bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2020–06–28
forty-nine papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit
  1. mTOR Signaling and SREBP Activity Increase FADS2 Expression and Can Activate Sapienate Biosynthesis.
  2. Autophagic lipid metabolism sustains mTORC1 activity in TSC-deficient neural stem cells.
  3. Limited Environmental Serine and Glycine Confer Brain Metastasis Sensitivity to PHGDH Inhibition.
  4. Therapeutic Manipulation of mtDNA Heteroplasmy: A Shifting Perspective.
  5. MICOS assembly controls mitochondrial inner membrane remodeling and crista junction redistribution to mediate cristae formation.
  6. Using arterial-venous analysis to characterize cancer metabolic consumption in patients.
  7. Mitochondrial F-type ATP synthase: multiple enzyme functions revealed by the membrane-embedded FO structure.
  8. CD28 Regulates Metabolic Fitness for Long-Lived Plasma Cell Survival.
  9. SSADH Variants Increase Susceptibility of U87 Cells to Mitochondrial Pro-Oxidant Insult.
  10. The Role of Mitochondrial Dynamics and Mitophagy in Carcinogenesis, Metastasis and Therapy.
  11. A quantitative LC-MS/MS method for analysis of mitochondrial -specific oxysterol metabolism.
  12. Symmetric arrangement of mitochondria:plasma membrane contacts between adjacent photoreceptor cells regulated by Opa1.
  13. Metabolic Landscape of a Genetically Engineered Mouse Model of IDH1 Mutant Glioma.
  14. Ubiquitination of PPAR-gamma by pVHL inhibits ACLY expression and lipid metabolism, is implicated in tumor progression.
  15. Opa1 Overexpression Protects from Early-Onset Mpv17-/--Related Mouse Kidney Disease.
  16. NAD+ Regeneration Rescues Lifespan, but Not Ataxia, in a Mouse Model of Brain Mitochondrial Complex I Dysfunction.
  17. Multifaceted Roles of Mitochondrial Components and Metabolites in Metabolic Diseases and Cancer.
  18. Ferroptosis and Cancer: Mitochondria Meet the "Iron Maiden" Cell Death.
  19. Deadly Encounter: Endosomes Meet Mitochondria to Initiate Apoptosis.
  20. SREBP1 regulates mitochondrial metabolism in oncogenic KRAS expressing NSCLC.
  21. Mitochondrial scenario: roles of mitochondrial dynamics in acute myocardial ischemia/reperfusion injury.
  22. The mitochondrial derived peptide humanin is a regulator of lifespan and healthspan.
  23. Hexokinase II dissociation alone cannot account for changes in heart mitochondrial function, morphology and sensitivity to permeability transition pore opening following ischemia.
  24. Consequences of Folding the Mitochondrial Inner Membrane.
  25. Spotlight on Circadian Genes and Colorectal Cancer Crosstalk.
  26. How and Why Are Cancers Acidic? Carbonic Anhydrase IX and the Homeostatic Control of Tumour Extracellular pH.
  27. Protein Biosynthesis in Mitochondria: Past Simple, Present Perfect, Future Indefinite.
  28. Self-assembled cGAMP-STINGΔTM signaling complex as a bioinspired platform for cGAMP delivery.
  29. Ornithine Decarboxylase, the rate-limiting enzyme of polyamine synthesis, modifies brain pathology in a mouse model of tuberous sclerosis complex.
  30. Novel mitochondrial and cytosolic purification pipeline for compartment-specific metabolomics in mammalian disease model tissues.
  31. Matrix Rigidity Controls Epithelial-Mesenchymal Plasticity and Tumor Metastasis via a Mechanoresponsive EPHA2/LYN Complex.
  32. Substrate Channeling via a Transient Protein-Protein Complex: The case of D-Glyceraldehyde-3-Phosphate Dehydrogenase and L-Lactate Dehydrogenase.
  33. Tumour metabolites hinder DNA repair.
  34. Adenosine/A2B Receptor Signaling Ameliorates the Effects of Aging and Counteracts Obesity.
  35. Cardiolipin is required for membrane docking of mitochondrial ribosomes and protein synthesis.
  36. Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis.
  37. Amino Acids as Regulators of Cell Metabolism.
  38. Resolving mitochondrial cristae: introducing a new model into the fold.
  39. The Critical Role of Cell Metabolism for Essential Neutrophil Functions.
  40. Metabolic Dynamics and Prediction of Gestational Age and Time to Delivery in Pregnant Women.
  41. Mitochondrial Transplantation: A Critical Analysis.
  42. PKCλ/ι Loss Induces Autophagy, Oxidative Phosphorylation, and NRF2 to Promote Liver Cancer Progression.
  43. Intracellular pH controls WNT downstream of glycolysis in amniote embryos.
  44. Protein arginine deiminase 4 antagonizes methylglyoxal-induced histone glycation.
  45. Convergent evolution of conserved mitochondrial pathways underlies repeated adaptation to extreme environments.
  46. Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes.
  47. Subunit composition of the mammalian serine-palmitoyltransferase defines the spectrum of straight and methyl-branched long-chain bases.
  48. Ageing, metabolism and the intestine.
  49. Robust detection of oncometabolic aberrations by 1H-13C heteronuclear single quantum correlation in intact biological specimens.
  1. Cell Rep. 2020 Jun 23. pii: S2211-1247(20)30787-7. [Epub ahead of print]31(12): 107806
    mTOR Signaling and SREBP Activity Increase FADS2 Expression and Can Activate Sapienate Biosynthesis.
    Mouna Triki, Gianmarco Rinaldi, Melanie Planque, Dorien Broekaert, Alina M Winkelkotte, Carina R Maier, Sudha Janaki Raman, Anke Vandekeere, Joke Van Elsen, Martin F Orth, Thomas G P Grünewald, Almut Schulze, Sarah-Maria Fendt.
      Cancer cells display an increased plasticity in their lipid metabolism, which includes the conversion of palmitate to sapienate via the enzyme fatty acid desaturase 2 (FADS2). We find that FADS2 expression correlates with mammalian target of rapamycin (mTOR) signaling and sterol regulatory element-binding protein 1 (SREBP-1) activity across multiple cancer types and is prognostic in some cancer types. Accordingly, activating mTOR signaling by deleting tuberous sclerosis complex 2 (Tsc2) or overexpression of SREBP-1/2 is sufficient to increase FADS2 mRNA expression and sapienate metabolism in mouse embryonic fibroblasts (MEFs) and U87 glioblastoma cells, respectively. Conversely, inhibiting mTOR signaling decreases FADS2 expression and sapienate biosynthesis in MEFs with Tsc2 deletion, HUH7 hepatocellular carcinoma cells, and orthotopic HUH7 liver xenografts. In conclusion, we show that mTOR signaling and SREBP activity are sufficient to activate sapienate metabolism by increasing FADS2 expression. Consequently, targeting mTOR signaling can reduce sapienate metabolism in vivo.
    Keywords:  FADS2; SCD1; SREBP; cancer; fatty acid metabolism; glioblastoma; hepatocellular carcinoma; mTOR; palmitate; palmitoleate; sapienate
    DOI:  https://doi.org/10.1016/j.celrep.2020.107806
  2. Nat Metab. 2019 Nov;1(11): 1127-1140
    Autophagic lipid metabolism sustains mTORC1 activity in TSC-deficient neural stem cells.
    Chenran Wang, Michael A Haas, Fuchun Yang, Syn Yeo, Takako Okamoto, Song Chen, Jian Wen, Pranjal Sarma, David R Plas, Jun-Lin Guan.
      Although mTORC1 negatively regulates autophagy in cultured cells, how autophagy impacts mTORC1 signaling, in particular in vivo, is less clear. Here we show that autophagy supports mTORC1 hyperactivation in NSCs lacking Tsc1, thereby promoting defects in NSC maintenance, differentiation, tumourigenesis, and the formation of the neurodevelopmental lesion of Tuberous Sclerosis Complex (TSC). Analysing mice that lack Tsc1 and the essential autophagy gene Fip200 in NSCs we find that TSC-deficient cells require autophagy to maintain mTORC1 hyperactivation under energy stress conditions, likely to provide lipids via lipophagy to serve as an alternative energy source for OXPHOS. In vivo, inhibition of lipophagy or its downstream catabolic pathway reverses defective phenotypes caused by Tsc1-null NSCs and reduces tumorigenesis in mouse models. These results reveal a cooperative function of selective autophagy in coupling energy availability with TSC pathogenesis and suggest a potential new therapeutic strategy to treat TSC patients.
    Keywords:  autophagy; energy stress; lipid catabolism; mTORC1; neural stem cells; tumorigenesis
    DOI:  https://doi.org/10.1038/s42255-019-0137-5
  3. Cancer Discov. 2020 Jun 22. pii: CD-19-1228. [Epub ahead of print]
    Limited Environmental Serine and Glycine Confer Brain Metastasis Sensitivity to PHGDH Inhibition.
    Bryan Ngo, Eugenie Kim, Victoria Osorio-Vasquez, Sophia Doll, Sophia Bustraan, Roger J Liang, Alba Luengo, Shawn M Davidson, Ahmed Ali, Gino B Ferraro, Grant M Fischer, Roozbeh Eskandari, Diane S Kang, Jing Ni, Ariana Plasger, Vinagolu K Rajasekhar, Edward R Kastenhuber, Sarah Bacha, Roshan K Sriram, Benjamin D Stein, Samuel F Bakhoum, Matija Snuderl, Paolo Cotzia, John H Healey, Nello Mainolfi, Vipin Suri, Adam Friedman, Mark Manfredi, David M Sabatini, Drew R Jones, Min Yu, Jean J Zhao, Rakesh K Jain, Kayvan R Keshari, Michael A Davies, Matthew G Vander Heiden, Eva Hernando, Matthias Mann, Lewis C Cantley, Michael E Pacold.
      A hallmark of metastasis is the adaptation of tumor cells to new environments. Metabolic constraints imposed by the serine and glycine-limited brain environment restrict metastatic tumor growth. How brain metastases overcome these growth-prohibitive conditions is poorly understood. Here, we demonstrate that 3-phosphoglycerate dehydrogenase (PHGDH), which catalyzes the rate-limiting step of glucose-derived serine synthesis, is a major determinant of brain metastasis in multiple human cancer types and preclinical models. Enhanced serine synthesis proved important for nucleotide production and cell proliferation in highly aggressive brain metastatic cells. In vivo, genetic suppression and pharmacological inhibition of PHGDH attenuated brain metastasis, but not extracranial tumor growth, and improved overall survival in mice. These results reveal that extracellular amino acid availability determines serine synthesis pathway dependence, and suggests that PHGDH inhibitors may be useful in the treatment of brain metastasis.
