Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging.
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging.
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DOI：
10.1038/s41592-022-01673-2
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发表时间：
2022-12
期刊：
影响因子：
48
通讯作者：
Lin, Charles P.
中科院分区：
文献类型：
--
作者：
Haase, Christa;Gustafsson, Karin;Mei, Shenglin;Yeh, Shu-Chi;Richter, Dmitry;Milosevic, Jelena;Turcotte, Raphael;Kharchenko, Peter, V;Sykes, David B.;Scadden, David T.;Lin, Charles P.
组织功能取决于细胞组织。虽然单个细胞的特性越来越多地被强大的单细胞测序技术破译，但了解它们的空间组织和时间演变仍然是一个重大挑战。在这里，我们介绍了Image-seq，这是一种技术，它提供了在图像引导下从特定空间位置分离的细胞的单细胞转录数据，从而保留了靶细胞的空间信息。它与原位和体内成像兼容，可以记录被分析细胞的时间和动态历史。从完整组织中分离细胞样品，并采用最先进的文库制备方案进行处理。因此，该技术将空间信息与来自单个完整细胞的高灵敏度RNA测序读数相结合。我们使用了高通量、基于液滴的测序以及SMARTseq-v4文库制备来证明其在骨髓和白血病生物学中的应用。我们发现DPP 4是急性髓细胞白血病早期进展过程中高度上调的基因，它标志着局限于特定骨髓微环境的更具增殖性的亚群。此外，Image-seq分离活的完整细胞的能力应使其与一系列下游单细胞分析工具（包括多组学方案）兼容。Image-seq在图像引导下从特定组织位置分离细胞，以通过单细胞RNA测序进行分析。该技术可以与体内成像相结合，以在测序之前记录细胞的时间和动态历史。
Tissue function depends on cellular organization. While the properties of individual cells are increasingly being deciphered using powerful single-cell sequencing technologies, understanding their spatial organization and temporal evolution remains a major challenge. Here, we present Image-seq, a technology that provides single-cell transcriptional data on cells that are isolated from specific spatial locations under image guidance, thus preserving the spatial information of the target cells. It is compatible with in situ and in vivo imaging and can document the temporal and dynamic history of the cells being analyzed. Cell samples are isolated from intact tissue and processed with state-of-the-art library preparation protocols. The technique therefore combines spatial information with highly sensitive RNA sequencing readouts from individual, intact cells. We have used both high-throughput, droplet-based sequencing as well as SMARTseq-v4 library preparation to demonstrate its application to bone marrow and leukemia biology. We discovered that DPP4 is a highly upregulated gene during early progression of acute myeloid leukemia and that it marks a more proliferative subpopulation that is confined to specific bone marrow microenvironments. Furthermore, the ability of Image-seq to isolate viable, intact cells should make it compatible with a range of downstream single-cell analysis tools including multi-omics protocols. Image-seq isolates cells from specific tissue locations under image guidance for analysis by single-cell RNA sequencing. The technique can be combined with in vivo imaging to document the temporal and dynamic history of the cells prior to sequencing.
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影响因子：
64.5
作者：
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