bims-mepmim 2022-10-30 papers

bims-mepmim

Biomed News

on Metabolites in pathological microenvironments and immunometabolism

Issue of 2022–10–30
forty-one papers selected by
Erika Mariana Palmieri, NIH/NCI Laboratory of Cancer ImmunoMetabolism

Lipids for CD8+ TILs: Beneficial or harmful?
The α-Ketoglutarate Dehydrogenase Complex as a Hub of Plasticity in Neurodegeneration and Regeneration.
UCP2 silencing restrains leukemia cell proliferation through glutamine metabolic remodeling.
The Glycosyltransferase Pathway: An Integrated Analysis of the Cell Metabolome.
NKT cells adopt a glutamine-addicted phenotype to regulate their homeostasis and function.
Metabolic control of CD47 expression through LAT2-mediated amino acid uptake promotes tumor immune evasion.
Synthetic metabolism without the TCA cycle.
Structural mechanism of SGLT1 inhibitors.
Lactate dehydrogenases promote glioblastoma growth and invasion via a metabolic symbiosis.
Hypoxia promotes osteogenesis by facilitating acetyl-CoA-mediated mitochondrial-nuclear communication.
Ferroptosis inhibition by lysosome-dependent catabolism of extracellular protein.
Structure and functionality of a multimeric human COQ7:COQ9 complex.
An Engineered Paper-Based 3D Co-Culture Model of Pancreatic Cancer to Study the Impact of Tissue Architecture and Microenvironmental Gradients on Cell Phenotype.
Tumor-associated macrophages expressing the transcription factor IRF8 promote T cell exhaustion in cancer.
Metabolic clearance of oxaloacetate and mitochondrial complex II respiration: Divergent control in skeletal muscle and brown adipose tissue.
Quantifying the contribution of triglycerides to metabolic resilience through the mixed meal model.
A Mass Spectrometry Imaging and Lipidomic Investigation Reveals Aberrant Lipid Metabolism in the Orthotopic Mouse Glioma.
KLF15 controls brown adipose tissue transcriptional flexibility and metabolism in response to various energetic demands.
Hepatic glutamine synthetase controls N5-methylglutamine in homeostasis and cancer.
Elevated pentose phosphate pathway flux supports appendage regeneration.
Human ultrarare genetic disorders of sulfur metabolism demonstrate redundancies in H2S homeostasis.
Spatial metabolomics reveals upregulation of several pyrophosphate-producing pathways in cortical bone of Hyp mice.
Divergent regulation of basement membrane trafficking by human macrophages and cancer cells.
Simplifying the B Complex: How Vitamins B6 and B9 Modulate One Carbon Metabolism in Cancer and Beyond.
Pyruvate prevents the onset of the cachectic features and metabolic alterations in myotubes downregulating STAT3 signaling.
Link between glucose metabolism and epithelial-to-mesenchymal transition drives triple-negative breast cancer migratory heterogeneity.
Limiting glutamine utilization activates a GCN2/TRAIL-R2/Caspase-8 apoptotic pathway in glutamine-addicted tumor cells.
OPA1 drives macrophage metabolism and functional commitment via p65 signaling.
Phospholipid imbalance impairs autophagosome completion.
Metabolic reconfiguration enables synthetic reductive metabolism in yeast.
Multi-omic analyses of changes in the tumor microenvironment of pancreatic adenocarcinoma following neoadjuvant treatment with anti-PD-1 therapy.
Ornithine decarboxylase supports ILC3 responses in infectious and autoimmune colitis through positive regulation of IL-22 transcription.
Metabolic features of innate lymphoid cells.
Kynurenine promotes neonatal heart regeneration by stimulating cardiomyocyte proliferation and cardiac angiogenesis.
REDD1 promotes obesity-induced metabolic dysfunction via atypical NF-κB activation.
A multienzyme S-nitrosylation cascade regulates cholesterol homeostasis.
Preface to Nitric Oxide Modulators in Health and Disease I.
Quick tips for re-using metabolomics data.
Cystine-dependent antiporters buffer against excess intracellular reactive sulfur species-induced stress.
PTEN directs developmental and metabolic signaling for innate-like T cell fate and tissue homeostasis.
The thioredoxin system: balancing redox responses in immune cells and tumors.

Front Immunol. 2022 ;13 1020422

Lipids for CD8+ TILs: Beneficial or harmful?

Duojiao Wu, Yuwen Chen.

  Lipids and lipid metabolism play crucial roles in regulating T cell function and are tightly related to the establishment of immune memory. It is reported that tumor-infiltrating CD8+T lymphocytes (CD8+TILs) burn fats to restore their impaired effector function due to the lack of glucose. Conversely, fatty acids (FAs) and cholesterol in the tumor microenvironment (TME) drive the CD8+ TILs dysfunction. The origin of dysfunctional CD8+ TILs shares important features with memory T cell's precursor, but whether lipids and/or lipid metabolism reprogramming directly influence the memory plasticity of dysfunctional CD8+ TILs remains elusive. It is necessary to understand the interplay between cellular lipid metabolism and dysfunction of CD8+ TILs in the case of targeting T cell's metabolism to synergize cancer immunotherapy. Therefore, in this review, we summarize the latest research on CD8+ TILs lipid metabolism, evaluate the impacts of lipids in the TME to CD8+ TILs, and highlight the significance of promoting memory phenotype cell formation by targeting CD8+ T cells lipid metabolism to provide longer duration of cancer immunotherapy efficacy.

Keywords:  CD8+ T cell; Exhausted T cell; cholesterol; fatty acid; fatty acid oxidation; metabolism; tumor microenvironment (TME)

DOI:  https://doi.org/10.3389/fimmu.2022.1020422
Int J Mol Sci. 2022 Oct 17. pii: 12403. [Epub ahead of print]23(20):

The α-Ketoglutarate Dehydrogenase Complex as a Hub of Plasticity in Neurodegeneration and Regeneration.

Grace E Hansen, Gary E Gibson.

  Abnormal glucose metabolism is central to neurodegeneration, and considerable evidence suggests that abnormalities in key enzymes of the tricarboxylic acid (TCA) cycle underlie the metabolic deficits. Significant recent advances in the role of metabolism in cancer provide new insight that facilitates our understanding of the role of metabolism in neurodegeneration. Research indicates that the rate-limiting step of the TCA cycle, the α-ketoglutarate dehydrogenase complex (KGDHC) and its substrate alpha ketoglutarate (KG), serve as a signaling hub that regulates multiple cellular processes: (1) is the rate-limiting step of the TCA cycle, (2) is sensitive to reactive oxygen species (ROS) and produces ROS, (3) determines whether KG is used for energy or synthesis of compounds to support growth, (4) regulates the cellular responses to hypoxia, (5) controls the post-translational modification of hundreds of cell proteins in the mitochondria, cytosol, and nucleus through succinylation, (6) controls critical aspects of transcription, (7) modulates protein signaling within cells, and (8) modulates cellular calcium. The primary focus of this review is to understand how reductions in KGDHC are translated to pathologically important changes that underlie both neurodegeneration and cancer. An understanding of each role is necessary to develop new therapeutic strategies to treat neurodegenerative disease.

Keywords:  Alzheimer’s disease; cell signaling; metabolic plasticity; mitochondria; oxidative stress; transcription; tricarboxylic acid cycle; α-ketoglutarate; α-ketoglutarate dehydrogenase complex

DOI:  https://doi.org/10.3390/ijms232012403
Front Immunol. 2022 ;13 960226

UCP2 silencing restrains leukemia cell proliferation through glutamine metabolic remodeling.

Tiphaine Sancerni, Ophélie Renoult, Angèle Luby, Cédric Caradeuc, Véronique Lenoir, Mikael Croyal, Céline Ransy, Esther Aguilar, Catherine Postic, Gildas Bertho, Renaud Dentin, Carina Prip-Buus, Claire Pecqueur, Marie-Clotilde Alves-Guerra.

  T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy derived from early T cell progenitors. Since relapsed T-ALL is associated with a poor prognosis improving initial treatment of patients is essential to avoid resistant selection of T-ALL. During initiation, development, metastasis and even in response to chemotherapy, tumor cells face strong metabolic challenges. In this study, we identify mitochondrial UnCoupling Protein 2 (UCP2) as a tricarboxylic acid (TCA) cycle metabolite transporter controlling glutamine metabolism associated with T-ALL cell proliferation. In T-ALL cell lines, we show that UCP2 expression is controlled by glutamine metabolism and is essential for their proliferation. Our data show that T-ALL cell lines differ in their substrate dependency and their energetic metabolism (glycolysis and oxidative). Thus, while UCP2 silencing decreases cell proliferation in all leukemia cells, it also alters mitochondrial respiration of T-ALL cells relying on glutamine-dependent oxidative metabolism by rewiring their cellular metabolism to glycolysis. In this context, the function of UCP2 in the metabolite export of malate enables appropriate TCA cycle to provide building blocks such as lipids for cell growth and mitochondrial respiration. Therefore, interfering with UCP2 function can be considered as an interesting strategy to decrease metabolic efficiency and proliferation rate of leukemia cells.

