DataSheet_2_Single-cell transcriptomics reveals striking heterogeneity and functional organization of dendritic and monocytic cells in the bovine mesenteric lymph node.xlsx

Dendritic and monocytic cells co-operate to initiate and shape adaptive immune responses in secondary lymphoid tissue. The complexity of this system is poorly understood, also because of the high phenotypic and functional plasticity of monocytic cells. We have sequenced mononuclear phagocytes in mesenteric lymph nodes (LN) of three adult cows at the single-cell level, revealing ten dendritic-cell (DC) clusters and seven monocyte/macrophage clusters with clearly distinct transcriptomic profiles. Among DC, we defined LN-resident subsets and their progenitors, as well as subsets of highly activated migratory DC differing in transcript levels for T-cell attracting chemokines. Our analyses also revealed a potential differentiation path for cDC2, resulting in a cluster of inflammatory cDC2 with close transcriptional similarity to putative DC3 and monocyte-derived DC. Monocytes and macrophages displayed sub-clustering mainly driven by pro- or anti-inflammatory expression signatures, including a small cluster of cycling, presumably self-renewing, macrophages. With this transcriptomic snapshot of LN-derived mononuclear phagocytes, we reveal functional properties and differentiation trajectories in a “command center of immunity”, and identify elements that are conserved across species.

树突状细胞（Dendritic cell）与单核细胞协同作用，启动并塑造次级淋巴组织中的适应性免疫应答。由于单核细胞具有高度的表型与功能可塑性，该系统的复杂性迄今尚未被充分阐明。本研究对3头成年奶牛肠系膜淋巴结（mesenteric lymph node, LN）中的单核吞噬细胞进行了单细胞测序，共鉴定出10个树突状细胞（Dendritic cell, DC）簇与7个单核细胞/巨噬细胞簇，各簇均具有显著差异的转录组特征。在DC中，我们明确了淋巴结驻留亚群及其祖细胞，同时还鉴定出高度活化的迁移性DC亚群，这类亚群在招募T细胞的趋化因子转录水平上存在差异。本研究分析还揭示了经典树突状细胞2型（cDC2）的潜在分化通路，最终生成一群炎性cDC2，其转录特征与推定的DC3及单核细胞衍生DC高度相似。单核细胞与巨噬细胞的亚簇划分主要由促炎或抗炎表达特征驱动，其中包含一小群处于增殖周期、推测具有自我更新能力的巨噬细胞。通过本次对淋巴结来源单核吞噬细胞的转录组快照分析，我们阐明了这一“免疫指挥中枢”内的功能特性与分化轨迹，并鉴定出跨物种保守的免疫相关元件。