    DOI:  https://doi.org/10.1158/2159-8290.CD-19-1228
  4. Trends Mol Med. 2020 Jul;pii: S1471-4914(20)30062-9. [Epub ahead of print]26(7): 698-709
    Therapeutic Manipulation of mtDNA Heteroplasmy: A Shifting Perspective.
    Christopher B Jackson, Doug M Turnbull, Michal Minczuk, Payam A Gammage.
      Mutations of mitochondrial DNA (mtDNA) often underlie mitochondrial disease, one of the most common inherited metabolic disorders. Since the sequencing of the human mitochondrial genome and the discovery of pathogenic mutations in mtDNA more than 30 years ago, a movement towards generating methods for robust manipulation of mtDNA has ensued, although with relatively few advances and some controversy. While developments in the transformation of mammalian mtDNA have stood still for some time, recent demonstrations of programmable nuclease-based technology suggest that clinical manipulation of mtDNA heteroplasmy may be on the horizon for these largely untreatable disorders. Here we review historical and recent developments in mitochondrially targeted nuclease technology and the clinical outlook for treatment of hereditary mitochondrial disease.
    Keywords:  gene therapy; heteroplasmy; mitoTALEN; mitochondrial disease; mtDNA; mtZFN
    DOI:  https://doi.org/10.1016/j.molmed.2020.02.006
  5. EMBO J. 2020 Jun 22. e104105
    MICOS assembly controls mitochondrial inner membrane remodeling and crista junction redistribution to mediate cristae formation.
    Till Stephan, Christian Brüser, Markus Deckers, Anna M Steyer, Francisco Balzarotti, Mariam Barbot, Tiana S Behr, Gudrun Heim, Wolfgang Hübner, Peter Ilgen, Felix Lange, David Pacheu-Grau, Jasmin K Pape, Stefan Stoldt, Thomas Huser, Stefan W Hell, Wiebke Möbius, Peter Rehling, Dietmar Riedel, Stefan Jakobs.
      Mitochondrial function is critically dependent on the folding of the mitochondrial inner membrane into cristae; indeed, numerous human diseases are associated with aberrant crista morphologies. With the MICOS complex, OPA1 and the F1 Fo -ATP synthase, key players of cristae biogenesis have been identified, yet their interplay is poorly understood. Harnessing super-resolution light and 3D electron microscopy, we dissect the roles of these proteins in the formation of cristae in human mitochondria. We individually disrupted the genes of all seven MICOS subunits in human cells and re-expressed Mic10 or Mic60 in the respective knockout cell line. We demonstrate that assembly of the MICOS complex triggers remodeling of pre-existing unstructured cristae and de novo formation of crista junctions (CJs) on existing cristae. We show that the Mic60-subcomplex is sufficient for CJ formation, whereas the Mic10-subcomplex controls lamellar cristae biogenesis. OPA1 stabilizes tubular CJs and, along with the F1 Fo -ATP synthase, fine-tunes the positioning of the MICOS complex and CJs. We propose a new model of cristae formation, involving the coordinated remodeling of an unstructured crista precursor into multiple lamellar cristae.
    Keywords:   MINFLUX ; cristae biogenesis; electron microscopy; nanoscopy; super-resolution microscopy
    DOI:  https://doi.org/10.15252/embj.2019104105
  6. Nat Commun. 2020 Jun 23. 11(1): 3169
    Using arterial-venous analysis to characterize cancer metabolic consumption in patients.
    Nanxiang Xiong, Xiaofei Gao, Hongyang Zhao, Feng Cai, Fang-Cheng Zhang, Ye Yuan, Weichao Liu, Fangping He, Lauren G Zacharias, Hong Lin, Hieu S Vu, Chao Xing, Dong-Xiao Yao, Fei Chen, Benyan Luo, Wenzhi Sun, Ralph J DeBerardinis, Hao Xu, Woo-Ping Ge.
      Understanding tumor metabolism holds the promise of new insights into cancer biology, diagnosis and treatment. To assess human cancer metabolism, here we report a method to collect intra-operative samples of blood from an artery directly upstream and a vein directly downstream of a brain tumor, as well as samples from dorsal pedal veins of the same patients. After performing targeted metabolomic analysis, we characterize the metabolites consumed and produced by gliomas in vivo by comparing the arterial supply and venous drainage. N-acetylornithine, D-glucose, putrescine, and L-acetylcarnitine are consumed in relatively large amounts by gliomas. Conversely, L-glutamine, agmatine, and uridine 5-monophosphate are produced in relatively large amounts by gliomas. Further we verify that D-2-hydroxyglutarate (D-2HG) is high in venous plasma from patients with isocitrate dehydrogenases1 (IDH1) mutations. Through these paired comparisons, we can exclude the interpatient variation that is present in plasma samples usually taken from the cubital vein.
    DOI:  https://doi.org/10.1038/s41467-020-16810-8
  7. Crit Rev Biochem Mol Biol. 2020 Jun 24. 1-13
    Mitochondrial F-type ATP synthase: multiple enzyme functions revealed by the membrane-embedded FO structure.
    Salvatore Nesci, Alessandra Pagliarani, Cristina Algieri, Fabiana Trombetti.
      Of the two main sectors of the F-type ATP synthase, the membrane-intrinsic FO domain is the one which, during evolution, has undergone the highest structural variations and changes in subunit composition. The FO complexity in mitochondria is apparently related to additional enzyme functions that lack in bacterial and thylakoid complexes. Indeed, the F-type ATP synthase has the main bioenergetic role to synthesize ATP by exploiting the electrochemical gradient built by respiratory complexes. The FO membrane domain, essential in the enzyme machinery, also participates in the bioenergetic cost of synthesizing ATP and in the formation of the cristae, thus contributing to mitochondrial morphology. The recent enzyme involvement in a high-conductance channel, which forms in the inner mitochondrial membrane and promotes the mitochondrial permeability transition, highlights a new F-type ATP synthase role. Point mutations which cause amino acid substitutions in FO subunits produce mitochondrial dysfunctions and lead to severe pathologies. The FO variability in different species, pointed out by cryo-EM analysis, mirrors the multiple enzyme functions and opens a new scenario in mitochondrial biology.
    Keywords:  F1FO-ATPase; FO domain; membrane; mitochondria; molecular mechanism; structure
    DOI:  https://doi.org/10.1080/10409238.2020.1784084
  8. Cell Rep. 2020 Jun 23. pii: S2211-1247(20)30796-8. [Epub ahead of print]31(12): 107815
    CD28 Regulates Metabolic Fitness for Long-Lived Plasma Cell Survival.
    Adam Utley, Colin Chavel, Shivana Lightman, G Aaron Holling, James Cooper, Peng Peng, Wensheng Liu, Benjamin G Barwick, Catherine M Gavile, Orla Maguire, Megan Murray-Dupuis, Cheryl Rozanski, Martha S Jordan, Taku Kambayashi, Scott H Olejniczak, Lawrence H Boise, Kelvin P Lee.
      Durable humoral immunity against epidemic infectious disease requires the survival of long-lived plasma cells (LLPCs). LLPC longevity is dependent on metabolic programs distinct from short-lived plasma cells (SLPCs); however, the mechanistic basis for this difference is unclear. We have previously shown that CD28, the prototypic T cell costimulatory receptor, is expressed on both LLPCs and SLPCs but is essential only for LLPC survival. Here we show that CD28 transduces pro-survival signaling specifically in LLPCs through differential SLP76 expression. CD28 signaling in LLPCs increased glucose uptake, mitochondrial mass/respiration, and reactive oxygen species (ROS) production. Unexpectedly, CD28-mediated regulation of mitochondrial respiration, NF-κB activation, and survival was ROS dependent. IRF4, a target of NF-κB, was upregulated by CD28 activation in LLPCs and decreased IRF4 levels correlated with decreased glucose uptake, mitochondrial mass, ROS, and CD28-mediated survival. Altogether, these data demonstrate that CD28 signaling induces a ROS-dependent metabolic program required for LLPC survival.
    Keywords:  CD28; IRF4; ROS; SLP76; metabolism; mitochondria; plasma cell
    DOI:  https://doi.org/10.1016/j.celrep.2020.107815
  9. Int J Mol Sci. 2020 Jun 19. pii: E4374. [Epub ahead of print]21(12):
    SSADH Variants Increase Susceptibility of U87 Cells to Mitochondrial Pro-Oxidant Insult.
    Giovanna Menduti, Alessandra Vitaliti, Concetta Rosa Capo, Daniele Lettieri-Barbato, Katia Aquilano, Patrizia Malaspina, Luisa Rossi.
      Succinate semialdehyde dehydrogenase (SSADH) is a mitochondrial enzyme, encoded by ALDH5A1, mainly involved in γ-aminobutyric acid (GABA) catabolism and energy supply of neuronal cells, possibly contributing to antioxidant defense. This study aimed to further investigate the antioxidant role of SSADH, and to verify if common SNPs of ALDH5A1 may affect SSADH activity, stability, and mitochondrial function. In this study, we used U87 glioblastoma cells as they represent a glial cell line. These cells were transiently transfected with a cDNA construct simultaneously harboring three SNPs encoding for a triple mutant (TM) SSADH protein (p.G36R/p.H180Y/p.P182L) or with wild type (WT) cDNA. SSADH activity and protein level were measured. Cell viability, lipid peroxidation, mitochondrial morphology, membrane potential (ΔΨ), and protein markers of mitochondrial stress were evaluated upon Paraquat treatment, in TM and WT transfected cells. TM transfected cells show lower SSADH protein content and activity, fragmented mitochondria, higher levels of peroxidized lipids, and altered ΔΨ than WT transfected cells. Upon Paraquat treatment, TM cells show higher cell death, lipid peroxidation, 4-HNE protein adducts, and lower ΔΨ, than WT transfected cells. These results reinforce the hypothesis that SSADH contributes to cellular antioxidant defense; furthermore, common SNPs may produce unstable, less active SSADH, which could per se negatively affect mitochondrial function and, under oxidative stress conditions, fail to protect mitochondria.
    Keywords:  4-HNE; ALDH5A1; GABA; SSA; SSADH; U87 cells; mitochondria; paraquat
    DOI:  https://doi.org/10.3390/ijms21124374
  10. Front Cell Dev Biol. 2020 ;8 413
    The Role of Mitochondrial Dynamics and Mitophagy in Carcinogenesis, Metastasis and Therapy.
    Yigang Wang, Hui-Hui Liu, Yu-Ting Cao, Lei-Lei Zhang, Fang Huang, Cong Yi.
