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Single cell RNA sequencing-based comparison of mouse splenic pDC, pDC-like cells, tDC, cDC1 and cDC2 at steady state and during a viral infection

ABSTRACT: Single cell RNA sequencing-based comparison of mouse splenic pDC, pDC-like cells, tDC, cDC1 and cDC2 at steady state and during a viral infection

PROVIDER: PRJNA806963 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18021517_1.fastq.gz	Fastqsanger.gz
	SRR18021517_2.fastq.gz	Fastqsanger.gz
	SRR18021518_1.fastq.gz	Fastqsanger.gz
	SRR18021518_2.fastq.gz	Fastqsanger.gz
	SRR18021519_1.fastq.gz	Fastqsanger.gz

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Single cell RNA sequencing-based comparison of mouse splenic pDC, pDC-like cells, tDC, cDC1 and cDC2 at steady state and during a viral infection

Project description:Plasmacytoid dendritic cells (pDC) are the main source of type I interferon (IFN) during viral infections. Their other functions are debated, due to a lack of tools to identify and target them in vivo without affecting pDC-like cells and transitional DC (tDC), which harbor overlapping phenotypes and transcriptomes but a higher efficacy for T cell activation. To overcome this bottleneck, we designed, generated and validated a pDC-Tomato reporter mouse. We bred pDC-Tomato with Zbtb46 GFP mice to yield the he ZeST mouse strain that enabled transcriptomic profiling of all splenic DC types, by single cell RNA sequencing, both at steady state and during the course of the infection with mouse cytomegalovirus (MCMV). Analyses of the transcriptomic dataset unraveled diverging activation of pDC-like cells vs tDC during the infection. This dataset and the associated specific gene modules will be useful to delineate the physiological functions of pDC versus other DC types.

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Project description:Conventional dendritic cells (cDC) consist of two functionally and phenotypically distinct subsets, cDC1 and cDC2, whose development is dependent on distinct sets of transcription factors. Interferon regulatory factor 8 (IRF8) is required at multiple stages of cDC1 development, but its role in mature cDC1 remains unclear. Here we used XCR1-cre to delete Irf8 in committed cDC1 and demonstrate that Irf8 is required for maintaining the identify of cDC1 but not their survival. In the absence of Irf8, committed cDC1 (“ex-cDC1”) acquired the transcriptional, functional and chromatin accessibility properties of cDC2. This conversion was independent on Irf4 and was associated with decreased accessibility in putative IRF8, Batf3 and composite AP-1-IRF (AICE) binding elements, together with increased accessibility of cDC2 associated transcription factor binding elements. Thus, IRF8 expression by committed cDC1 is required for preventing their conversion into cDC2.

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