ImmGen: Gene Expression and Regulation in Immune Cells

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The Immunological Genome Project (ImmGen) is a collaborative group of 15 Immunology and Computational Biology laboratories who perform, under standardized conditions, a thorough dissection of gene expression and its regulation in the mouse immune system. We also investigated how these respond to cytokines and immunologic challenges, how immune gene expression relates to chromatin configuration, and used cutting-edge computational algorithms to deduce regulatory connections. ImmGen data are publicly available on dedicated web and smartphone supports, using interactive graphic displays that make the results intuitive to users. These are now frequently used by the Immunology research community. The proposed continuation will harness the collective expertise of the ImmGen group to further develop this important public resource. (1) Expand and deepen the compendium, applying single-cell RNAseq to define very broadly the cast of cell-types at play in the immune system, their trajectories of differentiation, and their adaptation to specific organismal locations This effort will be complemented by deeper bulk profiling of cell-types thus identified. We will expand the analysis of cytokine signatures, continue to chart non-coding RNA (circRNAs), and persue the “OpenSource” program of coordinated sample contributions from the community. (2) Mechanistic Dissection of Immunogenomic Regulatory Networks focusing on a Core Set of 14 cell-types that represent all the major immunological lineages. We will generate high-resolution maps of transcription factor footprints by ultra-deep ATACseq; map 3D architectures by HiC chromosome conformation capture; apply ChIPseq to define enhancers and super-enhancers, chromatin modification domains and structural anchors; use machine learning approaches to integrate these complementary data into a comprehensive regulatory plan which spans from fine TF footprints to topologically associated domaiins; validate these inferences by collaborating with the KOMP project to analyze Core Set transcriptomes and chromatin configuration in mice with mutations in transcription factors that determine functionally relevant facets of immunocyte activity. (3): Public Display. ImmGen data have become a widely used resource in Immunology research, which will be maintained and curated. For scalability, cost-effectiveness, and to enable facile computation, we will develop and deploy cloud-based data storage and access solutions, compliant with NIH Commons guidelines. We will add to the existing databrowsers to allow users to query different facets of the expanding data (differential expression, regulatory network, chromatin states and architecture, cytokine signatures), increasing connectivity to other data sources. We will continue developing the popular mobile app, and explore the particular uses of that medium. ImmGen has positively impacted immunological research in the current decade, providing detailed and rigorous genomic resolution of immune populations, informed by a strong understanding of their immunology. This is what we will continue and amplify.