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The immune system can eliminate tumors, but checkpoints enable immune escape. Here, we identify immune evasion mechanisms using genome-scale in vivo CRISPR screens across cancer models treated with immune checkpoint blockade (ICB). We identify immune evasion genes and important immune inhibitory checkpoints conserved across cancers, including the non-classical major histocompatibility complex class I (MHC class I) molecule Qa-1

Adaptive thermogenesis has attracted much attention because of its ability to increase systemic energy expenditure and to counter obesity and diabetes1-3. Recent data have indicated that thermogenic fat cells use creatine to stimulate futile substrate cycling, dissipating chemical energy as heat4,5. This model was based on the super-stoichiometric relationship between the amount of creatine added to mitochondria and the quantity of oxygen consumed. Here we provide direct evidence for the molecular basis of this futile creatine cycling activity in mice. Thermogenic fat cells have robust phosphocreatine phosphatase activity, which is attributed to tissue-nonspecific alkaline phosphatase (TNAP). TNAP hydrolyses phosphocreatine to initiate a futile cycle of creatine dephosphorylation and phosphorylation. Unlike in other cells, TNAP in thermogenic fat cells is localized to the mitochondria, where futile creatine cycling occurs. TNAP expression is powerfully induced when mice are exposed to cold conditions, and its inhibition in isolated mitochondria leads to a loss of futile creatine cycling. In addition, genetic ablation of TNAP in adipocytes reduces whole-body energy expenditure and leads to rapid-onset obesity in mice, with no change in movement or feeding behaviour. These data illustrate the critical role of TNAP as a phosphocreatine phosphatase in the futile creatine cycle.

Mitophagy and mitochondrial integrated stress response (ISR) are 2 primary protective mechanisms to maintain functional mitochondria. Whether these 2 processes are coordinately regulated remains unclear. Here we show that mitochondrial fission 1 protein (Fis1), which is required for completion of mitophagy, serves as a signaling hub linking mitophagy and ISR. In mouse hepatocytes, high fat diet (HFD) feeding induces unresolved oxidative stress, defective mitophagy and enhanced type I interferon (IFN-I) response implicated in promoting metabolic inflammation. Adenoviral-mediated acute hepatic Fis1 overexpression is sufficient to reduce oxidative damage and improve glucose homeostasis in HFD-fed mice. RNA-Seq analysis reveals that Fis1 triggers a retrograde mitochondria-to-nucleus communication upregulating ISR genes encoding anti-oxidant defense, redox homeostasis, and proteostasis pathways. Fis1-mediated ISR also suppresses expression of IFN-I-stimulated genes through activating transcription factor 5 (Atf5), which inhibits the transactivation activity of interferon regulatory factor 3 (Irf3) known to control IFN-I production. Metabolite analysis demonstrates that Fis1 activation leads to accumulation of fumarate, a TCA cycle intermediate capable of increasing Atf5 activity. Consequently, hepatic Atf5 overexpression or monomethyl fumarate (MMF) treatment improves glucose homeostasis in HFD-fed mice. Collectively, these results support the potential use of small molecules targeting the Fis1-Atf5 axis, such as MMF, to treat metabolic diseases.

Epigenetic dysregulation is a defining feature of tumorigenesis that is implicated in immune escape1,2. Here, to identify factors that modulate the immune sensitivity of cancer cells, we performed in vivo CRISPR-Cas9 screens targeting 936 chromatin regulators in mouse tumour models treated with immune checkpoint blockade. We identified the H3K9 methyltransferase SETDB1 and other members of the HUSH and KAP1 complexes as mediators of immune escape3-5. We also found that amplification of SETDB1 (1q21.3) in human tumours is associated with immune exclusion and resistance to immune checkpoint blockade. SETDB1 represses broad domains, primarily within the open genome compartment. These domains are enriched for transposable elements (TEs) and immune clusters associated with segmental duplication events, a central mechanism of genome evolution6. SETDB1 loss derepresses latent TE-derived regulatory elements, immunostimulatory genes, and TE-encoded retroviral antigens in these regions, and triggers TE-specific cytotoxic T cell responses in vivo. Our study establishes SETDB1 as an epigenetic checkpoint that suppresses tumour-intrinsic immunogenicity, and thus represents a candidate target for immunotherapy.

