Universal recording of immune cell interactions in vivo. Universal recording of immune cell interactions in vivo

Immune cells rely on transient physical interactions with other immune and non-immune populations to regulate their function. To study these “kiss-and-run” interactions directly in vivo, we previously developed LIPSTIC (Labeling Immune Partnerships by SorTagging Intercellular Contacts), an approach that uses enzymatic transfer of a labeled substrate between the molecular partners CD40L and CD40 to label interacting cells. Reliance on this pathway limited the use of LIPSTIC to measuring interactions between CD4+ helper T cells and antigen presenting cells, however. Here, we report the development of a universal version of LIPSTIC (uLIPSTIC), which can record physical interactions both among immune cells and between immune and non-immune populations irrespective of the receptors and ligands involved. We show that uLIPSTIC can be used, among other things, to monitor the priming of CD8+ T cells by dendritic cells, reveal the steady-state cellular partners of regulatory T (Treg) cells, and identify germinal center (GC)-resident T follicular helper (Tfh) cells based on their ability to interact cognately with GC B cells. By coupling uLIPSTIC with single-cell transcriptomics, we build a catalog of the immune populations that physically interact with intestinal epithelial cells (IECs) at steady state and profile the evolution of the interactome of lymphocytic choriomeningitis virus (LCMV)-specific CD8+ T cells in multiple organs upon systemic infection. Thus, uLIPSTIC provides a broadly useful technology for measuring and understanding cell–cell interactions across multiple biological systems. Overall design: uLIPSTIC interaction-dependent transcriptomics of the immune interacting partners of intestinal epithelial cells in steady-state mice and of LCMV-specific (P14) CD8+ T cells upon infection with lymphocytic choriomeningitis virus (LCMV) Armstrong cells in mediastinal lymph nodes, spleen, liver, and lung. Please note that the HTO, Barcode sequence, and hashtagged sample information is included in the 'readme.txt'.

免疫细胞通过与其他免疫及非免疫群体发生瞬时物理相互作用，调控自身功能。为在体内直接研究这类“亲吻-跑开”式细胞相互作用，我们此前开发了LIPSTIC（Labeling Immune Partnerships by SorTagging Intercellular Contacts），该技术通过分子伴侣CD40L与CD40之间的标记底物酶促转移，对发生相互作用的细胞进行标记。然而，该技术依赖特定通路，这使得LIPSTIC仅能用于检测CD4+辅助T细胞与抗原呈递细胞之间的相互作用。本研究报道了通用版LIPSTIC（uLIPSTIC）的开发，该技术可记录免疫细胞之间，以及免疫与非免疫群体之间的物理相互作用，且不受所涉及受体和配体的限制。我们证实，uLIPSTIC可用于诸多场景，例如监测树突状细胞对CD8+ T细胞的致敏过程，揭示调节性T细胞（regulatory T cells, Treg）在稳态下的细胞互作伴侣，以及根据与生发中心（germinal center, GC）B细胞发生特异性认知相互作用的能力，识别驻留于生发中心的滤泡辅助T细胞（T follicular helper, Tfh）。通过将uLIPSTIC与单细胞转录组学相结合，我们构建了稳态下与肠道上皮细胞（intestinal epithelial cells, IECs）发生物理相互作用的免疫群体目录，并解析了全身感染后，淋巴细胞性脉络丛脑膜炎病毒（lymphocytic choriomeningitis virus, LCMV）特异性CD8+ T细胞在多个器官中的互作组演化轨迹。综上，uLIPSTIC为跨多个生物系统的细胞间相互作用的检测与研究提供了一项广泛适用的技术。

实验整体设计：对稳态小鼠中与肠道上皮细胞发生互作的免疫伴侣细胞，以及经淋巴细胞性脉络丛脑膜炎病毒（LCMV）Armstrong毒株感染后，纵隔淋巴结、脾脏、肝脏与肺脏内LCMV特异性（P14）CD8+ T细胞进行uLIPSTIC互作依赖型转录组学分析。

请注意，HTO、条形码序列及带标签的样本信息均包含于"readme.txt"文件中。