The ubiquitin-editing enzyme A20 controls NK cell homeostasis through regulation of mTOR activity and TNF

The ubiquitin-editing enzyme A20 is a well-known regulator of immune cell function and homeostasis. In addition, A20 protects cells from death in an ill-defined manner. While most studies focus on its role in the TNF-receptor complex, we here identify a novel component in the A20-mediated decision between life and death. Loss of A20 in NK cells led to spontaneous NK cell death and severe NK cell lymphopenia. The few remaining NK cells showed an immature, hyperactivated phenotype, hallmarked by the basal release of cytokines and cytotoxic molecules. NK-A20(-/-) cells were hypersensitive to TNF-induced cell death and could be rescued, at least partially, by a combined deficiency with TNF. Unexpectedly, rapamycin, a well-established inhibitor of mTOR, also strongly protected NK-A20(-/-) cells from death, and further studies revealed that A20 restricts mTOR activation in NK cells. This study therefore maps A20 as a crucial regulator of mTOR signaling and underscores the need for a tightly balanced mTOR pathway in NK cell homeostasis

Two distinct ubiquitin-binding motifs in A20 mediate its anti-inflammatory and cell-protective activities

Protein ubiquitination regulates protein stability and modulates the composition of signaling complexes. A20 is a negative regulator of inflammatory signaling, but the molecular mechanisms involved are ill understood. Here, we generated Tnfaip3 gene-targeted A20 mutant mice bearing inactivating mutations in the zinc finger 7 (ZnF7) and ZnF4 ubiquitin-binding domains, revealing that binding to polyubiquitin is essential for A20 to suppress inflammatory disease. We demonstrate that a functional ZnF7 domain was required for recruiting A20 to the tumor necrosis factor receptor 1 (TNFR1) signaling complex and to suppress inflammatory signaling and cell death. The combined inactivation of ZnF4 and ZnF7 phenocopied the postnatal lethality and severe multiorgan inflammation of A20-deficient mice. Conditional tissue-specific expression of mutant A20 further revealed the key role of ubiquitin-binding in myeloid and intestinal epithelial cells. Collectively, these results demonstrate that the anti-inflammatory and cytoprotective functions of A20 are largely dependent on its ubiquitin-binding properties. van Loo and colleagues provide insights into the action of the anti-inflammatory protein A20. The ZnF7 and ZnF4 ubiquitin-binding domains of A20 are both required to suppress inflammatory signaling and cell death; however, these zinc fingers operate via distinct mechanisms

The ubiquitin-editing enzyme A20 controls NK cell homeostasis through regulation of mTOR activity and TNF

The ubiquitin-editing enzyme A20 is a well-known regulator of immune cell function and homeostasis. In addition, A20 protects cells from death in an ill-defined manner. While most studies focus on its role in the TNF-receptor complex, we here identify a novel component in the A20-mediated decision between life and death. Loss of A20 in NK cells led to spontaneous NK cell death and severe NK cell lymphopenia. The few remaining NK cells showed an immature, hyperactivated phenotype, hallmarked by the basal release of cytokines and cytotoxic molecules. NK-A20−/− cells were hypersensitive to TNF-induced cell death and could be rescued, at least partially, by a combined deficiency with TNF. Unexpectedly, rapamycin, a wellestablished inhibitor of mTOR, also strongly protected NK-A20−/− cells from death, and further studies revealed that A20 restricts mTOR activation in NK cells. This study therefore maps A20 as a crucial regulator of mTOR signaling and underscores the need for a tightly balanced mTOR pathway in NK cell homeostasis

