bims-mepmim 2023-06-18 papers

bims-mepmim

Biomed News

on Metabolites in pathological microenvironments and immunometabolism

Issue of 2023–06–18
35 papers selected by
Erika Mariana Palmieri, NIH/NCI Laboratory of Cancer ImmunoMetabolism

Time-resolved proteomic analyses of senescence highlight metabolic rewiring of mitochondria.
Mitochondrial folate metabolism-mediated α-linolenic acid exhaustion masks liver fibrosis resolution.
Coenzyme biosynthesis in response to precursor availability reveals incorporation of β-alanine from pantothenate in prototrophic bacteria.
Energy substrate metabolism, mitochondrial structure and oxidative stress after cardiac ischemia-reperfusion in mice lacking UCP3.
A mitochondrial iron-responsive pathway regulated by DELE1.
Regulation of systemic metabolism by tissue-resident immune cell circuits.
Ceramide sensing by human SPT-ORMDL complex for establishing sphingolipid homeostasis.
Single cell and spatial sequencing define processes by which keratinocytes and fibroblasts amplify inflammatory responses in psoriasis.
RAB27B controls palmitoylation-dependent NRAS trafficking and signaling in myeloid leukemia.
Branched-chain keto acids inhibit mitochondrial pyruvate carrier and suppress gluconeogenesis in hepatocytes.
Microscopy-Directed Imaging Mass Spectrometry for Rapid High Spatial Resolution Molecular Imaging of Glomeruli.
Autophagy fuels mitochondrial function through regulation of iron metabolism in pancreatic cancer.
The structure of phosphatidylinositol remodeling MBOAT7 reveals its catalytic mechanism and enables inhibitor identification.
Direct stimulation of de novo nucleotide synthesis by O-GlcNAcylation.
Carnitine o-octanoyltransferase (CROT) is a p53 target that promotes oxidative metabolism and cell survival following nutrient starvation.
Itaconic acid underpins hepatocyte lipid metabolism in non-alcoholic fatty liver disease in male mice.
Senescent Macrophages Promote KRAS-Driven Lung Tumorigenesis.
Ketogenic diet promotes tumor ferroptosis but induces relative corticosterone deficiency that accelerates cachexia.
PERK signaling promotes mitochondrial elongation by remodeling membrane phosphatidic acid.
Reduced acetylation of TFAM promotes bioenergetic dysfunction in the failing heart.
Sfxn5 Regulation of Actin Polymerization for Neutrophil Spreading Depends on a Citrate-Cholesterol-PI(4,5)P2 Pathway.
IL-3 orchestrates ulcerative colitis pathogenesis by controlling the development and the recruitment of splenic reservoir neutrophils.
MCT4-dependent lactate secretion suppresses antitumor immunity in LKB1-deficient lung adenocarcinoma.
Deciphering the biosynthesis of a novel lipid in Mycobacterium tuberculosis expands the known roles of the nitroreductase superfamily.
Butyrate inhibits LPC-induced endothelial dysfunction by regulating nNOS-produced NO and ROS production.
Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids.
A 2.2 Å cryoEM structure of a quinol-dependent NO Reductase shows close similarity to respiratory oxidases.
Acetate controls endothelial-to-mesenchymal transition.
Tumor-derived prostaglandin E2 programs cDC1 dysfunction to impair intratumoral orchestration of anti-cancer T cell responses.
Itaconate trims the fat.
Activation of regulatory dendritic cells by Mertk coincides with a temporal wave of apoptosis in neonatal lungs.
Canonical BAF complex activity shapes the enhancer landscape that licenses CD8+ T cell effector and memory fates.
Defective extracellular matrix remodeling in brown adipose tissue is associated with fibro-inflammation and reduced diet-induced thermogenesis.
Cross talk between Paneth and tuft cells drives dysbiosis and inflammation in the gut mucosa.
Farnesyl diphosphate synthase exacerbates nonalcoholic steatohepatitis via the activation of AHR-CD36 axis.

Life Sci Alliance. 2023 Sep;pii: e202302127. [Epub ahead of print]6(9):

Time-resolved proteomic analyses of senescence highlight metabolic rewiring of mitochondria.

Jun Yong Kim, Ilian Atanassov, Frederik Dethloff, Lara Kroczek, Thomas Langer.

Mitochondrial dysfunction and cellular senescence are hallmarks of aging. However, the relationship between these two phenomena remains incompletely understood. In this study, we investigated the rewiring of mitochondria upon development of the senescent state in human IMR90 fibroblasts. Determining the bioenergetic activities and abundance of mitochondria, we demonstrate that senescent cells accumulate mitochondria with reduced OXPHOS activity, resulting in an overall increase of mitochondrial activities in senescent cells. Time-resolved proteomic analyses revealed extensive reprogramming of the mitochondrial proteome upon senescence development and allowed the identification of metabolic pathways that are rewired with different kinetics upon establishment of the senescent state. Among the early responding pathways, the degradation of branched-chain amino acid was increased, whereas the one carbon folate metabolism was decreased. Late-responding pathways include lipid metabolism and mitochondrial translation. These signatures were confirmed by metabolic flux analyses, highlighting metabolic rewiring as a central feature of mitochondria in cellular senescence. Together, our data provide a comprehensive view on the changes in mitochondrial proteome in senescent cells and reveal how the mitochondrial metabolism is rewired in senescent cells.

DOI: https://doi.org/10.26508/lsa.202302127
J Biol Chem. 2023 Jun 10. pii: S0021-9258(23)01937-3. [Epub ahead of print] 104909

Mitochondrial folate metabolism-mediated α-linolenic acid exhaustion masks liver fibrosis resolution.

Yanjie Gao, Bingfeng Zheng, Shuaiqi Xu, Zhibo Zhao, Wanyue Liu, Tingyu Wang, Manman Yuan, Xueqing Sun, Yang Tan, Qiang Xu, Xingxin Wu.

  Sustainable TGF-β1 signaling drives organ fibrogenesis. However, the cellular adaptation to maintain TGF-β1 signaling remains unclear. In this study, we revealed that dietary folate restriction promoted the resolution of liver fibrosis in mice with nonalcoholic steatohepatitis (NASH). In activated hepatic stellate cells (HSCs), folate shifted toward mitochondrial metabolism to sustain TGF-β1 signaling. Mechanistically, nontargeted metabolomics screening identified that α-linolenic acid (ALA) is exhausted by mitochondrial folate metabolism in activated HSCs. Knocking down serine hydroxymethyltransferase 2 (SHMT2) increases the bioconversion of ALA to docosahexaenoic acid (DHA) which inhibits TGF-β1 signaling. Finally, blocking mitochondrial folate metabolism promoted liver fibrosis resolution in NASH mice. In conclusion, mitochondrial folate metabolism/ALA exhaustion/TGF-βR1 reproduction is a feedforward signaling to sustain profibrotic TGF-β1 signaling and targeting mitochondrial folate metabolism is a promising strategy to enforce liver fibrosis resolution.

Keywords:  ALA; DHA; Hepatic stellate cells; Liver fibrosis resolution; Mitochondrial folate metabolism; SHMT2; TGF-β1 signaling

DOI:  https://doi.org/10.1016/j.jbc.2023.104909
J Biol Chem. 2023 Jun 12. pii: S0021-9258(23)01947-6. [Epub ahead of print] 104919

Coenzyme biosynthesis in response to precursor availability reveals incorporation of β-alanine from pantothenate in prototrophic bacteria.

Birgitta Ryback, Julia A Vorholt.