      Mitochondria are key cellular organelles and play vital roles in energy metabolism, apoptosis regulation and cellular homeostasis. Mitochondrial dynamics refers to the varying balance between mitochondrial fission and mitochondrial fusion that plays an important part in maintaining mitochondrial homeostasis and quality. Mitochondrial malfunction is involved in aging, metabolic disease, neurodegenerative disorders, and cancers. Mitophagy, a selective autophagy of mitochondria, can efficiently degrade, remove and recycle the malfunctioning or damaged mitochondria, and is crucial for quality control. In past decades, numerous studies have identified a series of factors that regulate mitophagy and are also involved in carcinogenesis, cancer cell migration and death. Therefore, it has become critically important to analyze signal pathways that regulate mitophagy to identify potential therapeutic targets. Here, we review recent progresses in mitochondrial dynamics, the mechanisms of mitophagy regulation, and the implications for understanding carcinogenesis, metastasis, treatment, and drug resistance.
    Keywords:  carcinogenesis; mitochondria; mitochondrial dynamics; mitophagy; therapy
    DOI:  https://doi.org/10.3389/fcell.2020.00413
  11. Redox Biol. 2020 Jun 01. pii: S2213-2317(20)30563-2. [Epub ahead of print]36 101595
    A quantitative LC-MS/MS method for analysis of mitochondrial -specific oxysterol metabolism.
    Khushboo Borah, Olivia J Rickman, Nikol Voutsina, Isaac Ampong, Dan Gao, Emma L Baple, Irundika Hk Dias, Andrew H Crosby, Helen R Griffiths.
      Oxysterols are critical regulators of inflammation and cholesterol metabolism in cells. They are oxidation products of cholesterol and may be differentially metabolised in subcellular compartments and in biological fluids. New analytical methods are needed to improve our understanding of oxysterol trafficking and the molecular interplay between the cellular compartments required to maintain cholesterol/oxysterol homeostasis. Here we describe a method for isolation of oxysterols using solid phase extraction and quantification by liquid chromatography-mass spectrometry, applied to tissue, cells and mitochondria. We analysed five monohydroxysterols; 24(S)-hydroxycholesterol, 25-hydroxycholesterol, 27-hydroxycholesterol, 7α-hydroxycholesterol, 7 ketocholesterol and three dihydroxysterols 7α-24(S)dihydroxycholesterol, 7α-25dihydroxycholesterol, 7α-27dihydroxycholesterol by LC-MS/MS following reverse phase chromatography. Our new method, using Triton and DMSO extraction, shows improved extraction efficiency and recovery of oxysterols from cellular matrix. We validated our method by reproducibly measuring oxysterols in mouse brain tissue and showed that mice fed a high fat diet had significantly lower levels of 24S/25diOHC, 27diOHC and 7ketoOHC. We measured oxysterols in mitochondria from peripheral blood mononuclear cells and highlight the importance of rapid cell isolation to minimise effects of handling and storage conditions on oxysterol composition in clinical samples. In addition, in vitro cell culture systems, of THP-1 monocytes and neuronal-like SH-SH5Y cells, showed mitochondrial-specific oxysterol metabolism and profiles were lineage specific. In summary, we describe a robust and reproducible method validated for improved recovery, quantitative linearity and detection, reproducibility and selectivity for cellular oxysterol analysis. This method enables subcellular oxysterol metabolism to be monitored and is versatile in its application to various biological and clinical samples.
    Keywords:  Blood; Brain oxysterol; Cholesterol; Dihydroxycholesterol; Liquid chromatography-mass spectrometry; Metabolism; Mitochondria; Monocytes; Neuroblastoma; Oxysterol; Peripheral blood mononuclear cell; Subcellular; Whole cell
    DOI:  https://doi.org/10.1016/j.redox.2020.101595
  12. Proc Natl Acad Sci U S A. 2020 Jun 22. pii: 202000304. [Epub ahead of print]
    Symmetric arrangement of mitochondria:plasma membrane contacts between adjacent photoreceptor cells regulated by Opa1.
    Ingrid P Meschede, Nicholas C Ovenden, Miguel C Seabra, Clare E Futter, Marcela Votruba, Michael E Cheetham, Thomas Burgoyne.
      Mitochondria are known to play an essential role in photoreceptor function and survival that enables normal vision. Within photoreceptors, mitochondria are elongated and extend most of the inner-segment length, where they supply energy for protein synthesis and the phototransduction machinery in the outer segment, as well as acting as a calcium store. Here, we examined the arrangement of the mitochondria within the inner segment in detail using three-dimensional (3D) electron microscopy techniques and show they are tethered to the plasma membrane in a highly specialized arrangement. Remarkably, mitochondria and their cristae openings align with those of neighboring inner segments. The pathway by which photoreceptors meet their high energy demands is not fully understood. We propose this to be a mechanism to share metabolites and assist in maintaining homeostasis across the photoreceptor cell layer. In the extracellular space between photoreceptors, Müller glial processes were identified. Due to the often close proximity to the inner-segment mitochondria, they may, too, play a role in the inner-segment mitochondrial arrangement as well as metabolite shuttling. OPA1 is an important factor in mitochondrial homeostasis, including cristae remodeling; therefore, we examined the photoreceptors of a heterozygous Opa1 knockout mouse model. The cristae structure in the Opa1 +/- photoreceptors was not greatly affected, but the mitochondria were enlarged and had reduced alignment to neighboring inner-segment mitochondria. This indicates the importance of key regulators in maintaining this specialized photoreceptor mitochondrial arrangement.
    Keywords:  contact sites; dominant optic atrophy; mitochondria; rod photoreceptors; tethers
    DOI:  https://doi.org/10.1073/pnas.2000304117
  13. Cancers (Basel). 2020 Jun 19. pii: E1633. [Epub ahead of print]12(6):
    Metabolic Landscape of a Genetically Engineered Mouse Model of IDH1 Mutant Glioma.
    Victor Ruiz-Rodado, Tomohiro Seki, Tyrone Dowdy, Adrian Lita, Meili Zhang, Sue Han, Chunzhang Yang, Murali K Cherukuri, Mark R Gilbert, Mioara Larion.
      Understanding the metabolic reprogramming of aggressive brain tumors has potential applications for therapeutics as well as imaging biomarkers. However, little is known about the nutrient requirements of isocitrate dehydrogenase 1 (IDH1) mutant gliomas. The IDH1 mutation involves the acquisition of a neomorphic enzymatic activity which generates D-2-hydroxyglutarate from α-ketoglutarate. In order to gain insight into the metabolism of these malignant brain tumors, we conducted metabolic profiling of the orthotopic tumor and the contralateral regions for the mouse model of IDH1 mutant glioma; as well as to examine the utilization of glucose and glutamine in supplying major metabolic pathways such as glycolysis and tricarboxylic acid (TCA). We also revealed that the main substrate of 2-hydroxyglutarate is glutamine in this model, and how this re-routing impairs its utilization in the TCA. Our 13C tracing analysis, along with hyperpolarized magnetic resonance experiments, revealed an active glycolytic pathway similar in both regions (tumor and contralateral) of the brain. Therefore, we describe the reprogramming of the central carbon metabolism associated with the IDH1 mutation in a genetically engineered mouse model which reflects the tumor biology encountered in glioma patients.
    Keywords:  13C-tracing; 2-hydroxyglutarate formation; IDH1-mutant gliomas; genetically engineered mouse models
    DOI:  https://doi.org/10.3390/cancers12061633
  14. Metabolism. 2020 Jun 23. pii: S0026-0495(20)30166-9. [Epub ahead of print] 154302
    Ubiquitination of PPAR-gamma by pVHL inhibits ACLY expression and lipid metabolism, is implicated in tumor progression.
    Kyung Hee Noh, Hyun Mi Kang, Wonbeak Yoo, Yoohong Min, Daehun Kim, Mijin Kim, Sihyung Wang, Jung Hwa Lim, Cho-Rok Jung.
       BACKGROUND: Intracellular lipid accumulation is associated with various diseases, particularly cancer. Mitochondrial dysfunction is considered as a cause of lipid accumulation; however, the related underlying mechanism remains unclear. Findings We found that Von Hippel-Lindau (VHL)-deficiency led to lipid accumulation and mitochondrial dysfunction in renal cell carcinoma cells. Moreover, VHL downregulated ATP-citrate lyase (ACLY), a key enzyme in de novo lipid synthesis, at the transcriptional level, which inhibited intracellular lipid accumulation in human renal carcinoma tissues. We identified PPARγ as the transcription factor regulating ACLY expression by binding to the cis-regulatory site PPRE on its promoter. VHL directly interacted with and promoted ubiquitination of PPARγ, leading to its degradation both in vitro and in vivo, resulting in the downregulation of ACLY. Furthermore, adenovirus-mediated VHL overexpression substantially ameliorated hepatic steatosis induced by a high-fat diet in db/db mice. Importantly, low VHL expression was associated with high ACLY expression and poor prognosis in human liver carcinoma in a dataset in The Cancer Genome Atlas.
    CONCLUSIONS: VHL plays role in cellular lipid metabolism via regulating mitochondria and targeting PPARγ, a transcription factor for ACLY independent of hypoxia-inducible factor 1α. A novel VHL-PPARγ-ACLY axis and its implication in fatty liver disease and cancer were uncovered.
    Keywords:  ACLY; Lipid metabolism; PPAR-gamma; Ubiquitination; Von Hippel-Lindau
    DOI:  https://doi.org/10.1016/j.metabol.2020.154302
  15. Mol Ther. 2020 Jun 12. pii: S1525-0016(20)30300-2. [Epub ahead of print]
    Opa1 Overexpression Protects from Early-Onset Mpv17-/--Related Mouse Kidney Disease.
    Marta Luna-Sanchez, Cristiane Benincá, Raffaele Cerutti, Gloria Brea-Calvo, Anna Yeates, Luca Scorrano, Massimo Zeviani, Carlo Viscomi.
      Moderate overexpression of Opa1, the master regulator of mitochondrial cristae morphology, significantly improved mitochondrial damage induced by drugs, surgical denervation, or oxidative phosphorylation (OXPHOS) defects due to specific impairment of a single mitochondrial respiratory chain complex. Here, we investigated the effectiveness of this approach in the Mpv17-/- mouse, characterized by profound, multisystem mitochondrial DNA (mtDNA) depletion. After the crossing with Opa1tg mice, we found a surprising anticipation of the severe, progressive focal segmental glomerulosclerosis, previously described in Mpv17-/- animals as a late-onset clinical feature (after 12-18 months of life). In contrast, Mpv17-/- animals from this new "mixed" strain died at 8-9 weeks after birth because of severe kidney failure However, Mpv17-/-::Opa1tg mice lived much longer than Mpv17-/- littermates and developed the kidney dysfunction much later. mtDNA content and OXPHOS activities were significantly higher in Mpv17-/-::Opa1tg than in Mpv17-/- kidneys and similar to those for wild-type (WT) littermates. Mitochondrial network and cristae ultrastructure were largely preserved in Mpv17-/-::Opa1tg versus Mpv17-/- kidney and isolated podocytes. Mechanistically, the protective effect of Opa1 overexpression in this model was mediated by a block in apoptosis due to the stabilization of the mitochondrial cristae. These results demonstrate that strategies aiming at increasing Opa1 expression or activity can be effective against mtDNA depletion syndromes.
