瑞典卡洛琳卡学院Martin Enge课题组开发出复杂组织中细胞相互作用分析的无监督方法。相关论文于2021年7月12日在线发表在《自然—方法学》杂志上。

研究人员开发出一种细胞相互作用的多重测序（CIM-SEQ），这是一种无监督的高通量方法，可用于分析组织中细胞类型之间的直接物理相互作用。CIM-SEQ基于未完全解离细胞的RNA测序，然后进行计算成分细胞类型。CIM-SEQ直接从排序数据中估计每个多功能集中的单元格数和单元格类型，使其与基于高吞吐量的液滴的方法兼容。

当应用于肠道上皮或整个肺和脾脏时，CIM-SEQ正确识别出已知的相互作用，包括不同细胞谱系和免疫细胞之间的相互作用。在结肠中，CIM-SEQ鉴定了表达伤口愈合标记PLET1的杯状细胞新亚型，其直接与结肠干细胞相邻。这些结果表明，CIM-SEQ广泛适用于不同组织类型中细胞型相互作用的无监督分析。 

据了解，复杂多细胞生物中的细胞同一性部分由细胞的物理组织确定。然而，大规模调查细胞蛋白酶仍然在技术上具有挑战性。

附：英文原文

Title: An unsupervised method for physical cell interaction profiling of complex tissues

Author: Nathanael Andrews, Jason T. Serviss, Natalie Geyer, Agneta B. Andersson, Ewa Dzwonkowska, Iva utevski, Rosan Heijboer, Ninib Baryawno, Marco Gerling, Martin Enge

Issue&Volume: 2021-07-12

Abstract: Cellular identity in complex multicellular organisms is determined in part by the physical organization of cells. However, large-scale investigation of the cellular interactome remains technically challenging. Here we develop cell interaction by multiplet sequencing (CIM-seq), an unsupervised and high-throughput method to analyze direct physical cell–cell interactions between cell types present in a tissue. CIM-seq is based on RNA sequencing of incompletely dissociated cells, followed by computational deconvolution into constituent cell types. CIM-seq estimates parameters such as number of cells and cell types in each multiplet directly from sequencing data, making it compatible with high-throughput droplet-based methods. When applied to gut epithelium or whole dissociated lung and spleen, CIM-seq correctly identifies known interactions, including those between different cell lineages and immune cells. In the colon, CIM-seq identifies a previously unrecognized goblet cell subtype expressing the wound-healing marker Plet1, which is directly adjacent to colonic stem cells. Our results demonstrate that CIM-seq is broadly applicable to unsupervised profiling of cell-type interactions in different tissue types.

DOI: 10.1038/s41592-021-01196-2

Source: https://www.nature.com/articles/s41592-021-01196-2