bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2020‒09‒13
forty papers selected by
Christian Frezza,

  1. SLC25A51 is a mammalian mitochondrial NAD+ transporter.
  2. The evolving metabolic landscape of chromatin biology and epigenetics.
  3. ER-mitochondria contacts promote mtDNA nucleoids active transportation via mitochondrial dynamic tubulation.
  4. Oxidative Metabolism Drives Immortalization of Neural Stem Cells during Tumorigenesis.
  5. Metabolic rivalry: circadian homeostasis and tumorigenesis.
  6. Dynamic changes in DICER levels in adipose tissue control metabolic adaptations to exercise.
  7. Structure of the dimeric ATP synthase from bovine mitochondria.
  8. Malic Enzyme Couples Mitochondria with Aerobic Glycolysis in Osteoblasts.
  9. Selective Lysosome Membrane Turnover Is Induced by Nutrient Starvation.
  10. PER1 interaction with GPX1 regulates metabolic homeostasis under oxidative stress.
  11. The malate-aspartate shuttle (Borst cycle): How it started and developed into a major metabolic pathway.
  12. Visualizing Subcellular Enrichment of Glycogen in Live Cancer Cells by Stimulated Raman Scattering.
  13. Mitochondrial respiration is required to provide amino acids during fermentative proliferation of fission yeast.
  14. Atf-6 Regulates Lifespan through ER-Mitochondrial Calcium Homeostasis.
  15. Hypoxia-mediated regulation of mitochondrial transcription factors in renal epithelial cells: implications for hypertensive renal physiology.
  16. AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation.
  17. The precursor of PI(3,4,5)P3 alleviates aging by activating daf-18(Pten) and independent of daf-16.
  18. Kinetic Trans-omic Analysis Reveals Key Regulatory Mechanisms for Insulin-Regulated Glucose Metabolism in Adipocytes.
  19. Organoids Model Transcriptional Hallmarks of Oncogenic KRAS Activation in Lung Epithelial Progenitor Cells.
  20. FIT2 is an acyl-coenzyme A diphosphatase crucial for endoplasmic reticulum homeostasis.
  21. Upregulation of CPT1A is essential for the tumor-promoting effect of adipocytes in colon cancer.
  22. Systematic analysis of nuclear gene function in respiratory growth and expression of the mitochondrial genome in S. cerevisiae.
  23. Ammonia inhibits energy metabolism in astrocytes in a rapid and glutamate dehydrogenase 2-dependent manner.
  24. Three cytosolic NAD-malate dehydrogenase isoforms of Arabidopsis thaliana: On the crossroad between energy fluxes and redox signaling.
  25. Mitochondrial biogenesis in organismal senescence and neurodegeneration.
  26. GFP fluorescence tagging alters dynamin-related protein 1 oligomerization dynamics and creates disassembly-refractory puncta to mediate mitochondrial fission.
  27. Metabolic Potential of Cancer Cells in Context of the Metastatic Cascade.
  28. Glutamine Metabolism Controls Stem Cell Fate Reversibility and Long-Term Maintenance in the Hair Follicle.
  29. NRF2 regulates the sensitivity of human NSCLC cells to cystine deprivation-induced ferroptosis via FOCAD-FAK signaling pathway.
  30. Dichotomous role of the human mitochondrial Na+/Ca2+/Li+ exchanger NCLX in colorectal cancer growth and metastasis.
  31. Membrane-tethering of cytochrome c accelerates regulated cell death in yeast.
  32. Exploitation of DHODH and p53 activation as therapeutic targets - a case study in polypharmacology.
  33. Protein crowding in the inner mitochondrial membrane.
  34. Adaptable haemodynamic endothelial cells for organogenesis and tumorigenesis.
  35. Yap/Taz promote the scavenging of extracellular nutrients through macropinocytosis.
  36. Ion Channels in Cancer: Orchestrators of Electrical Signaling and Cellular Crosstalk.
  37. The wasting-associated metabolite succinate disrupts myogenesis and impairs skeletal muscle regeneration.
  38. Structural mechanism of cGAS inhibition by the nucleosome.
  39. Cancer proteome and metabolite changes linked to SHMT2.
  40. Structural basis for sequestration and autoinhibition of cGAS by chromatin.
  1. Nature. 2020 Sep 09.
    SLC25A51 is a mammalian mitochondrial NAD+ transporter.
    Timothy S Luongo, Jared M Eller, Mu-Jie Lu, Marc Niere, Fabio Raith, Caroline Perry, Marc R Bornstein, Paul Oliphint, Lin Wang, Melanie R McReynolds, Marie E Migaud, Joshua D Rabinowitz, F Brad Johnson, Kai Johnsson, Mathias Ziegler, Xiaolu A Cambronne, Joseph A Baur.
      Mitochondria require nicotinamide adenine dinucleotide (NAD+) in order to carry out the fundamental processes that fuel respiration and mediate cellular energy transduction. Mitochondrial NAD+ transporters have been identified in yeast and plants1,2 but their very existence is controversial in mammals3-5. Here we demonstrate that mammalian mitochondria are capable of taking up intact NAD+ and identify SLC25A51 (an essential6,7 mitochondrial protein of previously unknown function, also known as MCART1) as a mammalian mitochondrial NAD+ transporter. Loss of SLC25A51 decreases mitochondrial but not whole-cell NAD+ content, impairs mitochondrial respiration, and blocks the uptake of NAD+ into isolated mitochondria. Conversely, overexpression of SLC25A51 or a nearly identical paralog, SLC25A52, increases mitochondrial NAD+ levels and restores NAD+ uptake into yeast mitochondria lacking endogenous NAD+ transporters. Together, these findings identify SLC25A51 as the first transporter capable of importing NAD+ into mammalian mitochondria.
    DOI:  https://doi.org/10.1038/s41586-020-2741-7
  2. Nat Rev Genet. 2020 Sep 09.
    The evolving metabolic landscape of chromatin biology and epigenetics.
    Ziwei Dai, Vijyendra Ramesh, Jason W Locasale.
      Molecular inputs to chromatin via cellular metabolism are modifiers of the epigenome. These inputs - which include both nutrient availability as a result of diet and growth factor signalling - are implicated in linking the environment to the maintenance of cellular homeostasis and cell identity. Recent studies have demonstrated that these inputs are much broader than had previously been known, encompassing metabolism from a wide variety of sources, including alcohol and microbiotal metabolism. These factors modify DNA and histones and exert specific effects on cell biology, systemic physiology and pathology. In this Review, we discuss the nature of these molecular networks, highlight their role in mediating cellular responses and explore their modifiability through dietary and pharmacological interventions.
    DOI:  https://doi.org/10.1038/s41576-020-0270-8
  3. Nat Commun. 2020 09 08. 11(1): 4471
    ER-mitochondria contacts promote mtDNA nucleoids active transportation via mitochondrial dynamic tubulation.
    Jinshan Qin, Yuting Guo, Boxin Xue, Peng Shi, Yang Chen, Qian Peter Su, Huiwen Hao, Shujuan Zhao, Congying Wu, Li Yu, Dong Li, Yujie Sun.