    Keywords:  Mpv17; Opa1; apoptosis; focal segmental glomerulosclerosis; mitochondrial DNA depletion; mitochondrial cristae; oxidative phosphorylation
    DOI:  https://doi.org/10.1016/j.ymthe.2020.06.010
  16. Cell Metab. 2020 Jun 16. pii: S1550-4131(20)30304-1. [Epub ahead of print]
    NAD+ Regeneration Rescues Lifespan, but Not Ataxia, in a Mouse Model of Brain Mitochondrial Complex I Dysfunction.
    Gregory S McElroy, Colleen R Reczek, Paul A Reyfman, Divakar S Mithal, Craig M Horbinski, Navdeep S Chandel.
      Mitochondrial complex I regenerates NAD+ and proton pumps for TCA cycle function and ATP production, respectively. Mitochondrial complex I dysfunction has been implicated in many brain pathologies including Leigh syndrome and Parkinson's disease. We sought to determine whether NAD+ regeneration or proton pumping, i.e., bioenergetics, is the dominant function of mitochondrial complex I in protection from brain pathology. We generated a mouse that conditionally expresses the yeast NADH dehydrogenase (NDI1), a single enzyme that can replace the NAD+ regeneration capability of the 45-subunit mammalian mitochondrial complex I without proton pumping. NDI1 expression was sufficient to dramatically prolong lifespan without significantly improving motor function in a mouse model of Leigh syndrome driven by the loss of NDUFS4, a subunit of mitochondrial complex I. Therefore, mitochondrial complex I activity in the brain supports organismal survival through its NAD+ regeneration capacity, while optimal motor control requires the bioenergetic function of mitochondrial complex I.
    Keywords:  Leigh syndrome; NAD; ataxia; metabolism; microglia; mitochondria; mitochondrial complex I; mitochondrial disease; neurodegeneration; neurometabolism
    DOI:  https://doi.org/10.1016/j.cmet.2020.06.003
  17. Int J Mol Sci. 2020 Jun 20. pii: E4405. [Epub ahead of print]21(12):
    Multifaceted Roles of Mitochondrial Components and Metabolites in Metabolic Diseases and Cancer.
    Jean Nakhle, Anne-Marie Rodriguez, Marie-Luce Vignais.
      Mitochondria are essential cellular components that ensure physiological metabolic functions. They provide energy in the form of adenosine triphosphate (ATP) through the electron transport chain (ETC). They also constitute a metabolic hub in which metabolites are used and processed, notably through the tricarboxylic acid (TCA) cycle. These newly generated metabolites have the capacity to feed other cellular metabolic pathways; modify cellular functions; and, ultimately, generate specific phenotypes. Mitochondria also provide intracellular signaling cues through reactive oxygen species (ROS) production. As expected with such a central cellular role, mitochondrial dysfunctions have been linked to many different diseases. The origins of some of these diseases could be pinpointed to specific mutations in both mitochondrial- and nuclear-encoded genes. In addition to their impressive intracellular tasks, mitochondria also provide intercellular signaling as they can be exchanged between cells, with resulting effects ranging from repair of damaged cells to strengthened progression and chemo-resistance of cancer cells. Several therapeutic options can now be envisioned to rescue mitochondria-defective cells. They include gene therapy for both mitochondrial and nuclear defective genes. Transferring exogenous mitochondria to target cells is also a whole new area of investigation. Finally, supplementing targeted metabolites, possibly through microbiota transplantation, appears as another therapeutic approach full of promises.
    Keywords:  cancer; electron transport chain (ETC); metabolism; metabolites; microbiota; mitochondria; mitochondria exchange; mitochondrial DNA (mtDNA); therapy; tricarboxylic acid (TCA) cycle
    DOI:  https://doi.org/10.3390/ijms21124405
  18. Cells. 2020 Jun 20. pii: E1505. [Epub ahead of print]9(6):
    Ferroptosis and Cancer: Mitochondria Meet the "Iron Maiden" Cell Death.
    Anna Martina Battaglia, Roberta Chirillo, Ilenia Aversa, Alessandro Sacco, Francesco Costanzo, Flavia Biamonte.
      Ferroptosis is a new type of oxidative regulated cell death (RCD) driven by iron-dependent lipid peroxidation. As major sites of iron utilization and master regulators of oxidative metabolism, mitochondria are the main source of reactive oxygen species (ROS) and, thus, play a role in this type of RCD. Ferroptosis is, indeed, associated with severe damage in mitochondrial morphology, bioenergetics, and metabolism. Furthermore, dysregulation of mitochondrial metabolism is considered a biochemical feature of neurodegenerative diseases linked to ferroptosis. Whether mitochondrial dysfunction can, per se, initiate ferroptosis and whether mitochondrial function in ferroptosis is context-dependent are still under debate. Cancer cells accumulate high levels of iron and ROS to promote their metabolic activity and growth. Of note, cancer cell metabolic rewiring is often associated with acquired sensitivity to ferroptosis. This strongly suggests that ferroptosis may act as an adaptive response to metabolic imbalance and, thus, may constitute a new promising way to eradicate malignant cells. Here, we review the current literature on the role of mitochondria in ferroptosis, and we discuss opportunities to potentially use mitochondria-mediated ferroptosis as a new strategy for cancer therapy.
    Keywords:  ROS; cancer; cell death; ferroptosis; iron; mitochondria
    DOI:  https://doi.org/10.3390/cells9061505
  19. Dev Cell. 2020 Jun 22. pii: S1534-5807(20)30419-6. [Epub ahead of print]53(6): 619-620
    Deadly Encounter: Endosomes Meet Mitochondria to Initiate Apoptosis.
    Mariella Vicinanza, David C Rubinsztein.
      Mitochondrial outer membrane permeabilization (MOMP) is a crucial event enabling apoptotic cell death. In this issue of Developmental Cell, Wang et al. reveal an interaction contributing to full MOMP execution, which depends on endosomes accumulating on apoptotic mitochondria. This causes mitochondrial lipid alterations that may contribute to functional pore assembly.
    DOI:  https://doi.org/10.1016/j.devcel.2020.05.030
  20. FASEB J. 2020 Jun 22.
    SREBP1 regulates mitochondrial metabolism in oncogenic KRAS expressing NSCLC.
    Christian F Ruiz, Emily D Montal, John A Haley, Alex J Bott, John D Haley.
      Cancer cells require extensive metabolic reprograming in order to provide the bioenergetics and macromolecular precursors needed to sustain a malignant phenotype. Mutant KRAS is a driver oncogene that is well-known for its ability to regulate the ERK and PI3K signaling pathways. However, it is now appreciated that KRAS can promote the tumor growth via upregulation of anabolic metabolism. We recently reported that oncogenic KRAS promotes a gene expression program of de novo lipogenesis in non-small cell lung cancer (NSCLC). To define the mechanism(s) responsible, we focused on the lipogenic transcription factor SREBP1. We observed that KRAS increases SREBP1 expression and genetic knockdown of SREBP1 significantly inhibited the cell proliferation of mutant KRAS-expressing cells. Unexpectedly, lipogenesis was not significantly altered in cells subject to SREBP1 knockdown. Carbon tracing metabolic studies showed a significant decrease in oxidative phosphorylation and RNA-seq data revealed a significant decrease in mitochondrial encoded subunits of the electron transport chain (ETC). Taken together, these data support a novel role, distinct from lipogenesis, of SREBP1 on mitochondrial function in mutant KRAS NSCLC.
    Keywords:  cancer metabolism; de novo lipogenesis; electron transport chain; oxidative phosphorylation
    DOI:  https://doi.org/10.1096/fj.202000052R
  21. J Recept Signal Transduct Res. 2020 Jun 25. 1-5
    Mitochondrial scenario: roles of mitochondrial dynamics in acute myocardial ischemia/reperfusion injury.
    David Mui, Ying Zhang.
      The main therapeutic strategy currently used for acute myocardial infarction (AMI) is to open occluded coronary arteries, a process defined as blood reperfusion. However, blood reperfusion will increase cardiac mortality, tissue damage and cardiac dysfunction in patients with AMI, which is mechanically defined as "ischemia/reperfusion (I/R) injury". It is currently believed that mitochondrial dynamics plays a key role in myocardial I/R, especially excessive mitochondrial fission, which is the main cause of cardiac dysfunction. Therefore, in the process of I/R injury, effective drug intervention and correct treatment strategies can be used to regulate mitochondrial dynamic balance to combat ischemia-reperfusion injury, which can play a huge role in improving the prognosis of patients. This review summarized the effects of mitochondrial fission and mitochondrial fusion balance on myocardial and mitochondrial functional changes during myocardial I/R injury. Finally, combined with the previous injury mechanisms, this review also briefly described some drug intervention that may be beneficial to clinical practice to improve the postoperative quality of life of patients with AMI.
    Keywords:  Ischemia reperfusion injury; heart; mitochondria; mitochondrial dynamics
    DOI:  https://doi.org/10.1080/10799893.2020.1784938
  22. Aging (Albany NY). 2020 Jun 23. 12
    The mitochondrial derived peptide humanin is a regulator of lifespan and healthspan.
    Kelvin Yen, Hemal H Mehta, Su-Jeong Kim, YanHe Lue, James Hoang, Noel Guerrero, Jenna Port, Qiuli Bi, Gerardo Navarrete, Sebastian Brandhorst, Kaitlyn Noel Lewis, Junxiang Wan, Ronald Swerdloff, Julie A Mattison, Rochelle Buffenstein, Carrie V Breton, Christina Wang, Valter Longo, Gil Atzmon, Douglas Wallace, Nir Barzilai, Pinchas Cohen.