Keywords:  UCP2; glutamine; leukemia; metabolism rewiring; metabolite carrier; mitochondria

DOI:  https://doi.org/10.3389/fimmu.2022.960226
Metabolites. 2022 Oct 21. pii: 1006. [Epub ahead of print]12(10):

The Glycosyltransferase Pathway: An Integrated Analysis of the Cell Metabolome.

Yannick Audet-Delage, Michèle Rouleau, Lyne Villeneuve, Chantal Guillemette.

  Nucleotide sugar-dependent glycosyltransferases (UGTs) are critical to the homeostasis of endogenous metabolites and the detoxification of xenobiotics. Their impact on the cell metabolome remains unknown. Cellular metabolic changes resulting from human UGT expression were profiled by untargeted metabolomics. The abundant UGT1A1 and UGT2B7 were studied as UGT prototypes along with their alternative (alt.) splicing-derived isoforms displaying structural differences. Nineteen biochemical routes were modified, beyond known UGT substrates. Significant variations in glycolysis and pyrimidine pathways, and precursors of the co-substrate UDP-glucuronic acid were observed. Bioactive lipids such as arachidonic acid and endocannabinoids were highly enriched by up to 13.3-fold (p < 0.01) in cells expressing the canonical enzymes. Alt. UGT2B7 induced drastic and unique metabolic perturbations, including higher glucose (18-fold) levels and tricarboxylic acid cycle (TCA) cycle metabolites and abrogated the effects of the UGT2B7 canonical enzyme when co-expressed. UGT1A1 proteins promoted the accumulation of branched-chain amino acids (BCAA) and TCA metabolites upstream of the mitochondrial oxoglutarate dehydrogenase complex (OGDC). Alt. UGT1A1 exacerbated these changes, likely through its interaction with the OGDC component oxoglutarate dehydrogenase-like (OGDHL). This study expands the breadth of biochemical pathways associated with UGT expression and establishes extensive connectivity between UGT enzymes, alt. proteins and other metabolic processes.

Keywords:  TCA cycle; cell metabolism; glucose; glucuronidation; lipids; metabolomics

DOI:  https://doi.org/10.3390/metabo12101006
Cell Rep. 2022 10 25. pii: S2211-1247(22)01366-3. [Epub ahead of print]41(4): 111516

NKT cells adopt a glutamine-addicted phenotype to regulate their homeostasis and function.

Ajay Kumar, Emily L Yarosz, Anthony Andren, Li Zhang, Costas A Lyssiotis, Cheong-Hee Chang.

  Natural killer T (NKT) cells operate distinctly different metabolic programming from CD4 T cells, including a strict requirement for glutamine to regulate cell homeostasis. However, the underlying mechanisms remain unknown. Here, we report that at a steady state, NKT cells have higher glutamine levels than CD4 T cells and that NKT cells increase glutaminolysis on activation. Activated NKT cells use glutamine to fuel the tricarboxylic acid cycle and glutathione synthesis. In addition, glutamine-derived nitrogen enables protein glycosylation via the hexosamine biosynthesis pathway (HBP). Each of these branches of glutamine metabolism seems to be critical for NKT cell homeostasis and mitochondrial functions. Glutaminolysis and HBP differentially regulate interleukin-4 (IL-4) and interferon γ (IFNγ) production. Glutamine metabolism appears to be controlled by AMP-activated protein kinase (AMPK)-mammalian target of rapamycin complex 1 (mTORC1) signaling. These findings highlight a distinct metabolic requirement of NKT cells compared with CD4 T cells, which may have therapeutic implications in the treatment of certain nutrient-restricted diseases.

Keywords:  CP: Immunology; HBP; PPP; ROS; glutathione; glycosylation; metabolism

DOI:  https://doi.org/10.1016/j.celrep.2022.111516
Nat Commun. 2022 Oct 23. 13(1): 6308

Metabolic control of CD47 expression through LAT2-mediated amino acid uptake promotes tumor immune evasion.

Zenan Wang, Binghao Li, Shan Li, Wenlong Lin, Zhan Wang, Shengdong Wang, Weida Chen, Wei Shi, Tao Chen, Hao Zhou, Eloy Yinwang, Wenkan Zhang, Haochen Mou, Xupeng Chai, Jiahao Zhang, Zhimin Lu, Zhaoming Ye.

Chemotherapy elicits tumor immune evasion with poorly characterized mechanisms. Here, we demonstrate that chemotherapy markedly enhances the expression levels of CD47 in osteosarcoma tissues, which are positively associated with patient mortality. We reveal that macrophages in response to chemotherapy secrete interleukin-18, which in turn upregulates expression of L-amino acid transporter 2 (LAT2) in tumor cells for substantially enhanced uptakes of leucine and glutamine, two potent stimulators of mTORC1. The increased levels of leucine and enhanced glutaminolysis activate mTORC1 and subsequent c-Myc-mediated transcription of CD47. Depletion of LAT2 or treatment of tumor cells with a LAT inhibitor downregulates CD47 with enhanced macrophage infiltration and phagocytosis of tumor cells, and sensitizes osteosarcoma to doxorubicin treatment in mice. These findings unveil a mutual regulation between macrophage and tumor cells that plays a critical role in tumor immune evasion and underscore the potential to intervene with the LAT2-mediated amino acid uptake for improving cancer therapies.

DOI: https://doi.org/10.1038/s41467-022-34064-4
Nat Metab. 2022 Oct 27.

Synthetic metabolism without the TCA cycle.

Steffen N Lindner, Markus Ralser.

DOI: https://doi.org/10.1038/s42255-022-00668-9
Nat Commun. 2022 Oct 28. 13(1): 6440

Structural mechanism of SGLT1 inhibitors.

Yange Niu, Wenhao Cui, Rui Liu, Sanshan Wang, Han Ke, Xiaoguang Lei, Lei Chen.

Sodium glucose co-transporters (SGLT) harness the electrochemical gradient of sodium to drive the uphill transport of glucose across the plasma membrane. Human SGLT1 (hSGLT1) plays a key role in sugar uptake from food and its inhibitors show promise in the treatment of several diseases. However, the inhibition mechanism for hSGLT1 remains elusive. Here, we present the cryo-EM structure of the hSGLT1-MAP17 hetero-dimeric complex in the presence of the high-affinity inhibitor LX2761. LX2761 locks the transporter in an outward-open conformation by wedging inside the substrate-binding site and the extracellular vestibule of hSGLT1. LX2761 blocks the putative water permeation pathway of hSGLT1. The structure also uncovers the conformational changes of hSGLT1 during transitions from outward-open to inward-open states.

DOI: https://doi.org/10.1038/s41467-022-33421-7
EMBO Mol Med. 2022 Oct 24. e15343

Lactate dehydrogenases promote glioblastoma growth and invasion via a metabolic symbiosis.

Joris Guyon, Ignacio Fernandez-Moncada, Claire M Larrieu, Cyrielle L Bouchez, Antonio C Pagano Zottola, Johanna Galvis, Tiffanie Chouleur, Audrey Burban, Kevin Joseph, Vidhya M Ravi, Heidi Espedal, Gro Vatne Røsland, Boutaina Daher, Aurélien Barre, Benjamin Dartigues, Slim Karkar, Justine Rudewicz, Irati Romero-Garmendia, Barbara Klink, Konrad Grützmann, Marie-Alix Derieppe, Thibaut Molinié, Nina Obad, Céline Léon, Giorgio Seano, Hrvoje Miletic, Dieter Henrik Heiland, Giovanni Marsicano, Macha Nikolski, Rolf Bjerkvig, Andreas Bikfalvi, Thomas Daubon.

  Lactate is a central metabolite in brain physiology but also contributes to tumor development. Glioblastoma (GB) is the most common and malignant primary brain tumor in adults, recognized by angiogenic and invasive growth, in addition to its altered metabolism. We show herein that lactate fuels GB anaplerosis by replenishing the tricarboxylic acid (TCA) cycle in absence of glucose. Lactate dehydrogenases (LDHA and LDHB), which we found spatially expressed in GB tissues, catalyze the interconversion of pyruvate and lactate. However, ablation of both LDH isoforms, but not only one, led to a reduction in tumor growth and an increase in mouse survival. Comparative transcriptomics and metabolomics revealed metabolic rewiring involving high oxidative phosphorylation (OXPHOS) in the LDHA/B KO group which sensitized tumors to cranial irradiation, thus improving mouse survival. When mice were treated with the antiepileptic drug stiripentol, which targets LDH activity, tumor growth decreased. Our findings unveil the complex metabolic network in which both LDHA and LDHB are integrated and show that the combined inhibition of LDHA and LDHB strongly sensitizes GB to therapy.

Keywords:  antiepileptic drug; energy metabolism; glioblastoma; invasion; lactate dehydrogenases

DOI:  https://doi.org/10.15252/emmm.202115343
EMBO J. 2022 Oct 24. e111239

Hypoxia promotes osteogenesis by facilitating acetyl-CoA-mediated mitochondrial-nuclear communication.