Metabolic pathways and inflammatory processes are under circadian regulation. While rhythmic immune cell recruitment is known to impact infection outcomes, whether the circadian clock modulates immunometabolism remains unclear. We find the molecular clock Bmal1 is induced by inflammatory stimulants, including Ifn-γ/lipopolysaccharide (M1) and tumor conditioned medium, to maintain mitochondrial metabolism under these metabolically stressed conditions in mouse macrophages. Upon M1 stimulation, myeloid-specificBmal1knockout (M-BKO) renders macrophages unable to sustain mitochondrial function, enhancing succinate dehydrogenase (SDH)-mediated mitochondrial ROS production and Hif-1α-dependent metabolic reprogramming and inflammatory damage. In tumor-associated macrophages, the aberrant Hif-1α activation and metabolic dysregulation by M-BKO contribute to an immunosuppressive tumor microenvironment. Consequently, M-BKO increases melanoma tumor burden, while administrating an SDH inhibitor dimethyl malonate suppresses tumor growth. Therefore, Bmal1 functions as a metabolic checkpoint integrating macrophage mitochondrial metabolism, redox homeostasis and effector functions. This Bmal1-Hif-1α regulatory loop may provide therapeutic opportunities for inflammatory diseases and immunotherapy.

Objective Alternative activation (M2) of adipose tissue resident macrophage (ATM) inhibits obesity-induced metabolic inflammation. The underlying mechanisms remain unclear. Recent studies have shown that dysregulated lipid homeostasis caused by increased lipolysis in white adipose tissue (WAT) in the obese state is a trigger of inflammatory responses. We investigated the role of M2 macrophages in lipotoxicity-induced inflammation. Methods We used microarray experiments to profile macrophage gene expression regulated by two M2 inducers, interleukin-4 (Il-4), and peroxisome proliferator-activated receptor delta/gamma (Pparδ/Pparγ) agonists. Functional validation studies were performed in bone marrow-derived macrophages and mice deprived of the signal transducer and activator of transcription 6 gene (Stat6; downstream effector of Il-4) or Pparδ/Pparγ genes (downstream effectors of Stat6). Palmitic acid (PA) and β-adrenergic agonist were employed to induce macrophage lipid loading in vitro and in vivo, respectively. Results Profiling of genes regulated by Il-4 or Pparδ/Pparγ agonists reveals that alternative activation promotes the cell survival program, while inhibiting that of inflammation-related cell death. Deletion of Stat6 or Pparδ/Pparγ increases the susceptibility of macrophages to PA-induced cell death. NLR family pyrin domain containing 3 (Nlrp3) inflammasome activation by PA in the presence of lipopolysaccharide is also increased in Stat6−/− macrophages and to a lesser extent, in Pparδ/γ−/− macrophages. In concert, β-adrenergic agonist-induced lipolysis results in higher levels of cell death and inflammatory markers in ATMs derived from myeloid-specific Pparδ/γ−/− or Stat6−/− mice. Conclusions Our data suggest that ATM cell death is closely linked to metabolic inflammation. Within WAT where concentrations of free fatty acids fluctuate, M2 polarization regulated by the Stat6-Ppar axis enhances ATM's tolerance to lipid-mediated stress, thereby maintaining the homeostatic state., Highlights • Cell survival is transcriptionally regulated by macrophage alternative activation. • Fatty acid-triggered cell death is increased in Pparδ/γ−/− or Stat6−/− macrophages. • Il-4-Stat6 signaling suppresses lipotoxicity-induced inflammasome activation. • The Stat6-Pparδ/γ axis protects ATMs against lipolysis-induced cell death in vivo.

Summary Inflammation can support or restrain cancer progression and the response to therapy. Here, we searched for primary regulators of cancer-inhibitory inflammation through deep profiling of inflammatory tumor microenvironments (TMEs) linked to immune-dependent control in mice. We found that early intratumoral accumulation of interferon gamma (IFN-γ)-producing natural killer (NK) cells induced a profound remodeling of the TME and unleashed cytotoxic T cell (CTL)-mediated tumor eradication. Mechanistically, tumor-derived prostaglandin E2 (PGE2) acted selectively on EP2 and EP4 receptors on NK cells, hampered the TME switch, and enabled immune evasion. Analysis of patient datasets across human cancers revealed distinct inflammatory TME phenotypes resembling those associated with cancer immune control versus escape in mice. This allowed us to generate a gene-expression signature that integrated opposing inflammatory factors and predicted patient survival and response to immune checkpoint blockade. Our findings identify features of the tumor inflammatory milieu associated with immune control of cancer and establish a strategy to predict immunotherapy outcomes., Graphical Abstract, Highlights • NK cells drive broad inflammatory remodeling characteristic of T-cell-inflamed tumors • PGE2 acting on EP2 and EP4 on NK cells prevents the TME switch enabling immune escape • Opposing inflammatory profiles found in many human cancer types have prognostic value • A signature capturing pro- and anti-tumor factors predicts response to immunotherapy, Inflammation can fuel or suppress cancer. Bonavita et al. identify NK cells as primary orchestrators of T cell inflammation in murine models and devise an inflammatory signature that predicts patient survival and response to immunotherapy in multiple malignancies.