  Coenzymes are important for all classes of enzymatic reactions and essential for cellular metabolism. Most coenzymes are synthesized from dedicated precursors, also referred to as vitamins, which prototrophic bacteria can either produce themselves from simpler substrates or take up from the environment. The extent to which prototrophs use supplied vitamins and whether externally available vitamins affect the size of intracellular coenzyme pools and control endogenous vitamin synthesis is currently largely unknown. Here, we studied coenzyme pool sizes and vitamin incorporation into coenzymes during growth on different carbon source and vitamin supplementation regimes using metabolomics approaches. We found that the model bacterium Escherichia coli incorporated pyridoxal, niacin, and pantothenate into pyridoxal 5'-phosphate, NAD, and coenzyme A (CoA), respectively. In contrast, riboflavin was not taken up and was produced exclusively endogenously. Coenzyme pools were mostly homeostatic and not affected by externally supplied precursors. Remarkably, we found that pantothenate is not incorporated into CoA as such but is first degraded to pantoate and β-alanine and then rebuilt. This pattern was conserved in various bacterial isolates, suggesting a preference for β-alanine over pantothenate utilization in CoA synthesis. Finally, we found that the endogenous synthesis of coenzyme precursors remains active when vitamins are supplied, which is consistent with described expression data of genes for enzymes involved in coenzyme biosynthesis under these conditions. Continued production of endogenous coenzymes may ensure rapid synthesis of the mature coenzyme under changing environmental conditions, protect against coenzyme limitation, and explain vitamin availability in naturally oligotrophic environments.

Keywords:  Bacterial metabolism; NAD biosynthesis; anaplerosis; biotin; biotin.; coenzyme A; coenzyme metabolism; flavin; flavin adenine dinucleotide (FAD); flavin mononucleotide (FMN); homeostasis; mass spectrometry (MS); metabolic shunt; metabolic tracer; metabolomics; microbiology; microbiome; nicotinamide adenine dinucleotide (NAD); overflow metabolism; pyridoxal phosphate; secretion; systems biology; transport; vitamin; β-alanine

DOI:  https://doi.org/10.1016/j.jbc.2023.104919
Free Radic Biol Med. 2023 Jun 07. pii: S0891-5849(23)00430-6. [Epub ahead of print]

Energy substrate metabolism, mitochondrial structure and oxidative stress after cardiac ischemia-reperfusion in mice lacking UCP3.

Patricia Sánchez-Pérez, Ana Mata, May-Kristin Torp, Elia López-Bernardo, Christina M Heiestad, Jan Magnus Aronsen, Antonio Molina-Iracheta, Luis J Jiménez-Borreguero, Pablo García-Roves, Ana S H Costa, Christian Frezza, Michael P Murphy, Kåre-Olav Stenslokken, Susana Cadenas.

  Myocardial ischemia-reperfusion (IR) injury may result in cardiomyocyte dysfunction. Mitochondria play a critical role in cardiomyocyte recovery after IR injury. The mitochondrial uncoupling protein 3 (UCP3) has been proposed to reduce mitochondrial reactive oxygen species (ROS) production and to facilitate fatty acid oxidation. As both mechanisms might be protective following IR injury, we investigated functional, mitochondrial structural, and metabolic cardiac remodeling in wild-type mice and in mice lacking UCP3 (UCP3-KO) after IR. Results showed that infarct size in isolated perfused hearts subjected to IR ex vivo was larger in adult and old UCP3-KO mice than in equivalent wild-type mice, and was accompanied by higher levels of creatine kinase in the effluent and by more pronounced mitochondrial structural changes. The greater myocardial damage in UCP3-KO hearts was confirmed in vivo after coronary artery occlusion followed by reperfusion. S1QEL, a suppressor of superoxide generation from site IQ in complex I, limited infarct size in UCP3-KO hearts, pointing to exacerbated superoxide production as a possible cause of the damage. Metabolomics analysis of isolated perfused hearts confirmed the reported accumulation of succinate, xanthine and hypoxanthine during ischemia, and a shift to anaerobic glucose utilization, which all recovered upon reoxygenation. The metabolic response to ischemia and IR was similar in UCP3-KO and wild-type hearts, being lipid and energy metabolism the most affected pathways. Fatty acid oxidation and complex I (but not complex II) activity were equally impaired after IR. Overall, our results indicate that UCP3 deficiency promotes enhanced superoxide generation and mitochondrial structural changes that increase the vulnerability of the myocardium to IR injury.

Keywords:  Energy metabolism; Ischemia-reperfusion injury; Mitochondrial respiration; Mitochondrial structure; Oxidative stress; UCP3 (uncoupling protein 3)

DOI:  https://doi.org/10.1016/j.freeradbiomed.2023.05.014
Mol Cell. 2023 Jun 15. pii: S1097-2765(23)00413-6. [Epub ahead of print]83(12): 2059-2076.e6

A mitochondrial iron-responsive pathway regulated by DELE1.

Yusuke Sekine, Ryan Houston, Eva-Maria Eckl, Evelyn Fessler, Derek P Narendra, Lucas T Jae, Shiori Sekine.

  The heme-regulated kinase HRI is activated under heme/iron deficient conditions; however, the underlying molecular mechanism is incompletely understood. Here, we show that iron-deficiency-induced HRI activation requires the mitochondrial protein DELE1. Notably, mitochondrial import of DELE1 and its subsequent protein stability are regulated by iron availability. Under steady-state conditions, DELE1 is degraded by the mitochondrial matrix-resident protease LONP1 soon after mitochondrial import. Upon iron chelation, DELE1 import is arrested, thereby stabilizing DELE1 on the mitochondrial surface to activate the HRI-mediated integrated stress response (ISR). Ablation of this DELE1-HRI-ISR pathway in an erythroid cell model enhances cell death under iron-limited conditions, suggesting a cell-protective role for this pathway in iron-demanding cell lineages. Our findings highlight mitochondrial import regulation of DELE1 as the core component of a previously unrecognized mitochondrial iron responsive pathway that elicits stress signaling following perturbation of iron homeostasis.

Keywords:  DELE1; HRI; LONP1; erythroid cells; integrated stress response; iron; mitochondria; mitochondrial import; mitochondrial proteostasis

DOI:  https://doi.org/10.1016/j.molcel.2023.05.031
Immunity. 2023 Jun 13. pii: S1074-7613(23)00218-2. [Epub ahead of print]56(6): 1168-1186

Regulation of systemic metabolism by tissue-resident immune cell circuits.

Joey H Li, Matthew R Hepworth, Timothy E O'Sullivan.

  Recent studies have demonstrated that tissue homeostasis and metabolic function are dependent on distinct tissue-resident immune cells that form functional cell circuits with structural cells. Within these cell circuits, immune cells integrate cues from dietary contents and commensal microbes in addition to endocrine and neuronal signals present in the tissue microenvironment to regulate structural cell metabolism. These tissue-resident immune circuits can become dysregulated during inflammation and dietary overnutrition, contributing to metabolic diseases. Here, we review the evidence describing key cellular networks within and between the liver, gastrointestinal tract, and adipose tissue that control systemic metabolism and how these cell circuits become dysregulated during certain metabolic diseases. We also identify open questions in the field that have the potential to enhance our understanding of metabolic health and disease.

Keywords:  cell circuits; immunometabolism; metabolism; systems immunology; tissue homeostasis; tissue-resident

DOI:  https://doi.org/10.1016/j.immuni.2023.05.001
Nat Commun. 2023 Jun 13. 14(1): 3475

Ceramide sensing by human SPT-ORMDL complex for establishing sphingolipid homeostasis.

Tian Xie, Peng Liu, Xinyue Wu, Feitong Dong, Zike Zhang, Jian Yue, Usha Mahawar, Faheem Farooq, Hisham Vohra, Qi Fang, Wenchen Liu, Binks W Wattenberg, Xin Gong.

The ORM/ORMDL family proteins function as regulatory subunits of the serine palmitoyltransferase (SPT) complex, which is the initiating and rate-limiting enzyme in sphingolipid biosynthesis. This complex is tightly regulated by cellular sphingolipid levels, but the sphingolipid sensing mechanism is unknown. Here we show that purified human SPT-ORMDL complexes are inhibited by the central sphingolipid metabolite ceramide. We have solved the cryo-EM structure of the SPT-ORMDL3 complex in a ceramide-bound state. Structure-guided mutational analyses reveal the essential function of this ceramide binding site for the suppression of SPT activity. Structural studies indicate that ceramide can induce and lock the N-terminus of ORMDL3 into an inhibitory conformation. Furthermore, we demonstrate that childhood amyotrophic lateral sclerosis (ALS) variants in the SPTLC1 subunit cause impaired ceramide sensing in the SPT-ORMDL3 mutants. Our work elucidates the molecular basis of ceramide sensing by the SPT-ORMDL complex for establishing sphingolipid homeostasis and indicates an important role of impaired ceramide sensing in disease development.

