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arXiv 2512.03497q-bio.QMcs.AIq-bio.CB
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细胞间通讯的推断与分析：生物机制、计算方法及未来机遇

Cell-cell Communication Inference and Analysis: Biological Mechanisms, Computational Approaches, and Future Opportunities

School of Mathematics and Statistics（数学与统计学学院）；NSF-Simons Center for Multiscale Cell Fate Research（多尺度细胞命运研究NSF-Simons中心）；Department of Mathematics（数学系）；Department of Developmental and Cell Biology（发育与细胞生物学系）

Xiangzheng Cheng, Haili Huang, Ye Su, Qing Nie, Xiufen Zou, Suoqin Jin

备注：
Published in CSIAM Transactions on Life Sciences (2026)
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AI总结：

本文综述了细胞间通讯的生物机制与计算方法，介绍超过140种推断方法，并讨论了该领域面临的挑战与未来机遇。

摘要：

在多细胞生物中，细胞通过细胞间通讯（CCC）协调活动，这对于发育、组织稳态和疾病进展至关重要。近年来，单细胞和空间组学技术的进步为系统推断和分析CCC提供了前所未有的机会，无论是通过整合配体-受体相互作用（LRIs）的先验知识，还是通过从头方法。已开发出多种计算方法，聚焦于方法学创新、复杂信号机制的精确建模以及更广泛的生物学问题研究。这些进展显著增强了我们分析CCC和生成生物学假设的能力。本文介绍了CCC的生物机制和建模策略，并概述了超过140种从单细胞和空间转录组数据推断CCC的计算方法，强调了方法学框架和生物学问题的多样性。最后，讨论了该领域快速发展的挑战和未来机遇，并通过交互式在线资源（https://cellchat.whu.edu.cn）总结了可用方法，以促进更高效的比较和选择。

英文摘要：

In multicellular organisms, cells coordinate their activities through cell-cell communication (CCC), which is crucial for development, tissue homeostasis, and disease progression. Recent advances in single-cell and spatial omics technologies provide unprecedented opportunities to systematically infer and analyze CCC from these omics data, either by integrating prior knowledge of ligand-receptor interactions (LRIs) or through de novo approaches. A variety of computational methods have been developed, focusing on methodological innovations, accurate modeling of complex signaling mechanisms, and investigation of broader biological questions. These advances have greatly enhanced our ability to analyze CCC and generate biological hypotheses. Here, we introduce the biological mechanisms and modeling strategies of CCC, and provide a focused overview of more than 140 computational methods for inferring CCC from single-cell and spatial transcriptomic data, emphasizing the diversity in methodological frameworks and biological questions. Finally, we discuss the current challenges and future opportunities in this rapidly evolving field, and summarize available methods in an interactive online resource (https://cellchat.whu.edu.cn) to facilitate more efficient method comparison and selection.

机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。

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