DECIphering the Tissue Imprinting of Plasmacytoid dendritic cells in homeostasis and during viral infections – DECITIP

Plasmacytoid dendritic cells (pDC) produce huge amounts of type I and III interferons (IFN) during most systemic viral infections. As the response to IFN activates both cell-intrinsic antiviral defense and innate and adaptive immunity, pDC are considered to exert key immunoactivating functions in anti-viral immunity. pDC are widely distributed in the body and located in both lymphoid organs (e.g. spleen) and non-lymphoid organs (e.g. gut, liver). Immunoactivating functions appear to be restricted to pDC residing in lymphoid organs, while gut and liver pDC have been proposed to exert immunosuppressive functions.
Organ-specific cell type(s), named niche, can instruct tissue-specific functions of resident immune cells, such as macrophages. Whether and how organ-specific niche cells regulate the nature and quality of pDC functions has not been elucidated. The gut-liver axis and, in particular, the microbiota can modulate the functions of the immune cells resident in the gastrointestinal tract and in the liver. However, whether this is the case for instructing the tolerogenic functions of the pDC residing in these organs is unknown.
We recently showed at the single cell level that, during MCMV infection, splenic IFN-producing pDC sequentially acquire five distinct functional activation states that are spatio-temporally regulated (Abbas et al. Nat Immunol 2020). At the peak of IFN production (states 1-3), pDC localize in the marginal zone, in tight proximity with MCMV-infected cells. Once IFN production has ceased, ex-IFN-producing pDC (states 4-5) acquire phenotypic and functional properties of antigen presenting cells, upregulate CCR7 and migrate to the T cell zone. However, whether and how splenic niches located in the marginal zone vs T cell zone instruct these distinct pDC activation states, and what is the impact of MCMV infection on these niches, is still unknown.
Our main aim is to understand whether and how the tissue environment shapes pDC functions in homeostasis and upon pathophysiological conditions. Specifically, we hypothesize that:
1) in homeostasis, the immunoactivating properties of splenic pDC vs tolerogenic properties of hepatic and intestinal pDC are instructed by organ-specific niches;
2) the gut-liver axis and, in particular, the microbiota shape the gene expression program and the functions of the pDC residing in these organs and, reciprocally, pDC can be involved in gut and liver homeostasis and functions;
3) during a systemic viral infection, virally-induced “niches” provide unique signals tuning pDC functional activation and plasticity.
To address these issues, we will take advantage of our novel and unique mouse models allowing specific identification of pDC by fluorescence, or selective and constitutive pDC depletion. We will develop an innovative systems biology approach to identify and characterize pDC niches, by using cutting-edge genomics technologies, including spatial transcriptomics (ST), single cell or single nucleus RNA sequencing (scRNA-Seq, snRNA-Seq), combined with advanced bioinformatics analyses and computational modelling. The niche cell identified and the related molecular circuits will be validated by using high throughput flow cytometry, spectral confocal microscopy analysis and functional assays, as already used in our recent collaborative publication to characterize the micro-anatomical location and functions of splenic pDC from MCMV-infected mice (Abbas et al. Nat Immunol 2020).