DOI: https://doi.org/10.1038/s41467-023-39274-y
Nat Commun. 2023 Jun 12. 14(1): 3455

Single cell and spatial sequencing define processes by which keratinocytes and fibroblasts amplify inflammatory responses in psoriasis.

Feiyang Ma, Olesya Plazyo, Allison C Billi, Lam C Tsoi, Xianying Xing, Rachael Wasikowski, Mehrnaz Gharaee-Kermani, Grace Hile, Yanyun Jiang, Paul W Harms, Enze Xing, Joseph Kirma, Jingyue Xi, Jer-En Hsu, Mrinal K Sarkar, Yutein Chung, Jeremy Di Domizio, Michel Gilliet, Nicole L Ward, Emanual Maverakis, Eynav Klechevsky, John J Voorhees, James T Elder, Jun Hee Lee, J Michelle Kahlenberg, Matteo Pellegrini, Robert L Modlin, Johann E Gudjonsson.

The immunopathogenesis of psoriasis, a common chronic inflammatory disease of the skin, is incompletely understood. Here we demonstrate, using a combination of single cell and spatial RNA sequencing, IL-36 dependent amplification of IL-17A and TNF inflammatory responses in the absence of neutrophil proteases, which primarily occur within the supraspinous layer of the psoriatic epidermis. We further show that a subset of SFRP2+ fibroblasts in psoriasis contribute to amplification of the immune network through transition to a pro-inflammatory state. The SFRP2+ fibroblast communication network involves production of CCL13, CCL19 and CXCL12, connected by ligand-receptor interactions to other spatially proximate cell types: CCR2+ myeloid cells, CCR7+ LAMP3+ dendritic cells, and CXCR4 expressed on both CD8+ Tc17 cells and keratinocytes, respectively. The SFRP2+ fibroblasts also express cathepsin S, further amplifying inflammatory responses by activating IL-36G in keratinocytes. These data provide an in-depth view of psoriasis pathogenesis, which expands our understanding of the critical cellular participants to include inflammatory fibroblasts and their cellular interactions.

DOI: https://doi.org/10.1038/s41467-023-39020-4
J Clin Invest. 2023 06 15. pii: e165510. [Epub ahead of print]133(12):

RAB27B controls palmitoylation-dependent NRAS trafficking and signaling in myeloid leukemia.

Jian-Gang Ren, Bowen Xing, Kaosheng Lv, Rachel A O'Keefe, Mengfang Wu, Ruoxing Wang, Kaylyn M Bauer, Arevik Ghazaryan, George M Burslem, Jing Zhang, Ryan M O'Connell, Vinodh Pillai, Elizabeth O Hexner, Mark R Philips, Wei Tong.

  RAS mutations are among the most prevalent oncogenic drivers in cancers. RAS proteins propagate signals only when associated with cellular membranes as a consequence of lipid modifications that impact their trafficking. Here, we discovered that RAB27B, a RAB family small GTPase, controlled NRAS palmitoylation and trafficking to the plasma membrane, a localization required for activation. Our proteomic studies revealed RAB27B upregulation in CBL- or JAK2-mutated myeloid malignancies, and its expression correlated with poor prognosis in acute myeloid leukemias (AMLs). RAB27B depletion inhibited the growth of CBL-deficient or NRAS-mutant cell lines. Strikingly, Rab27b deficiency in mice abrogated mutant but not WT NRAS-mediated progenitor cell growth, ERK signaling, and NRAS palmitoylation. Further, Rab27b deficiency significantly reduced myelomonocytic leukemia development in vivo. Mechanistically, RAB27B interacted with ZDHHC9, a palmitoyl acyltransferase that modifies NRAS. By regulating palmitoylation, RAB27B controlled c-RAF/MEK/ERK signaling and affected leukemia development. Importantly, RAB27B depletion in primary human AMLs inhibited oncogenic NRAS signaling and leukemic growth. We further revealed a significant correlation between RAB27B expression and sensitivity to MEK inhibitors in AMLs. Thus, our studies presented a link between RAB proteins and fundamental aspects of RAS posttranslational modification and trafficking, highlighting future therapeutic strategies for RAS-driven cancers.

Keywords:  Cancer; Cell Biology; Hematology; Signal transduction

DOI:  https://doi.org/10.1172/JCI165510
Cell Rep. 2023 Jun 12. pii: S2211-1247(23)00652-6. [Epub ahead of print]42(6): 112641

Branched-chain keto acids inhibit mitochondrial pyruvate carrier and suppress gluconeogenesis in hepatocytes.

Kiyoto Nishi, Akira Yoshii, Lauren Abell, Bo Zhou, Ricardo Frausto, Julia Ritterhoff, Timothy S McMillen, Ian Sweet, Yibin Wang, Chen Gao, Rong Tian.

  Branched-chain amino acid (BCAA) metabolism is linked to glucose homeostasis, but the underlying signaling mechanisms are unclear. We find that gluconeogenesis is reduced in mice deficient of Ppm1k, a positive regulator of BCAA catabolism, which protects against obesity-induced glucose intolerance. Accumulation of branched-chain keto acids (BCKAs) inhibits glucose production in hepatocytes. BCKAs suppress liver mitochondrial pyruvate carrier (MPC) activity and pyruvate-supported respiration. Pyruvate-supported gluconeogenesis is selectively suppressed in Ppm1k-deficient mice and can be restored with pharmacological activation of BCKA catabolism by BT2. Finally, hepatocytes lack branched-chain aminotransferase that alleviates BCKA accumulation via reversible conversion between BCAAs and BCKAs. This renders liver MPC most susceptible to circulating BCKA levels hence a sensor of BCAA catabolism.

Keywords:  CP: Metabolism; branched-chain amino acids; branched-chain keto acids; gluconeogenesis; mitochondrial pyruvate carrier; pyruvate

DOI:  https://doi.org/10.1016/j.celrep.2023.112641
J Am Soc Mass Spectrom. 2023 Jun 15.

Microscopy-Directed Imaging Mass Spectrometry for Rapid High Spatial Resolution Molecular Imaging of Glomeruli.

Allison B Esselman, Nathan Heath Patterson, Lukasz G Migas, Martin Dufresne, Katerina V Djambazova, Madeline E Colley, Raf Van de Plas, Jeffrey M Spraggins.

  The glomerulus is a multicellular functional tissue unit (FTU) of the nephron that is responsible for blood filtration. Each glomerulus contains multiple substructures and cell types that are crucial for their function. To understand normal aging and disease in kidneys, methods for high spatial resolution molecular imaging within these FTUs across whole slide images is required. Here we demonstrate a workflow using microscopy-driven selected sampling to enable 5 μm pixel size matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) of all glomeruli within whole slide human kidney tissues. Such high spatial resolution imaging entails large numbers of pixels, increasing the data acquisition times. Automating FTU-specific tissue sampling enables high-resolution analysis of critical tissue structures, while concurrently maintaining throughput. Glomeruli were automatically segmented using coregistered autofluorescence microscopy data, and these segmentations were translated into MALDI IMS measurement regions. This allowed high-throughput acquisition of 268 glomeruli from a single whole slide human kidney tissue section. Unsupervised machine learning methods were used to discover molecular profiles of glomerular subregions and differentiate between healthy and diseased glomeruli. Average spectra for each glomerulus were analyzed using Uniform Manifold Approximation and Projection (UMAP) and k-means clustering, yielding 7 distinct groups of differentiated healthy and diseased glomeruli. Pixel-wise k-means clustering was applied to all glomeruli, showing unique molecular profiles localized to subregions within each glomerulus. Automated microscopy-driven, FTU-targeted acquisition for high spatial resolution molecular imaging maintains high-throughput and enables rapid assessment of whole slide images at cellular resolution and identification of tissue features associated with normal aging and disease.

