Single nucleus RNA-Seq is not suitable for detection of microglial activation genes in humans

Single nucleus RNA-Seq (snRNA-Seq) is used as an alternative to single cell RNA-Seq, as it allows transcriptomic profiling of frozen tissue. However, it is unclear whether snRNA-Seq is able to detect cellular state in human tissue. Indeed, snRNA-Seq analyses of human brain samples have failed to detect a consistent microglial activation signature in Alzheimer's Disease. Our comparison of microglia from single cells and single nuclei of four human subjects revealed that, while the majority of genes showed similar relative abundances in cells and nuclei, a small population of genes (~1%) was depleted in nuclei compared to whole cells. This population was enriched for genes previously implicated in microglial activation, including APOE, CST3, SPP1, and CD74, comprising 18% of previously-identified microglial disease-associated genes. Given the low sensitivity of snRNA-Seq to detect many activation genes, we conclude that snRNA-Seq is not suited to detecting cellular activation in microglia in human disease. Overall design: Single nucleus and single cell sequencing of cortical tissue from 4 neurosurgical patients.

单细胞核RNA测序（Single nucleus RNA-Seq，snRNA-Seq）作为单细胞RNA测序（Single cell RNA-Seq）的替代技术，可对冰冻组织开展转录组谱分析。然而，目前尚不清楚snRNA-Seq能否检测人类组织中的细胞状态。
事实上，针对人类大脑样本的snRNA-Seq分析未能在阿尔茨海默病中检测到一致的小胶质细胞激活特征。
本研究对4名人类受试者的单细胞与单细胞核来源的小胶质细胞进行比较分析后发现：尽管绝大多数基因在细胞与细胞核内的相对表达量趋于一致，但一小部分基因（约占总基因的1%）在细胞核中的表达量相较于完整细胞显著降低。
该低表达基因群富集了此前被证实与小胶质细胞激活相关的基因，包括APOE、CST3、SPP1及CD74，这类基因占此前已鉴定的小胶质细胞疾病相关基因的18%。
鉴于snRNA-Seq在检测众多激活相关基因时灵敏度不足，本研究得出结论：snRNA-Seq不适用于检测人类疾病中小胶质细胞的细胞激活状态。
实验整体设计：对4名神经外科患者的大脑皮层组织开展单细胞核与单细胞测序。