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.This item is a part of the collection: https://doi.org/10.35092/yhjc.c.4753772If you use our data (including CITE-seq data) or code for your work please cite the following publication: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)AbstractResponses 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.General contact: John Tsang ([e-mail])Questions about software/code: Yuri Kotliarov ([e-mail])