Datasets to reproduce Figures 1-3 and associated Extended Data Figures

The CHI, HIPC-I (Stanford and Yale), Emory, Yellow fever and SLE data sets used in the study. Unpack this file to your working directory and keep the directory structure. The R codes can be downloaded from github (https://github.com/kotliary/baseline) into the R directory.<br>This item is a part of the collection: https://doi.org/10.35092/yhjc.c.4753772<br><b>If you use our data (including CITE-seq data) or code for your work please cite the following publication</b>:Kotliarov, Y., Sparks, R. et al. Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus. Nat. Med. DOI: https://doi.org/10.1038/s41591-020-0769-8 (2020)<br><b>Abstract</b><br>Responses to vaccination and to diseases vary widely across individuals, which may be partly due to baseline immune variations. Identifying such baseline predictors and their biological basis are of broad interest given their potential importance for cancer immunotherapy, disease outcomes, vaccination and infection responses. Here we uncover baseline blood transcriptional signatures predictive of antibody responses to both influenza and yellow fever vaccinations in healthy subjects. These same signatures evaluated at clinical quiescence are correlated with disease activity in systemic lupus erythematosus patients with plasmablast-associated flares. CITE-seq profiling of 82 surface proteins and transcriptomes of 53,201 single cells from healthy high and low influenza-vaccination responders revealed that our signatures reflect the extent of activation in a plasmacytoid dendritic cell—Type I IFN—T/B lymphocyte network. Our findings raise the prospect that modulating such immune baseline states may improve vaccine responsiveness and mitigate undesirable autoimmune disease activities.<br><br><b>General contact</b>: John Tsang ([e-mail])<b>Questions about software/code</b>: Yuri Kotliarov ([e-mail])<br>

本研究使用的数据集包括CHI、HIPC-I（斯坦福与耶鲁）、埃默里（Emory）、黄热病以及系统性红斑狼疮（SLE）数据集。请将此文件解压至您的工作目录，并保留原有目录结构。R代码可从GitHub（https://github.com/kotliary/baseline）下载至R目录下。<br>本条目隶属于数据集集合：https://doi.org/10.35092/yhjc.c.4753772<br><b>若您在研究中使用本数据集（包含CITE-seq（Cellular Indexing of Transcriptomes and Epitopes by Sequencing）数据）或代码，请引用以下文献</b>：Kotliarov, Y.、Sparks, R. 等。《广泛免疫激活构成健康个体疫苗应答与狼疮患者疾病活动的共同设定点特征》。《自然·医学》（Nat. Med.），DOI: https://doi.org/10.1038/s41591-020-0769-8 (2020)<br><b>摘要</b>：个体对疫苗接种与疾病的应答存在显著异质性，该差异在一定程度上源于基线免疫状态的不同。鉴于其在癌症免疫治疗、疾病转归、疫苗接种及感染应答中的潜在重要性，识别此类基线预测因子及其生物学基础具有广泛的研究价值。本研究揭示了可预测健康受试者针对流感与黄热病疫苗接种的抗体应答的基线血液转录特征。在临床静息状态下评估的上述特征，还与伴有浆母细胞相关发作的系统性红斑狼疮（SLE）患者的疾病活动度显著相关。本研究通过对82种表面蛋白进行CITE-seq分析，并对来自流感疫苗应答高低组健康受试者的53201个单细胞进行转录组测序，证实这些特征反映了浆细胞样树突状细胞（plasmacytoid dendritic cell）—I型干扰素（Type I IFN）—T/B淋巴细胞（T/B lymphocyte）网络的激活程度。本研究结果提示，调控此类免疫基线状态或可改善疫苗应答，并缓解不良自身免疫疾病活动。<br><br><b>通用咨询联系人</b>：John Tsang（[e-mail]）<b>软件/代码相关问题咨询</b>：Yuri Kotliarov（[e-mail]）