      A human cell contains hundreds to thousands of mitochondrial DNA (mtDNA) packaged into nucleoids. Currently, the segregation and allocation of nucleoids are thought to be passively determined by mitochondrial fusion and division. Here we provide evidence, using live-cell super-resolution imaging, that nucleoids can be actively transported via KIF5B-driven mitochondrial dynamic tubulation (MDT) activities that predominantly occur at the ER-mitochondria contact sites (EMCS). We further demonstrate that a mitochondrial inner membrane protein complex MICOS links nucleoids to Miro1, a KIF5B receptor on mitochondria, at the EMCS. We show that such active transportation is a mechanism essential for the proper distribution of nucleoids in the peripheral zone of the cell. Together, our work identifies an active transportation mechanism of nucleoids, with EMCS serving as a key platform for the interplay of nucleoids, MICOS, Miro1, and KIF5B to coordinate nucleoids segregation and transportation.
    DOI:  https://doi.org/10.1038/s41467-020-18202-4
  4. Cell. 2020 Aug 30. pii: S0092-8674(20)30947-8. [Epub ahead of print]
    Oxidative Metabolism Drives Immortalization of Neural Stem Cells during Tumorigenesis.
    François Bonnay, Ana Veloso, Victoria Steinmann, Thomas Köcher, Merve Deniz Abdusselamoglu, Sunanjay Bajaj, Elisa Rivelles, Lisa Landskron, Harald Esterbauer, Robert P Zinzen, Juergen A Knoblich.
      Metabolic reprogramming is a key feature of many cancers, but how and when it contributes to tumorigenesis remains unclear. Here we demonstrate that metabolic reprogramming induced by mitochondrial fusion can be rate-limiting for immortalization of tumor-initiating cells (TICs) and trigger their irreversible dedication to tumorigenesis. Using single-cell transcriptomics, we find that Drosophila brain tumors contain a rapidly dividing stem cell population defined by upregulation of oxidative phosphorylation (OxPhos). We combine targeted metabolomics and in vivo genetic screening to demonstrate that OxPhos is required for tumor cell immortalization but dispensable in neural stem cells (NSCs) giving rise to tumors. Employing an in vivo NADH/NAD+ sensor, we show that NSCs precisely increase OxPhos during immortalization. Blocking OxPhos or mitochondrial fusion stalls TICs in quiescence and prevents tumorigenesis through impaired NAD+ regeneration. Our work establishes a unique connection between cellular metabolism and immortalization of tumor-initiating cells.
    Keywords:  bioenergetics; cell immortalization; mitochondrial dynamics; neural stem cells; tumor heterogeneity; tumorigenesis
    DOI:  https://doi.org/10.1016/j.cell.2020.07.039
  5. Nat Rev Cancer. 2020 Sep 07.
    Metabolic rivalry: circadian homeostasis and tumorigenesis.
    Kenichiro Kinouchi, Paolo Sassone-Corsi.
      Circadian rhythms govern a large array of physiological and metabolic functions. Perturbations of the daily cycle have been linked to elevated risk of developing cancer as well as poor prognosis in patients with cancer. Also, expression of core clock genes or proteins is remarkably attenuated particularly in tumours of a higher stage or that are more aggressive, possibly linking the circadian clock to cellular differentiation. Emerging evidence indicates that metabolic control by the circadian clock underpins specific hallmarks of cancer metabolism. Indeed, to support cell proliferation and biomass production, the clock may direct metabolic processes of cancer cells in concert with non-clock transcription factors to control how nutrients and metabolites are utilized in a time-specific manner. We hypothesize that the metabolic switch between differentiation or stemness of cancer may be coupled to the molecular clockwork. Moreover, circadian rhythms of host organisms appear to dictate tumour growth and proliferation. This Review outlines recent discoveries of the interplay between circadian rhythms, proliferative metabolism and cancer, highlighting potential opportunities in the development of future therapeutic strategies.
    DOI:  https://doi.org/10.1038/s41568-020-0291-9
  6. Proc Natl Acad Sci U S A. 2020 Sep 08. pii: 202011243. [Epub ahead of print]
    Dynamic changes in DICER levels in adipose tissue control metabolic adaptations to exercise.
    Bruna B Brandão, Søren Madsen, Atefeh Rabiee, Matteo Oliverio, Gabriel P Ruiz, Danilo L Ferrucci, Jéssica L Branquinho, Daniela Razolli, Silas Pinto, Thomas S Nielsen, William T Festuccia, Adriano S Martins, Beatriz A Guerra, Thiago L Knittel, Ditte Søgaard, Steen Larsen, Jørn W Helge, Josef Brandauer, Lício A Velloso, Brice Emanuelli, Jan-Wilhelm Kornfeld, C Ronald Kahn, Sara G Vienberg, Juleen R Zierath, Jonas T Treebak, Marcelo A Mori.
      DICER is a key enzyme in microRNA (miRNA) biogenesis. Here we show that aerobic exercise training up-regulates DICER in adipose tissue of mice and humans. This can be mimicked by infusion of serum from exercised mice into sedentary mice and depends on AMPK-mediated signaling in both muscle and adipocytes. Adipocyte DICER is required for whole-body metabolic adaptations to aerobic exercise training, in part, by allowing controlled substrate utilization in adipose tissue, which, in turn, supports skeletal muscle function. Exercise training increases overall miRNA expression in adipose tissue, and up-regulation of miR-203-3p limits glycolysis in adipose under conditions of metabolic stress. We propose that exercise training-induced DICER-miR-203-3p up-regulation in adipocytes is a key adaptive response that coordinates signals from working muscle to promote whole-body metabolic adaptations.
    Keywords:  adipose tissue; cross-talk; exercise; metabolic flexibility; microRNA
    DOI:  https://doi.org/10.1073/pnas.2011243117
  7. Proc Natl Acad Sci U S A. 2020 Sep 08. pii: 202013998. [Epub ahead of print]
    Structure of the dimeric ATP synthase from bovine mitochondria.
    Tobias E Spikes, Martin G Montgomery, John E Walker.
      The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial matrix via the proton inlet half channel proceeds via a Grotthus mechanism, and a similar mechanism may operate in the exit half channel. The structure has given information about the architecture and mechanical constitution and properties of the peripheral stalk, part of the membrane extrinsic region of the stator, and how the action of the peripheral stalk damps the side-to-side rocking motions that occur in the enzyme complex during the catalytic cycle. It also describes wedge structures in the membrane domains of each monomer, where the skeleton of each wedge is provided by three α-helices in the membrane domains of the b-subunit to which the supernumerary subunits e, f, and g and the membrane domain of subunit A6L are bound. Protein voids in the wedge are filled by three specifically bound cardiolipin molecules and two other phospholipids. The external surfaces of the wedges link the monomeric complexes together into the dimeric structures and provide a pivot to allow the monomer-monomer interfaces to change during catalysis and to accommodate other changes not related directly to catalysis in the monomer-monomer interface that occur in mitochondrial cristae. The structure of the bovine dimer also demonstrates that the structures of dimeric ATP synthases in a tetrameric porcine enzyme have been seriously misinterpreted in the membrane domains.
