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在单细胞分辨率下从空间奥米克数据中识别和描述组织中的细胞

Jingyang Qian^1,2, Xin Shao^3,4,5, Hudong Bao¹

¹College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.

Nature communications

|February 16, 2025

概括

scNiche是一个新的计算框架,用于使用空间奥米克数据识别细胞. 它准确地描述了细胞微环境,并且在疾病和正常组织分析中优于现有的方法.

科学领域:

计算生物学计算生物学
空间奥米克斯空间奥米克斯
细胞微环境细胞微环境

背景情况:

了解组织中的细胞利基至关重要,但具有挑战性.
空间奥米克数据为细胞社区提供了新的见解.

研究的目的:

介绍scNiche,一个用于细胞利基识别的计算框架.
以单细胞分辨率从空间奥米克数据中描述细胞.

主要方法:

开发了scNiche,一个计算框架.
使用模拟和生物数据集 (空间蛋白质组学,空间转录组学) 的基准 scNiche.
应用 scNiche 对人类三阴性乳腺癌和小鼠肝脏组织.

主要成果:

scNiche 能够有效且稳定地识别细胞.
scNiche的性能优于现有的方法.
揭示了微环境对乳腺癌细胞表型的影响.
剖析了特定患者的利基,并发现了特定疾病的肝损伤利基.

结论:

scNiche 能够从单细胞空间奥米克数据解码细胞微环境.
在不同组织和条件中识别和表征细胞方面表现出强大的表现.

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