Keywords:  MALDI IMS; glomeruli; high spatial resolution imaging; high-throughput; human kidney; lipids; molecular imaging; multimodal; targeted; unsupervised machine learning; whole slide imaging

DOI:  https://doi.org/10.1021/jasms.3c00033
Autophagy. 2023 Jun 13. 1-2

Autophagy fuels mitochondrial function through regulation of iron metabolism in pancreatic cancer.

Subhadip Mukhopadhyay, Joel Encarnacion-Rosado, Alec C Kimmelman.

  Pancreatic ductal adenocarcinoma (PDAC) has one of the lowest 5-year survival rates of any cancer in the United States. Our previous work has shown that autophagy can promote PDAC progression. We recently established the importance of autophagy in regulating bioavailable iron to control mitochondrial metabolism in PDAC. We found that inhibition of autophagy in PDAC leads to mitochondrial dysfunction due to abrogation of succinate dehydrogenase complex iron sulfur subunit B (SDHB) expression. Additionally, we observed that cancer-associated fibroblasts (CAFs) can provide iron to autophagy-inhibited PDAC tumor cells, thereby increasing their resistance to autophagy inhibition. To impede such metabolic compensation, we used a low iron diet together with autophagy inhibition and demonstrated a significant improvement of tumor response in syngeneic PDAC models.Abbreviations: PDAC: Pancreatic ductal adenocarcinoma; CAFs: cancer-associated fibroblasts; SDHB: succinate dehydrogenase complex iron sulfur subunit B; ISCA1: iron sulfur cluster assembly protein 1; FPN: ferroportin; LIP: labile iron pool; FAC: ferric ammonium chloride; OCR: oxygen consumption rate; OXPHOS: oxidative phosphorylation, IL6: interleukin 6; Fe-S: iron sulfur; ATP: adenosine triphosphate.

Keywords:  Autophagy; cancer associated fibroblasts; iron metabolism; lysosome; mitochondria; pancreatic ductal adenocarcinoma

DOI:  https://doi.org/10.1080/15548627.2023.2223473
Nat Commun. 2023 Jun 14. 14(1): 3533

The structure of phosphatidylinositol remodeling MBOAT7 reveals its catalytic mechanism and enables inhibitor identification.

Kun Wang, Chia-Wei Lee, Xuewu Sui, Siyoung Kim, Shuhui Wang, Aidan B Higgs, Aaron J Baublis, Gregory A Voth, Maofu Liao, Tobias C Walther, Robert V Farese.

Cells remodel glycerophospholipid acyl chains via the Lands cycle to adjust membrane properties. Membrane-bound O-acyltransferase (MBOAT) 7 acylates lyso-phosphatidylinositol (lyso-PI) with arachidonyl-CoA. MBOAT7 mutations cause brain developmental disorders, and reduced expression is linked to fatty liver disease. In contrast, increased MBOAT7 expression is linked to hepatocellular and renal cancers. The mechanistic basis of MBOAT7 catalysis and substrate selectivity are unknown. Here, we report the structure and a model for the catalytic mechanism of human MBOAT7. Arachidonyl-CoA and lyso-PI access the catalytic center through a twisted tunnel from the cytosol and lumenal sides, respectively. N-terminal residues on the ER lumenal side determine phospholipid headgroup selectivity: swapping them between MBOATs 1, 5, and 7 converts enzyme specificity for different lyso-phospholipids. Finally, the MBOAT7 structure and virtual screening enabled identification of small-molecule inhibitors that may serve as lead compounds for pharmacologic development.

DOI: https://doi.org/10.1038/s41467-023-38932-5
Nat Chem Biol. 2023 Jun 12.

Direct stimulation of de novo nucleotide synthesis by O-GlcNAcylation.

Lulu Chen, Qi Zhou, Pingfeng Zhang, Wei Tan, Yingge Li, Ziwen Xu, Junfeng Ma, Gary M Kupfer, Yanxin Pei, Qibin Song, Huadong Pei.

O-linked β-N-acetyl glucosamine (O-GlcNAc) is at the crossroads of cellular metabolism, including glucose and glutamine; its dysregulation leads to molecular and pathological alterations that cause diseases. Here we report that O-GlcNAc directly regulates de novo nucleotide synthesis and nicotinamide adenine dinucleotide (NAD) production upon abnormal metabolic states. Phosphoribosyl pyrophosphate synthetase 1 (PRPS1), the key enzyme of the de novo nucleotide synthesis pathway, is O-GlcNAcylated by O-GlcNAc transferase (OGT), which triggers PRPS1 hexamer formation and relieves nucleotide product-mediated feedback inhibition, thereby boosting PRPS1 activity. PRPS1 O-GlcNAcylation blocked AMPK binding and inhibited AMPK-mediated PRPS1 phosphorylation. OGT still regulates PRPS1 activity in AMPK-deficient cells. Elevated PRPS1 O-GlcNAcylation promotes tumorigenesis and confers resistance to chemoradiotherapy in lung cancer. Furthermore, Arts-syndrome-associated PRPS1 R196W mutant exhibits decreased PRPS1 O-GlcNAcylation and activity. Together, our findings establish a direct connection among O-GlcNAc signals, de novo nucleotide synthesis and human diseases, including cancer and Arts syndrome.

DOI: https://doi.org/10.1038/s41589-023-01354-x
J Biol Chem. 2023 Jun 10. pii: S0021-9258(23)01936-1. [Epub ahead of print] 104908

Carnitine o-octanoyltransferase (CROT) is a p53 target that promotes oxidative metabolism and cell survival following nutrient starvation.

Jack D Sanford, Derek Franklin, Gabriella A Grois, Aiwen Jin, Yanping Zhang.

  Whereas it is known that p53 broadly regulates cell metabolism, the specific activities that mediate this regulation remain partially understood. Here, we identified carnitine o-octanoyltransferase (CROT) as a p53 transactivation target that is upregulated by cellular stresses in a p53-dependent manner. CROT is a peroxisomal enzyme catalyzing very long-chain fatty acids (VLCFAs) conversion to medium chain fatty acids (MCFAs) that can be absorbed by mitochondria during β-oxidation. p53 induces CROT transcription through binding to consensus response elements in the 5'-UTR of CROT mRNA. Overexpression of wild type but not enzymatically inactive mutant CROT promotes mitochondrial oxidative respiration, while down-regulation of CROT inhibits mitochondrial oxidative respiration. Nutrient depletion induces p53-dependent CROT expression that facilitates cell growth and survival; in contrast cells deficient in CROT have blunted cell growth and reduced survival during nutrient depletion. Together, these data are consistent with a model where p53-regulated CROT expression allows cells to be more efficiently utilizing stored VLCFAs to survive nutrient depletion stresses.

Keywords:  CROT; nutrient starvation; oxidative metabolism; p53

DOI:  https://doi.org/10.1016/j.jbc.2023.104908
Nat Metab. 2023 Jun 12.

Itaconic acid underpins hepatocyte lipid metabolism in non-alcoholic fatty liver disease in male mice.

Jonathan M Weiss, Erika M Palmieri, Marieli Gonzalez-Cotto, Ian A Bettencourt, Emily L Megill, Nathaniel W Snyder, Daniel W McVicar.

Itaconate, the product of the decarboxylation of cis-aconitate, regulates numerous biological processes. We and others have revealed itaconate as a regulator of fatty acid β-oxidation, generation of mitochondrial reactive oxygen species and the metabolic interplay between resident macrophages and tumors. In the present study, we show that itaconic acid is upregulated in human non-alcoholic steatohepatitis and a mouse model of non-alcoholic fatty liver disease. Male mice deficient in the gene responsible for itaconate production (immunoresponsive gene (Irg)-1) have exacerbated lipid accumulation in the liver, glucose and insulin intolerance and mesenteric fat deposition. Treatment of mice with the itaconate derivative, 4-octyl itaconate, reverses dyslipidemia associated with high-fat diet feeding. Mechanistically, itaconate treatment of primary hepatocytes reduces lipid accumulation and increases their oxidative phosphorylation in a manner dependent upon fatty acid oxidation. We propose a model whereby macrophage-derived itaconate acts in trans upon hepatocytes to modulate the liver's ability to metabolize fatty acids.

