CytoSignal Detects Locations and Dynamics of Ligand-Receptor Signaling at Cellular Resolution from Spatial Transcriptomic Data (Part 2)

Nearby cells within tissues communicate through ligand-receptor signaling interactions. Emerging spatial transcriptomic technologies provide a tremendous opportunity to systematically detect ligand-receptor signaling, but no method operates at cellular resolution in the spatial context. We developed CytoSignal to infer the locations and dynamics of cell-cell communication at cellular resolution from spatial transcriptomic data. CytoSignal is based on the simple insight that signaling is a protein-protein interaction that occurs at a specific tissue location when ligand and receptor are expressed in close spatial proximity. Our cellular-resolution, spatially-resolved signaling scores allow several novel types of analyses: we identify spatial gradients in signaling strength; separately quantify the locations of contact-dependent and diffusible interactions; and detect signaling-associated differentially expressed genes. Additionally, we can predict the temporal dynamics of a signaling interaction at each spatial location. CytoSignal is compatible with nearly every kind of spatial transcriptomic technology including FISH-based protocols and spot-based protocols without deconvolution. We experimentally validate our results in situ by proximity ligation assay, confirming that CytoSignal scores closely match the tissue locations of ligand-receptor protein-protein interactions. Our work addresses the field's current need for a robust and scalable tool to detect cell-cell signaling interactions and their dynamics at cellular resolution from spatial transcriptomic data.组织内的邻近细胞通过配体-受体（ligand-receptor）信号传导相互作用进行通讯。新兴的空间转录组学（spatial transcriptomic）技术为系统性检测配体-受体信号传导提供了绝佳机遇，但目前尚无方法能够在空间环境下以细胞分辨率（cellular resolution）开展此类分析。 我们开发了CytoSignal工具，旨在从空间转录组学数据中以细胞分辨率推断细胞间通讯的位置与动态过程。CytoSignal的核心逻辑十分简洁：信号传导本质是一种蛋白质-蛋白质相互作用（protein-protein interaction），当配体与受体在空间上紧密邻近表达时，该作用便会在特定组织位置发生。我们提出的细胞分辨率空间解析信号评分支持多种新型分析：可识别信号传导强度的空间梯度；分别量化接触依赖性与可扩散性相互作用的位置；并检测与信号传导相关的差异表达基因（differentially expressed genes）。此外，我们还可预测每个空间位置处信号传导相互作用的时间动态过程。 CytoSignal可兼容几乎所有类型的空间转录组学技术，包括基于荧光原位杂交（FISH）的实验方案与无需解卷积（deconvolution）的基于斑点的实验方案。 我们通过邻近连接试验（proximity ligation assay）在原位对结果进行了实验验证，证实CytoSignal评分与配体-受体蛋白质-蛋白质相互作用的组织位置高度吻合。本研究满足了该领域当前的迫切需求：开发一款稳健且可扩展的工具，能够从空间转录组学数据中以细胞分辨率检测细胞间信号传导相互作用及其动态过程。