    Keywords:  Grotthus chain; bovine mitochondria; dimeric ATP synthase; structure; torque generation
    DOI:  https://doi.org/10.1073/pnas.2013998117
  8. Cell Rep. 2020 Sep 08. pii: S2211-1247(20)31097-4. [Epub ahead of print]32(10): 108108
    Malic Enzyme Couples Mitochondria with Aerobic Glycolysis in Osteoblasts.
    Wen-Chih Lee, Xing Ji, Itzhak Nissim, Fanxin Long.
      The metabolic program of osteoblasts, the chief bone-making cells, remains incompletely understood. Here in murine calvarial cells, we establish that osteoblast differentiation under aerobic conditions is coupled with a marked increase in glucose consumption and lactate production but reduced oxygen consumption. As a result, aerobic glycolysis accounts for approximately 80% of the ATP production in mature osteoblasts. In vivo tracing with 13C-labeled glucose in the mouse shows that glucose in bone is readily metabolized to lactate but not organic acids in the TCA cycle. Glucose tracing in osteoblast cultures reveals that pyruvate is carboxylated to form malate integral to the malate-aspartate shuttle. RNA sequencing (RNA-seq) identifies Me2, encoding the mitochondrial NAD-dependent isoform of malic enzyme, as being specifically upregulated during osteoblast differentiation. Knockdown of Me2 markedly reduces the glycolytic flux and impairs osteoblast proliferation and differentiation. Thus, the mitochondrial malic enzyme functionally couples the mitochondria with aerobic glycolysis in osteoblasts.
    Keywords:  TCA cycle; aerobic glycolysis; bone; differentiation; malate-aspartate shuttle; malic enzyme; metabolic tracing; metabolism; mitochondria; osteoblast
    DOI:  https://doi.org/10.1016/j.celrep.2020.108108
  9. Dev Cell. 2020 Aug 31. pii: S1534-5807(20)30666-3. [Epub ahead of print]
    Selective Lysosome Membrane Turnover Is Induced by Nutrient Starvation.
    Chan Lee, Lilian Lamech, Eleanor Johns, Michael Overholtzer.
      Lysosome function is essential for cellular homeostasis, but quality-control mechanisms that maintain healthy lysosomes remain poorly characterized. Here, we developed a method to measure lysosome turnover and use this to identify a selective mechanism of membrane degradation that involves lipidation of the autophagy protein LC3 onto lysosomal membranes and the formation of intraluminal vesicles through microautophagy. This mechanism is induced in response to metabolic stress resulting from glucose starvation or by treatment with pharmacological agents that induce osmotic stress on lysosomes. Cells lacking ATG5, an essential component of the LC3 lipidation machinery, show reduced ability to regulate lysosome size and degradative capacity in response to activation of this mechanism. These findings identify a selective mechanism of lysosome membrane turnover that is induced by stress and uncover a function for LC3 lipidation in regulating lysosome size and activity through microautophagy.
    Keywords:  ATG5; LAP; LC3; ammonium; autophagy; glucose; glutamine; lysosome; metabolism; microautophagy
    DOI:  https://doi.org/10.1016/j.devcel.2020.08.008
  10. Redox Biol. 2020 Aug 26. pii: S2213-2317(20)30899-5. [Epub ahead of print]37 101694
    PER1 interaction with GPX1 regulates metabolic homeostasis under oxidative stress.
    Qi Sun, Yunxia Yang, Zhongqiu Wang, Xiao Yang, Yan Gao, Yang Zhao, Wenhao Ge, Junhao Liu, Xi Xu, Wei Guan, Dan Weng, Shiming Wang, Junsong Wang, Jianfa Zhang.
      Metabolism serves mammalian feeding and active behavior, and is controlled by circadian clock. The molecular mechanism by which clock factors regulate metabolic homeostasis under oxidative stress is unclear. Here, we have characterized that the daily oxygen consumption rhythm was deregulated in Per1 deficient mice. Per1 deficiency impaired daily mitochondrial dynamics and deregulated cellular GPx-related ROS fluctuations in the peripheral organs. We identified that PER1 enhanced GPx activity through PER1/GPX1 interaction in cytoplasm, consequently improving the oxidative phosphorylation efficiency of mitochondria. Per1 expression was specifically elevated in the fasting peripheral organs for protecting mitochondrial from oxidation stress. These observations reveal that Per1-driven mitochondrial dynamics is a critical effector mechanism for the regulation of mitochondrial function in response to oxidation stress.
    Keywords:  GPX1; Metabolic rhythm; Oxidation stress; PER1; ROS
    DOI:  https://doi.org/10.1016/j.redox.2020.101694
  11. IUBMB Life. 2020 Sep 11.
    The malate-aspartate shuttle (Borst cycle): How it started and developed into a major metabolic pathway.
    Piet Borst.
      This article presents a personal and critical review of the history of the malate-aspartate shuttle (MAS), starting in 1962 and ending in 2020. The MAS was initially proposed as a route for the oxidation of cytosolic NADH by the mitochondria in Ehrlich ascites cell tumor lacking other routes, and to explain the need for a mitochondrial aspartate aminotransferase (glutamate oxaloacetate transaminase 2 [GOT2]). The MAS was soon adopted in the field as a major pathway for NADH oxidation in mammalian tissues, such as liver and heart, even though the energetics of the MAS remained a mystery. Only in the 1970s, LaNoue and coworkers discovered that the efflux of aspartate from mitochondria, an essential step in the MAS, is dependent on the proton-motive force generated by the respiratory chain: for every aspartate effluxed, mitochondria take up one glutamate and one proton. This makes the MAS in practice uni-directional toward oxidation of cytosolic NADH, and explains why the free NADH/NAD ratio is much higher in the mitochondria than in the cytosol. The MAS is still a very active field of research. Most recently, the focus has been on the role of the MAS in tumors, on cells with defects in mitochondria and on inborn errors in the MAS. The year 2019 saw the discovery of two new inborn errors in the MAS, deficiencies in malate dehydrogenase 1 and in aspartate transaminase 2 (GOT2). This illustrates the vitality of ongoing MAS research.
    Keywords:  MAS; NADH/NAD ratio; aspartate; citrate-malate cycle; glycerol-1-P cycle; inborn errors; reductive carboxylation
    DOI:  https://doi.org/10.1002/iub.2367
  12. Anal Chem. 2020 Sep 09.
    Visualizing Subcellular Enrichment of Glycogen in Live Cancer Cells by Stimulated Raman Scattering.
    Dongkwan Lee, Jiajun Du, Rona Yu, Yapeng Su, James R Heath, Lu Wei.