DOI: https://doi.org/10.1038/s42255-023-00801-2
Cancer Discov. 2023 Jun 16. OF1

Senescent Macrophages Promote KRAS-Driven Lung Tumorigenesis.

Senescent macrophages in the tumor microenvironment support lung tumor initiation and immunosuppression.

DOI: https://doi.org/10.1158/2159-8290.CD-RW2023-092
Cell Metab. 2023 Jun 07. pii: S1550-4131(23)00185-7. [Epub ahead of print]

Ketogenic diet promotes tumor ferroptosis but induces relative corticosterone deficiency that accelerates cachexia.

Miriam Ferrer, Nicholas Mourikis, Emma E Davidson, Sam O Kleeman, Marta Zaccaria, Jill Habel, Rachel Rubino, Qing Gao, Thomas R Flint, Lisa Young, Claire M Connell, Michael J Lukey, Marcus D Goncalves, Eileen P White, Ashok R Venkitaraman, Tobias Janowitz.

  Glucose dependency of cancer cells can be targeted with a high-fat, low-carbohydrate ketogenic diet (KD). However, in IL-6-producing cancers, suppression of the hepatic ketogenic potential hinders the utilization of KD as energy for the organism. In IL-6-associated murine models of cancer cachexia, we describe delayed tumor growth but accelerated cachexia onset and shortened survival in mice fed KD. Mechanistically, this uncoupling is a consequence of the biochemical interaction of two NADPH-dependent pathways. Within the tumor, increased lipid peroxidation and, consequently, saturation of the glutathione (GSH) system lead to the ferroptotic death of cancer cells. Systemically, redox imbalance and NADPH depletion impair corticosterone biosynthesis. Administration of dexamethasone, a potent glucocorticoid, increases food intake, normalizes glucose levels and utilization of nutritional substrates, delays cachexia onset, and extends the survival of tumor-bearing mice fed KD while preserving reduced tumor growth. Our study emphasizes the need to investigate the effects of systemic interventions on both the tumor and the host to accurately assess therapeutic potential. These findings may be relevant to clinical research efforts that investigate nutritional interventions such as KD in patients with cancer.

Keywords:  GDF-15; IL-6; NADPH; cachexia; cancer; corticosterone; ferroptosis; ketogenic diet; lipid peroxidation; steroid

DOI:  https://doi.org/10.1016/j.cmet.2023.05.008
EMBO J. 2023 Jun 12. e113908

PERK signaling promotes mitochondrial elongation by remodeling membrane phosphatidic acid.

Valerie Perea, Christian Cole, Justine Lebeau, Vivian Dolina, Kelsey R Baron, Aparajita Madhavan, Jeffery W Kelly, Danielle A Grotjahn, R Luke Wiseman.

  Endoplasmic reticulum (ER) stress and mitochondrial dysfunction are linked in the onset and pathogenesis of numerous diseases. This has led to considerable interest in defining the mechanisms responsible for regulating mitochondria during ER stress. The PERK signaling arm of the unfolded protein response (UPR) has emerged as a prominent ER stress-responsive signaling pathway that regulates diverse aspects of mitochondrial biology. Here, we show that PERK activity promotes adaptive remodeling of mitochondrial membrane phosphatidic acid (PA) to induce protective mitochondrial elongation during acute ER stress. We find that PERK activity is required for ER stress-dependent increases in both cellular PA and YME1L-dependent degradation of the intramitochondrial PA transporter PRELID1. These two processes lead to the accumulation of PA on the outer mitochondrial membrane where it can induce mitochondrial elongation by inhibiting mitochondrial fission. Our results establish a new role for PERK in the adaptive remodeling of mitochondrial phospholipids and demonstrate that PERK-dependent PA regulation adapts organellar shape in response to ER stress.

Keywords:  endoplasmic reticulum (ER) stress; mitochondrial morphology; phosphatidic acid; unfolded protein response (UPR)

DOI:  https://doi.org/10.15252/embj.2023113908
iScience. 2023 Jun 16. 26(6): 106942

Reduced acetylation of TFAM promotes bioenergetic dysfunction in the failing heart.

Manling Zhang, Ning Feng, Zishan Peng, Dharendra Thapa, Michael W Stoner, Janet R Manning, Charles F McTiernan, Xue Yang, Michael J Jurczak, Danielle Guimaraes, Krithika Rao, Sruti Shiva, Brett A Kaufman, Michael N Sack, Iain Scott.

  General control of amino acid synthesis 5-like 1 (GCN5L1) was previously identified as a key regulator of protein lysine acetylation in mitochondria. Subsequent studies demonstrated that GCN5L1 regulates the acetylation status and activity of mitochondrial fuel substrate metabolism enzymes. However, the role of GCN5L1 in response to chronic hemodynamic stress is largely unknown. Here, we show that cardiomyocyte-specific GCN5L1 knockout mice (cGCN5L1 KO) display exacerbated heart failure progression following transaortic constriction (TAC). Mitochondrial DNA and protein levels were decreased in cGCN5L1 KO hearts after TAC, and isolated neonatal cardiomyocytes with reduced GCN5L1 expression had lower bioenergetic output in response to hypertrophic stress. Loss of GCN5L1 expression led to a decrease in the acetylation status of mitochondrial transcription factor A (TFAM) after TAC in vivo, which was linked to a reduction in mtDNA levels in vitro. Together, these data suggest that GCN5L1 may protect from hemodynamic stress by maintaining mitochondrial bioenergetic output.

Keywords:  Hematology; Molecular biology; Physiology

DOI:  https://doi.org/10.1016/j.isci.2023.106942
J Immunol. 2023 Jun 16. pii: ji2200863. [Epub ahead of print]

Sfxn5 Regulation of Actin Polymerization for Neutrophil Spreading Depends on a Citrate-Cholesterol-PI(4,5)P2 Pathway.

Huan Zhang, Ling Meng, Yang Liu, Jinlong Jiang, Zhenting He, Jingjing Qin, Cuihong Wang, Meiting Yang, Ke He, Jie Yang, Ketong Chen, Qinke He, Wenwen Tang, Sijia Fan, Chunguang Ren.

Cell spreading is an initial and critical step in neutrophil adhesion and migration, leading to neutrophil recruitment to inflammatory tissues. Sideroflexin (Sfxn) family proteins are metabolite transporters located in the mitochondrial membrane. Recombinant SFXN5 protein is a citrate transporter in vitro; however, whether Sfxn5 regulates any cellular behavior or function remains unknown. In this study, we found that small interfering RNA transfection or morpholino injection achieving Sfxn5 deficiency in neutrophils significantly decreased neutrophil recruitment in mice and zebrafish, respectively. Sfxn5 deficiency impaired neutrophil spreading and spreading-associated cellular phenotypes, such as cell adhesion, chemotaxis, and ROS production. Actin polymerization is critical for neutrophil spreading, and we found that actin polymerization in spreading neutrophils was partially inhibited by Sfxn5 deficiency. Mechanistically, we observed that the levels of cytosolic citrate and its downstream metabolic products, acetyl-CoA and cholesterol, were decreased in Sfxn5-deficient neutrophils. The levels of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), a mediator for the regulation of actin polymerization by cholesterol, were reduced in the plasma membrane of Sfxn5-deficient neutrophils. Exogenous supplementation with citrate or cholesterol partially reversed the reduction in PI(4,5)P2 levels, defective neutrophil actin polymerization, and cell spreading. Altogether, we demonstrated that Sfxn5 maintains cytosolic citrate levels and ensures the synthesis of sufficient cholesterol to promote actin polymerization in a PI(4,5)P2-dependent manner during neutrophil spreading, which is essential for the eventual inflammatory recruitment of neutrophils. Our study revealed the importance of Sfxn5 in neutrophil spreading and migration, thus identifying, to our knowledge, for the first time, the physiological cellular functions of the Sfxn5 gene.

