Expression profiling by high throughput sequencing
Summary
Cytokines mediate cell-cell communication in the immune system and represent important therapeutic targets. While there have been in-depth studies of individual cytokines, we lack a global view of the responses of each major immune cell type to each cytokine. To address this gap we created the Immune Dictionary — a compendium of single-cell transcriptomic profiles of over 17 immune cell types in response to each of 86 cytokines in murine lymph nodes in vivo. A cytokine-centric view of the dictionary revealed that most cytokines induce highly cell-type-specific responses. For example, the inflammatory cytokine IL-1β induced distinct gene programs in almost every cell type. A cell-type-centric view identified both known and previously uncharacterized cytokine-induced polarization states in every immune cell type, such as a polyfunctional state of NK cells induced by IL-18. Based on the dictionary, we developed companion software, Immune Response Enrichment Analysis (IREA), for assessing immune cell polarization and cytokine activities in any transcriptomic data, and applied it to infer cytokine networks in tumors following immune checkpoint blockade therapy. Our dictionary generates new hypotheses for cytokine functions, illuminates pleiotropic effects of cytokines, expands our knowledge of activation states in each immune cell type, and provides a framework to deduce the roles of specific cytokines and cell-cell communication networks in any immune response.
Overall design
We systematically profiled single-cell transcriptomic responses in vivo to 86 cytokines. The 86 cytokines were selected to represent most of the members in each major cytokine family, including: IL-1 (IL-1α/1β/Ra/18/33/36α/36Ra), common γ chain (IL-2/4/7/9/15/21), common β chain (GM-CSF/IL-3/IL-5), IL-6 (IL-6/11/27*/31, LIF, OSM, CT-1, NP), IL-12 (IL-12/23/27*/Y), IL-10 (IL-10/19/20/22/24), IL-17 (IL-17A-F), interferon (IFN-α1/β/ε/κ/γ/λ2), TNF (TNFSF1-15, 13B, 18), complement (C3a, C5a), and a small number of representative cytokines from other protein families with less well-characterized immune functions (e.g.,Persephins, Adiponectin). Carrier-free cytokines were freshly reconstituted and administered into distinct wild-type C57BL6/J mice (3 mice per cytokine as biological replicates). PBS (vehicle) treated samples were included in each batch as controls. Draining lymph nodes were collected 4 hours after treatment and freshly processed using an optimized protocol for viable cell recovery. Data quality, including batch-to-batch consistency, was experimentally strictly controlled for and computationally verified. Single-cell profiling of lymph node cells was performed Chromium Single Cell 3’ Library & Gel Bead v3 Kit (10x Genomics) to generate single-cell transcriptomes for 386,703 cells that passed quality control.
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