A cross-disease human microglial framework identifies disease-enriched subsets and tool compounds for microglial polarization.

Human microglia play a pivotal role in neurological diseases, but few targeted therapies that directly modulate microglial state or function exist due to an incomplete understanding of microglial heterogeneity. We use single-cell RNA sequencing to profile live human microglia from autopsies or surgical resections across diverse neurological diseases and central nervous system regions. We observe a central divide between oxidative and heterocyclic metabolism and identify subsets associated with antigen presentation, motility, and proliferation. Specific subsets are enriched in susceptibility genes for neurodegenerative diseases or the disease-associated microglial signature. We validate subtypes in situ with an RNAscope-immunofluorescence pipeline and leverage our dataset as a classification resource, finding that iPSC model systems recapitulate substantial in vivo heterogeneity. Finally, we identify and validate candidates for chemically inducing subtype-specific states in vitro, showing that Camptothecin downregulates the transcriptional signature of disease-enriched subsets and upregulates a signature previously shown to be depleted in Alzheimer’s. Comparative bulk RNA-sequencing data of HMC cells treated with one of several drugs or DMSO control.

人类小胶质细胞（human microglia）在神经系统疾病中发挥关键作用，但由于对小胶质细胞异质性的认知尚不充分，目前可直接调控小胶质细胞状态与功能的靶向治疗方案极为匮乏。本研究采用单细胞RNA测序（single-cell RNA sequencing）技术，对来自多种神经系统疾病患者的尸检或手术切除样本中的存活人类小胶质细胞进行转录组分析，覆盖多个中枢神经系统（central nervous system）区域。研究观察到氧化代谢与杂环代谢之间存在核心分化差异，并鉴定出与抗原呈递、细胞运动及增殖相关的小胶质细胞亚群。部分特异性亚群富集神经退行性疾病易感基因，或呈现疾病相关小胶质细胞特征谱。我们通过RNAscope-免疫荧光（RNAscope-immunofluorescence）联用体系对上述亚群进行了原位验证，并将本数据集作为分类参考资源，证实诱导多能干细胞（induced pluripotent stem cell, iPSC）模型可复现体内大量的小胶质细胞异质性。最后，我们筛选并验证了可在体外诱导亚型特异性状态的化学候选化合物，实验表明喜树碱（Camptothecin）可下调疾病富集亚群的转录特征谱，并上调此前被证实于阿尔茨海默病（Alzheimer’s disease）中表达缺失的特征谱。本数据集同时包含经数种药物或二甲基亚砜（DMSO）对照处理的人类小胶质细胞（HMC）的批量RNA测序对比数据。