Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq1_LPS_ABX]

Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer's disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration. Overall design: Following either lipopolysaccharide (LPS), antibiotics (ABX), or PBS (N) treatment, microglia from early stage (ES) and late stage (LS) 5xfAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq.

鉴于阿尔茨海默病（Alzheimer's disease, AD）细胞靶向治疗的潜在前景，小胶质细胞的空间异质性仍是一个至关重要却鲜有研究的科学问题。目前学界对与斑块区域相邻或无关联的空间特异性小胶质细胞状态的动态变化，及其在体内对神经退行性变的选择性调控作用仍知之甚少。迄今为止，相关研究主要聚焦于病理相关小胶质细胞。本研究结合新型多色荧光命运图谱技术、单细胞转录组分析、表观遗传谱分析、先进免疫组织化学技术与计算建模方法，全面解析了雌性小鼠神经退行性变过程中斑块相关与非斑块相关小胶质细胞的相互关系。该研究方法使我们得以在阿尔茨海默病小鼠模型中，将非斑块相关小胶质细胞鉴定为一种独特且高度动态的小胶质细胞状态，并对其进行了特征解析。与此前认为其为被动旁观者亚群的认知相反，非斑块相关小胶质细胞可调控病理网络扩张，快速响应环境信号，且其向斑块相关小胶质细胞的转化可在疾病进程中被特异性调控。因此，对空间分隔的小胶质细胞状态动态变化及其独特分子特征的这一解析，有望为神经退行性变阶段的状态特异性治疗干预开辟全新的潜在研究路径。实验整体设计：将小鼠分为脂多糖（lipopolysaccharide, LPS）、抗生素（antibiotics, ABX）及磷酸盐缓冲液（PBS, N）处理组，分别采集早期病程（ES）与晚期病程（LS）的5xfAD阳性及阴性小鼠的小胶质细胞，通过荧光激活细胞分选（fluorescence-activated cell sorting, FACS）进行分选后，采用单细胞RNA测序（single cell RNA seq）进行分析。