瑞士洛桑大学Giovanni Ciriello研究小组发现，CellCharter可揭示与组织重塑和细胞可塑性相关的空间细胞微环境。相关论文于2023年12月8日在线发表在《自然—遗传学》杂志上。

研究人员介绍一种算法框架CellCharter，用于识别、描述和比较空间解析数据集中的细胞微环境。CellCharter的表现优于现有方法，它能在使用不同技术生成的数据集（包括数百个样本和数百万个细胞）中有效识别细胞微环境。在多个人类肺癌队列中，CellCharter发现了由肿瘤相关中性粒细胞和表达缺氧和细胞迁移标记的癌细胞组成的细胞微环境。这种癌细胞状态在空间上与增殖性更强的肿瘤细胞簇隔离，并与肿瘤相关中性粒细胞浸润和独立患者队列中的不良预后有关。

总之，CellCharter可以进行跨数据类型和技术的系统分析，以解读空间组织结构与细胞可塑性之间的联系。

据了解，组织以细胞微环境为单位，其组成和相互作用可通过空间全息技术进行研究。然而，组织构成的系统分析却受到数据规模和多样性的挑战。

附：英文原文

Title: CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity

Author: Varrone, Marco, Tavernari, Daniele, Santamaria-Martnez, Albert, Walsh, Logan A., Ciriello, Giovanni

Issue&Volume: 2023-12-08

Abstract: Tissues are organized in cellular niches, the composition and interactions of which can be investigated using spatial omics technologies. However, systematic analyses of tissue composition are challenged by the scale and diversity of the data. Here we present CellCharter, an algorithmic framework to identify, characterize, and compare cellular niches in spatially resolved datasets. CellCharter outperformed existing approaches and effectively identified cellular niches across datasets generated using different technologies, and comprising hundreds of samples and millions of cells. In multiple human lung cancer cohorts, CellCharter uncovered a cellular niche composed of tumor-associated neutrophil and cancer cells expressing markers of hypoxia and cell migration. This cancer cell state was spatially segregated from more proliferative tumor cell clusters and was associated with tumor-associated neutrophil infiltration and poor prognosis in independent patient cohorts. Overall, CellCharter enables systematic analyses across data types and technologies to decode the link between spatial tissue architectures and cell plasticity.

DOI: 10.1038/s41588-023-01588-4

Source: https://www.nature.com/articles/s41588-023-01588-4