Novel pathways in NK cell biology

On a daily basis, human beings are faced with millions of potential pathogens. Sometimes even our very own cells turn against us, thereby inducing autoimmune disorders or malignancies. Luckily, with the help of our immune system, we spend most of our lives in good health. Although the immune system comprises many distinct cell types that are typically divided over two major branches, natural killer (NK) cells form an exception to this classification. In line with the innate immune system, NK cells are one of the first cells to respond to incoming threats (usually viruses or cancer) by releasing large amounts of cytokines. In line with the adaptive branch, NK cells resemble lymphocytes, as apparent by their cytotoxic potential and capacity to form memory. Irrespective of the many regulators that have already been established in the context of NK cell biology, this thesis identifies two novel, distinct regulators of NK cell homeostasis and function, and provides evidence for the in vivo relevance of both NK cell regulators, either in health or upon disease. The inositol-requiring enzyme 1 (IRE1) and its main downstream target X-box-binding protein 1 (XBP1) are best known for their role in the unfolded protein response (UPR), an adaptive cellular response initiated upon the accumulation of unfolded proteins in the endoplasmic reticulum (ER). Aside from its mere canonical role in restoring ER homeostasis, IRE1’s non-canonical roles in the immune system have gained increased attention over the past years. In Chapter 3 we sought to determine the potential role of IRE1 in NK cell biology, both in health and disease. While IRE1 is dispensable for basal NK cell homeostasis, NK cells need IRE1 for proper clonal-like expansion upon challenge with murine cytomegalovirus infection. By single cell RNA sequencing, we showed that the proliferative defect in IRE1-deficient NK cells could be attributed to IRE1’s canonical role. We thus conclude that proliferating NK cells require proper protein folding in the ER to maintain the required metabolic fitness that enables vigorous proliferation upon viral challenge. In a second part, we turned our attention towards the ubiquitin-editing enzyme A20. Besides its role in dampening pro-inflammatory nuclear factor kappa B (NF-κB) signaling, A20 is also well-known for protecting distinct cell types from death. In this regard, NK cells formed no exception to this rule as NK cells succumbed in absence of A20. Intriguingly, this already occurred in steady state and the few remaining A20-deficient NK cells were hyperactive. This identifies A20’s indispensable role in NK cell homeostasis. Mechanistically, two distinct pathways downstream of A20, tumor necrosis factor (TNF) and mechanistic target of rapamycin (mTOR), were identified. Although working in a synergistic manner, both pathways operated independently as NK cell death could only be rescued upon simultaneous blockade of both TNF and mTOR. While literature had already established the intimate link between A20 and TNF-induced cell death, the link between A20 and mTOR was entirely novel in the NK cell field. How A20 exactly affects mTOR to flip the switch to NK cell death, remains to be elucidated. All in all, this thesis brings IRE1 and A20 forward as novel metabolic regulators of NK cell biology. While IRE1’s role only becomes apparent upon viral challenge, A20 is a bona fide regulator of basal NK cell homeostasis. We nevertheless propose that further research should aim at unraveling a potential alternative explanation for IRE1’s role in virus-driven NK cell proliferation as well as substantiate how A20 affects mTOR to flip the switch to NK cell death

Opposing regulation and roles for PHD3 in lung dendritic cells and alveolar macrophages

The prolyl hydroxylase domain-containing enzymes (PHDs) are important metabolic sensors of the cell and its environment, which might be employed to alert cells of the immune system. These enzymes regulate the expression of the hypoxia inducible factor (HIF) isoforms and NF-kappa B, crucial transcription factors controlling cellular metabolism and inflammation. PHD/HIF signaling is activated in the allergic lung and is proposed as a potential druggable pathway. Here, we investigated the regulation and role of the PHD isoforms in CD11c-expressing dendritic cells (DCs) and macrophages (M phi), sensors of the environment and crucial antigen-presenting cells in the pathogenesis of asthma. Although PHD2 and PHD3 were expressed in baseline, stimulation with house dust mite (HDM) allergen, hypoxia, and TLR4 ligands induced the expression of PHD3 in DCs. Conditional deletion or overexpression of PHD3 in CD11c(hi) cells had minor effects on DCs and alveolar M phi biology in steady state. However, when put into competition with wild-type counterparts in mixed chimeric mice, alveolar M phi uniquely required PHD3 for optimal reconstitution of the alveolar space. Using genetic and chemical approaches, we were unable to find a clear role for PHD3 or the other PHD isoforms in DCs in asthma development. These data show cell-specific competitive advantage of PHD3 expression in antigen-presenting cells, but question whether therapeutic manipulation of PHDs in DCs would offer therapeutic benefit in asthma

Emerging role of the unfolded protein response in tumor immunosurveillance

Disruption of endoplasmic reticulum (ER) homeostasis results in ER stress and activation of the unfolded protein response (UPR). This response alleviates cell stress, and is activated in both tumor cells and tumor infiltrating immune cells. The UPR plays a dual function in cancer biology, acting as a barrier to tumorigenesis at the premalignant stage, while fostering cancer maintenance in established tumors. In infiltrating immune cells, the UPR has been involved in both immunosurveillance and immunosuppressive functions. This review aims to decipher the role of the UPR at different stages of tumorigenesis and how the UPR shapes the balance between immunosurveillance and immune escape. This knowledge may improve existing UPR-targeted therapies and the design of novel strategies for cancer treatment

Canonical IRE1 function needed to sustain vigorous natural killer cell proliferation during viral infection

