathways are shared in microglia responses to age and AD across species, respectively. (2) Differences: IL1RAPL1 and SPP1 as marker genes are more identifiable in human microglia compared to their mouse counterparts. Most genes of DEGs associated with age or AD exhibit different trends between humans and mice. Pseudotime analyses demonstrate varying cell density trends in microglial subpopulations, depending on age or AD across species.ConclusionsMouse Apoe and Cell_Apoe maybe serve as proxies for studying human AD, while Cx3cr1 and Cell_Cx3cr1 are suitable for human aging studies. However, AD mouse models (App_NL_G_F) have limitations in studying human genes like IL1RAPL1 and SPP1 related to AD. Thus, mouse models cannot fully replace human samples for AD and aging research.

研究目的 为指导动物实验开展，我们在单细胞核RNA测序（single-nucleus RNA sequencing, snRNA-seq）或单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）层面，探究了人类与小鼠在衰老及阿尔茨海默病（Alzheimer’s disease, AD）中的异同。研究方法 我们从人类死后海马体数据集GSE198323中提取小胶质细胞（microglia）。分别以人类数据集GSE198323与小鼠数据集GSE127892为研究对象，对比与AD或衰老相关的小胶质细胞亚群的分布特征及细胞数量占比。采用Seurat R包与harmony R包进行数据分析及批次效应校正。通过FindMarkers函数结合MAST检验识别差异表达基因（differentially expressed genes, DEGs）。针对与衰老和AD相关的DEGs中的共有基因，我们采用多种生物信息学技术开展人类与小鼠的跨物种对比分析，并分别对衰老相关DEGs及AD相关DEGs中的基因进行解析。利用同源基因开展跨物种分析，并通过Monocle2对人类与小鼠的拟时间序列进行对比分析。研究结果 (1) 相似性：无论在人类还是小鼠中，小胶质细胞亚群Cell_APOE/Apoe的占比在AD组与正常对照组（normal control, NC）中均呈现一致的变化趋势。代表稳态小胶质细胞的Cell_CX3CR1/Cx3cr1亚群占比，在跨物种的正常对照组中随衰老进程保持稳定。跨物种中小胶质细胞对衰老与AD的应答分别共享结核相关通路与FcγR介导的吞噬通路。(2) 差异性：与小鼠相比，IL1RAPL1和SPP1作为标记基因在人类小胶质细胞中更具识别性。绝大多数与衰老或AD相关的DEGs在人类与小鼠中呈现不同的表达趋势。拟时间序列分析显示，跨物种间小胶质细胞亚群的细胞密度变化趋势因衰老或AD状态而异。研究结论 小鼠Apoe及Cell_Apoe或可作为研究人类AD的替代模型，而Cx3cr1及Cell_Cx3cr1则适用于人类衰老相关研究。然而，AD小鼠模型（App_NL_G_F）在研究人类AD相关基因如IL1RAPL1和SPP1时存在局限性。因此，小鼠模型无法完全替代人类样本用于AD与衰老相关研究。