威康桑格研究所Mohammad Lotfollahi研究组在研究中取得进展。他们揭示了空间分辨组学数据中细胞龛的定量表征。2025年3月18日出版的《自然—遗传学》杂志发表了这项成果。

为了解决这一问题，该研究组介绍了NicheCompass，这是一种图形深度学习方法，它对细胞通信进行建模，以学习编码信号事件的可解释细胞嵌入，从而能够识别生态位及其底层过程。与现有的方法不同，NicheCompass基于沟通途径定量表征利基，并始终优于其他方法。研究小组通过绘制同主题胚胎发育期间的组织结构和描绘人类癌症的肿瘤龛，包括空间参考制图应用，展示了它的多功能性。最后，该研究组将其功能扩展到空间多组学，展示了与来自不同测序平台的数据集的跨技术集成，并构建了包含840万个细胞的整个无主题大脑空间图谱，突出了NicheCompass的可扩展性。总的来说，NicheCompass提供了一个可扩展的框架，用于通过信号事件识别和分析利基市场。

据悉，空间组学能够表征组织内协调特定功能的共定位细胞群落。这些群落或生态位是由相邻细胞之间的相互作用形成的，然而现有的计算方法很少利用这种相互作用来识别和表征它们。

附：英文原文

Title: Quantitative characterization of cell niches in spatially resolved omics data

Author: Birk, Sebastian, Bonafonte-Pards, Irene, Feriz, Adib Miraki, Boxall, Adam, Agirre, Eneritz, Memi, Fani, Maguza, Anna, Yadav, Anamika, Armingol, Erick, Fan, Rong, Castelo-Branco, Gonalo, Theis, Fabian J., Bayraktar, Omer Ali, Talavera-Lpez, Carlos, Lotfollahi, Mohammad

Issue&Volume: 2025-03-18

Abstract: Spatial omics enable the characterization of colocalized cell communities that coordinate specific functions within tissues. These communities, or niches, are shaped by interactions between neighboring cells, yet existing computational methods rarely leverage such interactions for their identification and characterization. To address this gap, here we introduce NicheCompass, a graph deep-learning method that models cellular communication to learn interpretable cell embeddings that encode signaling events, enabling the identification of niches and their underlying processes. Unlike existing methods, NicheCompass quantitatively characterizes niches based on communication pathways and consistently outperforms alternatives. We show its versatility by mapping tissue architecture during mouse embryonic development and delineating tumor niches in human cancers, including a spatial reference mapping application. Finally, we extend its capabilities to spatial multi-omics, demonstrate cross-technology integration with datasets from different sequencing platforms and construct a whole mouse brain spatial atlas comprising 8.4 million cells, highlighting NicheCompass’ scalability. Overall, NicheCompass provides a scalable framework for identifying and analyzing niches through signaling events.

DOI: 10.1038/s41588-025-02120-6

Source: https://www.nature.com/articles/s41588-025-02120-6