Andromachi Pouikli, Monika Maleszewska, Swati Parekh, Ming Yang, Chrysa Nikopoulou, Juan Jose Bonfiglio, Constantine Mylonas, Tonantzi Sandoval, Anna-Lena Schumacher, Yvonne Hinze, Ivan Matic, Christian Frezza, Peter Tessarz.

  Bone-derived mesenchymal stem cells (MSCs) reside in a hypoxic niche that maintains their differentiation potential. While hypoxia (low oxygen concentration) was reported to critically support stem cell function and osteogenesis, the molecular events triggering changes in stem cell fate decisions in response to normoxia (high oxygen concentration) remain elusive. Here, we study the impact of normoxia on mitochondrial-nuclear communication during stem cell differentiation. We show that normoxia-cultured murine MSCs undergo profound transcriptional alterations which cause irreversible osteogenesis defects. Mechanistically, high oxygen promotes chromatin compaction and histone hypo-acetylation, particularly on promoters and enhancers of osteogenic genes. Although normoxia induces metabolic rewiring resulting in elevated acetyl-CoA levels, histone hypo-acetylation occurs due to the trapping of acetyl-CoA inside mitochondria owing to decreased citrate carrier (CiC) activity. Restoring the cytosolic acetyl-CoA pool remodels the chromatin landscape and rescues the osteogenic defects. Collectively, our results demonstrate that the metabolism-chromatin-osteogenesis axis is perturbed upon exposure to high oxygen levels and identifies CiC as a novel, oxygen-sensitive regulator of the MSC function.

Keywords:  histone acetylation; hypoxia; mesenchymal stem cells; metabolism; osteogenesis

DOI:  https://doi.org/10.15252/embj.2022111239
Cell Chem Biol. 2022 Oct 24. pii: S2451-9456(22)00360-9. [Epub ahead of print]

Ferroptosis inhibition by lysosome-dependent catabolism of extracellular protein.

David A Armenta, Nouf N Laqtom, Grace Alchemy, Wentao Dong, Danielle Morrow, Carson D Poltorack, David A Nathanson, Monther Abu-Remalieh, Scott J Dixon.

  Cancer cells need a steady supply of nutrients to evade cell death and proliferate. Depriving cancer cells of the amino acid cystine can trigger the non-apoptotic cell death process of ferroptosis. Here, we report that cancer cells can evade cystine deprivation-induced ferroptosis by uptake and catabolism of the cysteine-rich extracellular protein albumin. This protective mechanism is enhanced by mTORC1 inhibition and involves albumin degradation in the lysosome, predominantly by cathepsin B (CTSB). CTSB-dependent albumin breakdown followed by export of cystine from the lysosome via the transporter cystinosin fuels the synthesis of glutathione, which suppresses lethal lipid peroxidation. When cancer cells are grown under non-adherent conditions as spheroids, mTORC1 pathway activity is reduced, and albumin supplementation alone affords considerable protection against ferroptosis. These results identify the catabolism of extracellular protein within the lysosome as a mechanism that can inhibit ferroptosis in cancer cells.

Keywords:  ROS; albumin; cancer; cathepsin; cell death; cysteine; ferroptosis; glutathione; lysosome; mTOR

DOI:  https://doi.org/10.1016/j.chembiol.2022.10.006
Mol Cell. 2022 Oct 21. pii: S1097-2765(22)00960-1. [Epub ahead of print]

Structure and functionality of a multimeric human COQ7:COQ9 complex.

Mateusz Manicki, Halil Aydin, Luciano A Abriata, Katherine A Overmyer, Rachel M Guerra, Joshua J Coon, Matteo Dal Peraro, Adam Frost, David J Pagliarini.

  Coenzyme Q (CoQ) is a redox-active lipid essential for core metabolic pathways and antioxidant defense. CoQ is synthesized upon the mitochondrial inner membrane by an ill-defined "complex Q" metabolon. Here, we present structure-function analyses of a lipid-, substrate-, and NADH-bound complex comprising two complex Q subunits: the hydroxylase COQ7 and the lipid-binding protein COQ9. We reveal that COQ7 adopts a ferritin-like fold with a hydrophobic channel whose substrate-binding capacity is enhanced by COQ9. Using molecular dynamics, we further show that two COQ7:COQ9 heterodimers form a curved tetramer that deforms the membrane, potentially opening a pathway for the CoQ intermediates to translocate from the bilayer to the proteins' lipid-binding sites. Two such tetramers assemble into a soluble octamer with a pseudo-bilayer of lipids captured within. Together, these observations indicate that COQ7 and COQ9 cooperate to access hydrophobic precursors within the membrane and coordinate subsequent synthesis steps toward producing CoQ.

Keywords:  COQ7; COQ9; coenzyme Q; di-iron proteins; mitochondria; protein-lipid complex; protein-membrane interaction; quinone biosynthesis

DOI:  https://doi.org/10.1016/j.molcel.2022.10.003
Adv Healthc Mater. 2022 Oct 29. e2201846

An Engineered Paper-Based 3D Co-Culture Model of Pancreatic Cancer to Study the Impact of Tissue Architecture and Microenvironmental Gradients on Cell Phenotype.

Jose L Cadavid, Simon Latour, Ferris Nowlan, Ileana L Co, Natalie Landon-Brace, Bradly G Wouters, Barbara T Grünwald, Mark Nitz, Hartland Jackson, Alison P McGuigan.

  The spatial configuration of cells in the tumor microenvironment (TME) affects both cancer and fibroblast cell phenotypes contributing to the clinical challenge of tumour heterogeneity and therapeutic resistance. This is a particular challenge in stroma-rich pancreatic ductal adenocarcinoma. Here, we describe a versatile system to study the impact of tissue architecture on cell phenotype using PDAC as a model system. This fully human system encompassing both primary pancreatic stellate cells and primary organoid cells uses the TRACER platform to allow the creation of user-defined TME architectures that have been inferred from clinical PDAC samples and are analyzed by a CyTOF pipeline to characterize cells extracted from the system. By performing high dimensional characterization using CyTOF, we demonstrate that tissue architecture leads to distinct hypoxia and proliferation gradients. Furthermore, phenotypic markers for both cell types are also graded in ways that cannot be explained by either hypoxia or co-culture alone. This demonstrates the importance of using complex models encompassing cancer cells, stromal cells and allowing control over architecture to explore the impact of tissue architecture on cell phenotype. We anticipate that our model will help decipher how tissue architecture and cell interactions regulate cell phenotype and hence cellular and tissue heterogeneity. This article is protected by copyright. All rights reserved.

Keywords:  3D model; fibroblasts; hypoxia; patient-derived organoids; tissue architecture; tumor microenvironment

DOI:  https://doi.org/10.1002/adhm.202201846
Immunity. 2022 Oct 21. pii: S1074-7613(22)00543-X. [Epub ahead of print]

Tumor-associated macrophages expressing the transcription factor IRF8 promote T cell exhaustion in cancer.

Briana G Nixon, Fengshen Kuo, LiangLiang Ji, Ming Liu, Kristelle Capistrano, Mytrang Do, Ruth A Franklin, Xiaodi Wu, Emily R Kansler, Raghvendra M Srivastava, Tanaya A Purohit, Alejandro Sanchez, Lynda Vuong, Chirag Krishna, Xinxin Wang, Herbert C Morse Iii, James J Hsieh, Timothy A Chan, Kenneth M Murphy, James J Moon, A Ari Hakimi, Ming O Li.

  Tumors are populated by antigen-presenting cells (APCs) including macrophage subsets with distinct origins and functions. Here, we examined how cancer impacts mononuclear phagocytic APCs in a murine model of breast cancer. Tumors induced the expansion of monocyte-derived tumor-associated macrophages (TAMs) and the activation of type 1 dendritic cells (DC1s), both of which expressed and required the transcription factor interferon regulatory factor-8 (IRF8). Although DC1s mediated cytotoxic T lymphocyte (CTL) priming in tumor-draining lymph nodes, TAMs promoted CTL exhaustion in the tumor, and IRF8 was required for TAMs' ability to present cancer cell antigens. TAM-specific IRF8 deletion prevented exhaustion of cancer-cell-reactive CTLs and suppressed tumor growth. Tumors from patients with immune-infiltrated renal cell carcinoma had abundant TAMs that expressed IRF8 and were enriched for an IRF8 gene expression signature. Furthermore, the TAM-IRF8 signature co-segregated with CTL exhaustion signatures across multiple cancer types. Thus, CTL exhaustion is promoted by TAMs via IRF8.

Keywords:  IRF8; T cell exhaustion; antigen presentation; antigen-presenting cell; tumor-associated macrophage

DOI:  https://doi.org/10.1016/j.immuni.2022.10.002
Biochim Biophys Acta Bioenerg. 2022 Oct 19. pii: S0005-2728(22)00400-5. [Epub ahead of print]1864(1): 148930

Metabolic clearance of oxaloacetate and mitochondrial complex II respiration: Divergent control in skeletal muscle and brown adipose tissue.