Epigenetic alterations are defining features of many tumor types and have recently been implicated in tumor immunity. However, the epigenetic mechanisms that mediate immune sensitivity or resistance in cancer cells are poorly characterized. To systematically identify epigenetic regulators of immune evasion in cancer, we performed in vivo loss of function CRISPR screens against 936 chromatin regulator genes in syngeneic murine tumor models treated with immune checkpoint blockade. These screens identified SETDB1, an H3K9-methyltransferase, and associated members of the HUSH and KAP1 complexes as intrinsic mediators of immune evasion in cancer cells. We also found that amplification of SETDB1 (1q21) in certain human tumors is associated with immune exclusion and resistance to immune checkpoint blockade. Mechanistically, we find that SETDB1 targets broad domains, hundreds of kilobases in size, that are predominantly located within the open genome compartment “A” (i.e., euchromatin). These SETDB1 domains show strong enrichment for transposable elements (TEs) of the LTR family, and gene loci that arose through segmental duplication events, a key driver of mammalian genome evolution. Setdb1 KO derepresses latent regulatory elements at TEs within these regions and leads to the transcriptional up-regulation of nearby immune genes, including canonical stimulatory ligands of the NKG2D receptor. SETDB1 loss also triggers the activation of hundreds of TEs with the potential to encode retroviral proteins (Gag, Pol, Env), and promotes immune responses dependent on CD8+ T cells and tumor expression of MHC Class I. Our study establishes SETDB1 as an epigenetic checkpoint that represses intrinsic immunogenicity in cancer cells, and thus represents a novel target to enhance the efficacy and scope of immunotherapy. Citation Format: Jingyi Wu, Arvin Iracheta-Vellve, James Patti, Jeffrey Hsu, Thomas Davis, Deborah Dele-Oni, Peter Du, Jeffrey Ishizuka, Sarah Kim, Susan Klaeger, Nelson Knudsen, Brian Miller, Tung Nguyen, Emily Robitschek, Emily Schneider, Margaret Zimmer, Jacob Jaffe, John Doench, W. Nicholas Haining, Kathleen Yates, Robert Manguso, Bradley Bernstein, Gabriel K. Griffin. Epigenetic silencing by SETDB1 represses tumor-cell intrinsic immunogenicity [abstract]. In: Abstracts: AACR Virtual Special Conference: Tumor Immunology and Immunotherapy; 2020 Oct 19-20. Philadelphia (PA): AACR; Cancer Immunol Res 2021;9(2 Suppl):Abstract nr PO009.

SummaryMitochondria undergo architectural/functional changes in response to metabolic inputs. How this process is regulated in physiological feeding/fasting states remains unclear. Here we show that mitochondrial dynamics (notably fission and mitophagy) and biogenesis are transcriptional targets of the circadian regulator Bmal1 in mouse liver and exhibit a metabolic rhythm in sync with diurnal bioenergetic demands. Bmal1 loss-of-function causes swollen mitochondria incapable of adapting to different nutrient conditions accompanied by diminished respiration and elevated oxidative stress. Consequently, liver-specific Bmal1 knockout (LBmal1KO) mice accumulate oxidative damage and develop hepatic insulin resistance. Restoration of hepatic Bmal1 activities in high-fat-fed mice improves metabolic outcomes, whereas expression of Fis1, a fission protein that promotes quality control, rescues morphological/metabolic defects of LBmal1KO mitochondria. Interestingly, Bmal1 homolog AHA-1 in C. elegans retains the ability to modulate oxidative metabolism and lifespan despite lacking circadian regulation. These results suggest clock genes are evolutionarily conserved energetics regulators.

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.

