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<p>MicroRNAs are released from cells in extracellular vesicles (EVs), representing an essential mode of cell–cell communication (CCC) via a regulatory effect on gene expression. Single-cell RNA-sequencing technologies have ushered in an era of elucidating CCC at single-cell resolution. Herein, we present miRTalk, a pioneering approach for inferring CCC mediated by EV-derived miRNA-target interactions (MiTIs). The benchmarking against simulated and real-world datasets demonstrates the superior performance of miRTalk, and the application to four disease scenarios reveals the in-depth MiTI-mediated CCC mechanisms. Collectively, miRTalk can infer EV-derived MiTI-mediated CCC with scRNA-seq data, providing new insights into the intercellular dynamics of biological processes.</p>

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Extracellular vesicle-derived miRNA-mediated cell–cell communication inference for single-cell transcriptomic data with miRTalk

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年4月14日

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  • Xin Shao,
  • Lingqi Yu,
  • Chengyu Li,
  • Jingyang Qian,
  • Xinyu Yang,
  • Haihong Yang,
  • Jie Liao,
  • Xueru Fan,
  • Xiao Xu,
  • Xiaohui Fan

摘要

MicroRNAs are released from cells in extracellular vesicles (EVs), representing an essential mode of cell–cell communication (CCC) via a regulatory effect on gene expression. Single-cell RNA-sequencing technologies have ushered in an era of elucidating CCC at single-cell resolution. Herein, we present miRTalk, a pioneering approach for inferring CCC mediated by EV-derived miRNA-target interactions (MiTIs). The benchmarking against simulated and real-world datasets demonstrates the superior performance of miRTalk, and the application to four disease scenarios reveals the in-depth MiTI-mediated CCC mechanisms. Collectively, miRTalk can infer EV-derived MiTI-mediated CCC with scRNA-seq data, providing new insights into the intercellular dynamics of biological processes.