      Humanin is a member of a new family of peptides that are encoded by short open reading frames within the mitochondrial genome. It is conserved in animals and is both neuroprotective and cytoprotective. Here we report that in C. elegans the overexpression of humanin is sufficient to increase lifespan, dependent on daf-16/Foxo. Humanin transgenic mice have many phenotypes that overlap with the worm phenotypes and, similar to exogenous humanin treatment, have increased protection against toxic insults. Treating middle-aged mice twice weekly with the potent humanin analogue HNG, humanin improves metabolic healthspan parameters and reduces inflammatory markers. In multiple species, humanin levels generally decline with age, but here we show that levels are surprisingly stable in the naked mole-rat, a model of negligible senescence. Furthermore, in children of centenarians, who are more likely to become centenarians themselves, circulating humanin levels are much greater than age-matched control subjects. Further linking humanin to healthspan, we observe that humanin levels are decreased in human diseases such as Alzheimer's disease and MELAS (Mitochondrial Encephalopathy, Lactic Acidosis, and Stroke-like episodes). Together, these studies are the first to demonstrate that humanin is linked to improved healthspan and increased lifespan.
    Keywords:  aging; humanin; mitochondria; peptides
    DOI:  https://doi.org/10.18632/aging.103534
  23. PLoS One. 2020 ;15(6): e0234653
    Hexokinase II dissociation alone cannot account for changes in heart mitochondrial function, morphology and sensitivity to permeability transition pore opening following ischemia.
    Gonçalo C Pereira, Laura Lee, Nadiia Rawlings, Joke Ouwendijk, Joanne E Parker, Tatyana N Andrienko, Jeremy M Henley, Andrew P Halestrap.
      We previously demonstrated that hexokinase II (HK2) dissociation from mitochondria during cardiac ischemia correlates with cytochrome c (cyt-c) loss, oxidative stress and subsequent reperfusion injury. However, whether HK2 release is the primary signal mediating this ischemia-induced mitochondrial dysfunction was not established. To investigate this, we studied the effects of dissociating HK2 from isolated heart mitochondria. Mitochondria isolated from Langendorff-perfused rat hearts before and after 30 min global ischemia ± ischemic preconditioning (IPC) were subject to in vitro dissociation of HK2 by incubation with glucose-6-phosphate at pH 6.3. Prior HK2 dissociation from pre- or end-ischemic heart mitochondria had no effect on their cyt-c release, respiration (± ADP) or mitochondrial permeability transition pore (mPTP) opening. Inner mitochondrial membrane morphology was assessed indirectly by monitoring changes in light scattering (LS) and confirmed by transmission electron microscopy. Although no major ultrastructure differences were detected between pre- and end-ischemia mitochondria, the amplitude of changes in LS was reduced in the latter. This was prevented by IPC but not mimicked in vitro by HK2 dissociation. We also observed more Drp1, a mitochondrial fission protein, in end-ischemia mitochondria. IPC failed to prevent this increase but did decrease mitochondrial-associated dynamin 2. In vitro HK2 dissociation alone cannot replicate ischemia-induced effects on mitochondrial function implying that in vivo dissociation of HK2 modulates end-ischemia mitochondrial function indirectly perhaps involving interaction with mitochondrial fission proteins. The resulting changes in mitochondrial morphology and cristae structure would destabilize outer / inner membrane interactions, increase cyt-c release and enhance mPTP sensitivity to [Ca2+].
    DOI:  https://doi.org/10.1371/journal.pone.0234653
  24. Front Physiol. 2020 ;11 536
    Consequences of Folding the Mitochondrial Inner Membrane.
    Carmen A Mannella.
      A fundamental first step in the evolution of eukaryotes was infolding of the chemiosmotic membrane of the endosymbiont. This allowed the proto-eukaryote to amplify ATP generation while constraining the volume dedicated to energy production. In mitochondria, folding of the inner membrane has evolved into a highly regulated process that creates specialized compartments (cristae) tuned to optimize function. Internalizing the inner membrane also presents complications in terms of generating the folds and maintaining mitochondrial integrity in response to stresses. This review describes mechanisms that have evolved to regulate inner membrane topology and either preserve or (when appropriate) rupture the outer membrane.
    Keywords:  chemiosmosis; crista junctions; cristae; membrane remodeling; membrane topology; mitochondria
    DOI:  https://doi.org/10.3389/fphys.2020.00536
  25. Endocr Metab Immune Disord Drug Targets. 2020 Jun 24.
    Spotlight on Circadian Genes and Colorectal Cancer Crosstalk.
    Senthilkumar Rajendran, Silvia Barbon, Salvatore Pucciarelli.
      Mammalian physiology is regulated by circadian clock through oscillating feedback loops controlling cellular processes and behaviors. Recent findings have led to an interesting connection between circadian disruption and colorectal cancer progression and incidence through controlling the hallmarks of cancer namely, cell cycle, cell metabolism and cell death. Deeper understanding of the circadian mechanisms that define the colorectal cancer pathophysiology is the need of the hour to define a chronotherapy for improving colorectal cancer patient survival. This review identifies the key areas in which circadian genes interact with cellular pathways to modify the outcome with respect to colorectal cancer incidence and progression.
    Keywords:  Circadian pathway; cancer cell metabolism. ; cell cycle; cell death; chronotherapy; colorectal cancer
    DOI:  https://doi.org/10.2174/1871530320666200624192517
  26. Cancers (Basel). 2020 Jun 18. pii: E1616. [Epub ahead of print]12(6):
    How and Why Are Cancers Acidic? Carbonic Anhydrase IX and the Homeostatic Control of Tumour Extracellular pH.
    Shen-Han Lee, John R Griffiths.
      The acidic tumour microenvironment is now recognized as a tumour phenotype that drives cancer somatic evolution and disease progression, causing cancer cells to become more invasive and to metastasise. This property of solid tumours reflects a complex interplay between cellular carbon metabolism and acid removal that is mediated by cell membrane carbonic anhydrases and various transport proteins, interstitial fluid buffering, and abnormal tumour-associated vessels. In the past two decades, a convergence of advances in the experimental and mathematical modelling of human cancers, as well as non-invasive pH-imaging techniques, has yielded new insights into the physiological mechanisms that govern tumour extracellular pH (pHe). In this review, we examine the mechanisms by which solid tumours maintain a low pHe, with a focus on carbonic anhydrase IX (CAIX), a cancer-associated cell surface enzyme. We also review the accumulating evidence that suggest a role for CAIX as a biological pH-stat by which solid tumours stabilize their pHe. Finally, we highlight the prospects for the clinical translation of CAIX-targeted therapies in oncology.
    Keywords:  cancer metabolism; cancer microenvironment; carbonic anhydrase IX; magnetic resonance spectroscopy; models of tumour pH regulation; pH measurement in vivo; pH-stat; tumour pH
    DOI:  https://doi.org/10.3390/cancers12061616
  27. Biochemistry (Mosc). 2020 Mar;85(3): 257-263
    Protein Biosynthesis in Mitochondria: Past Simple, Present Perfect, Future Indefinite.
    S A Levitskii, M V Baleva, I V Chicherin, I A Krasheninnikov, P A Kamenski.
      Mitochondria are obligate organelles of most eukaryotic cells that perform many different functions important for cellular homeostasis. The main role of mitochondria is supplying cells with energy in a form of ATP, which is synthesized in a chain of oxidative phosphorylation reactions on the organelle inner membrane. It is commonly believed now that mitochondria have the endosymbiotic origin. In the course of evolution, they have lost most of their genetic material as a result of genome reduction and gene transfer to the nucleus. The majority of mitochondrial proteins are synthesized in the cytosol and then imported to the mitochondria. However, almost all known mitochondria still contain genomes that are maintained and expressed. The processes of protein biosynthesis in the mitochondria - mitochondrial translation - substantially differs from the analogous processes in bacteria and the cytosol of eukaryotic cells. Mitochondrial translation is characterized by a high degree of specialization and specific regulatory mechanisms. In this review, we analyze available information on the common principles of mitochondrial translation with emphasis on the molecular mechanisms of translation initiation in the mitochondria of yeast and mammalian cells.
    DOI:  https://doi.org/10.1134/S0006297920030013
  28. Sci Adv. 2020 Jun;6(24): eaba7589
    Self-assembled cGAMP-STINGΔTM signaling complex as a bioinspired platform for cGAMP delivery.
    Yanpu He, Celestine Hong, Emily Z Yan, Samantha J Fletcher, Ge Zhu, Mengdi Yang, Yingzhong Li, Xin Sun, Darrell J Irvine, Jiahe Li, Paula T Hammond.
      The stimulator of interferon (IFN) genes (STING) pathway constitutes a highly important part of immune responses against various cancers and infections. Consequently, administration of STING agonists such as cyclic GMP-AMP (cGAMP) has been identified as a promising approach to target these diseases. In cancer cells, STING signaling is frequently impaired by epigenetic silencing of STING; hence, conventional delivery of only its agonist cGAMP may be insufficient to trigger STING signaling. In this work, while expression of STING lacking the transmembrane (TM) domain is known to be unresponsive to STING agonists and is dominant negative when coexpressed with the full-length STING inside cells, we observed that the recombinant TM-deficient STING protein complexed with cGAMP could effectively trigger STING signaling when delivered in vitro and in vivo, including in STING-deficient cell lines. Thus, this bioinspired method using TM-deficient STING may present a universally applicable platform for cGAMP delivery.
    DOI:  https://doi.org/10.1126/sciadv.aba7589
  29. Hum Mol Genet. 2020 Jun 26. pii: ddaa121. [Epub ahead of print]
    Ornithine Decarboxylase, the rate-limiting enzyme of polyamine synthesis, modifies brain pathology in a mouse model of tuberous sclerosis complex.
    David Kapfhamer, James McKenna, Caroline J Yoon, Tracy Murray-Stewart, Robert A Casero, Michael J Gambello.
      Tuberous sclerosis complex (TSC) is a rare autosomal dominant neurodevelopmental disorder characterized by variable expressivity. TSC results from inactivating variants within the TSC1 or TSC2 genes, leading to constitutive activation of mechanistic Target of Rapamycin Complex 1 (mTORC1) signaling. Using a mouse model of TSC (Tsc2-RG) in which the Tsc2 gene is deleted in radial glial precursors and their neuronal and glial descendants, we observed increased ornithine decarboxylase (ODC) enzymatic activity and concentration of its product, putrescine. To test if increased ODC activity and dysregulated polyamine metabolism contributes to the neurodevelopmental defects of Tsc2-RG mice, we used pharmacologic and genetic approaches to reduce ODC activity in Tsc2-RG mice, followed by histologic assessment of brain development. We observed that decreasing ODC activity and putrescine levels in Tsc2-RG mice worsened many of the neurodevelopmental phenotypes, including brain growth and neuronal migration defects, astrogliosis and oxidative stress. These data suggest a protective effect of increased ODC activity and elevated putrescine that modify the phenotype in this developmental Tsc2-RG model.
