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从单细胞转录组学数据中解读细胞命运决定的驱动调节器,使用CEFCON

Peizhuo Wang^1,2, Xiao Wen³, Han Li¹

¹Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China.

Nature communications

|December 20, 2023

概括

一个新的网络框架CEFCON准确地推断基因调节网络,并从单细胞RNA测序数据中确定控制细胞命运决定的驱动因素,从而推进细胞系谱映射. 这个工具提供了对细胞分化机制的关键见解.

科学领域:

计算生物学计算生物学
基因组学就是基因组学.
系统生物学系统生物学

背景情况:

单细胞技术促进了动态细胞命运映射.
鉴定基因调节网络和细胞命运决定中的驱动因素仍然具有挑战性.

研究的目的:

介绍CEFCON,一种基于网络的框架,用于从单细胞RNA测序 (scRNA-seq) 数据中推断基因调节网络 (GRNs) 和识别细胞命运决定的驱动调节者.
使用网络控制理论建模细胞命运动态,揭示与细胞状态相关的关键生物过程.

主要方法:

利用带有注意力机制的图形神经网络,从scRNA-seq数据中构建细胞系特异的GRN.
应用网络控制理论来建模细胞命运动态,并识别驱动器调节器和基因模块.
对GRN和驾驶员监管器识别的基线方法进行了广泛的基准测试.

主要成果:

与现有方法相比,CEFCON在GRN构建,驱动器调节器识别和基因模块识别方面表现出卓越的表现.
应用于小鼠造血干细胞分化,CEFCON确定了三个发育谱系的关键驱动调节者.
识别的监管机构提供了对干细胞分化的网络控制见解.

结论:

CEFCON是使用scRNA-seq数据剖析细胞命运决定背后的机制的强大工具.
该框架增强了对基因调控动态和细胞分化驱动因素的理解.

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