Despite important advances in studying experimental and clinical acute kidney injury (AKI), the pathogenesis of this disease remains incompletely understood. Single cell sequencing studies have closed this knowledge gap by characterizing the transcriptomic signature of different cell types within the kidney. However, the spatial distribution of injury can be regional and affect cells heterogeneously. We first optimized coordination of spatial transcriptomics and single nuclear sequencing datasets, mapping 30 dominant cell types to a human nephrectomy sample. The predicted cell type spots corresponded with the underlying hematoxylin and eosin histopathology. To study the implications of acute kidney injury on the distribution of transcript expression, we then characterized the spatial transcriptomic signature of two murine AKI models: ischemia reperfusion injury (IRI) and cecal ligation puncture (CLP). Localized regions of reduced overall expression were found associated with tissue injury pathways. Using single cell sequencing, we deconvoluted the signature of each spatial transcriptomic spot, identifying patterns of colocalization between immune and epithelial cells. As expected, neutrophils infiltrated the renal medullary outer stripe in the ischemia model. Atf3 was identified as a chemotactic factor in S3 proximal tubule cells. In the CLP model, infiltrating macrophages dominated the outer cortical signature and Mdk was identified as a corresponding chemotactic factor. The regional distribution of these immune cells was validated with multiplexed CO-Detection by inDEXing (CODEX) immunofluorescence. Spatial transcriptomic sequencing can aid in uncovering the mechanisms driving immune cell infiltration and allow detection of relevant subpopulations in single cell sequencing. The complementarity of these technologies facilitates the development of a transcriptomic kidney atlas in health and disease.

中文翻译：

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空间转录组学和单细胞测序的整合确定了急性肾损伤中免疫和上皮细胞串扰的潜在表达模式

尽管在研究实验性和临床急性肾损伤（AKI）方面取得了重要进展，但该病的发病机理仍未完全了解。单细胞测序研究通过表征肾脏内不同细胞类型的转录组特征，填补了这一知识鸿沟。但是，损伤的空间分布可能是区域性的，并且会异质地影响细胞。我们首先优化了空间转录组学和单核测序数据集的协调，将30种优势细胞类型映射到人类肾切除术样本。预测的细胞类型斑点对应于潜在的苏木精和曙红组织病理学。为了研究急性肾脏损伤对转录表达的分布的影响，我们然后表征了两种鼠AKI模型的空间转录组特征：缺血再灌注损伤（IRI）和盲肠结扎穿刺（CLP）。发现总表达降低的局部区域与组织损伤途径相关。使用单细胞测序，我们对每个空间转录组斑点的特征进行去卷积，确定免疫细胞和上皮细胞之间共定位的模式。如预期的那样，中性粒细胞浸润在缺血模型的肾髓外条纹中。Atf3被确定为S3近端小管细胞的趋化因子。在CLP模型中，浸润性巨噬细胞占了皮质外信号的主要部分，Mdk被确定为相应的趋化因子。这些免疫细胞的区域分布通过inDEXing（CODEX）免疫荧光技术通过多重CO检测进行了验证。空间转录组测序可以帮助揭示驱动免疫细胞浸润的机制，并允许在单细胞测序中检测相关的亚群。这些技术的互补性促进了健康和疾病方面的转录组肾脏图谱的发展。