ATAC-seq analysis of immune responses from bone marrow derived dendritic cells stimulated with 7 pattern recognition receptor (PRR) ligands along with their pairwise and triplet combinations

The immune system makes decisions in response to combinations of multiple microbial inputs. We do not understand the combinatorial logic governing how higher-order combinations of microbial signals shape immune responses. Here, using coculture experiments and statistical analyses, we discover a general property for the combinatorial sensing of microbial signals, whereby the effects of triplet combinations of microbial signals on immune responses can be predicted by combining the effects of single and pairs. Mechanistically, we find that singles and pairs dictate the information signaled by triplets in mouse and human DCs at the levels of transcription, chromatin and protein secretion. We exploit this simplifying property to develop cell-based immunotherapies prepared with adjuvant combinations that trigger protective responses in mouse models of cancer. We conclude that the processing of multiple input signals by innate immune cells is governed by pairwise effects, which will inform the rationale combination of adjuvants to manipulate immunity. Genome wide chromatin accessbility profiles of mouse bone marrow derived dendritic cells stimulated for 6 hours with 3 random triplet PRR ligand combinations and their constituting single and pair ligand combinations generated by ATAC-seq in duplicates using illumina NextSeq 550

免疫系统会针对多种微生物输入的组合做出决策。目前我们尚未阐明支配高阶微生物信号组合如何塑造免疫应答的组合逻辑。本研究通过共培养实验与统计学分析，发现了微生物信号组合感知的一项通用特性：微生物信号三联组合对免疫应答的影响，可通过单信号与双信号组合的影响进行预测。在机制层面，我们发现在小鼠与人类树突状细胞（dendritic cells, DCs）中，单信号与双信号组合决定了三联信号所传递的信息，覆盖转录、染色质与蛋白质分泌多个层面。我们利用这一简化特性，开发了基于佐剂组合的细胞免疫疗法，该疗法可在小鼠癌症模型中触发保护性免疫应答。本研究得出结论：先天免疫细胞（innate immune cells）对多输入信号的处理由成对信号效应支配，这一发现将为合理组合佐剂以调控免疫应答提供理论依据。本研究使用Illumina NextSeq 550平台进行重复转座酶可及性染色质测序（ATAC-seq）实验，对经3种随机模式识别受体（Pattern Recognition Receptor, PRR）配体三联组合及其对应的单配体、双配体组合刺激6小时的小鼠骨髓源性树突状细胞，获取了其全基因组染色质可及性图谱。