Vonficht Dominik, Jopp-Saile Lea, Yousefian Schayan, Flore Viktoria, Simó Vesperinas Inés, Teuber Ruth, Avanesyan Bogdan, Luo Yanjiang, Röthemeier Caroline, Grünschläger Florian, Fernandez-Vaquero Mirian, Fregona Vincent, Ordoñez-Rueda Diana, Schmalbrock Laura K, Deininger Luca, Yamachui Sitcheu Angelo Jovin, Gu Zuguang, Funk Maja C, Mikut Ralf, Heikenwälder Mathias, Eggert Angelika, von Stackelberg Arend, Kobold Sebastian, Krönke Jan, Keller Ulrich, Trumpp Andreas, Hegazy Ahmed N, Eckert Cornelia, Hübschmann Daniel, Haas Simon
Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany.
Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
Nat Methods. 2025 Aug 7. doi: 10.1038/s41592-025-02744-w.
Cellular interactions are of fundamental importance, orchestrating organismal development, tissue homeostasis and immunity. Recently, powerful methods that use single-cell genomic technologies to dissect physically interacting cells have been developed. However, these approaches are characterized by low cellular throughput, long processing times and high costs and are typically restricted to predefined cell types. Here we introduce Interact-omics, a cytometry-based framework to accurately map cellular landscapes and cellular interactions across all immune cell types at ultra-high resolution and scale. We demonstrate the utility of our approach to study kinetics, mode of action and personalized response prediction of immunotherapies, and organism-wide shifts in cellular composition and cellular interaction dynamics following infection in vivo. Our scalable framework can be applied a posteriori to existing cytometry datasets or incorporated into newly designed cytometry-based studies to map cellular interactions with a broad range of applications from fundamental biology to applied biomedicine.
细胞间相互作用至关重要，它协调着机体发育、组织稳态和免疫。最近，已开发出利用单细胞基因组技术剖析物理相互作用细胞的强大方法。然而，这些方法存在细胞通量低、处理时间长和成本高的特点，并且通常局限于预定义的细胞类型。在此，我们介绍Interact-omics，这是一种基于流式细胞术的框架，能够以超高分辨率和规模精确绘制所有免疫细胞类型的细胞图谱和细胞间相互作用。我们展示了我们的方法在研究免疫疗法的动力学、作用方式和个性化反应预测，以及体内感染后机体范围内细胞组成和细胞相互作用动态变化方面的效用。我们可扩展的框架可事后应用于现有的流式细胞术数据集，或纳入新设计的基于流式细胞术的研究中，以绘制细胞间相互作用，其具有从基础生物学到应用生物医学的广泛应用。