IL-13 hits the gym Interleukin-13 (IL-13) is a cytokine secreted by T cells, innate lymphoid cells (ILC2s), and granulocytes. It acts as a central mediator in allergy and antihelminth defense with various effects. Knudsen et al. report a distinct role for IL-13 in exercise and metabolism (see the Perspective by Correia and Ruas). Mice subjected to endurance training showed increases in circulating IL-13, which correlated with ILC2 expansion in the muscles. By contrast, exercise-induced increases in muscle fatty acid utilization and mitochondrial biogenesis were erased when mice lacked IL-13. Activation of signaling pathways downstream of the muscle IL-13 receptor was key to this effect. Intramuscular injection of adenoviral IL-13 could recapitulate exercise-induced metabolic reprogramming. This signaling pathway may have evolved to combat the metabolic stresses of parasite infection. Science , this issue p. eaat3987 ; see also p. 470

Bioenergetics homeostasis is important for cells to sustain normal functions and defend against injury. The genetic controls of bioenergetics homeostasis, especially lipid metabolism, remain poorly understood in chronic obstructive pulmonary disease (COPD), the third leading cause of death in the world. Additionally, the biological function of most of the susceptibility genes identified from genome-wide association studies (GWASs) in COPD remains unclear. Here, we aimed to address (1) how fatty acid oxidation (FAO), specifically β-oxidation, a key lipid metabolism pathway that provides energy to cells, contributes to cigarette smoke (CS)-induced COPD; and (2) whether-and if so, how-FAM13A (family with sequence similarity 13 member A), a well-replicated COPD GWAS gene, modulates the FAO pathway. We demonstrated that CS induced expression of carnitine palmitoyltransferase 1A (CPT1A), a key mitochondrial enzyme for the FAO pathway, thereby enhancing FAO. Pharmacological inhibition of FAO by etomoxir blunted CS-induced reactive oxygen species accumulation and cell death in lung epithelial cells. FAM13A promoted FAO, possibly by interacting with and activating sirutin 1, and increasing expression of CPT1A. Furthermore, CS-induced cell death was reduced in lungs from Fam13a-/- mice. Our results suggest that FAM13A, the COPD GWAS gene, shapes the cellular metabolic response to CS exposure by promoting the FAO pathway, which may contribute to COPD development.

Mononuclear phagocytes (MNPs) are a highly heterogeneous group of cells that play important roles in maintaining the body’s homeostasis. Here, we found CD301b (also known as MGL2), a lectin commonly used as a marker for alternatively-activated macrophages (M2), was selectively expressed by a subset of CD11b+CD11c+MHCII+ MNPs in multiple organs including adipose tissues. Depleting CD301b+ MNPs in vivo led to a significant weight loss with increased insulin sensitivity and a marked reduction in serum RELM α, a multifunctional cytokine produced by MNPs. Reconstituting RELM α in CD301b+ MNP-depleted animals restored body weight and normoglycemia. Thus, CD301b+ MNPs play crucial roles in maintaining glucose metabolism and net energy balance.

Objective: Angiogenesis is crucial to maintain tissue homeostasis under nutrient and oxygen deprivation (ischemia). Although considerable evidence supports that angiogenesis is regulated by hypoxia-HIF1α induction of vascular endothelial growth factor (VEGF), the role of nutrient deprivation in angiogenesis is poorly defined. Approach and Results: We report that nutrient deprivation in the form of dietary sulfur amino acid restriction (Methionine/cysteine Restriction; MR) promotes VEGF expression and functional growth of new capillaries in skeletal muscle of mice (Fig.1 A, B). This occurred independently of hypoxia or HIF1α, but instead required the amino acid-sensing eIF2α kinase GCN2 and the transcription factor ATF4 (Fig. 1C). In addition to increased VEGF, nutrient deprivation boosted production of the pro-angiogenic gas hydrogen sulfide (H 2 S) via increased GCN2/ATF4-dependent expression of the H 2 S-generating enzyme cystathionine-gamma-lyase (CGL). The genetic requirement for CGL in angiogenesis triggered by nutrient deprivation, exercise or local VEGF overexpression, as well as the ability of local CGL overexpression to promote angiogenesis in vivo, revealed the critical importance of CGL-derived H 2 S in angiogenesis (Fig. 1D). Finally, plasma H 2 S was reduced in patients with vascular disease (versus non-diseased age-matched controls), and correlated with 2-year survival following vascular surgery (Fig.1 E, F). Conclusions: These data reveal a nutrient-sensing pathway targetable by diet as a previously unrecognized central regulator of VEGF expression and angiogenesis independent of canonical hypoxic signaling. This discovery points to novel dietary interventions and GCN2/ATF4/CGL/H 2 S-based strategies to manipulate angiogenesis. Figure 1

