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Harnessing systems immunology to unravel dendritic cell subset biology

Final Report Summary - SYSTEMSDENDRITIC (Harnessing systems immunology to unravel dendritic cell subset biology)

Dendritic cells (DCs) are a heterogeneous family of mononuclear phagocytes poised at the interface between innate and adaptive immunity. They can exert both direct effector innate immune functions for the control of pathogens or tumors as well as orchestrate the induction and functional polarization of innate and adaptive lymphocyte responses including to promote either tolerance or immunity. Hence, the manipulation of DCs bears great promises for treating many diseases. However, to advance towards this aim, it is necessary to better understand DC heterogeneity, in particular whether certain DC types bear crucial, non-redundant, functions to promote health over disease. Plasmacytoid DCs (pDCs) are a major source of the antiviral cytokines type I interferons (IFN-I) in vivo early on after viral infections. However, their physiological role for antiviral defense remains obscure. Their ability to produce IFN-I is dispensable in modern humans in developed countries. Type 1 classical DCs (cDC1s) are characterized by the expression of the chemokine receptor XCR1. They excel at activating CD8+ cytotoxic T lymphocytes (CTLs). In particular, cDC1s are particularly efficient at presenting to CTLs exogenous antigens engulfed from infected or dying cells, a process known as antigen cross-presentation. However, when we started our project, the extent and the importance of the physiological functions of cDC1s remained largely to be understood. The immunogenic maturation of cDC1s requires their ability to respond to IFN-I. Therefore, we hypothesized that the induction of efficient CTL responses able to control viruses or tumors may require a cross-talk between pDCs and cDC1s. Overall, our major aim was to investigate whether and how pDCs and cDC1s contribute to immune protection against intracellular pathogens. Such studies had been hampered by lack of adequate mutant mouse models for specific in vivo tracking, depletion or genetic manipulation of DCs, by the extreme difficulty of working with ex vivo isolated human cDC1s due to their rarity and fragility, and by the lack of adequate in vitro models of human cDC1s. Thus, our experimental strategy was in a part based on the generation, or characterization, and use of innovative, dedicated mouse models. We largely focused on innate and CTL immune responses during infections of mice with the intracellular bacteria Listeria monocytogenes (Lm) or with mouse cytomegalovirus (MCMV). This included i) gene expression profiling of DCs during infections, to characterize their activation state in a broad and unbiased way, and to infer from there novel hypotheses, ii) using already existing mutant mice to examine the impact of cDC1 or pDC depletion or of Xcr1 genetic inactivation on natural killer (NK) and CTL responses, and iii) generating novel mutant mouse models for conditional inactivation of target genes in cDC1s or pDCs and investigation of its impact on immunity to infections. These studies led to major discoveries. First, we demonstrated that the maturation of DCs is a much more complex process than generally considered, and we discovered novel gene modules associated with the functional polarization of DCs towards tolerance versus immunogenicity. Second, we discovered that cDC1s are not only crucial for the priming of naïve CTLs but also promote the efficient reactivation of memory CTLs upon secondary challenges, and we deciphered some of the underlying cellular and molecular mechanisms. These published results, as well as other ones not yet publicly disclosed, have led us to hypothesize a division of labor between DC types, and a crucial role of IFN-I and antigen cross-presentation in this process. Finally, to facilitate experimental testing in human cells of the functions and molecular regulations validated in mice, we developed a novel in vitro differentiation model of human DCs from cord blood CD34+ hematopoietic progenitors, yielding high numbers of bona fide pDCs and cDC1s. These novel tools and knowledge will fuel the design of next generation prophylactic vaccines or immunotherapies against cancer or chronic infections by intracellular pathogens.