Neonatal imprinting of mesenteric lymph node stroma modulates tolerogenic properties of dendritic cells [scRNA-seq]

Gut-draining mesenteric lymph nodes (mLNs) play a key role in peripheral tolerance towards food and commensal antigens by providing an optimal microenvironment for efficient de novo induction of Foxp3+ regulatory T cells (Tregs). We recently identified mLN stromal cells as critical cellular players in this process and demonstrated that their tolerogenic properties are imprinted by microbiota. Here, we show that this imprinting process already takes place in the neonatal phase and renders the mLN stromal cell compartment resistant to inflammatory perturbations later in life. Utilizing LN transplantation, RNA-seq and single-cell RNA-seq allowed identification of stably imprinted expression signatures in mLN fibroblastic stromal cells. We dissected common stromal cell subsets across gut-draining mLNs and skin-draining LNs with location-specific immunomodulatory functions, such as subset-specific expression of Aldh1a2/3. Accordingly, mLN stromal cells shaped resident dendritic cells to attain high Treg-inducing capacity in a Bmp2-dependent manner. Thus, crosstalk between mLN stromal and resident dendritic cells provides a robust feedback mechanism for the maintenance of intestinal tolerance. Single-cell transcriptomic analysis of skin-draining pLNs (inguinal and axillary) or mLNs (small intestinal and colon/caecum-draining) cell populations.肠道引流型肠系膜淋巴结（mesenteric lymph nodes, mLNs）可通过为高效从头诱导Foxp3阳性调节性T细胞（Tregs）提供最优微环境，在针对食物与共生抗原的外周免疫耐受中发挥关键作用。我们近期明确了肠系膜淋巴结基质细胞是该过程中的关键细胞组分，并证实其致耐受特性由菌群印记塑造。本研究发现，这种印记过程早在新生阶段即已启动，并使得肠系膜淋巴结基质细胞群在后续生命进程中可抵抗炎性扰动。借助淋巴结移植技术、RNA测序（RNA-seq）与单细胞RNA测序（single-cell RNA-seq），我们得以鉴定出肠系膜淋巴结成纤维细胞样基质细胞中稳定存在的印记表达特征。我们对肠道引流型肠系膜淋巴结与皮肤引流型淋巴结中具有位置特异性免疫调节功能的常见基质细胞亚群进行了解析，例如乙醛脱氢酶1a2/3（Aldh1a2/3）的亚群特异性表达。相应地，肠道引流型肠系膜淋巴结基质细胞可通过骨形态发生蛋白2（Bmp2）依赖性方式，调控驻留型树突状细胞以获得高效的Treg诱导能力。综上，肠道引流型肠系膜淋巴结基质细胞与驻留型树突状细胞间的细胞串扰，为维持肠道免疫耐受提供了一套稳健的反馈调控机制。本数据集包含皮肤引流型外周淋巴结（pLNs，含腹股沟淋巴结与腋窝淋巴结）以及肠道引流型肠系膜淋巴结（mLNs，含小肠引流与结肠/盲肠引流亚型）的细胞群体的单细胞转录组分析数据。