Adipose tissue is comprised of a community of different immune cells that contributes to regulation of energy storage and release by adipocytes. The population of various immune cells is dynamic, undergoing phenotypic and compositional changes in response to physiologic (e.g., fasting vs. feeding) and pathologic (e.g., lean vs. obese) stimuli. Cumulative evidence suggests that a regulatory or anti-inflammatory immune phenotype promotes metabolic homeostasis, whereas a proinflammatory response is associated with metabolic dysregulation (1). Accordingly, lean, healthy white adipose tissue (WAT) is home to a population of alternatively activated macrophages (M2s) as well as immune cells that mediate M2 polarization, such as eosinophils, CD4+ T-helper type (Th) 2 cells, and regulatory T cells (Tregs) (1). During obesity, WAT is infiltrated by additional classically activated macrophages (M1s), neutrophils, mast cells, and CD8+ T cells that release proinflammatory cytokines, thereby sustaining metabolic inflammation, or meta-inflammation (2). Although the changes in immune repertoires associated with different metabolic states are well characterized, mechanisms underlying the switches in immune phenotypes remain unclear. Due to their roles in skewing immune cell responses, multiple cytokines have been suggested to play a role in the development of meta-inflammation in obesity. The first studies to recognize that obesity is associated with inflammation identified tumor necrosis factor-α (TNFα) as a mediator of WAT insulin resistance. TNFα produced by infiltrating M1s triggers the activation of Jun NH2-terminal kinase and inhibitor of κB kinase β causing antagonistic phosphorylation of insulin receptor …

Angiogenesis, the formation of new blood vessels by endothelial cells (EC), is an adaptive response to oxygen/nutrient deprivation orchestrated by vascular endothelial growth factor (VEGF) upon ischemia or exercise. Hypoxia is the best-understood trigger of VEGF expression via the transcription factor HIF1α. Nutrient deprivation is inseparable from hypoxia during ischemia, yet its role in angiogenesis is poorly characterized. Here, we identified sulfur amino acid restriction as a proangiogenic trigger, promoting increased VEGF expression, migration and sprouting in EC in vitro, and increased capillary density in mouse skeletal muscle in vivo, via the GCN2/ATF4 amino acid starvation response pathway independent of hypoxia or HIF1α. We also identified a requirement for cystathionine-γ-lyase in VEGF-dependent angiogenesis via increased hydrogen sulfide (H(2)S) production. H(2)S mediated its proangiogenic effects in part by inhibiting mitochondrial electron transport and oxidative phosphorylation, resulting in increased glucose uptake and glycolytic ATP production.

Metabolic regulation and immune signaling are closely linked, as evidenced by both the physical proximity between metabolic cells (e.g., adipocytes and hepatocytes) and resident macrophages as well as the progression of inflammation in metabolic syndrome. Contrasting the reactions to pathogen infections, meta-inflammation describes a novel type of low-grade, unresolvable immune response that is in the causal pathway to metabolic dysregulation (1). Although how meta-inflammation is initiated remains unclear, the T-helper cell type 1 (Th1)/Th2 (or M1/M2) paradigm provides a simplified view of how immune cells are involved in readjusting metabolic set points in response to nutrient intake (2). It appears that Th1 cytokines (e.g., interleukin [IL]-12 and interferon-γ [IFNγ]) or Th1 polarized immune cells promote insulin resistance, whereas Th2 signaling (e.g., IL-4 and IL-13) sustains metabolic homeostasis (3). In mouse genetic models, for example, tipping the Th1/Th2 balance toward one specific spectrum leads to the expected outcome (4). As such, immunometabolism has become an attractive target to treat metabolic diseases. Members of the signal transducer and activator of the transcription (STAT) family are transcription factors that mediate the signaling events of many cytokines in immune and nonimmune cells (5–7). The seven mammalian STAT proteins each contain a DNA-binding domain, a transactivation domain, and an Src homology 2 (SH2) domain; the latter is required for dimerization (5). When cytokines are bound to cell …