DOI: https://doi.org/10.4049/jimmunol.2200863
Cell Rep. 2023 Jun 08. pii: S2211-1247(23)00648-4. [Epub ahead of print]42(6): 112637

IL-3 orchestrates ulcerative colitis pathogenesis by controlling the development and the recruitment of splenic reservoir neutrophils.

Alan Bénard, Anke Mittelstädt, Bettina Klösch, Karolina Glanz, Jan Müller, Janina Schoen, Björn Nüse, Maximilian Brunner, Elisabeth Naschberger, Michael Stürzl, Jochen Mattner, Luis E Muñoz, Kai Sohn, Robert Grützmann, Georg F Weber.

  Inflammatory bowel diseases (IBDs) are a global health issue with an increasing incidence. Although the pathogenesis of IBDs has been investigated intensively, the etiology of IBDs remains enigmatic. Here, we report that interleukin-3 (Il-3)-deficient mice are more susceptible and exhibit increased intestinal inflammation during the early stage of experimental colitis. IL-3 is locally expressed in the colon by cells harboring a mesenchymal stem cell phenotype and protects by promoting the early recruitment of splenic neutrophils with high microbicidal capability into the colon. Mechanistically, IL-3-dependent neutrophil recruitment involves CCL5+ PD-1high LAG-3high T cells, STAT5, and CCL20 and is sustained by extramedullary splenic hematopoiesis. During acute colitis, Il-3-/- show, however, increased resistance to the disease as well as reduced intestinal inflammation. Altogether, this study deepens our understanding of IBD pathogenesis, identifies IL-3 as an orchestrator of intestinal inflammation, and reveals the spleen as an emergency reservoir for neutrophils during colonic inflammation.

Keywords:  CCL5; CP: Immunology; colitis; interleukin-3; neutrophils; spleen

DOI:  https://doi.org/10.1016/j.celrep.2023.112637
Cancer Cell. 2023 Jun 12. pii: S1535-6108(23)00182-4. [Epub ahead of print]

MCT4-dependent lactate secretion suppresses antitumor immunity in LKB1-deficient lung adenocarcinoma.

Yu Qian, Ana Galan-Cobo, Irene Guijarro, Minghao Dang, David Molkentine, Alissa Poteete, Fahao Zhang, Qi Wang, Jing Wang, Edwin Parra, Apekshya Panda, Jacy Fang, Ferdinandos Skoulidis, Ignacio I Wistuba, Svena Verma, Taha Merghoub, Jedd D Wolchok, Kwok-Kin Wong, Ralph J DeBerardinis, John D Minna, Natalie I Vokes, Catherine B Meador, Justin F Gainor, Linghua Wang, Alexandre Reuben, John V Heymach.

  Inactivating STK11/LKB1 mutations are genomic drivers of primary resistance to immunotherapy in KRAS-mutated lung adenocarcinoma (LUAD), although the underlying mechanisms remain unelucidated. We find that LKB1 loss results in enhanced lactate production and secretion via the MCT4 transporter. Single-cell RNA profiling of murine models indicates that LKB1-deficient tumors have increased M2 macrophage polarization and hypofunctional T cells, effects that could be recapitulated by the addition of exogenous lactate and abrogated by MCT4 knockdown or therapeutic blockade of the lactate receptor GPR81 expressed on immune cells. Furthermore, MCT4 knockout reverses the resistance to PD-1 blockade induced by LKB1 loss in syngeneic murine models. Finally, tumors from STK11/LKB1 mutant LUAD patients demonstrate a similar phenotype of enhanced M2-macrophages polarization and hypofunctional T cells. These data provide evidence that lactate suppresses antitumor immunity and therapeutic targeting of this pathway is a promising strategy to reversing immunotherapy resistance in STK11/LKB1 mutant LUAD.

Keywords:  LKB1; MCT4; PD-1; T cell activation; immunotherapy resistance; lactate; lung adenocarcinoma; macrophage polarization; metabolism

DOI:  https://doi.org/10.1016/j.ccell.2023.05.015
J Biol Chem. 2023 Jun 14. pii: S0021-9258(23)01952-X. [Epub ahead of print] 104924

Deciphering the biosynthesis of a novel lipid in Mycobacterium tuberculosis expands the known roles of the nitroreductase superfamily.

Jason C Grigg, Janine N Copp, Jessica M C Krekhno, Jie Liu, Aygun Ibrahimova, Lindsay D Eltis.

  Mycobacterium tuberculosis's (Mtb) success as a pathogen is due in part to its sophisticated lipid metabolic programs, both catabolic and biosynthetic. Several of Mtb's lipids have specific roles in pathogenesis, but the identity and roles of many are unknown. Here, we demonstrated that the tyz gene cluster in Mtb, previously implicated in resistance to oxidative stress and survival in macrophages, encodes the biosynthesis of acyl-oxazolones. Heterologous expression of tyzA (Rv2336), tyzB (Rv2338c) and tyzC (Rv2337c) resulted in the biosynthesis of C12:0-tyrazolone as the predominant compound, and the C12:0-tyrazolone was identified in Mtb lipid extracts. TyzA catalyzed the N-acylation of L-amino acids, with highest specificity for L-Tyr and L-Phe and lauroyl-CoA (kcat/KM = 5.9 ± 0.8 × 103 M-1s-1). In cell extracts, TyzC, a flavin-dependent oxidase (FDO) of the nitroreductase (NTR) superfamily, catalyzed the O2-dependent desaturation of the N-acyl-L-Tyr produced by TyzA, while TyzB, a ThiF homolog, catalyzed its ATP-dependent cyclization. The substrate preference of TyzB and TyzC appear to determine the identity of the acyl-oxazolone. Phylogenetic analyses revealed that the NTR superfamily includes a large number of broadly distributed FDOs, including five in Mtb that likely catalyze the desaturation of lipid species. Finally, TCA1, a molecule with activity against drug-resistant and persistent tuberculosis, failed to inhibit the cyclization activity of TyzB, the proposed secondary target of TCA1. Overall, this study identifies a novel class of Mtb lipids, clarifies the role of a potential drug target, and expands our understanding of the NTR superfamily.

Keywords:  N-acyl amino acid; NTR; actinobacteria; acyltransferase; enzyme; flavin; mycobacteria; oxazolone

DOI:  https://doi.org/10.1016/j.jbc.2023.104924
Nitric Oxide. 2023 Jun 10. pii: S1089-8603(23)00050-2. [Epub ahead of print]

Butyrate inhibits LPC-induced endothelial dysfunction by regulating nNOS-produced NO and ROS production.

Melissa Tainan Silva Dias, Edenil Costa Aguilar, Gianne Paul Campos, Natalia Fernanda do Couto, Luciano Dos Santos Aggum Capettini, Weslley Fernandes Braga, Luciana de Oliveira Andrade, Jacqueline Alvarez-Leite.

Lipids oxidation is a key risk factor for cardiovascular diseases. Lysophosphatidylcholine (LPC), the major component of oxidized LDL, is an important triggering agent for endothelial dysfunction and atherogenesis. Sodium butyrate, a short-chain fatty acid, has demonstrated atheroprotective properties. So, we evaluate the role of butyrate in LPC-induced endothelial dysfunction. Vascular response to phenylephrine (Phe) and acetylcholine (Ach) was performed in aortic rings from male mice (C57BL/6J). The aortic rings were incubated with LPC (10 μM) and butyrate (0.01 or 0.1 Mm), with or without TRIM (an nNOS inhibitor). Endothelial cells (EA.hy296) were incubated with LPC and butyrate to evaluate nitric oxide (NO) and reactive oxygen species (ROS) production, calcium influx, and the expression of total and phosphorylated nNOS and ERK½. We found that butyrate inhibited LPC-induced endothelial dysfunction by improving nNOS activity in aortic rings. In endothelial cells, butyrate reduced ROS production and increased nNOS-related NO release, by improving nNOS activation (phosphorylation at Ser1412). Additionally, butyrate prevented the increase in cytosolic calcium and inhibited ERk½ activation by LPC. In conclusion, butyrate inhibited LPC-induced vascular dysfunction by increasing nNOS-derived NO and reducing ROS production. Butyrate restored nNOS activation, which was associated with calcium handling normalization and reduction of ERK½ activation.