Liping Yu, Brian D Fink, Ritu Som, Adam J Rauckhorst, Eric B Taylor, William I Sivitz.

  At low inner mitochondrial membrane potential (ΔΨ) oxaloacetate (OAA) accumulates in the organelles concurrently with decreased complex II-energized respiration. This is consistent with ΔΨ-dependent OAA inhibition of succinate dehydrogenase. To assess the metabolic importance of this process, we tested the hypothesis that perturbing metabolic clearance of OAA in complex II-energized mitochondria would alter O2 flux and, further, that this would occur in both ΔΨ and tissue-dependent fashion. We carried out respiratory and metabolite studies in skeletal muscle and interscapular brown adipose tissue (IBAT) directed at the effect of OAA transamination to aspartate (catalyzed by the mitochondrial form of glutamic-oxaloacetic transaminase, Got2) on complex II-energized respiration. Addition of low amounts of glutamate to succinate-energized mitochondria at low ΔΨ increased complex II (succinate)-energized respiration in muscle but had little effect in IBAT mitochondria. The transaminase inhibitor, aminooxyacetic acid, increased OAA concentrations and impaired succinate-energized respiration in muscle but not IBAT mitochondria at low but not high ΔΨ. Immunoblotting revealed that Got2 expression was far greater in muscle than IBAT mitochondria. Because we incidentally observed metabolism of OAA to pyruvate in IBAT mitochondria, more so than in muscle mitochondria, we also examined the expression of mitochondrial oxaloacetate decarboxylase (ODX). ODX was detected only in IBAT mitochondria. In summary, at low but not high ΔΨ, mitochondrial transamination clears OAA preventing loss of complex II respiration: a process far more active in muscle than IBAT mitochondria. We also provide evidence that OAA decarboxylation clears OAA to pyruvate in IBAT mitochondria.

Keywords:  Brown adipose tissue; Mitochondria; Mitochondrial complex II; Muscle; Oxaloacetate; Succinate dehydrogenase

DOI:  https://doi.org/10.1016/j.bbabio.2022.148930
iScience. 2022 Nov 18. 25(11): 105206

Quantifying the contribution of triglycerides to metabolic resilience through the mixed meal model.

Shauna D O'Donovan, Balázs Erdős, Doris M Jacobs, Anne J Wanders, E Louise Thomas, Jimmy D Bell, Milena Rundle, Gary Frost, Ilja C W Arts, Lydia A Afman, Natal A W van Riel.

  Despite the pivotal role played by elevated circulating triglyceride levels in the pathophysiology of cardio-metabolic diseases many of the indices used to quantify metabolic health focus on deviations in glucose and insulin alone. We present the Mixed Meal Model, a computational model describing the systemic interplay between triglycerides, free fatty acids, glucose, and insulin. We show that the Mixed Meal Model can capture deviations in the post-meal excursions of plasma glucose, insulin, and triglyceride that are indicative of features of metabolic resilience; quantifying insulin resistance and liver fat; validated by comparison to gold-standard measures. We also demonstrate that the Mixed Meal Model is generalizable, applying it to meals with diverse macro-nutrient compositions. In this way, by coupling triglycerides to the glucose-insulin system the Mixed Meal Model provides a more holistic assessment of metabolic resilience from meal response data, quantifying pre-clinical metabolic deteriorations that drive disease development in overweight and obesity.

Keywords:  Human metabolism; In silico biology; Nutrition; Systems biology

DOI:  https://doi.org/10.1016/j.isci.2022.105206
J Lipid Res. 2022 Oct 20. pii: S0022-2275(22)00137-7. [Epub ahead of print] 100304

A Mass Spectrometry Imaging and Lipidomic Investigation Reveals Aberrant Lipid Metabolism in the Orthotopic Mouse Glioma.

Hay-Yan J Wang, Chiung-Yin Huang, Kuo-Chen Wei, Kuo-Chen Hung.

  Lipids perform multiple biological functions, and reflect the physiology and pathology of cells, tissues, and organs. Here we sought to understand lipid content in relation to tumor pathology by characterizing phospholipids (PLs) and sphingolipids (SLs) in the orthotopic mouse glioma using matrix-assisted laser desorption-ionization mass spectrometry imaging (MALDI-MSI) and liquid chromatography tandem mass spectrometry (LC-MS/MS). Unsupervised clustering analysis of the MALDI-MSI data segmented the coronal tumoral brain section into ten histopathologically salient regions. Heterogeneous decrease of the common saturated phosphatidylcholines (PCs) in the tumor was accompanied by the increase of analogous PCs with one or two additional fatty acyl double-bonds, and increased lysophosphatidylcholines (LPCs). Polyunsaturated fatty acyl-PCs and ether PCs highlighted the striatal tumor margins, while the distributions of other PCs differentiated the cortical and striatal tumor parenchyma. We detected a reduction of sphingomyelin (SM) d18:1/18:0 and the heterogeneous mild increase of SM d18:1/16:0 in the tumor, while ceramides accumulated only in a small patch deep in the tumoral parenchyma. LC-MS/MS analyses of PLs and SLs complemented the MALDI-MSI observation, providing a snapshot of these lipids in the tumor. Finally, the proposed mechanisms responsible for the tumoral lipid changes were contrasted with our interrogation of gene expression in human glioma. Together, these lipidomic results unveil the aberrant and heterogeneous lipid metabolism in mouse glioma where multiple lipid-associated signaling pathways underline the tumor features, promote the survival, growth, proliferation, and invasion of different tumor cell populations, and implicate the management strategy of a multiple-target approach for glioma and related brain malignancies.

Keywords:  ceramides; lipid-associated signaling pathways; lipidomics; liquid chromatography tandem mass spectrometry; matrix-assisted laser desorption-ionization mass spectrometry imaging; phosphatidylcholine; phospholipids; sphingolipids; tumor pathology; unsupervised clustering analysis

DOI:  https://doi.org/10.1016/j.jlr.2022.100304
iScience. 2022 Nov 18. 25(11): 105292

KLF15 controls brown adipose tissue transcriptional flexibility and metabolism in response to various energetic demands.

Liyan Fan, Alexander F Lesser, David R Sweet, Komal S Keerthy, Yuan Lu, Ernest R Chan, Vinesh Vinayachandran, Olga Ilkayeva, Tapatee Das, Christopher B Newgard, Mukesh K Jain.

  Brown adipose tissue (BAT) is a specialized metabolic organ responsible for non-shivering thermogenesis. Recently, its activity has been shown to be critical in systemic metabolic health through its utilization and consumption of macronutrients. In the face of energetically demanding states, metabolic flexibility and systemic coordination of nutrient partitioning is requisite for health and survival. In this study, we elucidate BAT's differential transcriptional adaptations in response to multiple nutrient challenges and demonstrate its context-dependent prioritization of lipid, glucose, and amino acid metabolism. We show that the transcription factor Krüppel-like factor 15 (KLF15) plays a critical role in BAT metabolic flexibility. BAT-specific loss of KLF15 results in widespread changes in circulating metabolites and severely compromised thermogenesis in response to high energy demands, indicative of impaired nutrient utilization and metabolic flexibility. Together, our data demonstrate KLF15 in BAT plays an indispensable role in partitioning resources to maintain homeostasis and ensure survival.

Keywords:  Cell biology; Human metabolism; Molecular biology

DOI:  https://doi.org/10.1016/j.isci.2022.105292
Nat Chem Biol. 2022 Oct 24.

Hepatic glutamine synthetase controls N5-methylglutamine in homeostasis and cancer.

Victor H Villar, Maria Francesca Allega, Ruhi Deshmukh, Tobias Ackermann, Mark A Nakasone, Johan Vande Voorde, Thomas M Drake, Janina Oetjen, Algernon Bloom, Colin Nixon, Miryam Müller, Stephanie May, Ee Hong Tan, Lars Vereecke, Maude Jans, Gillian Blancke, Daniel J Murphy, Danny T Huang, David Y Lewis, Thomas G Bird, Owen J Sansom, Karen Blyth, David Sumpton, Saverio Tardito.

Glutamine synthetase (GS) activity is conserved from prokaryotes to humans, where the ATP-dependent production of glutamine from glutamate and ammonia is essential for neurotransmission and ammonia detoxification. Here, we show that mammalian GS uses glutamate and methylamine to produce a methylated glutamine analog, N5-methylglutamine. Untargeted metabolomics revealed that liver-specific GS deletion and its pharmacological inhibition in mice suppress hepatic and circulating levels of N5-methylglutamine. This alternative activity of GS was confirmed in human recombinant enzyme and cells, where a pathogenic mutation in the active site (R324C) promoted the synthesis of N5-methylglutamine over glutamine. N5-Methylglutamine is detected in the circulation, and its levels are sustained by the microbiome, as demonstrated by using germ-free mice. Finally, we show that urine levels of N5-methylglutamine correlate with tumor burden and GS expression in a β-catenin-driven model of liver cancer, highlighting the translational potential of this uncharacterized metabolite.

