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Single-cell RNA-seq dictionary of in vivo immune responses to cytokines

ABSTRACT: Single-cell RNA-seq dictionary of in vivo immune responses to cytokines

PROVIDER: PRJNA834959 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19078500.fastq.gz	Fastqsanger.gz
	SRR19078501.fastq.gz	Fastqsanger.gz
	SRR19078502.fastq.gz	Fastqsanger.gz
	SRR19078503.fastq.gz	Fastqsanger.gz
	SRR19078504.fastq.gz	Fastqsanger.gz

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Single-cell RNA-seq dictionary of in vivo immune responses to cytokines

Project description: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.

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