    DOI:  https://doi.org/10.1093/hmg/ddaa121
  30. Metabolomics. 2020 Jun 23. 16(7): 78
    Novel mitochondrial and cytosolic purification pipeline for compartment-specific metabolomics in mammalian disease model tissues.
    Gunter van der Walt, Roan Louw.
       INTRODUCTION: Mitochondria represent an important milieu for studying the pathogenesis of several major diseases. The need for organelle-level metabolic resolution exists, as mitochondrial/cytosolic metabolites are often diluted beyond detection limits in complex samples. Compartment-specific studies are still hindered by the lack of efficient, cost-effective fractioning methods-applicable to laboratories of all financial/analytical standing.
    OBJECTIVES: We established a novel mitochondrial/cytosolic purification pipeline for complimentary GC-TOF-MS and 1H-NMR metabolomics using robust, commercially available fractionation strategies.
    METHODS: Magnetic based mitochondria isolation kits (MACS) were adapted for this purpose, accompanied by cytosolic filtering. Yield was assessed through the percentage recovery of citrate synthase (CS; a mitochondrial marker), purity by immunoblotting against compartment-specific proteins and integrity interrogated through the respiratory coupling ratio (RCR). The effects of the kit-based buffers on MS/NMR analyses of pure metabolite standards were evaluated. Finally, biological applicability to mammalian disease models was shown using Ndufs4 mouse brain tissue.
    RESULTS: With minor modifications, MACS produced around 60% more mitochondria compared to a differential centrifugation method. Less than 15% of lysosomal LAMP-2 protein was found in the MACS isolates, confirming relative purity-while RCR's above 6 indicate sufficient mitochondrial integrity. The filtering approach effectively depleted mitochondria from the cytosolic fraction, as indicated by negligible Hsp60 and CS levels. Our GC-MS pilot yielded 60-70 features per fraction, while NMR analyses could quantify 6-10 of the most abundant compounds in each fraction.
    CONCLUSION: This study provides a simple and flexible solution for mitochondrial and cytosolic metabolomics in animal model tissues, towards large-scale application of such methodologies in disease research.
    Keywords:  Compartment-specific metabolomics; Cytosol; Gas chromatography time-of-flight mass spectrometry (GC-TOF–MS); MACS; Mitochondria; Proton nuclear magnetic resonance (1H-NMR)
    DOI:  https://doi.org/10.1007/s11306-020-01697-9
  31. Dev Cell. 2020 Jun 12. pii: S1534-5807(20)30420-2. [Epub ahead of print]
    Matrix Rigidity Controls Epithelial-Mesenchymal Plasticity and Tumor Metastasis via a Mechanoresponsive EPHA2/LYN Complex.
    Laurent Fattet, Hae-Yun Jung, Mike W Matsumoto, Brandon E Aubol, Aditya Kumar, Joseph A Adams, Albert C Chen, Robert L Sah, Adam J Engler, Elena B Pasquale, Jing Yang.
      Mechanical cues from the extracellular matrix (ECM) regulate various cellular processes via distinct mechanotransduction pathways. In breast cancer, increased ECM stiffness promotes epithelial-to-mesenchymal transition (EMT), cell invasion, and metastasis. Here, we identify a mechanosensitive EPHA2/LYN protein complex regulating EMT and metastasis in response to increasing ECM stiffness during tumor progression. High ECM stiffness leads to ligand-independent phosphorylation of ephrin receptor EPHA2, which recruits and activates the LYN kinase. LYN phosphorylates the EMT transcription factor TWIST1 to release TWIST1 from its cytoplasmic anchor G3BP2 to enter the nucleus, thus triggering EMT and invasion. Genetic and pharmacological inhibition of this pathway prevents breast tumor invasion and metastasis in vivo. In human breast cancer samples, activation of this pathway correlates with collagen fiber alignment, a marker of increasing ECM stiffness. Our findings reveal an EPHA2/LYN/TWIST1 mechanotransduction pathway that responds to mechanical signals from the tumor microenvironment to drive EMT, invasion, and metastasis.
    Keywords:  ECM stiffness and breast cancer; EMT; EPHA2; LYN; TWIST1; epithelial-mesenchymal transition; matrix stiffness; mechanotransduction; metastasis
    DOI:  https://doi.org/10.1016/j.devcel.2020.05.031
  32. Sci Rep. 2020 Jun 26. 10(1): 10404
    Substrate Channeling via a Transient Protein-Protein Complex: The case of D-Glyceraldehyde-3-Phosphate Dehydrogenase and L-Lactate Dehydrogenase.
    Željko M Svedružić, Ivica Odorčić, Christopher H Chang, Draženka Svedružić.
      Substrate channeling studies have frequently failed to provide conclusive results due to poor understanding of this subtle phenomenon. We analyzed the mechanism of NADH-channeling from D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) to L-lactate Dehydrogenase (LDH) using enzymes from different cells. Enzyme kinetics studies showed that LDH activity with free NADH and GAPDH-NADH complex always take place in parallel. The channeling is observed only in assays that mimic cytosolic conditions where free NADH concentration is negligible and the GAPDH-NADH complex is dominant. Molecular dynamics and protein-protein interaction studies showed that LDH and GAPDH can form a leaky channeling complex only at the limiting NADH concentrations. Surface calculations showed that positive electric field between the NAD(H) binding sites on LDH and GAPDH tetramers can merge in the LDH-GAPDH complex. NAD(H)-channeling within the LDH-GAPDH complex can be an extension of NAD(H)-channeling within each tetramer. In the case of a transient LDH-(GAPDH-NADH) complex, the relative contribution from the channeled and the diffusive paths depends on the overlap between the off-rates for the LDH-(GAPDH-NADH) complex and the GAPDH-NADH complex. Molecular evolution or metabolic engineering protocols can exploit substrate channeling for metabolic flux control by fine-tuning substrate-binding affinity for the key enzymes in the competing reaction paths.
    DOI:  https://doi.org/10.1038/s41598-020-67079-2
  33. Nature. 2020 Jun;582(7813): 492-494
    Tumour metabolites hinder DNA repair.
    Lei-Lei Chen, Yue Xiong.
      
    Keywords:  Cancer; Metabolism
    DOI:  https://doi.org/10.1038/d41586-020-01569-1
  34. Cell Metab. 2020 Jun 22. pii: S1550-4131(20)30307-7. [Epub ahead of print]
    Adenosine/A2B Receptor Signaling Ameliorates the Effects of Aging and Counteracts Obesity.
    Thorsten Gnad, Gemma Navarro, Minna Lahesmaa, Laia Reverte-Salisa, Francesca Copperi, Arnau Cordomi, Jennifer Naumann, Aileen Hochhäuser, Saskia Haufs-Brusberg, Daniela Wenzel, Frank Suhr, Naja Zenius Jespersen, Camilla Scheele, Volodymyr Tsvilovskyy, Christian Brinkmann, Joern Rittweger, Christian Dani, Mathias Kranz, Winnie Deuther-Conrad, Holger K Eltzschig, Tarja Niemi, Markku Taittonen, Peter Brust, Pirjo Nuutila, Leonardo Pardo, Bernd K Fleischmann, Matthias Blüher, Rafael Franco, Wilhelm Bloch, Kirsi A Virtanen, Alexander Pfeifer.
      The combination of aging populations with the obesity pandemic results in an alarming rise in non-communicable diseases. Here, we show that the enigmatic adenosine A2B receptor (A2B) is abundantly expressed in skeletal muscle (SKM) as well as brown adipose tissue (BAT) and might be targeted to counteract age-related muscle atrophy (sarcopenia) as well as obesity. Mice with SKM-specific deletion of A2B exhibited sarcopenia, diminished muscle strength, and reduced energy expenditure (EE), whereas pharmacological A2B activation counteracted these processes. Adipose tissue-specific ablation of A2B exacerbated age-related processes and reduced BAT EE, whereas A2B stimulation ameliorated obesity. In humans, A2B expression correlated with EE in SKM, BAT activity, and abundance of thermogenic adipocytes in white fat. Moreover, A2B agonist treatment increased EE from human adipocytes, myocytes, and muscle explants. Mechanistically, A2B forms heterodimers required for adenosine signaling. Overall, adenosine/A2B signaling links muscle and BAT and has both anti-aging and anti-obesity potential.
    Keywords:  GPCR; adenosine; adenosine receptor A2B; aging; brown adipose tissue; browning; energy metabolism; muscle; obesity; sarcopenia
    DOI:  https://doi.org/10.1016/j.cmet.2020.06.006
  35. J Cell Sci. 2020 Jun 23. pii: jcs.240374. [Epub ahead of print]
    Cardiolipin is required for membrane docking of mitochondrial ribosomes and protein synthesis.
    Richard G Lee, Junjie Gao, Stefan J Siira, Anne-Marie Shearwood, Judith A Ermer, Vinzenz Hofferek, James C Mathews, Minghao Zheng, Gavin E Reid, Oliver Rackham, Aleksandra Filipovska.
      The mitochondrial inner membrane contains a unique phospholipid known as cardiolipin (CL), which stabilises the protein complexes embedded in the membrane and supports its overall structure. Recent evidence indicates that the mitochondrial ribosome may associate with the inner membrane to facilitate co-translational insertion of the hydrophobic oxidative phosphorylation (OXPHOS) proteins into the inner membrane. We generated three mutant knockout cell lines for the cardiolipin biosynthesis gene Crls1 to investigate the effects of cardiolipin loss on mitochondrial protein synthesis. Reduced CL levels caused altered mitochondrial morphology and transcriptome-wide changes that were accompanied by reduced uncoordinated mitochondrial translation rates and impaired respiratory supercomplex formation. Aberrant protein synthesis was caused by impaired formation and distribution of mitochondrial ribosomes. Reduction or loss of cardiolipin resulted in divergent mitochondrial and endoplasmic reticulum stress responses. We show that cardiolipin is required to stabilise the interaction of the mitochondrial ribosome with the membrane via its association with OXA1 during active translation. This interaction facilitates insertion of newly synthesised mitochondrial proteins into the inner membrane and stabilises the respiratory supercomplexes.
    Keywords:  Mitochondrial membranes; Mitochondrial ribosomes; Protein synthesis
    DOI:  https://doi.org/10.1242/jcs.240374
  36. Nat Commun. 2020 Jun 23. 11(1): 3165
    Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis.
    Elizabeth R Morris, Sarah J Caswell, Simone Kunzelmann, Laurence H Arnold, Andrew G Purkiss, Geoff Kelly, Ian A Taylor.