DOI: https://doi.org/10.1038/s41589-022-01154-9
Cell Rep. 2022 Oct 25. pii: S2211-1247(22)01408-5. [Epub ahead of print]41(4): 111552

Elevated pentose phosphate pathway flux supports appendage regeneration.

Jeet H Patel, Daniel J Ong, Claire R Williams, LuLu K Callies, Andrea E Wills.

  A fundamental step in regeneration is rapid growth to replace lost tissue. Cells must generate sufficient lipids, nucleotides, and proteins to fuel rapid cell division. To define metabolic pathways underlying regenerative growth, we undertake a multimodal investigation of metabolic reprogramming in Xenopus tropicalis appendage regeneration. Regenerating tissues have increased glucose uptake; however, inhibition of glycolysis does not decrease regeneration. Instead, glucose is funneled to the pentose phosphate pathway (PPP), which is essential for full tail regeneration. Liquid chromatography-mass spectrometry (LC-MS) metabolite profiling reveals increased nucleotide and nicotinamide intermediates required for cell division. Using single-cell RNA sequencing (scRNA-seq), we find that highly proliferative cells have increased transcription of PPP enzymes and not glycolytic enzymes. Further, PPP inhibition results in decreased cell division specifically in regenerating tissue. Our results inform a model wherein regenerating tissues direct glucose toward the PPP, yielding nucleotide precursors to drive regenerative cell proliferation.

Keywords:  CP: Developmental biology; CP: Metabolism; Xenopus tropicalis; glucose metabolism; glycolysis; pentose phosphate pathway; proliferation; regeneration

DOI:  https://doi.org/10.1016/j.celrep.2022.111552
Redox Biol. 2022 Oct 18. pii: S2213-2317(22)00289-0. [Epub ahead of print]58 102517

Human ultrarare genetic disorders of sulfur metabolism demonstrate redundancies in H2S homeostasis.

Viktor Kožich, Bernd C Schwahn, Jitka Sokolová, Michaela Křížková, Tamas Ditroi, Jakub Krijt, Youssef Khalil, Tomáš Křížek, Tereza Vaculíková-Fantlová, Blanka Stibůrková, Philippa Mills, Peter Clayton, Kristýna Barvíková, Holger Blessing, Jolanta Sykut-Cegielska, Carlo Dionisi-Vici, Serena Gasperini, Ángeles García-Cazorla, Tobias B Haack, Tomáš Honzík, Pavel Ješina, Alice Kuster, Lucia Laugwitz, Diego Martinelli, Francesco Porta, René Santer, Guenter Schwarz, Peter Nagy.

  Regulation of H2S homeostasis in humans is poorly understood. Therefore, we assessed the importance of individual enzymes in synthesis and catabolism of H2S by studying patients with respective genetic defects. We analyzed sulfur compounds (including bioavailable sulfide) in 37 untreated or insufficiently treated patients with seven ultrarare enzyme deficiencies and compared them to 63 controls. Surprisingly, we observed that patients with severe deficiency in cystathionine β-synthase (CBS) or cystathionine γ-lyase (CSE) - the enzymes primarily responsible for H2S synthesis - exhibited increased and normal levels of bioavailable sulfide, respectively. However, an approximately 21-fold increase of urinary homolanthionine in CBS deficiency strongly suggests that lacking CBS activity is compensated for by an increase in CSE-dependent H2S synthesis from accumulating homocysteine, which suggests a control of H2S homeostasis in vivo. In deficiency of sulfide:quinone oxidoreductase - the first enzyme in mitochondrial H2S oxidation - we found normal H2S concentrations in a symptomatic patient and his asymptomatic sibling, and elevated levels in an asymptomatic sibling, challenging the requirement for this enzyme in catabolizing H2S under physiological conditions. Patients with ethylmalonic encephalopathy and sulfite oxidase/molybdenum cofactor deficiencies exhibited massive accumulation of thiosulfate and sulfite with formation of large amounts of S-sulfocysteine and S-sulfohomocysteine, increased renal losses of sulfur compounds and concomitant strong reduction in plasma total cysteine. Our results demonstrate the value of a comprehensive assessment of sulfur compounds in severe disorders of homocysteine/cysteine metabolism and provide evidence for redundancy and compensatory mechanisms in the maintenance of H2S homeostasis.

Keywords:  Cystathionine β-synthase; Cystathionine γ-lyase; Molybdenum cofactor; Persulfide dioxygenase; Sulfide:quinone oxidoreductase; Sulfite oxidase

DOI:  https://doi.org/10.1016/j.redox.2022.102517
JCI Insight. 2022 Oct 24. pii: e162138. [Epub ahead of print]7(20):

Spatial metabolomics reveals upregulation of several pyrophosphate-producing pathways in cortical bone of Hyp mice.

Achim Buck, Verena M Prade, Thomas Kunzke, Reinhold G Erben, Axel Walch.

  Patients with the renal phosphate-wasting disease X-linked hypophosphatemia (XLH) and Hyp mice, the murine homolog of XLH, are characterized by loss-of-function mutations in phosphate-regulating endopeptidase homolog X-linked (PHEX), leading to excessive secretion of the bone-derived phosphotropic hormone FGF23. The mineralization defect in patients with XLH and Hyp mice is caused by a combination of hypophosphatemia and local accumulation of mineralization-inhibiting molecules in bone. However, the mechanism by which PHEX deficiency regulates bone cell metabolism remains elusive. Here, we used spatial metabolomics by employing matrix-assisted laser desorption/ionization (MALDI) Fourier-transform ion cyclotron resonance mass spectrometry imaging (MSI) of undecalcified bone cryosections to characterize in situ metabolic changes in bones of Hyp mice in a holistic, unbiased manner. We found complex changes in Hyp bone metabolism, including perturbations in pentose phosphate, purine, pyrimidine, and phospholipid metabolism. Importantly, our study identified an upregulation of several biochemical pathways involved in intra- and extracellular production of the mineralization inhibitor pyrophosphate in the bone matrix of Hyp mice. Our data emphasize the utility of MSI-based spatial metabolomics in bone research and provide holistic in situ insights as to how Phex deficiency-induced changes in biochemical pathways in bone cells are linked to impaired bone mineralization.

Keywords:  Bone Biology; Bone disease; Mouse models

DOI:  https://doi.org/10.1172/jci.insight.162138
Nat Commun. 2022 Oct 27. 13(1): 6409

Divergent regulation of basement membrane trafficking by human macrophages and cancer cells.

Julian C Bahr, Xiao-Yan Li, Tamar Y Feinberg, Long Jiang, Stephen J Weiss.

Macrophages and cancer cells populations are posited to navigate basement membrane barriers by either mobilizing proteolytic enzymes or deploying mechanical forces. Nevertheless, the relative roles, or identity, of the proteinase -dependent or -independent mechanisms used by macrophages versus cancer cells to transmigrate basement membrane barriers harboring physiologically-relevant covalent crosslinks remains ill-defined. Herein, both macrophages and cancer cells are shown to mobilize membrane-anchored matrix metalloproteinases to proteolytically remodel native basement membranes isolated from murine tissues while infiltrating the underlying interstitial matrix ex vivo. In the absence of proteolytic activity, however, only macrophages deploy actomyosin-generated forces to transmigrate basement membrane pores, thereby providing the cells with proteinase-independent access to the interstitial matrix while simultaneously exerting global effects on the macrophage transcriptome. By contrast, cancer cell invasive activity is reliant on metalloproteinase activity and neither mechanical force nor changes in nuclear rigidity rescue basement membrane transmigration. These studies identify membrane-anchored matrix metalloproteinases as key proteolytic effectors of basement membrane remodeling by macrophages and cancer cells while also defining the divergent invasive strategies used by normal and neoplastic cells to traverse native tissue barriers.

DOI: https://doi.org/10.1038/s41467-022-34087-x
Metabolites. 2022 Oct 11. pii: 961. [Epub ahead of print]12(10):

Simplifying the B Complex: How Vitamins B6 and B9 Modulate One Carbon Metabolism in Cancer and Beyond.

Carolina N Franco, Laurence J Seabrook, Steven T Nguyen, Jack T Leonard, Lauren V Albrecht.

  Vitamin B micronutrients are essential regulators of one carbon metabolism that ensures human health. Vitamin B9, or folate, lies at the heart of the folate cycle and converges with the methionine cycle to complete the one carbon pathway. Additionally, vitamin B6 contributes by orchestrating the flux of one carbon cycling. Dysregulation of vitamin B contributes to altered biochemical signaling that manifests in a spectrum of human diseases. This review presents an analysis of the past, present, and future work, highlighting the interplay between folate and vitamin B6 in one carbon metabolism. Emerging insights include advances in metabolomic-based mass spectrometry and the use of live-cell metabolic labeling. Cancer is used as a focal point to dissect vitamin crosstalk and highlight new insights into the roles of folate and vitamin B6 in metabolic control. This collection of vitamin-based research detailing the trends of one carbon metabolism in human disease exemplifies how the future of personalized medicine could unfold using this new base of knowledge and ultimately provide next-generation therapeutics.