      Glycogen, a branched glucose polymer, helps regulate glucose homeostasis through immediate storage and release of glucose. Re-programming of glycogen metabolism has recently been suggested to play an emerging role in cancer progression and tumorigene-sis. However, regulation of metabolic rewiring for glycogen synthesis and breakdown in cancer cells remains less understood. De-spite the availability of various glycogen detection methods, selective visualization of glycogen in living cells with high spatial resolution has proven to be highly challenging. Here, we present an optical imaging strategy to visualize glycogen in live cancer cells with minimal perturbation by combining stimulated Raman scattering microscopy with metabolic incorporation of deuterium-labeled glucose. We revealed the subcellular enrichment of glycogen in live cancer cells and achieved specific glycogen mapping through distinct spectral identification. Using our method, different glycogen metabolic phenotypes were characterized in a series of patient-derived BRAF-mutant melanoma cell-lines. Our results indicate that cell-lines manifesting high glycogen storage level showed increased tolerance to glucose deficiency among the studied melanoma phenotypes. Our method opens up the possibility for non-invasive study of complex glycogen metabolism at subcellular resolution and may help reveal new features of glycogen regulation in cancer systems.
    DOI:  https://doi.org/10.1021/acs.analchem.0c02348
  13. EMBO Rep. 2020 Sep 07. e50845
    Mitochondrial respiration is required to provide amino acids during fermentative proliferation of fission yeast.
    Michal Malecki, Stephan Kamrad, Markus Ralser, Jürg Bähler.
      When glucose is available, many organisms repress mitochondrial respiration in favour of aerobic glycolysis, or fermentation in yeast, that suffices for ATP production. Fission yeast cells, however, rely partially on respiration for rapid proliferation under fermentative conditions. Here, we determined the limiting factors that require respiratory function during fermentation. When inhibiting the electron transport chain, supplementation with arginine was necessary and sufficient to restore rapid proliferation. Accordingly, a systematic screen for mutants growing poorly without arginine identified mutants defective in mitochondrial oxidative metabolism. Genetic or pharmacological inhibition of respiration triggered a drop in intracellular levels of arginine and amino acids derived from the Krebs cycle metabolite alpha-ketoglutarate: glutamine, lysine and glutamic acid. Conversion of arginine into these amino acids was required for rapid proliferation when blocking the respiratory chain. The respiratory block triggered an immediate gene expression response diagnostic of TOR inhibition, which was muted by arginine supplementation or without the AMPK-activating kinase Ssp1. The TOR-controlled proteins featured biased composition of amino acids reflecting their shortage after respiratory inhibition. We conclude that respiration supports rapid proliferation in fermenting fission yeast cells by boosting the supply of Krebs cycle-derived amino acids.
    Keywords:   S. pombe ; arginine; cellular metabolism; fermentation; respiration
    DOI:  https://doi.org/10.15252/embr.202050845
  14. Cell Rep. 2020 Sep 08. pii: S2211-1247(20)31114-1. [Epub ahead of print]32(10): 108125
    Atf-6 Regulates Lifespan through ER-Mitochondrial Calcium Homeostasis.
    Kristopher Burkewitz, Gaomin Feng, Sneha Dutta, Charlotte A Kelley, Michael Steinbaugh, Erin J Cram, William B Mair.
      Individually, dysfunction of both the endoplasmic reticulum (ER) and mitochondria has been linked to aging, but how communication between these organelles might be targeted to promote longevity is unclear. Here, we provide evidence that, in Caenorhabditis elegans, inhibition of the conserved unfolded protein response (UPRER) mediator, activating transcription factor (atf)-6, increases lifespan by modulating calcium homeostasis and signaling to mitochondria. Atf-6 loss confers longevity via downregulation of the ER calcium buffer, calreticulin. ER calcium release via the inositol triphosphate receptor (IP3R/itr-1) is required for longevity, while IP3R/itr-1 gain of function is sufficient to extend lifespan. Highlighting coordination between organelles, the mitochondrial calcium import channel mcu-1 is also required for atf-6 longevity. IP3R inhibition leads to impaired mitochondrial bioenergetics and hyperfusion, which is sufficient to suppress long life in atf-6 mutants. This study reveals the importance of organellar calcium handling as a critical output for the UPRER in determining the quality of aging.
    Keywords:  InsP3R; UPR; aging; calreticulin; interorganelle communication; longevity
    DOI:  https://doi.org/10.1016/j.celrep.2020.108125
  15. Hypertens Res. 2020 Sep 11.
    Hypoxia-mediated regulation of mitochondrial transcription factors in renal epithelial cells: implications for hypertensive renal physiology.
    Bhargavi Natarajan, Vikas Arige, Abrar A Khan, S Santosh Reddy, Manoj K Barthwal, Nitish R Mahapatra.
      Kidneys have a high resting metabolic rate and low partial pressure of oxygen due to enhanced mitochondrial oxygen consumption and ATP production needed for active solute transport. Heightened mitochondrial activity leads to progressively increasing hypoxia from the renal cortex to the renal medulla. Renal hypoxia is prominent in hypertensive rats due to increased sodium reabsorption within the nephrons, which demands higher energy production by oxidative phosphorylation (OXPHOS). Consequently, spontaneously hypertensive rats (SHR) display greater oxygen deficiency (hypoxia) than normotensive Wistar Kyoto rats (WKY). Here, we sought to investigate the expression of key proteins for mitochondrial biogenesis in SHR and WKY, and study the regulation of mitochondrial transcription factors (mtTFs) under in vitro hypoxic conditions in renal epithelial cells. We report that renal expressions of hypoxia-inducible factor-1-alpha (HIF-1α), peroxisome proliferator-activated receptor-gamma coactivator-1-alpha (PGC-1α), mtTFs, and OXPHOS proteins are elevated in SHR compared to WKY. In addition, our experiments in cultured kidney cells demonstrate that acute hypoxia augments the expression of these genes. Furthermore, we show that the transcripts of HIF-1α and mtTFs are positively correlated in various human tissues. We reveal, for the first time to our knowledge, that HIF-1α transactivates mtTF genes by direct interaction with their promoters in rat kidney epithelial cells (NRK-52E) under acute hypoxia. Concomitant increases in the mitochondrial DNA and RNA, and OXPHOS proteins are observed. Taken together, this study suggests that hypoxia within the renal epithelial cells may enhance mitochondrial function to meet the energy demand in proximal tubular cells during prehypertensive stages in kidneys of young SHR.
    Keywords:  hypoxia; mitochondrial biogenesis; mitochondrial transcription factors; renal epithelial cells; spontaneously hypertensive rats
    DOI:  https://doi.org/10.1038/s41440-020-00539-4
  16. Genes Dev. 2020 Sep 10.
    AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation.
    Jeanine L Van Nostrand, Kristina Hellberg, En-Ching Luo, Eric L Van Nostrand, Alina Dayn, Jingting Yu, Maxim N Shokhirev, Yelena Dayn, Gene W Yeo, Reuben J Shaw.
