小柯机器人

美国德克萨斯大学MD安德森癌症中心Nicholas E. Navin研究组的最新研究揭示了组织中单细胞转录组空间图。2022年3月21日，国际学术期刊《自然-生物技术》发表了这一成果。

研究人员研发一种称为CellTrek的计算方法，它将单细胞RNA测序和空间转录组数据集结合起来，通过共嵌入和度量学习方法实现单细胞空间映射。研究人员使用模拟和原位杂交数据集对CellTrek进行了基准测试，证明了它的准确性和稳健性。然后，研究人员将CellTrek应用于现有小鼠大脑和肾脏的数据集，表明CellTrek可以检测不同细胞类型和细胞状态的拓扑模式。研究人员对两个导管原位癌组织进行了单细胞RNA测序和空间转录组学实验，并应用CellTrek来识别仅在不同导管中存在的肿瘤亚克隆，以及与肿瘤区域相邻特定T细胞的状态。该数据表明，CellTrek可以准确地映射不同组织类型中的单个细胞，以解析它们的空间位置。

据悉，单细胞RNA测序方法可以分析单细胞的转录组，但不能保留空间信息。相反，空间转录组学分析可以分析组织切片中的空间位置关系，但无法达到单细胞分辨率。

附：英文原文

Title: Spatial charting of single-cell transcriptomes in tissues

Author: Wei, Runmin, He, Siyuan, Bai, Shanshan, Sei, Emi, Hu, Min, Thompson, Alastair, Chen, Ken, Krishnamurthy, Savitri, Navin, Nicholas E.

Issue&Volume: 2022-03-21

Abstract: Single-cell RNA sequencing methods can profile the transcriptomes of single cells but cannot preserve spatial information. Conversely, spatial transcriptomics assays can profile spatial regions in tissue sections, but do not have single-cell resolution. Here, we developed a computational method called CellTrek that combines these two datasets to achieve single-cell spatial mapping through coembedding and metric learning approaches. We benchmarked CellTrek using simulation and in situ hybridization datasets, which demonstrated its accuracy and robustness. We then applied CellTrek to existing mouse brain and kidney datasets and showed that CellTrek can detect topological patterns of different cell types and cell states. We performed single-cell RNA sequencing and spatial transcriptomics experiments on two ductal carcinoma in situ tissues and applied CellTrek to identify tumor subclones that were restricted to different ducts, and specific T cell states adjacent to the tumor areas. Our data show that CellTrek can accurately map single cells in diverse tissue types to resolve their spatial organization. CellTrek maps single cells to their spatial coordinates in tissues.

DOI: 10.1038/s41587-022-01233-1

Source: https://www.nature.com/articles/s41587-022-01233-1

Nature Biotechnology：《自然—生物技术》，创刊于1996年。隶属于施普林格·自然出版集团，最新IF：68.164
官方网址：https://www.nature.com/nbt/
投稿链接：https://mts-nbt.nature.com/cgi-bin/main.plex