      SAMHD1 regulates cellular 2'-deoxynucleoside-5'-triphosphate (dNTP) homeostasis by catalysing the hydrolysis of dNTPs into 2'-deoxynucleosides and triphosphate. In CD4+ myeloid lineage and resting T-cells, SAMHD1 blocks HIV-1 and other viral infections by depletion of the dNTP pool to a level that cannot support replication. SAMHD1 mutations are associated with the autoimmune disease Aicardi-Goutières syndrome and hypermutated cancers. Furthermore, SAMHD1 sensitises cancer cells to nucleoside-analogue anti-cancer therapies and is linked with DNA repair and suppression of the interferon response to cytosolic nucleic acids. Nevertheless, despite its requirement in these processes, the fundamental mechanism of SAMHD1-catalysed dNTP hydrolysis remained unknown. Here, we present structural and enzymological data showing that SAMHD1 utilises an active site, bi-metallic iron-magnesium centre that positions a hydroxide nucleophile in-line with the Pα-O5' bond to catalyse phosphoester bond hydrolysis. This precise molecular mechanism for SAMHD1 catalysis, reveals how SAMHD1 down-regulates cellular dNTP and modulates the efficacy of nucleoside-based anti-cancer and anti-viral therapies.
    DOI:  https://doi.org/10.1038/s41467-020-16983-2
  37. Biochemistry (Mosc). 2020 Apr;85(4): 393-408
    Amino Acids as Regulators of Cell Metabolism.
    S V Nesterov, L S Yaguzhinsky, G I Podoprigora, Ya R Nartsissov.
      In this review, we discuss the principles of regulation and synchronization of metabolic processes in mammalian cells using a two-component model of cell metabolism consisting of a controlling signaling system that regulates major enzymatic cascades and executive metabolic system that directly performs biosynthetic reactions. This approach has allowed us to distinguish two transitional metabolic states (from catabolism to anabolism and vice versa) accompanied by major rearrangements in the signaling system. The signaling system of natural amino acids was selected, because amino acids are involved in both signaling and executive metabolic subsystems of general cell metabolism. We have developed a graphical representation of metabolic events that allowed us to demonstrate the succession of processes occurring in both metabolic subsystems during complete metabolic cycle in a non-dividing cell. An important revealed feature of the amino acid signaling system is that the signaling properties of amino acid are determined not only by their molecular structure, but also by the location within the cell. Four major signaling groups of amino acids have been identified that localize to lysosomes, mitochondria, cytosol, and extracellular space adjacent to the plasma membrane. Although these amino acids groups are similar in the composition, they have different receptors. We also proposed a scheme for the metabolism regulation by amino acids signaling that can serve as a basis for developing more complete spatio-temporal picture of metabolic regulation involving a wide variety of intracellular signaling cascades.
    DOI:  https://doi.org/10.1134/S000629792004001X
  38. EMBO J. 2020 Jun 22. e105714
    Resolving mitochondrial cristae: introducing a new model into the fold.
    Kate McArthur, Michael T Ryan.
      The many functions of mitochondria-the powerhouses of our cells-are intimately linked with their ultrastructure and network morphology. In this issue, Stephan et al (2020) apply a tour de force of microscopic techniques to examine the contributions of specific mitochondrial proteins to crista architecture.
    DOI:  https://doi.org/10.15252/embj.2020105714
  39. Cell Physiol Biochem. 2020 Jun 27. 54(4): 629-647
    The Critical Role of Cell Metabolism for Essential Neutrophil Functions.
    Rui Curi, Adriana Cristina Levada-Pires, Eliane Borges da Silva, Sarah de Oliveira Poma, Raquel Freitas Zambonatto, Paola Domenech, Mariana Mendes de Almeida, Raquel Bragante Gritte, Talita Souza-Siqueira, Renata Gorjão, Philip Newsholme, Tania Cristina Pithon-Curi.
      Neutrophils were traditionally considered as short-lived cells with abundant secretory and protein synthetic activity. Recent studies, however, indicate neutrophils are in reality a heterogeneous population of cells. Neutrophils differentiate from pluripotent stem cells in the bone marrow, and can further mature in the blood stream and can have different phenotypes in health and disease conditions. Neutrophils undergo primary functions such as phagocytosis, production of reactive oxygen species (ROS), release of lipid mediators and inflammatory proteins (mainly cytokines), and apoptosis. Neutrophils stimulate other neutrophils and trigger a cascade of immune and inflammatory responses. The underpinning intracellular metabolisms that support these neutrophil functions are herein reported. It has been known for many decades that neutrophils utilize glucose as a primary fuel and produce lactate as an end product of glycolysis. Neutrophils metabolize glucose through glycolysis and the pentose- phosphate pathway (PPP). Mitochondrial glucose oxidation is very low. The PPP provides the reduced nicotinamide adenine dinucleotide phosphate (NADPH) for the NADPH-oxidase (NOX) complex activity to produce superoxide from oxygen. These cells also utilize glutamine and fatty acids to produce the required adenosine triphosphate (ATP) and precursors for the synthesis of molecules that trigger functional outcomes. Neutrophils obtained from rat intraperitoneal cavity and incubate for 1 hour at 37°C metabolize glutamine at higher rate than that of glucose. Glutamine delays neutrophil apoptosis and maintains optimal NOX activity for superoxide production. Under limited glucose provision, neutrophils move to fatty acid oxidation (FAO) to obtain the required energy for the cell function. FAO is mainly associated with neutrophil differentiation and maturation. Hypoxia, hormonal dysfunction, and physical exercise markedly change neutrophil metabolism. It is now become clear that neutrophil metabolism underlies the heterogeneity of neutrophil phenotypes and should be intense focus of investigation.
    Keywords:  Inflammation; Glutamine; Glucose; Hormones; Physical Exercise
    DOI:  https://doi.org/10.33594/000000245
  40. Cell. 2020 Jun 25. pii: S0092-8674(20)30564-X. [Epub ahead of print]181(7): 1680-1692.e15
    Metabolic Dynamics and Prediction of Gestational Age and Time to Delivery in Pregnant Women.
    Liang Liang, Marie-Louise Hee Rasmussen, Brian Piening, Xiaotao Shen, Songjie Chen, Hannes Röst, John K Snyder, Robert Tibshirani, Line Skotte, Norman Cy Lee, Kévin Contrepois, Bjarke Feenstra, Hanyah Zackriah, Michael Snyder, Mads Melbye.
      Metabolism during pregnancy is a dynamic and precisely programmed process, the failure of which can bring devastating consequences to the mother and fetus. To define a high-resolution temporal profile of metabolites during healthy pregnancy, we analyzed the untargeted metabolome of 784 weekly blood samples from 30 pregnant women. Broad changes and a highly choreographed profile were revealed: 4,995 metabolic features (of 9,651 total), 460 annotated compounds (of 687 total), and 34 human metabolic pathways (of 48 total) were significantly changed during pregnancy. Using linear models, we built a metabolic clock with five metabolites that time gestational age in high accordance with ultrasound (R = 0.92). Furthermore, two to three metabolites can identify when labor occurs (time to delivery within two, four, and eight weeks, AUROC ≥ 0.85). Our study represents a weekly characterization of the human pregnancy metabolome, providing a high-resolution landscape for understanding pregnancy with potential clinical utilities.
    Keywords:  delivery prediction; gestational age; human pregnancy; longitudinal profiling; machine learning; metabolic clock; metabolic pathways; metabolomics
    DOI:  https://doi.org/10.1016/j.cell.2020.05.002
  41. Biochemistry (Mosc). 2020 May;85(5): 636-641
    Mitochondrial Transplantation: A Critical Analysis.
    B V Chernyak.
      "Mitochondrial transplantation" refers to a procedure for introducing isolated mitochondria into a damaged area of a heart or other organ. A considerable amount of data has been accumulated on the therapeutic effects of "mitochondrial transplantation" in animals with ischemic heart damage. In 2017, the first attempts were made to apply this procedure in a clinic. The authors of the method suggest that exogenous mitochondria penetrate into cardiomyocytes, retaining functional activity, and compensate for impaired energy output of endogenous mitochondria. This hypothesis contradicts the well-known fact of loss of mitochondrial functions in the presence of high concentrations of Ca2+, which are characteristic of the extracellular medium. This review critically considers the possible mechanisms of the therapeutic effect of "mitochondrial transplantation".
    DOI:  https://doi.org/10.1134/S0006297920050132
  42. Cancer Cell. 2020 Jun 09. pii: S1535-6108(20)30268-3. [Epub ahead of print]
    PKCλ/ι Loss Induces Autophagy, Oxidative Phosphorylation, and NRF2 to Promote Liver Cancer Progression.
    Yotaro Kudo, Masayuki Sugimoto, Esperanza Arias, Hiroaki Kasashima, Thekla Cordes, Juan F Linares, Angeles Duran, Yuki Nakanishi, Naoko Nakanishi, Antoine L'Hermitte, Alex Campos, Nadia Senni, Tarmo Rooslid, Lewis R Roberts, Ana Maria Cuervo, Christian M Metallo, Michael Karin, Maria T Diaz-Meco, Jorge Moscat.
      Oxidative stress plays a critical role in liver tissue damage and in hepatocellular carcinoma (HCC) initiation and progression. However, the mechanisms that regulate autophagy and metabolic reprogramming during reactive oxygen species (ROS) generation, and how ROS promote tumorigenesis, still need to be fully understood. We show that protein kinase C (PKC) λ/ι loss in hepatocytes promotes autophagy and oxidative phosphorylation. This results in ROS generation, which through NRF2 drives HCC through cell-autonomous and non-autonomous mechanisms. Although PKCλ/ι promotes tumorigenesis in oncogene-driven cancer models, emerging evidence demonstrate that it is a tumor suppressor in more complex carcinogenic processes. Consistently, PKCλ/ι levels negatively correlate with HCC histological tumor grade, establishing this kinase as a tumor suppressor in liver cancer.
    Keywords:  NRF2; PKCζ; PKCι; PKCλ; atypical PKC; autophagy; hepatocellular carcinoma; metabolic reprogramming; oxidative phosphorylation; reactive oxygen species
    DOI:  https://doi.org/10.1016/j.ccell.2020.05.018
  43. Nature. 2020 Jun 24.
    Intracellular pH controls WNT downstream of glycolysis in amniote embryos.
    Masayuki Oginuma, Yukiko Harima, Oscar A Tarazona, Margarete Diaz-Cuadros, Arthur Michaut, Tohru Ishitani, Fengzhu Xiong, Olivier Pourquié.