      Despite being the frontline therapy for type 2 diabetes, the mechanisms of action of the biguanide drug metformin are still being discovered. In particular, the detailed molecular interplays between the AMPK and the mTORC1 pathway in the hepatic benefits of metformin are still ill defined. Metformin-dependent activation of AMPK classically inhibits mTORC1 via TSC/RHEB, but several lines of evidence suggest additional mechanisms at play in metformin inhibition of mTORC1. Here we investigated the role of direct AMPK-mediated serine phosphorylation of RAPTOR in a new Raptor AA mouse model, in which AMPK phospho-serine sites Ser722 and Ser792 of RAPTOR were mutated to alanine. Metformin treatment of primary hepatocytes and intact murine liver requires AMPK regulation of both RAPTOR and TSC2 to fully inhibit mTORC1, and this regulation is critical for both the translational and transcriptional response to metformin. Transcriptionally, AMPK and mTORC1 were both important for regulation of anabolic metabolism and inflammatory programs triggered by metformin treatment. The hepatic transcriptional response in mice on high-fat diet treated with metformin was largely ablated by AMPK deficiency under the conditions examined, indicating the essential role of this kinase and its targets in metformin action in vivo.
    Keywords:  AMPK; RAPTOR; STAT3; TSC2; mTOR; metformin
    DOI:  https://doi.org/10.1101/gad.339895.120
  17. Nat Commun. 2020 Sep 08. 11(1): 4496
    The precursor of PI(3,4,5)P3 alleviates aging by activating daf-18(Pten) and independent of daf-16.
    Dawei Shi, Xian Xia, Aoyuan Cui, Zhongxiang Xiong, Yizhen Yan, Jing Luo, Guoyu Chen, Yingying Zeng, Donghong Cai, Lei Hou, Joseph McDermott, Yu Li, Hong Zhang, Jing-Dong J Han.
      Aging is characterized by the loss of homeostasis and the general decline of physiological functions, accompanied by various degenerative diseases and increased rates of mortality. Aging targeting small molecule screens have been performed many times, however, few have focused on endogenous metabolic intermediates-metabolites. Here, using C. elegans lifespan assays, we conducted a worm metabolite screen and identified an eukaryotes conserved metabolite, myo-inositol (MI), to extend lifespan, increase mobility and reduce fat content. Genetic analysis of enzymes in MI metabolic pathway suggest that MI alleviates aging through its derivative PI(4,5)P2. MI and PI(4,5)P2 are precursors of PI(3,4,5)P3, which is negatively related to longevity. The longevity effect of MI is dependent on the tumor suppressor gene, daf-18 (homologous to mouse Pten), independent of its classical pathway downstream genes, akt or daf-16. Furthermore, we found MI effects on aging and lifespan act through mitophagy regulator PTEN induced kinase-1 (pink-1) and mitophagy. MI's anti-aging effect is also conserved in mouse, indicating a conserved mechanism in mammals.
    DOI:  https://doi.org/10.1038/s41467-020-18280-4
  18. iScience. 2020 Aug 20. pii: S2589-0042(20)30671-4. [Epub ahead of print]23(9): 101479
    Kinetic Trans-omic Analysis Reveals Key Regulatory Mechanisms for Insulin-Regulated Glucose Metabolism in Adipocytes.
    Satoshi Ohno, Lake-Ee Quek, James R Krycer, Katsuyuki Yugi, Akiyoshi Hirayama, Satsuki Ikeda, Futaba Shoji, Kumi Suzuki, Tomoyoshi Soga, David E James, Shinya Kuroda.
      Insulin regulates glucose metabolism through thousands of regulatory mechanisms; however, which regulatory mechanisms are keys to control glucose metabolism remains unknown. Here, we performed kinetic trans-omic analysis by integrating isotope-tracing glucose flux and phosphoproteomic data from insulin-stimulated adipocytes and built a kinetic mathematical model to identify key allosteric regulatory and phosphorylation events for enzymes. We identified nine reactions regulated by allosteric effectors and one by enzyme phosphorylation and determined the regulatory mechanisms for three of these reactions. Insulin stimulated glycolysis by promoting Glut4 activity by enhancing phosphorylation of AS160 at S595, stimulated fatty acid synthesis by promoting Acly activity through allosteric activation by glucose 6-phosphate or fructose 6-phosphate, and stimulated glutamate synthesis by alleviating allosteric inhibition of Gls by glutamate. Most of glycolytic reactions were regulated by amounts of substrates and products. Thus, phosphorylation or allosteric modulator-based regulation of only a few key enzymes was sufficient to change insulin-induced metabolism.
    Keywords:  Biological Sciences; Mathematical Biosciences; Metabolic Flux Analyisis; Metabolomics; Omics; Proteomics; Systems Biology
    DOI:  https://doi.org/10.1016/j.isci.2020.101479
  19. Cell Stem Cell. 2020 Aug 22. pii: S1934-5909(20)30360-X. [Epub ahead of print]
    Organoids Model Transcriptional Hallmarks of Oncogenic KRAS Activation in Lung Epithelial Progenitor Cells.
    Antonella F M Dost, Aaron L Moye, Marall Vedaie, Linh M Tran, Eileen Fung, Dar Heinze, Carlos Villacorta-Martin, Jessie Huang, Ryan Hekman, Julian H Kwan, Benjamin C Blum, Sharon M Louie, Samuel P Rowbotham, Julio Sainz de Aja, Mary E Piper, Preetida J Bhetariya, Roderick T Bronson, Andrew Emili, Gustavo Mostoslavsky, Gregory A Fishbein, William D Wallace, Kostyantyn Krysan, Steven M Dubinett, Jane Yanagawa, Darrell N Kotton, Carla F Kim.
      Mutant KRAS is a common driver in epithelial cancers. Nevertheless, molecular changes occurring early after activation of oncogenic KRAS in epithelial cells remain poorly understood. We compared transcriptional changes at single-cell resolution after KRAS activation in four sample sets. In addition to patient samples and genetically engineered mouse models, we developed organoid systems from primary mouse and human induced pluripotent stem cell-derived lung epithelial cells to model early-stage lung adenocarcinoma. In all four settings, alveolar epithelial progenitor (AT2) cells expressing oncogenic KRAS had reduced expression of mature lineage identity genes. These findings demonstrate the utility of our in vitro organoid approaches for uncovering the early consequences of oncogenic KRAS expression. This resource provides an extensive collection of datasets and describes organoid tools to study the transcriptional and proteomic changes that distinguish normal epithelial progenitor cells from early-stage lung cancer, facilitating the search for targets for KRAS-driven tumors.
    Keywords:  KRAS; alveolar; developmental programs; early-stage lung cancer; iPSC; loss of differentiation; organoid; single-cell RNA sequencing; stage IA lung adenocarcinoma; tumor progression
    DOI:  https://doi.org/10.1016/j.stem.2020.07.022
  20. J Cell Biol. 2020 Oct 05. pii: e202006111. [Epub ahead of print]219(10):
    FIT2 is an acyl-coenzyme A diphosphatase crucial for endoplasmic reticulum homeostasis.
