Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
10X Genomics, Pleasanton, CA, USA.
Nat Commun. 2024 Feb 15;15(1):1396. doi: 10.1038/s41467-024-45752-8.
Emerging spatially resolved transcriptomics technologies allow for the measurement of gene expression in situ at cellular resolution. We apply direct RNA hybridization-based in situ sequencing (dRNA HybISS, Cartana part of 10xGenomics) to compare male and female healthy mouse kidneys and the male kidney injury and repair timecourse. A pre-selected panel of 200 genes is used to identify cell state dynamics patterns during injury and repair. We develop a new computational pipeline, CellScopes, for the rapid analysis, multi-omic integration and visualization of spatially resolved transcriptomic datasets. The resulting dataset allows us to resolve 13 kidney cell types within distinct kidney niches, dynamic alterations in cell state over the course of injury and repair and cell-cell interactions between leukocytes and kidney parenchyma. At late timepoints after injury, C3+ leukocytes are enriched near pro-inflammatory, failed-repair proximal tubule cells. Integration of snRNA-seq dataset from the same injury and repair samples also allows us to impute the spatial localization of genes not directly measured by dRNA HybISS.
新兴的空间分辨转录组学技术可实现细胞分辨率下原位基因表达的测量。我们应用基于直接 RNA 杂交的原位测序 (dRNA HybISS，10xGenomics 的 Cartana 部分) 来比较健康雄性和雌性小鼠的肾脏以及雄性肾脏损伤和修复的时间过程。使用预先选择的 200 个基因面板来鉴定损伤和修复过程中的细胞状态动力学模式。我们开发了一种新的计算管道 CellScopes，用于快速分析、多组学整合和可视化空间分辨转录组数据集。由此产生的数据集使我们能够在不同的肾脏龛位中分辨出 13 种肾脏细胞类型、损伤和修复过程中细胞状态的动态变化以及白细胞和肾脏实质之间的细胞间相互作用。在损伤后晚期，C3+白细胞在富含促炎的、修复失败的近端肾小管细胞附近富集。对同一损伤和修复样本的 snRNA-seq 数据集进行整合还使我们能够推断未直接通过 dRNA HybISS 测量的基因的空间定位。