      Formation of the body of vertebrate embryos proceeds sequentially by posterior addition of tissues from the tail bud. Cells of the tail bud and the posterior presomitic mesoderm, which control posterior elongation1, exhibit a high level of aerobic glycolysis that is reminiscent of the metabolic status of cancer cells experiencing the Warburg effect2,3. Glycolytic activity downstream of fibroblast growth factor controls WNT signalling in the tail bud3. In the neuromesodermal precursors of the tail bud4, WNT signalling promotes the mesodermal fate that is required for sustained axial elongation, at the expense of the neural fate3,5. How glycolysis regulates WNT signalling in the tail bud is currently unknown. Here we used chicken embryos and human tail bud-like cells differentiated in vitro from induced pluripotent stem cells to show that these cells exhibit an inverted pH gradient, with the extracellular pH lower than the intracellular pH, as observed in cancer cells6. Our data suggest that glycolysis increases extrusion of lactate coupled to protons via the monocarboxylate symporters. This contributes to elevating the intracellular pH in these cells, which creates a favourable chemical environment for non-enzymatic β-catenin acetylation downstream of WNT signalling. As acetylated β-catenin promotes mesodermal rather than neural fate7, this ultimately leads to activation of mesodermal transcriptional WNT targets and specification of the paraxial mesoderm in tail bud precursors. Our work supports the notion that some tumour cells reactivate a developmental metabolic programme.
    DOI:  https://doi.org/10.1038/s41586-020-2428-0
  44. Nat Commun. 2020 Jun 26. 11(1): 3241
    Protein arginine deiminase 4 antagonizes methylglyoxal-induced histone glycation.
    Qingfei Zheng, Adewola Osunsade, Yael David.
      Protein arginine deiminase 4 (PAD4) facilitates the post-translational citrullination of the core histones H3 and H4. While the precise epigenetic function of this modification has not been resolved, it has been shown to associate with general chromatin decompaction and compete with arginine methylation. Recently, we found that histones are subjected to methylglyoxal (MGO)-induced glycation on nucleophilic side chains, particularly arginines, under metabolic stress conditions. These non-enzymatic adducts change chromatin architecture and the epigenetic landscape by competing with enzymatic modifications, as well as changing the overall biophysical properties of the fiber. Here, we report that PAD4 antagonizes histone MGO-glycation by protecting the reactive arginine sites, as well as by converting already-glycated arginine residues into citrulline. Moreover, we show that similar to the deglycase DJ-1, PAD4 is overexpressed and histone citrullination is upregulated in breast cancer tumors, suggesting an additional mechanistic link to PAD4's oncogenic properties.
    DOI:  https://doi.org/10.1038/s41467-020-17066-y
  45. Proc Natl Acad Sci U S A. 2020 Jun 25. pii: 202004223. [Epub ahead of print]
    Convergent evolution of conserved mitochondrial pathways underlies repeated adaptation to extreme environments.
    Ryan Greenway, Nick Barts, Chathurika Henpita, Anthony P Brown, Lenin Arias Rodriguez, Carlos M Rodríguez Peña, Sabine Arndt, Gigi Y Lau, Michael P Murphy, Lei Wu, Dingbo Lin, Michael Tobler, Joanna L Kelley, Jennifer H Shaw.
      Extreme environments test the limits of life; yet, some organisms thrive in harsh conditions. Extremophile lineages inspire questions about how organisms can tolerate physiochemical stressors and whether the repeated colonization of extreme environments is facilitated by predictable and repeatable evolutionary innovations. We identified the mechanistic basis underlying convergent evolution of tolerance to hydrogen sulfide (H2S)-a toxicant that impairs mitochondrial function-across evolutionarily independent lineages of a fish (Poecilia mexicana, Poeciliidae) from H2S-rich springs. Using comparative biochemical and physiological analyses, we found that mitochondrial function is maintained in the presence of H2S in sulfide spring P. mexicana but not ancestral lineages from nonsulfidic habitats due to convergent adaptations in the primary toxicity target and a major detoxification enzyme. Genome-wide local ancestry analyses indicated that convergent evolution of increased H2S tolerance in different populations is likely caused by a combination of selection on standing genetic variation and de novo mutations. On a macroevolutionary scale, H2S tolerance in 10 independent lineages of sulfide spring fishes across multiple genera of Poeciliidae is correlated with the convergent modification and expression changes in genes associated with H2S toxicity and detoxification. Our results demonstrate that the modification of highly conserved physiological pathways associated with essential mitochondrial processes mediates tolerance to physiochemical stress. In addition, the same pathways, genes, and-in some instances-codons are implicated in H2S adaptation in lineages that span 40 million years of evolution.
    Keywords:  adaptive evolution; comparative physiology; ecological genomics; hydrogen sulfide; phylogenetic comparative analysis
    DOI:  https://doi.org/10.1073/pnas.2004223117
  46. Nat Genet. 2020 Jun 22.
    Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes.
    Jennifer M Luppino, Daniel S Park, Son C Nguyen, Yemin Lan, Zhuxuan Xu, Rebecca Yunker, Eric F Joyce.
      The human genome can be segmented into topologically associating domains (TADs), which have been proposed to spatially sequester genes and regulatory elements through chromatin looping. Interactions between TADs have also been suggested, presumably because of variable boundary positions across individual cells. However, the nature, extent and consequence of these dynamic boundaries remain unclear. Here, we combine high-resolution imaging with Oligopaint technology to quantify the interaction frequencies across both weak and strong boundaries. We find that chromatin intermingling across population-defined boundaries is widespread but that the extent of permissibility is locus-specific. Cohesin depletion, which abolishes domain formation at the population level, does not induce ectopic interactions but instead reduces interactions across all boundaries tested. In contrast, WAPL or CTCF depletion increases inter-domain contacts in a cohesin-dependent manner. Reduced chromatin intermingling due to cohesin loss affects the topology and transcriptional bursting frequencies of genes near boundaries. We propose that cohesin occasionally bypasses boundaries to promote incorporation of boundary-proximal genes into neighboring domains.
    DOI:  https://doi.org/10.1038/s41588-020-0647-9
  47. Proc Natl Acad Sci U S A. 2020 Jun 23. pii: 202002391. [Epub ahead of print]
    Subunit composition of the mammalian serine-palmitoyltransferase defines the spectrum of straight and methyl-branched long-chain bases.
    Museer A Lone, Andreas J Hülsmeier, Essa M Saied, Gergely Karsai, Christoph Arenz, Arnold von Eckardstein, Thorsten Hornemann.
      Sphingolipids (SLs) are chemically diverse lipids that have important structural and signaling functions within mammalian cells. SLs are commonly defined by the presence of a long-chain base (LCB) that is normally formed by the conjugation of l-serine and palmitoyl-CoA. This pyridoxal 5-phosphate (PLP)-dependent reaction is mediated by the enzyme serine-palmitoyltransferase (SPT). However, SPT can also metabolize other acyl-CoAs, in the range of C14 to C18, forming a variety of LCBs that differ by structure and function. Mammalian SPT consists of three core subunits: SPTLC1, SPTLC2, and SPTLC3. Whereas SPTLC1 and SPTLC2 are ubiquitously expressed, SPTLC3 expression is restricted to certain tissues only. The influence of the individual subunits on enzyme activity is not clear. Using cell models deficient in SPTLC1, SPTLC2, and SPTLC3, we investigated the role of each subunit on enzyme activity and the LCB product spectrum. We showed that SPTLC1 is essential for activity, whereas SPTLC2 and SPTLC3 are partly redundant but differ in their enzymatic properties. SPTLC1 in combination with SPTLC2 specifically formed C18, C19, and C20 LCBs while the combination of SPTLC1 and SPTLC3 yielded a broader product spectrum. We identified anteiso-branched-C18 SO (meC18SO) as the primary product of the SPTLC3 reaction. The meC18SO was synthesized from anteiso-methyl-palmitate, in turn synthesized from a precursor metabolite generated in the isoleucine catabolic pathway. The meC18SO is metabolized to ceramides and complex SLs and is a constituent of human low- and high-density lipoproteins.
    Keywords:  long-chain base; omega-3-methyl-sphingosine; serine-palmitoyltransferase
    DOI:  https://doi.org/10.1073/pnas.2002391117
  48. EMBO Rep. 2020 Jun 21. e50047
    Ageing, metabolism and the intestine.
    Maja C Funk, Jun Zhou, Michael Boutros.
      The intestinal epithelium serves as a dynamic barrier to the environment and integrates a variety of signals, including those from metabolites, commensal microbiota, immune responses and stressors upon ageing. The intestine is constantly challenged and requires a high renewal rate to replace damaged cells in order to maintain its barrier function. Essential for its renewal capacity are intestinal stem cells, which constantly give rise to progenitor cells that differentiate into the multiple cell types present in the epithelium. Here, we review the current state of research of how metabolism and ageing control intestinal stem cell function and epithelial homeostasis. We focus on recent insights gained from model organisms that indicate how changes in metabolic signalling during ageing are a major driver for the loss of stem cell plasticity and epithelial homeostasis, ultimately affecting the resilience of an organism and limiting its lifespan. We compare findings made in mouse and Drosophila and discuss differences and commonalities in the underlying signalling pathways and mechanisms in the context of ageing.
    Keywords:  ageing; epithelial barriers; intestinal homeostasis; metabolism; stem cells
    DOI:  https://doi.org/10.15252/embr.202050047
  49. Commun Biol. 2020 Jun 25. 3(1): 328
    Robust detection of oncometabolic aberrations by 1H-13C heteronuclear single quantum correlation in intact biological specimens.
    Yasaman Barekatain, Victoria C Yan, Kenisha Arthur, Jeffrey J Ackroyd, Sunada Khadka, John De Groot, Jason T Huse, Florian L Muller.
      Magnetic resonance (MR) spectroscopy has potential to non-invasively detect metabolites of diagnostic significance for precision oncology. Yet, many metabolites have similar chemical shifts, yielding highly convoluted 1H spectra of intact biological material and limiting diagnostic utility. Here, we show that hydrogen-carbon heteronuclear single quantum correlation (1H-13C HSQC) offers dramatic improvements in sensitivity compared to one-dimensional (1D) 13C NMR and significant signal deconvolution compared to 1D 1H spectra in intact biological settings. Using a standard NMR spectroscope with a cryoprobe but without specialized signal enhancing features such as magic angle spinning, metabolite extractions or 13C-isotopic enrichment, we obtain well-resolved 2D 1H-13C HSQC spectra in live cancer cells, in ex vivo freshly dissected xenografted tumors and resected primary tumors. This method can identify tumors with specific oncometabolite alterations such as IDH mutations by 2-hydroxyglutarate and PGD-deleted tumors by gluconate. Results suggest potential of 1H-13C HSQC as a non-invasive diagnostic in precision oncology.
    DOI:  https://doi.org/10.1038/s42003-020-1055-5
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