    Michel Becuwe, Laura M Bond, Antonio F M Pinto, Sebastian Boland, Niklas Mejhert, Shane D Elliott, Marcelo Cicconet, Morven M Graham, Xinran N Liu, Olga Ilkayeva, Alan Saghatelian, Tobias C Walther, Robert V Farese.
      The endoplasmic reticulum is a cellular hub of lipid metabolism, coordinating lipid synthesis with continuous changes in metabolic flux. Maintaining ER lipid homeostasis despite these fluctuations is crucial to cell function and viability. Here, we identify a novel mechanism that is crucial for normal ER lipid metabolism and protects the ER from dysfunction. We identify the molecular function of the evolutionarily conserved ER protein FIT2 as a fatty acyl-coenzyme A (CoA) diphosphatase that hydrolyzes fatty acyl-CoA to yield acyl 4'-phosphopantetheine. This activity of FIT2, which is predicted to be active in the ER lumen, is required in yeast and mammalian cells for maintaining ER structure, protecting against ER stress, and enabling normal lipid storage in lipid droplets. Our findings thus solve the long-standing mystery of the molecular function of FIT2 and highlight the maintenance of optimal fatty acyl-CoA levels as key to ER homeostasis.
    DOI:  https://doi.org/10.1083/jcb.202006111
  21. Cell Death Dis. 2020 Sep 10. 11(9): 736
    Upregulation of CPT1A is essential for the tumor-promoting effect of adipocytes in colon cancer.
    Xiaopeng Xiong, Yang-An Wen, Rachelle Fairchild, Yekaterina Y Zaytseva, Heidi L Weiss, B Mark Evers, Tianyan Gao.
      Colon tumors grow in an adipose tissue-enriched microenvironment. Locally advanced colon cancers often invade into surrounding adipose tissue with a direct contact with adipocytes. We have previously shown that adipocytes promote tumor growth by modulating cellular metabolism. Here we demonstrate that carnitine palmitoyltransferase I (CPT1A), a key enzyme controlling fatty acid oxidation (FAO), was upregulated in colon cancer cells upon exposure to adipocytes or fatty acids. In addition, CPT1A expression was increased in invasive tumor cells within the adipose tissue compared to tumors without direct contact with adipocytes. Silencing CPT1A abolished the protective effect provided by fatty acids against nutrient deprivation and reduced tumor organoid formation in 3D culture and the expression of genes associated with cancer stem cells downstream of Wnt/β-catenin. Mechanistically, CPT1A-dependent FAO promoted the acetylation and nuclear translocation of β-catenin. Furthermore, knockdown of CPT1A blocked the tumor-promoting effect of adipocytes in vivo and inhibited xenograft tumor initiation. Taken together, our findings identify CPT1A-depedent FAO as an essential metabolic pathway that enables the interaction between adipocytes and colon cancer cells.
    DOI:  https://doi.org/10.1038/s41419-020-02936-6
  22. Microb Cell. 2020 Jun 30. 7(9): 234-249
    Systematic analysis of nuclear gene function in respiratory growth and expression of the mitochondrial genome in S. cerevisiae.
    Maria Stenger, Duc Tung Le, Till Klecker, Benedikt Westermann.
      The production of metabolic energy in form of ATP by oxidative phosphorylation depends on the coordinated action of hundreds of nuclear-encoded mitochondrial proteins and a handful of proteins encoded by the mitochondrial genome (mtDNA). We used the yeast Saccharomyces cerevisiae as a model system to systematically identify the genes contributing to this process. Integration of genome-wide high-throughput growth assays with previously published large data sets allowed us to define with high confidence a set of 254 nuclear genes that are indispensable for respiratory growth. Next, we induced loss of mtDNA in the yeast deletion collection by growth on ethidium bromide-containing medium and identified twelve genes that are essential for viability in the absence of mtDNA (i.e. petite-negative). Replenishment of mtDNA by cytoduction showed that respiratory-deficient phenotypes are highly variable in many yeast mutants. Using a mitochondrial genome carrying a selectable marker, ARG8 m , we screened for mutants that are specifically defective in maintenance of mtDNA and mitochondrial protein synthesis. We found that up to 176 nuclear genes are required for expression of mitochondria-encoded proteins during fermentative growth. Taken together, our data provide a comprehensive picture of the molecular processes that are required for respiratory metabolism in a simple eukaryotic cell.
    Keywords:  mitochondria; mitochondrial DNA; oxidative phosphorylation; petite mutant; yeast
    DOI:  https://doi.org/10.15698/mic2020.09.729
  23. Dis Model Mech. 2020 Sep 11. pii: dmm.047134. [Epub ahead of print]
    Ammonia inhibits energy metabolism in astrocytes in a rapid and glutamate dehydrogenase 2-dependent manner.
    Leonie Drews, Marcel Zimmermann, Philipp Westhoff, Dominik Brilhaus, Rebecca E Poss, Laura Bergmann, Constanze Wiek, Peter Brenneisen, Roland P Piekorz, Tabea Mettler-Altmann, Andreas P M Weber, Andreas S Reichert.
      Astrocyte dysfunction is a primary factor in hepatic encephalopathy (HE) impairing neuronal activity under hyperammonemia. In particular the early events causing ammonia-induced toxicity to astrocytes are not well understood. Using established cellular HE models, we show that mitochondria rapidly undergo fragmentation in a reversible manner upon hyperammonemia. Further, within a timescale of minutes mitochondrial respiration and glycolysis were hampered which occurred in a pH-independent manner. Using metabolomics an accumulation of numerous amino acids, including branched chain amino acids and glucose was observed. Metabolomic tracking of 15N-labeled ammonia showed rapid incorporation of 15N into glutamate and glutamate-derived amino acids. Downregulating human GLUD2, encoding mitochondrial glutamate dehydrogenase 2 (GDH2), inhibiting GDH2 activity by SIRT4 overexpression, and supplementing cells with glutamate or glutamine alleviated ammonia-induced inhibition of mitochondrial respiration. Metabolomic tracking of 13C-glutamine showed that hyperammonemia can inhibit anaplerosis of TCA-cycle intermediates. Contrary to its classical anaplerotic role, we show that under hyperammonemia GDH2 rather catalyzes the removal of ammonia by reductive amination of α-ketoglutarate which efficiently and rapidly inhibits the TCA-cycle. Overall, we propose a critical GDH2-dependent mechanism in HE models that on the one hand helps to remove ammonia but on the other hand impairs energy metabolism in mitochondria rapidly.
    Keywords:  Brain energy metabolism; Glutamate dehydrogenase; Hepatic encephalopathy; Hyperammonemia; Mitochondria; TCA-cycle
    DOI:  https://doi.org/10.1242/dmm.047134
  24. Biochem J. 2020 Sep 08. pii: BCJ20200240. [Epub ahead of print]
    Three cytosolic NAD-malate dehydrogenase isoforms of Arabidopsis thaliana: On the crossroad between energy fluxes and redox signaling.
    Aleksandra Liszka, Regina Schimpf, Krupskaya Ivannova Cartuche Zaruma, Annika Buhr, Thorsten Seidel, Stefan Walter, Johannes Knuesting, Anna Dreyer, Karl-Josef Dietz, Renate Scheibe, Jennifer Selinski.