DOI: https://doi.org/10.1016/j.niox.2023.05.006
Nat Commun. 2023 Jun 16. 14(1): 3599

Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids.

Ana Martínez-Val, Kyle Fort, Claire Koenig, Leander Van der Hoeven, Giulia Franciosa, Thomas Moehring, Yasushi Ishihama, Yu-Ju Chen, Alexander Makarov, Yue Xuan, Jesper V Olsen.

Achieving sufficient coverage of regulatory phosphorylation sites by mass spectrometry (MS)-based phosphoproteomics for signaling pathway reconstitution is challenging, especially when analyzing tiny sample amounts. To address this, we present a hybrid data-independent acquisition (DIA) strategy (hybrid-DIA) that combines targeted and discovery proteomics through an Application Programming Interface (API) to dynamically intercalate DIA scans with accurate triggering of multiplexed tandem mass spectrometry (MSx) scans of predefined (phospho)peptide targets. By spiking-in heavy stable isotope labeled phosphopeptide standards covering seven major signaling pathways, we benchmark hybrid-DIA against state-of-the-art targeted MS methods (i.e., SureQuant) using EGF-stimulated HeLa cells and find the quantitative accuracy and sensitivity to be comparable while hybrid-DIA also profiles the global phosphoproteome. To demonstrate the robustness, sensitivity, and biomedical potential of hybrid-DIA, we profile chemotherapeutic agents in single colon carcinoma multicellular spheroids and evaluate the phospho-signaling difference of cancer cells in 2D vs 3D culture.

DOI: https://doi.org/10.1038/s41467-023-39347-y
Nat Commun. 2023 Jun 09. 14(1): 3416

A 2.2 Å cryoEM structure of a quinol-dependent NO Reductase shows close similarity to respiratory oxidases.

Alex J Flynn, Svetlana V Antonyuk, Robert R Eady, Stephen P Muench, S Samar Hasnain.

Quinol-dependent nitric oxide reductases (qNORs) are considered members of the respiratory heme-copper oxidase superfamily, are unique to bacteria, and are commonly found in pathogenic bacteria where they play a role in combating the host immune response. qNORs are also essential enzymes in the denitrification pathway, catalysing the reduction of nitric oxide to nitrous oxide. Here, we determine a 2.2 Å cryoEM structure of qNOR from Alcaligenes xylosoxidans, an opportunistic pathogen and a denitrifying bacterium of importance in the nitrogen cycle. This high-resolution structure provides insight into electron, substrate, and proton pathways, and provides evidence that the quinol binding site not only contains the conserved His and Asp residues but also possesses a critical Arg (Arg720) observed in cytochrome bo3, a respiratory quinol oxidase.

DOI: https://doi.org/10.1038/s41467-023-39140-x
Cell Metab. 2023 Jun 08. pii: S1550-4131(23)00203-6. [Epub ahead of print]

Acetate controls endothelial-to-mesenchymal transition.

Xiaolong Zhu, Yunyun Wang, Ioana Soaita, Heon-Woo Lee, Hosung Bae, Nabil Boutagy, Anna Bostwick, Rong-Mo Zhang, Caitlyn Bowman, Yanying Xu, Sophie Trefely, Yu Chen, Lingfeng Qin, William Sessa, George Tellides, Cholsoon Jang, Nathaniel W Snyder, Luyang Yu, Zoltan Arany, Michael Simons.

  Endothelial-to-mesenchymal transition (EndMT), a process initiated by activation of endothelial TGF-β signaling, underlies numerous chronic vascular diseases and fibrotic states. Once induced, EndMT leads to a further increase in TGF-β signaling, thus establishing a positive-feedback loop with EndMT leading to more EndMT. Although EndMT is understood at the cellular level, the molecular basis of TGF-β-driven EndMT induction and persistence remains largely unknown. Here, we show that metabolic modulation of the endothelium, triggered by atypical production of acetate from glucose, underlies TGF-β-driven EndMT. Induction of EndMT suppresses the expression of the enzyme PDK4, which leads to an increase in ACSS2-dependent Ac-CoA synthesis from pyruvate-derived acetate. This increased Ac-CoA production results in acetylation of the TGF-β receptor ALK5 and SMADs 2 and 4 leading to activation and long-term stabilization of TGF-β signaling. Our results establish the metabolic basis of EndMT persistence and unveil novel targets, such as ACSS2, for the potential treatment of chronic vascular diseases.

Keywords:  ACSS2; ALK5; PDK4; acetate; acetyl-CoA; atherosclerosis; endfothelial cells; endothelial-to-mesenchymal transition; transforming growth factor beta signaling

DOI:  https://doi.org/10.1016/j.cmet.2023.05.010
Immunity. 2023 Jun 13. pii: S1074-7613(23)00228-5. [Epub ahead of print]56(6): 1341-1358.e11

Tumor-derived prostaglandin E2 programs cDC1 dysfunction to impair intratumoral orchestration of anti-cancer T cell responses.

Felix Bayerl, Philippa Meiser, Sainitin Donakonda, Anna Hirschberger, Sebastian B Lacher, Anna-Marie Pedde, Chris D Hermann, Anais Elewaut, Moritz Knolle, Lukas Ramsauer, Thomas J Rudolph, Simon Grassmann, Rupert Öllinger, Nicole Kirchhammer, Marcel Trefny, Martina Anton, Dirk Wohlleber, Bastian Höchst, Anne Zaremba, Achim Krüger, Roland Rad, Anna C Obenauf, Dirk Schadendorf, Alfred Zippelius, Veit R Buchholz, Barbara U Schraml, Jan P Böttcher.

  Type 1 conventional dendritic cells (cDC1s) are critical for anti-cancer immunity. Protective anti-cancer immunity is thought to require cDC1s to sustain T cell responses within tumors, but it is poorly understood how this function is regulated and whether its subversion contributes to immune evasion. Here, we show that tumor-derived prostaglandin E2 (PGE2) programmed a dysfunctional state in intratumoral cDC1s, disabling their ability to locally orchestrate anti-cancer CD8+ T cell responses. Mechanistically, cAMP signaling downstream of the PGE2-receptors EP2 and EP4 was responsible for the programming of cDC1 dysfunction, which depended on the loss of the transcription factor IRF8. Blockade of the PGE2-EP2/EP4-cDC1 axis prevented cDC1 dysfunction in tumors, locally reinvigorated anti-cancer CD8+ T cell responses, and achieved cancer immune control. In human cDC1s, PGE2-induced dysfunction is conserved and associated with poor cancer patient prognosis. Our findings reveal a cDC1-dependent intratumoral checkpoint for anti-cancer immunity that is targeted by PGE2 for immune evasion.

Keywords:  T cells; cancer immunotherapy; dendritic cells; immune evasion; prostaglandin E2; tumor microenvironment

DOI:  https://doi.org/10.1016/j.immuni.2023.05.011
Nat Metab. 2023 Jun 12.

Itaconate trims the fat.

Rory Turner, Thekla Cordes, Martina Wallace.

DOI: https://doi.org/10.1038/s42255-023-00819-6
Sci Immunol. 2023 Jun 23. 8(84): eadc9081

Activation of regulatory dendritic cells by Mertk coincides with a temporal wave of apoptosis in neonatal lungs.

Aaron Silva-Sanchez, Selene Meza-Perez, Mingyong Liu, Sara L Stone, Leopoldo Flores-Romo, Eric Ubil, Frances E Lund, Alexander F Rosenberg, Troy D Randall.

