Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium.
Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; UK Dementia Research Institute at University College London, University College London, London, UK.
Cell Rep. 2020 Sep 29;32(13):108189. doi: 10.1016/j.celrep.2020.108189.
Single-nucleus RNA sequencing (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 reveals that, although most genes show similar relative abundances in cells and nuclei, a small population of genes (∼1%) is depleted in nuclei compared to whole cells. This population is 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 for detecting cellular activation in microglia in human disease.
单细胞 RNA 测序 (snRNA-seq) 可作为单细胞 RNA 测序的替代方法，因为它可以对冷冻组织进行转录组分析。然而，目前尚不清楚 snRNA-seq 是否能够检测人类组织中的细胞状态。事实上，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。我们比较了来自四个供体的单细胞和单个核的小胶质细胞，结果表明，尽管大多数基因在细胞和核中的相对丰度相似，但一小部分基因（~1%）在核中比在整个细胞中耗竭。这群基因富含先前与小胶质细胞激活有关的基因，包括 APOE、CST3、SPP1 和 CD74，占先前确定的与小胶质细胞疾病相关基因的 18%。鉴于 snRNA-seq 检测许多激活基因的灵敏度较低，我们得出结论，snRNA-seq 不适合用于检测人类疾病中小胶质细胞的细胞激活。