The unfolded protein response (UPR) aims to restore ER homeostasis under conditions of high protein folding load, a function primarily serving secretory cells. Additional, non-canonical UPR functions have recently been unraveled in immune cells. We addressed the function of the inositol-requiring enzyme 1 (IRE1) signaling branch of the UPR in NK cells in homeostasis and microbial challenge. Cell-intrinsic compound deficiency of IRE1 and its downstream transcription factor XBP1 in NKp46+ NK cells, did not affect basal NK cell homeostasis, or overall outcome of viral MCMV infection. However, mixed bone marrow chimeras revealed a competitive advantage in the proliferation of IRE1-sufficient Ly49H+ NK cells after viral infection. CITE-Seq analysis confirmed strong induction of IRE1 early upon infection, concomitant with the activation of a canonical UPR signature. Therefore, we conclude that IRE1/XBP1 activation is required during vigorous NK cell proliferation early upon viral infection, as part of a canonical UPR response.</p

The unfolded-protein-response sensor IRE-1α regulates the function of CD8α⁺ dendritic cells

The role of the unfolded protein response (UPR) and endoplasmic reticulum (ER) stress in homeostasis of the immune system is incompletely understood. Here we found that dendritic cells (DCs) constitutively activated the UPR sensor IRE-1 alpha and its target, the transcription factor XBP-1, in the absence of ER stress. Loss of XBP-1 in CD11c(+) cells led to defects in phenotype, ER homeostasis and antigen presentation by CD8 alpha(+) conventional DCs, yet the closely related CD11b(+) DCs were unaffected. Whereas the dysregulated ER in XBP-1-deficient DCs resulted from loss of XBP-1 transcriptional activity, the phenotypic and functional defects resulted from regulated IRE-1 alpha-dependent degradation (RIDD) of mRNAs, including those encoding CD18 integrins and components of the major histocompatibility complex (MHC) class I machinery. Thus, a precisely regulated feedback circuit involving IRE-1 alpha and XBP-1 controls the homeostasis of CD8 alpha(+) conventional DCs

LXR signaling controls homeostatic dendritic cell maturation

Dendritic cells (DCs) mature in an immunogenic or tolerogenic manner depending on the context in which an antigen is perceived, preserving the balance between immunity and tolerance. Whereas the pathways driving immunogenic maturation in response to infectious insults are well-characterized, the signals that drive tolerogenic maturation during homeostasis are still poorly understood. We found that the engulfment of apoptotic cells triggered homeostatic maturation of conventional cDC1s within the spleen. This maturation process could be mimicked by engulfment of empty, non-adjuvanted lipid nanoparticles (LNPs), was marked by intracellular accumulation of cholesterol, and highly unique to type 1 DCs. Engulfment of either apoptotic cells or cholesterol-rich LNPs led to activation of the LXR pathway, which promotes the efflux of cellular cholesterol, and repressed genes associated with immunogenic maturation. In contrast, simultaneous engagement of TLR3 to mimic viral infection via administration of poly(I:C)-adjuvanted LNPs repressed the LXR pathway, thus delaying cellular cholesterol efflux and inducing genes that promote T cell-mediated immunity. These data demonstrate that conserved cellular cholesterol efflux pathways are differentially regulated in in tolerogenic versus immunogenic cDC1s and suggest that administration of non-adjuvanted cholesterol-rich LNPs may be an approach for inducing tolerogenic DC maturation

The unfolded-protein-response sensor IRE-1α regulates the function of CD8α+ dendritic cells

The role of the unfolded protein response (UPR) and endoplasmic reticulum (ER) stress in homeostasis of the immune system is incompletely understood. Here we found that dendritic cells (DCs) constitutively activated the UPR sensor IRE-1 alpha and its target, the transcription factor XBP-1, in the absence of ER stress. Loss of XBP-1 in CD11c(+) cells led to defects in phenotype, ER homeostasis and antigen presentation by CD8 alpha(+) conventional DCs, yet the closely related CD11b(+) DCs were unaffected. Whereas the dysregulated ER in XBP-1-deficient DCs resulted from loss of XBP-1 transcriptional activity, the phenotypic and functional defects resulted from regulated IRE-1 alpha-dependent degradation (RIDD) of mRNAs, including those encoding CD18 integrins and components of the major histocompatibility complex (MHC) class I machinery. Thus, a precisely regulated feedback circuit involving IRE-1 alpha and XBP-1 controls the homeostasis of CD8 alpha(+) conventional DCs