Keywords:  B6; B9; CEST-MRI; aptamer; cancer; fluorescent sensors; folate; metabolic probe; methionine; methylation; one carbon metabolism; post-translational modification; pyridoxine

DOI:  https://doi.org/10.3390/metabo12100961
FASEB J. 2022 Nov;36(11): e22598

Pyruvate prevents the onset of the cachectic features and metabolic alterations in myotubes downregulating STAT3 signaling.

Michele Mannelli, Tania Gamberi, Rachele Garella, Francesca Magherini, Roberta Squecco, Tania Fiaschi.

  Cachexia is a systemic disease associated with several pathologies, including cancer, that leads to excessive weight loss due to enhanced protein degradation. Previously, we showed that cachectic features in myotubes are provoked by a metabolic shift toward lactic fermentation. Our previous results led us to hyphotesise that increasing pyruvate concentration could impede the metabolic modifications responsible for induction of cachexia in myotubes. Here, we demonstrated that the addition of sodium pyruvate in conditioned media from CT26 colon cancer cells (CM CT26) prevents the onset of either phenotypic and metabolic cachectic features. Myotubes treated with CM CT26 containing sodium pyruvate show a phenotype similar to the healthy counterpart and display lactate production, oxygen consumption, and pyruvate dehydrogenase activity as control myotubes. The use of the Mitochondrial Pyruvate Carrier inhibitor UK5099, highlights the importance of mitochondrial pyruvate amount in the prevention of cachexia. Indeed, UK5099-treated myotubes show cachectic features as those observed in myotubes treated with CM CT26. Finally, we found that sodium pyruvate is able to decrease STAT3 phosphorylation level, a signaling pathway involved in the induction of cachexia in myotubes. Collectively, our results show that cachexia in myotubes could be prevented by the utilization of sodium pyruvate which impedes the metabolic modifications responsible for the acquisition of the cachectic features.

Keywords:  cancer cachexia; metabolism; pyruvate

DOI:  https://doi.org/10.1096/fj.202200848R
iScience. 2022 Oct 21. 25(10): 105190

Link between glucose metabolism and epithelial-to-mesenchymal transition drives triple-negative breast cancer migratory heterogeneity.

Samantha C Schwager, Jenna A Mosier, Reethi S Padmanabhan, Addison White, Qinzhe Xing, Lauren A Hapach, Paul V Taufalele, Ismael Ortiz, Cynthia A Reinhart-King.

  Intracellular and environmental cues result in heterogeneous cancer cell populations with different metabolic and migratory behaviors. Although glucose metabolism and epithelial-to-mesenchymal transition have previously been linked, we aim to understand how this relationship fuels cancer cell migration. We show that while glycolysis drives single-cell migration in confining microtracks, fast and slow cells display different migratory sensitivities to glycolysis and oxidative phosphorylation inhibition. Phenotypic sorting of highly and weakly migratory subpopulations (MDA+, MDA-) reveals that more mesenchymal, highly migratory MDA+ preferentially use glycolysis while more epithelial, weakly migratory MDA- utilize mitochondrial respiration. These phenotypes are plastic and MDA+ can be made less glycolytic, mesenchymal, and migratory and MDA- can be made more glycolytic, mesenchymal, and migratory via modulation of glucose metabolism or EMT. These findings reveal an intrinsic link between EMT and glucose metabolism that controls migration. Identifying mechanisms fueling phenotypic heterogeneity is essential to develop targeted metastatic therapeutics.

Keywords:  Biological sciences; cancer; human metabolism; physiology

DOI:  https://doi.org/10.1016/j.isci.2022.105190
Cell Death Dis. 2022 Oct 27. 13(10): 906

Limiting glutamine utilization activates a GCN2/TRAIL-R2/Caspase-8 apoptotic pathway in glutamine-addicted tumor cells.

Rosario Yerbes, Rocío Mora-Molina, F Javier Fernández-Farrán, Laura Hiraldo, Abelardo López-Rivas, Carmen Palacios.

Oncogenic transformation leads to changes in glutamine metabolism that make transformed cells highly dependent on glutamine for anabolic growth and survival. Herein, we investigated the cell death mechanism activated in glutamine-addicted tumor cells in response to the limitation of glutamine metabolism. We show that glutamine starvation triggers a FADD and caspase-8-dependent and mitochondria-operated apoptotic program in tumor cells that involves the pro-apoptotic TNF-related apoptosis-inducing ligand receptor 2 (TRAIL-R2), but is independent of its cognate ligand TRAIL. In glutamine-depleted tumor cells, activation of the amino acid-sensing general control nonderepressible-2 kinase (GCN2) is responsible for TRAIL-R2 upregulation, caspase-8 activation, and apoptotic cell death. Interestingly, GCN2-dependent ISR signaling induced by methionine starvation also leads to TRAIL-R2 upregulation and apoptosis. Moreover, pharmacological inhibition of transaminases activates a GCN2 and TRAIL-R2-dependent apoptotic mechanism that is inhibited by non-essential amino acids (NEAA). In addition, metabolic stress upon glutamine deprivation also results in GCN2-independent FLICE-inhibitory protein (FLIP) downregulation facilitating caspase-8 activation and apoptosis. Importantly, downregulation of the long FLIP splice form (FLIPL) and apoptosis upon glutamine deprivation are inhibited in the presence of a membrane-permeable α-ketoglutarate. Collectively, our data support a model in which limiting glutamine utilization in glutamine-addicted tumor cells triggers a previously unknown cell death mechanism regulated by GCN2 that involves the TRAIL-R2-mediated activation of the extrinsic apoptotic pathway.

DOI: https://doi.org/10.1038/s41419-022-05346-y
Cell Death Differ. 2022 Oct 28.

OPA1 drives macrophage metabolism and functional commitment via p65 signaling.

Ricardo Sánchez-Rodríguez, Caterina Tezze, Andrielly H R Agnellini, Roberta Angioni, Francisca C Venegas, Chiara Cioccarelli, Fabio Munari, Nicole Bertoldi, Marcella Canton, Maria Andrea Desbats, Leonardo Salviati, Rosanna Gissi, Alessandra Castegna, Maria Eugenia Soriano, Marco Sandri, Luca Scorrano, Antonella Viola, Barbara Molon.

Macrophages are essential players for the host response against pathogens, regulation of inflammation and tissue regeneration. The wide range of macrophage functions rely on their heterogeneity and plasticity that enable a dynamic adaptation of their responses according to the surrounding environmental cues. Recent studies suggest that metabolism provides synergistic support for macrophage activation and elicitation of desirable immune responses; however, the metabolic pathways orchestrating macrophage activation are still under scrutiny. Optic atrophy 1 (OPA1) is a mitochondria-shaping protein controlling mitochondrial fusion, cristae biogenesis and respiration; clear evidence shows that the lack or dysfunctional activity of this protein triggers the accumulation of metabolic intermediates of the TCA cycle. In this study, we show that OPA1 has a crucial role in macrophage activation. Selective Opa1 deletion in myeloid cells impairs M1-macrophage commitment. Mechanistically, Opa1 deletion leads to TCA cycle metabolite accumulation and defective NF-κB signaling activation. In an in vivo model of muscle regeneration upon injury, Opa1 knockout macrophages persist within the damaged tissue, leading to excess collagen deposition and impairment in muscle regeneration. Collectively, our data indicate that OPA1 is a key metabolic driver of macrophage functions.

DOI: https://doi.org/10.1038/s41418-022-01076-y
EMBO J. 2022 Oct 27. e110771

Phospholipid imbalance impairs autophagosome completion.

Alexandra Polyansky, Oren Shatz, Milana Fraiberg, Eyal Shimoni, Tali Dadosh, Muriel Mari, Fulvio M Reggiori, Chao Qin, Xianlin Han, Zvulun Elazar.

  Autophagy, a conserved eukaryotic intracellular catabolic pathway, maintains cell homeostasis by lysosomal degradation of cytosolic material engulfed in double membrane vesicles termed autophagosomes, which form upon sealing of single-membrane cisternae called phagophores. While the role of phosphatidylinositol 3-phosphate (PI3P) and phosphatidylethanolamine (PE) in autophagosome biogenesis is well-studied, the roles of other phospholipids in autophagy remain rather obscure. Here we utilized budding yeast to study the contribution of phosphatidylcholine (PC) to autophagy. We reveal for the first time that genetic loss of PC biosynthesis via the CDP-DAG pathway leads to changes in lipid composition of autophagic membranes, specifically replacement of PC by phosphatidylserine (PS). This impairs closure of the autophagic membrane and autophagic flux. Consequently, we show that choline-dependent recovery of de novo PC biosynthesis via the CDP-choline pathway restores autophagosome formation and autophagic flux in PC-deficient cells. Our findings therefore implicate phospholipid metabolism in autophagosome biogenesis.

Keywords:  autophagosome biogenesis; autophagy; phagophore; phospholipids

DOI:  https://doi.org/10.15252/embj.2022110771
Nat Metab. 2022 Oct 27.