Multiple mechanisms restrain inflammation in neonates, most likely to prevent tissue damage caused by overly robust immune responses against newly encountered pathogens. Here, we identify a population of pulmonary dendritic cells (DCs) that express intermediate levels of CD103 (CD103int) and appear in the lungs and lung-draining lymph nodes of mice between birth and 2 weeks of age. CD103int DCs express XCR1 and CD205 and require expression of the transcription factor BATF3 for development, suggesting that they belong to the cDC1 lineage. In addition, CD103int DCs express CCR7 constitutively and spontaneously migrate to the lung-draining lymph node, where they promote stromal cell maturation and lymph node expansion. CD103int DCs mature independently of microbial exposure and TRIF- or MyD88-dependent signaling and are transcriptionally related to efferocytic and tolerogenic DCs as well as mature, regulatory DCs. Correlating with this, CD103int DCs show limited ability to stimulate proliferation and IFN-γ production by CD8+ T cells. Moreover, CD103int DCs acquire apoptotic cells efficiently, in a process that is dependent on the expression of the TAM receptor, Mertk, which drives their homeostatic maturation. The appearance of CD103int DCs coincides with a temporal wave of apoptosis in developing lungs and explains, in part, dampened pulmonary immunity in neonatal mice. Together, these data suggest a mechanism by which DCs sense apoptotic cells at sites of noninflammatory tissue remodeling, such as tumors or the developing lungs, and limit local T cell responses.

DOI: https://doi.org/10.1126/sciimmunol.adc9081
Immunity. 2023 Jun 13. pii: S1074-7613(23)00222-4. [Epub ahead of print]56(6): 1303-1319.e5

Canonical BAF complex activity shapes the enhancer landscape that licenses CD8+ T cell effector and memory fates.

Bryan McDonald, Brent Y Chick, Nasiha S Ahmed, Mannix Burns, Shixin Ma, Eduardo Casillas, Dan Chen, Thomas H Mann, Carolyn O'Connor, Nasun Hah, Diana C Hargreaves, Susan M Kaech.

  CD8+ T cells provide host protection against pathogens by differentiating into distinct effector and memory cell subsets, but how chromatin is site-specifically remodeled during their differentiation is unclear. Due to its critical role in regulating chromatin and enhancer accessibility through its nucleosome remodeling activities, we investigated the role of the canonical BAF (cBAF) chromatin remodeling complex in antiviral CD8+ T cells during infection. ARID1A, a subunit of cBAF, was recruited early after activation and established de novo open chromatin regions (OCRs) at enhancers. Arid1a deficiency impaired the opening of thousands of activation-induced enhancers, leading to loss of TF binding, dysregulated proliferation and gene expression, and failure to undergo terminal effector differentiation. Although Arid1a was dispensable for circulating memory cell formation, tissue-resident memory (Trm) formation was strongly impaired. Thus, cBAF governs the enhancer landscape of activated CD8+ T cells that orchestrates TF recruitment and activity and the acquisition of specific effector and memory differentiation states.

Keywords:  ARID1A; BAF complex; CD8(+) T cells; antiviral immunity; chromatin remodeling; effector T cell; epigenetics; immunotherapy; memory T cell

DOI:  https://doi.org/10.1016/j.immuni.2023.05.005
Cell Rep. 2023 Jun 13. pii: S2211-1247(23)00651-4. [Epub ahead of print]42(6): 112640

Defective extracellular matrix remodeling in brown adipose tissue is associated with fibro-inflammation and reduced diet-induced thermogenesis.

Vanessa Pellegrinelli, Elizabeth Figueroa-Juárez, Isabella Samuelson, Mueez U-Din, Sonia Rodriguez-Fdez, Samuel Virtue, Jennifer Leggat, Cankut Çubuk, Vivian J Peirce, Tarja Niemi, Mark Campbell, Sergio Rodriguez-Cuenca, Joaquin Dopazo Blázquez, Stefania Carobbio, Kirsi A Virtanen, Antonio Vidal-Puig.

  The relevance of extracellular matrix (ECM) remodeling is reported in white adipose tissue (AT) and obesity-related dysfunctions, but little is known about the importance of ECM remodeling in brown AT (BAT) function. Here, we show that a time course of high-fat diet (HFD) feeding progressively impairs diet-induced thermogenesis concomitantly with the development of fibro-inflammation in BAT. Higher markers of fibro-inflammation are associated with lower cold-induced BAT activity in humans. Similarly, when mice are housed at thermoneutrality, inactivated BAT features fibro-inflammation. We validate the pathophysiological relevance of BAT ECM remodeling in response to temperature challenges and HFD using a model of a primary defect in the collagen turnover mediated by partial ablation of the Pepd prolidase. Pepd-heterozygous mice display exacerbated dysfunction and BAT fibro-inflammation at thermoneutrality and in HFD. Our findings show the relevance of ECM remodeling in BAT activation and provide a mechanism for BAT dysfunction in obesity.

Keywords:  CP: Metabolism; PEPD; brown adipose tissue; extracellular matrix; fibrosis; obesity

DOI:  https://doi.org/10.1016/j.celrep.2023.112640
Proc Natl Acad Sci U S A. 2023 Jun 20. 120(25): e2219431120

Cross talk between Paneth and tuft cells drives dysbiosis and inflammation in the gut mucosa.

Nathalie Coutry, Julie Nguyen, Salima Soualhi, François Gerbe, Victoria Meslier, Valérie Dardalhon, Mathieu Almeida, Benoit Quinquis, Florence Thirion, Fabien Herbert, Imène Gasmi, Ali Lamrani, Alicia Giordano, Pierre Cesses, Laure Garnier, Steeve Thirard, Denis Greuet, Chantal Cazevieille, Florence Bernex, Christelle Bressuire, Douglas Winton, Ichiro Matsumoto, Hervé M Blottière, Naomi Taylor, Philippe Jay.

  Gut microbiota imbalance (dysbiosis) is increasingly associated with pathological conditions, both within and outside the gastrointestinal tract. Intestinal Paneth cells are considered to be guardians of the gut microbiota, but the events linking Paneth cell dysfunction with dysbiosis remain unclear. We report a three-step mechanism for dysbiosis initiation. Initial alterations in Paneth cells, as frequently observed in obese and inflammatorybowel diseases patients, cause a mild remodeling of microbiota, with amplification of succinate-producing species. SucnR1-dependent activation of epithelial tuft cells triggers a type 2 immune response that, in turn, aggravates the Paneth cell defaults, promoting dysbiosis and chronic inflammation. We thus reveal a function of tuft cells in promoting dysbiosis following Paneth cell deficiency and an unappreciated essential role of Paneth cells in maintaining a balanced microbiota to prevent inappropriate activation of tuft cells and deleterious dysbiosis. This succinate-tuft cell inflammation circuit may also contribute to the chronic dysbiosis observed in patients.

Keywords:  Paneth cells; antimicrobial peptides; gut inflammation; microbiota dysbiosis; tuft cells

DOI:  https://doi.org/10.1073/pnas.2219431120
FASEB J. 2023 07;37(7): e23035

Farnesyl diphosphate synthase exacerbates nonalcoholic steatohepatitis via the activation of AHR-CD36 axis.

Jun Liu, Xinxin Zhang, Yufei Zhang, Minyi Qian, Maohui Yang, Song Yang, Lirui Wang.

  Nonalcoholic steatohepatitis (NASH) has become a major concern that threatens human health worldwide. The underlying pathogenesis was crucial but remained poorly understood. Here, we found that the expression of hepatic farnesyl diphosphate synthase (FDPS) was increased in mice and patients with NASH. Elevated FDPS levels were positively correlated with NASH severity. Overexpression of FDPS in mice provoked increased lipid accumulation, inflammation, and fibrosis, while hepatic FDPS deficiency protected mice from NASH progression. Importantly, pharmacological inhibition of FDPS with clinically used alendronate remarkably attenuated NASH-associated phenotypes in mice. Mechanistically, we demonstrated that FDPS increased its downstream product farnesyl pyrophosphate levels, which could function as an aryl hydrocarbon receptor (AHR) agonist to upregulate the expression of fatty acid translocase CD36, to accelerate the development of NASH. Collectively, these findings suggest that FDPS exacerbates NASH via AHR-CD36 axis and identify FDPS as a promising target for NASH therapy.

Keywords:  AHR; AHR-CD36 axis; ALN; FDPS; NASH

DOI:  https://doi.org/10.1096/fj.202300433RR