Krawczyk
Laboratory

Project Area 1: Epigenetic and metabolic mechanisms regulating dendritic cell function

Context- and subset-specific response allows dendritic cells (DCs) to fine-tune immune responses, ensuring appropriate reactions to diverse challenges. This remarkable plasticity of DCs is central to their roles in orchestrating context-specific immune responses.

Metabolism and epigenetic programming play crucial roles in shaping DC function. As DCs transition from an immature to an activated state, they undergo significant metabolic reprogramming. Likewise, they undergo significant epigenetic programming that is both context- (e.g., infection type) and subset-specific.

Our group has shown that DCs engage in Warburg metabolism upon activation and depend on glycolysis for their survival and inflammatory functions (Krawczyk et al., 2010). However, DCs with varying inflammatory phenotypes (from weak to strong) all rely on the induction of glycolysis for functions such as migration from tissues to lymph nodes where they initiate immune responses (Guak et al., 2018). One of the most striking differences of differentially activated DCs is the maintenance of mitochondrial metabolism. We found that PGC-1β is a crucial driver of mitochondrial metabolism, but also suppresses inflammatory gene expression (Guak et al., 2022). These findings suggest the molecules that regulate metabolic programming of DCs directly impact their inflammatory capabilities.

DCs respond rapidly to environmental cues. We hypothesized that, in addition to being poised at the cellular level, DCs must also be epigenetically poised to swiftly express specific genes tailored to combat distinct threats. Further, it is well established that DCs that previously have been activated are significantly impaired in responding to new threats. Thus, DC activation needs to be tightly regulated and restrained at steady state to ensure an effective response.

We discovered that the restraint of DC activation at homeostasis is reliant on epigenetic regulators PCGF6 and KDM5C. PCGF6 is a component of the polycomb repressor complex (PRC1.6), which represses gene expression via histone ubiquitylation. PCGF6 interacts with the histone lysine demethylase KDM5C to jointly restrain DC activation (Boukhaled et al., 2016). Upon DC activation, PCGF6 is rapidly downregulated to relieve inhibition. Mechanistically, we also discovered that the micro-RNA, miR-9, is rapidly upregulated upon DC activation and targets PCGF6 and other negative regulators of DC activation to facilitate DC activation (Cordeiro et al., 2020).

To further explore these mechanisms, we generated mice with DC-specific deficiencies in KDM5C and PCGF6. Our findings revealed that KDM5C-deficient DCs exhibit abnormalities, including altered subset heterogeneity, spontaneous activation at steady state and impaired response to stimuli (Guak, Weiland et al., 2024). In Guak, Weiland et al. (2024), we characterize a previously undescribed population of plasmacytoid DCs that are more abundant in the absence of KDM5C, and that pDCs are effective APCs for CD8 T cells in the context of infection. We found that KDM5C restrains inflammatory gene expression while promoting the expression of mitochondrial metabolism genes. In the absence of KDM5C in DCs, mice are less able to control viral infection. Conversely, deletion of PCGF6 had minimal impact on DC function and heterogeneity, indicating that KDM5C likely serves as the primary repressor of steady-state gene activation.

We currently are investigating subset-specific metabolic and epigenetic programming of DC subsets in vivo. We now know that bone marrow-derived dendritic cell (BMDC) programming does not fully recapitulate the metabolic profiles of DCs that develop naturally in vivo, in part because of nutrient availability, signals from the microenvironment and developmental differences between BMDC and DCs in physiological settings. In addition to glycolysis, DCs engage in multiple metabolic pathways following activation, and we are exploring how specific metabolic pathways, and epigenetic programming mechanisms support DC activation with the goal of improving DC-based therapies through modulating these pathways.

Current efforts are focused on the intersection of epigenetic and metabolic programming of DCs.