Metabolic reconfiguration enables synthetic reductive metabolism in yeast.

Tao Yu, Quanli Liu, Xiang Wang, Xiangjian Liu, Yun Chen, Jens Nielsen.

Cell proliferation requires the integration of catabolic processes to provide energy, redox power and biosynthetic precursors. Here we show how the combination of rational design, metabolic rewiring and recombinant expression enables the establishment of a decarboxylation cycle in the yeast cytoplasm. This metabolic cycle can support growth by supplying energy and increased provision of NADPH or NADH in the cytosol, which can support the production of highly reduced chemicals such as glycerol, succinate and free fatty acids. With this approach, free fatty acid yield reached 40% of theoretical yield, which is the highest yield reported for Saccharomyces cerevisiae to our knowledge. This study reports the implementation of a synthetic decarboxylation cycle in the yeast cytosol, and its application in achieving high yields of valuable chemicals in cell factories. Our study also shows that, despite extensive regulation of catabolism in yeast, it is possible to rewire the energy metabolism, illustrating the power of biodesign.

DOI: https://doi.org/10.1038/s42255-022-00654-1
Cancer Cell. 2022 Oct 21. pii: S1535-6108(22)00492-5. [Epub ahead of print]

Multi-omic analyses of changes in the tumor microenvironment of pancreatic adenocarcinoma following neoadjuvant treatment with anti-PD-1 therapy.

Keyu Li, Joseph A Tandurella, Jessica Gai, Qingfeng Zhu, Su Jin Lim, Dwayne L Thomas, Tao Xia, Guanglan Mo, Jacob T Mitchell, Janelle Montagne, Melissa Lyman, Ludmila V Danilova, Jacquelyn W Zimmerman, Benedict Kinny-Köster, Tengyi Zhang, Linda Chen, Alex B Blair, Thatcher Heumann, Rose Parkinson, Jennifer N Durham, Amol K Narang, Robert A Anders, Christopher L Wolfgang, Daniel A Laheru, Jin He, Arsen Osipov, Elizabeth D Thompson, Hao Wang, Elana J Fertig, Elizabeth M Jaffee, Lei Zheng.

  Successful pancreatic ductal adenocarcinoma (PDAC) immunotherapy necessitates optimization and maintenance of activated effector T cells (Teff). We prospectively collected and applied multi-omic analyses to paired pre- and post-treatment PDAC specimens collected in a platform neoadjuvant study of granulocyte-macrophage colony-stimulating factor-secreting allogeneic PDAC vaccine (GVAX) vaccine ± nivolumab (anti-programmed cell death protein 1 [PD-1]) to uncover sensitivity and resistance mechanisms. We show that GVAX-induced tertiary lymphoid aggregates become immune-regulatory sites in response to GVAX + nivolumab. Higher densities of tumor-associated neutrophils (TANs) following GVAX + nivolumab portend poorer overall survival (OS). Increased T cells expressing CD137 associated with cytotoxic Teff signatures and correlated with increased OS. Bulk and single-cell RNA sequencing found that nivolumab alters CD4+ T cell chemotaxis signaling in association with CD11b+ neutrophil degranulation, and CD8+ T cell expression of CD137 was required for optimal T cell activation. These findings provide insights into PD-1-regulated immune pathways in PDAC that should inform more effective therapeutic combinations that include TAN regulators and T cell activators.

Keywords:  CD137; IL-8; RNA sequencing; Th17; anti-PD-1 antibody; immune checkpoint inhibitor; multiplex immunohistochemistry; pancreatic cancer; tumor-associated neutrophils; vaccine therapy

DOI:  https://doi.org/10.1016/j.ccell.2022.10.001
Proc Natl Acad Sci U S A. 2022 Nov 08. 119(45): e2214900119

Ornithine decarboxylase supports ILC3 responses in infectious and autoimmune colitis through positive regulation of IL-22 transcription.

Vincent Peng, Siyan Cao, Tihana Trsan, Jennifer K Bando, Julian Avila-Pacheco, John L Cleveland, Clary Clish, Ramnik J Xavier, Marco Colonna.

  Group 3 innate lymphoid cells (ILC3s) are RORγT+ lymphocytes that are predominately enriched in mucosal tissues and produce IL-22 and IL-17A. They are the innate counterparts of Th17 cells. While Th17 lymphocytes utilize unique metabolic pathways in their differentiation program, it is unknown whether ILC3s make similar metabolic adaptations. We employed single-cell RNA sequencing and metabolomic profiling of intestinal ILC subsets to identify an enrichment of polyamine biosynthesis in ILC3s, converging on the rate-limiting enzyme ornithine decarboxylase (ODC1). In vitro and in vivo studies demonstrated that exogenous supplementation with the polyamine putrescine or its biosynthetic substrate, ornithine, enhanced ILC3 production of IL-22. Conditional deletion of ODC1 in ILC3s impaired mouse antibacterial defense against Citrobacter rodentium infection, which was associated with a decrease in anti-microbial peptide production by the intestinal epithelium. Furthermore, in a model of anti-CD40 colitis, deficiency of ODC1 in ILC3s markedly reduced the production of IL-22 and severity of inflammatory colitis. We conclude that ILC3-intrinsic polyamine biosynthesis facilitates efficient defense against enteric pathogens as well as exacerbates autoimmune colitis, thus representing an attractive target to modulate ILC3 function in intestinal disease.

Keywords:  IL-22; enteritis; innate lymphoid cells; ornithine decarboxylase; polyamines

DOI:  https://doi.org/10.1073/pnas.2214900119
J Exp Med. 2022 Nov 07. pii: e20221140. [Epub ahead of print]219(11):

Metabolic features of innate lymphoid cells.

Huiyang Yu, Nicolas Jacquelot, Gabrielle T Belz.

Innate and adaptive immune cells are found in distinct tissue niches where they orchestrate immune responses. This requires intrinsic and temporal metabolic adaptability to coordinately activate the immune response cascade. Dysregulation of this program is a key feature of immunosuppression. Direct or indirect metabolic immune cell reprogramming may offer new approaches to modulate immune cells behavior for therapy to overcome dysregulation. In this review, we explored how metabolism regulates lymphocytes beyond the classical T cell subsets. We focus on the innate lymphoid cell (ILC) family, highlighting the distinct metabolic characteristics of these cells, the impact of environmental factors, and the receptors that could alter immune cell functions through manipulation of metabolic pathways to potentially prevent or treat various diseases.

DOI: https://doi.org/10.1084/jem.20221140
Nat Commun. 2022 Oct 26. 13(1): 6371

Kynurenine promotes neonatal heart regeneration by stimulating cardiomyocyte proliferation and cardiac angiogenesis.

Donghong Zhang, Jinfeng Ning, Tharmarajan Ramprasath, Changjiang Yu, Xiaoxu Zheng, Ping Song, Zhonglin Xie, Ming-Hui Zou.

Indoleamine 2,3 dioxygenase-1 (IDO1) catalyzes tryptophan-kynurenine metabolism in many inflammatory and cancer diseases. Of note, acute inflammation that occurs immediately after heart injury is essential for neonatal cardiomyocyte proliferation and heart regeneration. However, the IDO1-catalyzed tryptophan metabolism during heart regeneration is largely unexplored. Here, we find that apical neonatal mouse heart resection surgery led to rapid and consistent increases in cardiac IDO1 expression and kynurenine accumulation. Cardiac deletion of Ido1 gene or chemical inhibition of IDO1 impairs heart regeneration. Mechanistically, elevated kynurenine triggers cardiomyocyte proliferation by activating the cytoplasmic aryl hydrocarbon receptor-SRC-YAP/ERK pathway. In addition, cardiomyocyte-derived kynurenine transports to endothelial cells and stimulates cardiac angiogenesis by promoting aryl hydrocarbon receptor nuclear translocation and enhancing vascular endothelial growth factor A expression. Notably, Ahr deletion prevents indoleamine 2,3 dioxygenase -kynurenine-associated heart regeneration. In summary, increasing indoleamine 2,3 dioxygenase-derived kynurenine level promotes cardiac regeneration by functioning as an endogenous regulator of cardiomyocyte proliferation and cardiac angiogenesis.

DOI: https://doi.org/10.1038/s41467-022-33734-7
Nat Commun. 2022 Oct 22. 13(1): 6303

REDD1 promotes obesity-induced metabolic dysfunction via atypical NF-κB activation.

Dong-Keon Lee, Taesam Kim, Junyoung Byeon, Minsik Park, Suji Kim, Joohwan Kim, Seunghwan Choi, Gihwan Lee, Chanin Park, Keun Woo Lee, Yong Jung Kwon, Jeong-Hyung Lee, Young-Guen Kwon, Young-Myeong Kim.

