Dupuis Louise, Debeaupuis Orianne, Simon Franck, Isambert Hervé
CNRS UMR168, Institut Curie, 75005 Paris, France.
Inserm U1163, Institut Imagine, 75005 Paris, France.
Nucleic Acids Res. 2025 Jul 7;53(W1):W125-W131. doi: 10.1093/nar/gkaf404.
Understanding cell-cell communication (CCC) pathways from single-cell or spatial transcriptomic data is key to unraveling biological processes. Recently, multiple CCC methods have been developed but primarily focus on refining ligand-receptor (L-R) interaction scores. A critical gap for a more comprehensive picture of cellular crosstalks lies in the integration of upstream and downstream intracellular pathways in the sender and receiver cells. We report here CausalCCC, https://miic.curie.fr/causalCCC.php, an interactive web server, which addresses this need by reconstructing gene-gene interaction pathways across two or more interacting cell types from single-cell or spatial transcriptomic data. CausalCCC includes a graphical introduction and a demo dataset within the workbench page as well as a comprehensive tutorial. CausalCCC methodology integrates a robust and scalable causal network reconstruction method, multivariate information-based inductive causation, with internally computed L-R pairs using LIANA+ (including CellphoneDBv5, SingleCellSignalR, Connectome, NATMI, and Log2FC). Alternatively, user-defined L-R pairs from any CCC methods can also be uploaded. We showcase here CausalCCC on different single-cell and spatial transcriptomic datasets from three original CCC methods (NicheNet, CellChat, and Misty). CausalCCC web server offers unique interactive visualization tools dedicated to single-cell data practitioners seeking to go beyond L-R scores and explore extended CCC pathways across multiple interacting cell types.
从单细胞或空间转录组数据中理解细胞间通信(CCC)途径是揭示生物学过程的关键。最近,已经开发了多种CCC方法,但主要集中在优化配体-受体(L-R)相互作用得分上。对于更全面了解细胞间串扰而言,一个关键差距在于整合发送细胞和接收细胞中上游和下游细胞内途径。我们在此报告CausalCCC,网址为https://miic.curie.fr/causalCCC.php,这是一个交互式网络服务器,它通过从单细胞或空间转录组数据中重建两种或更多相互作用细胞类型之间的基因-基因相互作用途径来满足这一需求。CausalCCC在工作台页面中包括图形介绍和演示数据集以及全面的教程。CausalCCC方法将一种强大且可扩展的因果网络重建方法——基于多变量信息的归纳因果关系,与使用LIANA+(包括CellphoneDBv5、SingleCellSignalR、Connectome、NATMI和Log2FC)内部计算的L-R对相结合。或者,也可以上传来自任何CCC方法的用户定义L-R对。我们在此展示了CausalCCC在来自三种原始CCC方法(NicheNet、CellChat和Misty)的不同单细胞和空间转录组数据集上的应用。CausalCCC网络服务器为寻求超越L-R得分并探索多种相互作用细胞类型之间扩展CCC途径的单细胞数据从业者提供了独特的交互式可视化工具。
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