      In yeast and animal cells, mitochondrial disturbances resulting from imbalances in the respiratory chain require malate dehydrogenase (MDH) activities for re-directing fluxes of reducing equivalents. In plants, in addition to mitochondria, plastids use malate valves to counterbalance and maintain redox-homeostasis. Arabidopsis expresses three cytosolic MDH isoforms, namely cyMDH1, cyMDH2, and cyMDH3, the latter possessing an N-terminal extension carrying a unique cysteine residue C2. In this study, redox-effects on activity and structure of all three cyMDH isoforms were analyzed in vitro. cyMDH1 and cyMDH2 were reversibly inactivated by diamide treatment, accompanied by dimerization via disulfide-bridge formation. In contrast, cyMDH3 forms dimers and higher oligomers upon oxidation, but its low specific activity is redox-independent. In the presence of glutathione, cyMDH1 and cyMDH2 are protected from dimerization and inactivation. In contrast, cyMDH3 still dimerizes but does not form oligomers any longer. From analyses of single and double cysteine mutants and structural modeling of cyMDH3, we conclude that the presence of C2 and C336 allows for multiple cross-links in the higher molecular weight complexes comprising disulfides within the dimer as well as between monomers of two different dimers. Furthermore, nuclear localization of cyMDH isoforms was significantly increased under oxidizing conditions in isolated Arabidopsis protoplasts, in particular of isoform cyMDH3. The unique cyMDH3 C2-C2-linked dimer is, therefore, a good candidate as a redox-sensor taking over moonlighting functions upon disturbances of energy metabolism, as shown previously for the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase (GAPDH) where oxidative modification of the sensitive catalytic cysteine residues induces nuclear translocation.
    Keywords:  Arabidopsis thaliana; S-glutathionylation; energy metabolism; malate dehydrogenase; redox signalling; small molecules
    DOI:  https://doi.org/10.1042/BCJ20200240
  25. Mech Ageing Dev. 2020 Sep 03. pii: S0047-6374(20)30141-X. [Epub ahead of print] 111345
    Mitochondrial biogenesis in organismal senescence and neurodegeneration.
    Ioanna Daskalaki, Nektarios Tavernarakis.
      Mitochondrial biogenesis is indispensable for organismal homeostasis. The semi-autonomous nature of mitochondria makes their biogenesis rather complex, as it requires the contribution of the nucleus, the cytoplasm and the organelle itself. Recently, several transcription regulators, RNA binding proteins and outer mitochondrial membrane (OMM) components have been implicated in the regulation of the process. Both the expression and the abundance of several of these factors are altered during ageing, and their impairment can have diverse, yet principally detrimental, effects on lifespan. These findings converge on the notion that mitochondrial biogenesis is an age-modulated process that, when perturbed, compromises survival. Notably, core brain functions are dependent on mitochondrial metabolite availability. Indeed, emerging evidence indicates that mitochondrial biogenesis regulators play important roles in the onset and progression of severe neurodegenerative syndromes such as AD, PD and HD. These devastating human pathologies remain incurable to date. A better understanding of the mechanisms that govern mitochondrial biogenesis could facilitate the development of effective pharmaceutical interventions against these diseases.
    Keywords:  Ageing; Mitochondrial biogenesis; Neurodegeneration; Organismal Senescence; Transcription factor; mRNA translation
    DOI:  https://doi.org/10.1016/j.mad.2020.111345
  26. Sci Rep. 2020 Sep 08. 10(1): 14777
    GFP fluorescence tagging alters dynamin-related protein 1 oligomerization dynamics and creates disassembly-refractory puncta to mediate mitochondrial fission.
    Felipe Montecinos-Franjola, Brianna L Bauer, Jason A Mears, Rajesh Ramachandran.
      Green fluorescent protein (GFP)-tagging is the prevalent strategy to monitor protein dynamics in living cells. However, the consequences of appending the bulky GFP moiety to the protein of interest are rarely investigated. Here, using a powerful combination of quantitative fluorescence spectroscopic and imaging techniques, we have examined the oligomerization dynamics of the GFP-tagged mitochondrial fission GTPase dynamin-related protein 1 (Drp1) both in vitro and in vivo. We find that GFP-tagged Drp1 exhibits impaired oligomerization equilibria in solution that corresponds to a greatly diminished cooperative GTPase activity in comparison to native Drp1. Consequently, GFP-tagged Drp1 constitutes aberrantly stable, GTP-resistant supramolecular assemblies both in vitro and in vivo, neither of which reflects a more dynamic native Drp1 oligomerization state. Indeed, GFP-tagged Drp1 is detected more frequently per unit length over mitochondria in Drp1-null mouse embryonic fibroblasts (MEFs) compared to wild-type (wt) MEFs, indicating that the drastically reduced GTP turnover restricts oligomer disassembly from the mitochondrial surface relative to mixed oligomers comprising native and GFP-tagged Drp1. Yet, GFP-tagged Drp1 retains the capacity to mediate membrane constriction in vitro and mitochondrial division in vivo. These findings suggest that instead of robust assembly-disassembly dynamics, persistent Drp1 higher-order oligomerization over membranes is sufficient for mitochondrial fission.
    DOI:  https://doi.org/10.1038/s41598-020-71655-x
  27. Cells. 2020 Sep 05. pii: E2035. [Epub ahead of print]9(9):
    Metabolic Potential of Cancer Cells in Context of the Metastatic Cascade.
    Mohaned Benzarti, Catherine Delbrouck, Laura Neises, Nicole Kiweler, Johannes Meiser.
      The metastatic cascade is a highly plastic and dynamic process dominated by cellular heterogeneity and varying metabolic requirements. During this cascade, the three major metabolic pillars, namely biosynthesis, RedOx balance, and bioenergetics, have variable importance. Biosynthesis has superior significance during the proliferation-dominated steps of primary tumour growth and secondary macrometastasis formation and only minor relevance during the growth-independent processes of invasion and dissemination. Consequently, RedOx homeostasis and bioenergetics emerge as conceivable metabolic key determinants in cancer cells that disseminate from the primary tumour. Within this review, we summarise our current understanding on how cancer cells adjust their metabolism in the context of different microenvironments along the metastatic cascade. With the example of one-carbon metabolism, we establish a conceptual view on how the same metabolic pathway can be exploited in different ways depending on the current cellular needs during metastatic progression.
    Keywords:  ROS; RedOx balance; bioenergetics; biosynthesis; cancer metabolism; hypoxia; metabolic plasticity; metastasis; one-carbon metabolism; tumour microenvironment
    DOI:  https://doi.org/10.3390/cells9092035
  28. Cell Metab. 2020 Aug 31. pii: S1550-4131(20)30424-1. [Epub ahead of print]
    Glutamine Metabolism Controls Stem Cell Fate Reversibility and Long-Term Maintenance in the Hair Follicle.