Regulated in development and DNA damage response 1 (REDD1) expression is upregulated in response to metabolic imbalance and obesity. However, its role in obesity-associated complications is unclear. Here, we demonstrate that the REDD1-NF-κB axis is crucial for metabolic inflammation and dysregulation. Mice lacking Redd1 in the whole body or adipocytes exhibited restrained diet-induced obesity, inflammation, insulin resistance, and hepatic steatosis. Myeloid Redd1-deficient mice showed similar results, without restrained obesity and hepatic steatosis. Redd1-deficient adipose-derived stem cells lost their potential to differentiate into adipocytes; however, REDD1 overexpression stimulated preadipocyte differentiation and proinflammatory cytokine expression through atypical IKK-independent NF-κB activation by sequestering IκBα from the NF-κB/IκBα complex. REDD1 with mutated Lys219/220Ala, key amino acid residues for IκBα binding, could not stimulate NF-κB activation, adipogenesis, and inflammation in vitro and prevented obesity-related phenotypes in knock-in mice. The REDD1-atypical NF-κB activation axis is a therapeutic target for obesity, meta-inflammation, and metabolic complications.

DOI: https://doi.org/10.1038/s41467-022-34110-1
Cell Rep. 2022 Oct 25. pii: S2211-1247(22)01394-8. [Epub ahead of print]41(4): 111538

A multienzyme S-nitrosylation cascade regulates cholesterol homeostasis.

Colin T Stomberski, Nicholas M Venetos, Hua-Lin Zhou, Zhaoxia Qian, Bryce R Collison, Seth J Field, Richard T Premont, Jonathan S Stamler.

  Accumulating evidence suggests that protein S-nitrosylation is enzymatically regulated and that specificity in S-nitrosylation derives from dedicated S-nitrosylases and denitrosylases that conjugate and remove S-nitrosothiols, respectively. Here, we report that mice deficient in the protein denitrosylase SCoR2 (S-nitroso-Coenzyme A Reductase 2; AKR1A1) exhibit marked reductions in serum cholesterol due to reduced secretion of the cholesterol-regulating protein PCSK9. SCoR2 associates with endoplasmic reticulum (ER) secretory machinery to control an S-nitrosylation cascade involving ER cargo-selection proteins SAR1 and SURF4, which moonlight as S-nitrosylases. SAR1 acts as a SURF4 nitrosylase and SURF4 as a PCSK9 nitrosylase to inhibit PCSK9 secretion, while SCoR2 counteracts nitrosylase activity by promoting PCSK9 denitrosylation. Inhibition of PCSK9 by an NO-based drug requires nitrosylase activity, and small-molecule inhibition of SCoR2 phenocopies the PCSK9-mediated reductions in cholesterol observed in SCoR2-deficient mice. Our results reveal enzymatic machinery controlling cholesterol levels through S-nitrosylation and suggest a distinct treatment paradigm for cardiovascular disease.

Keywords:  COPII; CP: Metabolism; CP: Molecular biology; PCSK9; denitrosylation; hypercholesterolemia; nitric oxide; nitrosylase cascade; transnitrosylation

DOI:  https://doi.org/10.1016/j.celrep.2022.111538
Molecules. 2022 Oct 12. pii: 6820. [Epub ahead of print]27(20):

Preface to Nitric Oxide Modulators in Health and Disease I.

Cristina Maccallini, Rosa Amoroso.

Nitric oxide (NO) is a small free radical molecule biosynthesized by nitric oxide synthases (NOS), a family of oxidoreductases responsible for the conversion of the natural substrate L-arginine into L-citrulline and NO [...].

DOI: https://doi.org/10.3390/molecules27206820
Nat Cell Biol. 2022 Oct 24.

Quick tips for re-using metabolomics data.

Ethan Stancliffe, Gary J Patti.

DOI: https://doi.org/10.1038/s41556-022-01019-2
Redox Biol. 2022 Oct 17. pii: S2213-2317(22)00286-5. [Epub ahead of print]57 102514

Cystine-dependent antiporters buffer against excess intracellular reactive sulfur species-induced stress.

Masahiro Akiyama, Takamitsu Unoki, Hanako Aoki, Akiyuki Nishimura, Yasuhiro Shinkai, Eiji Warabi, Kazuhiro Nishiyama, Yuka Furumoto, Naohiko Anzai, Takaaki Akaike, Motohiro Nishida, Yoshito Kumagai.

  Reactive sulfur species (RSS) play a role in redox homeostasis; however, adaptive cell responses to excessive intracellular RSS are not well understood. Therefore, in this study, we generated transgenic (Tg) mice overexpressing cystathionine gamma-lyase (CSE) to produce excessive RSS. Contrary to expectations, tissue concentrations of RSS, such as cysteine persulfide (CysSSH), were comparable in both wild-type and CSE Tg mice, but the plasma concentrations of CysSSH were significantly higher in CSE Tg mice than in wild-type mice. This export of surplus intracellular RSS was also observed in primary hepatocytes of CSE Tg mice. Exposure of primary hepatocytes to the RSS generator sodium tetrasulfide (Na2S4) resulted in an initial increase in the intracellular concentration of RSS, which later returned to basal levels after export into the extracellular space. Interestingly, among all amino acids, cystine (CysSSCys) was found to be essential for CysSSH export from primary mouse hepatocytes, HepG2 cells, and HEK293 cells during Na2S4 exposure, suggesting that the cystine/glutamate transporter (SLC7A11) contributes, at least partially, to CysSSH export. We established HepG2 cell lines with knockout and overexpression of SLC7A11 and used them to confirm SLC7A11 as the predominant antiporter of CysSSCys and CysSSH. We observed that the poor efflux of excess CysSSH from the cell enhanced cellular stresses induced by Na2S4 exposure, such as polysulfidation of intracellular proteins, mitochondrial damage, and cytotoxicity. These results suggest the presence of a cellular response to excess intracellular RSS that involves the extracellular efflux of excess CysSSH by a cystine-dependent transporter to maintain intracellular redox homeostasis.

Keywords:  Antiporter; Cystathionine gamma-lyase; Cysteine persulfide; Cystine; Sulfur stress

DOI:  https://doi.org/10.1016/j.redox.2022.102514
Nat Cell Biol. 2022 Oct 27.

PTEN directs developmental and metabolic signaling for innate-like T cell fate and tissue homeostasis.

Daniel Bastardo Blanco, Nicole M Chapman, Jana L Raynor, Chengxian Xu, Wei Su, Anil Kc, Wei Li, Seon Ah Lim, Stefan Schattgen, Hao Shi, Isabel Risch, Yu Sun, Yogesh Dhungana, Yunjung Kim, Jun Wei, Sherri Rankin, Geoffrey Neale, Paul G Thomas, Kai Yang, Hongbo Chi.

Phosphatase and tensin homologue (PTEN) is frequently mutated in human cancer, but its roles in lymphopoiesis and tissue homeostasis remain poorly defined. Here we show that PTEN orchestrates a two-step developmental process linking antigen receptor and IL-23-Stat3 signalling to type-17 innate-like T cell generation. Loss of PTEN leads to pronounced accumulation of mature IL-17-producing innate-like T cells in the thymus. IL-23 is essential for their accumulation, and ablation of IL-23 or IL-17 signalling rectifies the reduced survival of female PTEN-haploinsufficient mice that model human patients with PTEN mutations. Single-cell transcriptome and network analyses revealed the dynamic regulation of PTEN, mTOR and metabolic activities that accompanied type-17 cell programming. Furthermore, deletion of mTORC1 or mTORC2 blocks PTEN loss-driven type-17 cell accumulation, and this is further shaped by the Foxo1 and Stat3 pathways. Collectively, our study establishes developmental and metabolic signalling networks underpinning type-17 cell fate decisions and their functional effects at coordinating PTEN-dependent tissue homeostasis.

DOI: https://doi.org/10.1038/s41556-022-01011-w
Eur J Immunol. 2022 Oct 25.

The thioredoxin system: balancing redox responses in immune cells and tumors.

Jonathan Muri, Manfred Kopf.

  The thioredoxin (TRX) system is an important contributor to cellular redox balance and regulates cell growth, apoptosis, gene expression, and antioxidant defense in nearly all living cells. Oxidative stress, the imbalance between reactive oxygen species (ROS) and antioxidants, can lead cell death and tissue damage, thereby contributing to ageing and to the development of several diseases, including cardiovascular and allergic diseases, diabetes, and neurological disorders. Targeting its activity is also considered as a promising strategy in the treatment of cancer. Over the past years, immunologists have established an essential function of TRX for activation, proliferation, and responses in T cells, B cells, and macrophages. Upon activation, immune cells rearrange their redox system and activate the TRX pathway to promote proliferation through sustainment of nucleotide biosynthesis and to support inflammatory responses in myeloid cells by allowing NF-κB and NLRP3 inflammasome responses. Consequently, targeting the TRX system may therapeutically be exploited to inhibit immune responses in inflammatory conditions. In this review, we summarize recent insights revealing key roles of the TRX pathway in immune cells in health and disease, and lessons learnt for cancer therapy. This article is protected by copyright. All rights reserved.

Keywords:  TRX system ⋅ Immunoregulation ⋅ ROS ⋅ Cancer ⋅ Cellular redox

DOI:  https://doi.org/10.1002/eji.202249948