    Christine S Kim, Xiaolei Ding, Kira Allmeroth, Leah C Biggs, Olivia I Kolenc, Nina L'Hoest, Carlos Andrés Chacón-Martínez, Christian Edlich-Muth, Patrick Giavalisco, Kyle P Quinn, Martin S Denzel, Sabine A Eming, Sara A Wickström.
      Stem cells reside in specialized niches that are critical for their function. Upon activation, hair follicle stem cells (HFSCs) exit their niche to generate the outer root sheath (ORS), but a subset of ORS progeny returns to the niche to resume an SC state. Mechanisms of this fate reversibility are unclear. We show that the ability of ORS cells to return to the SC state requires suppression of a metabolic switch from glycolysis to oxidative phosphorylation and glutamine metabolism that occurs during early HFSC lineage progression. HFSC fate reversibility and glutamine metabolism are regulated by the mammalian target of rapamycin complex 2 (mTORC2)-Akt signaling axis within the niche. Deletion of mTORC2 results in a failure to re-establish the HFSC niche, defective hair follicle regeneration, and compromised long-term maintenance of HFSCs. These findings highlight the importance of spatiotemporal control of SC metabolic states in organ homeostasis.
    Keywords:  Akt; Hif1; cell fate; glutamine; hair follicle; hypoxia; mTOR; mTORC2; metabolism; stem cell
    DOI:  https://doi.org/10.1016/j.cmet.2020.08.011
  29. Redox Biol. 2020 Aug 27. pii: S2213-2317(20)30907-1. [Epub ahead of print]37 101702
    NRF2 regulates the sensitivity of human NSCLC cells to cystine deprivation-induced ferroptosis via FOCAD-FAK signaling pathway.
    Pengfei Liu, Di Wu, Jinyue Duan, Hexin Xiao, Yulai Zhou, Lei Zhao, Yetong Feng.
      Transcription factor nuclear factor-erythroid 2-like 2 (NRF2) mainly regulates cellular antioxidant response, redox homeostasis and metabolic balance. Our previous study illustrated the translational significance of NRF2-mediated transcriptional repression, and the transcription of FOCAD gene might be negatively regulated by NRF2. However, the detailed mechanism and the related significance remain unclear. In this study, we mainly explored the effect of NRF2-FOCAD signaling pathway on ferroptosis regulation in human non-small-cell lung carcinoma (NSCLC) model. Our results confirmed the negative regulation relationship between NRF2 and FOCAD, which was dependent on NRF2-Replication Protein A1 (RPA1)-Antioxidant Response Elements (ARE) complex. In addition, FOCAD promoted the activity of focal adhesion kinase (FAK), which further enhanced the sensitivity of NSCLC cells to cysteine deprivation-induced ferroptosis via promoting the tricarboxylic acid (TCA) cycle and the activity of Complex I in mitochondrial electron transport chain (ETC). However, FOCAD didn't affect GPX4 inhibition-induced ferroptosis. Moreover, the treatment with the combination of NRF2 inhibitor (brusatol) and erastin showed better therapeutic action against NSCLC in vitro and in vivo than single treatment, and the improved therapeutic function partially depended on the activation of FOCAD-FAK signal. Taken together, our study indicates the close association of NRF2-FOCAD-FAK signaling pathway with cysteine deprivation-induced ferroptosis, and elucidates a novel insight into the ferroptosis-based therapeutic approach for the patients with NSCLC.
    Keywords:  FAK; FOCAD; Ferroptosis; Mitochondria; NRF2; NSCLC
    DOI:  https://doi.org/10.1016/j.redox.2020.101702
  30. Elife. 2020 Sep 11. pii: e59686. [Epub ahead of print]9
    Dichotomous role of the human mitochondrial Na+/Ca2+/Li+ exchanger NCLX in colorectal cancer growth and metastasis.
    Trayambak Pathak, Maxime Gueguinou, Vonn Walter, Celine Delierneux, Martin T Johnson, Xuexin Zhang, Ping Xin, Ryan E Yoast, Scott M Emrich, Gregory R Yochum, Israel Sekler, Walter A Koltun, Donald L Gill, Nadine Hempel, Mohamed Trebak.
      Despite the established role of mitochondria in cancer, the mechanisms by which mitochondrial Ca2+ (mtCa2+) regulates tumorigenesis remain incompletely understood. The crucial role of mtCa2+ in tumorigenesis is highlighted by altered expression of proteins mediating mtCa2+ uptake and extrusion in cancer. Here, we demonstrate decreased expression of the mitochondrial Na+/Ca2+/Li+ exchanger NCLX (SLC8B1) in human colorectal tumors and its association with advanced-stage disease in patients. Downregulation of NCLX causes mtCa2+ overload, mitochondrial depolarization, decreased expression of cell-cycle genes and reduced tumor size in xenograft and spontaneous colorectal cancer mouse models. Concomitantly, NCLX downregulation drives metastatic spread, chemoresistance, and expression of epithelial-to-mesenchymal, hypoxia, and stem cell pathways. Mechanistically, mtCa2+ overload leads to increased mitochondrial reactive oxygen species, which activate HIF1α signaling supporting metastasis of NCLX-null tumor cells. Thus, loss of NCLX is a novel driver of metastasis, indicating that regulation of mtCa2+ is a novel therapeutic approach in metastatic colorectal cancer.
    Keywords:  human; molecular biophysics; mouse; structural biology
    DOI:  https://doi.org/10.7554/eLife.59686
  31. Cell Death Dis. 2020 Sep 05. 11(9): 722
    Membrane-tethering of cytochrome c accelerates regulated cell death in yeast.
    Alexandra Toth, Andreas Aufschnaiter, Olga Fedotovskaya, Hannah Dawitz, Pia Ädelroth, Sabrina Büttner, Martin Ott.
      Intrinsic apoptosis as a modality of regulated cell death is intimately linked to permeabilization of the outer mitochondrial membrane and subsequent release of the protein cytochrome c into the cytosol, where it can participate in caspase activation via apoptosome formation. Interestingly, cytochrome c release is an ancient feature of regulated cell death even in unicellular eukaryotes that do not contain an apoptosome. Therefore, it was speculated that cytochrome c release might have an additional, more fundamental role for cell death signalling, because its absence from mitochondria disrupts oxidative phosphorylation. Here, we permanently anchored cytochrome c with a transmembrane segment to the inner mitochondrial membrane of the yeast Saccharomyces cerevisiae, thereby inhibiting its release from mitochondria during regulated cell death. This cytochrome c retains respiratory growth and correct assembly of mitochondrial respiratory chain supercomplexes. However, membrane anchoring leads to a sensitisation to acetic acid-induced cell death and increased oxidative stress, a compensatory elevation of cellular oxygen-consumption in aged cells and a decreased chronological lifespan. We therefore conclude that loss of cytochrome c from mitochondria during regulated cell death and the subsequent disruption of oxidative phosphorylation is not required for efficient execution of cell death in yeast, and that mobility of cytochrome c within the mitochondrial intermembrane space confers a fitness advantage that overcomes a potential role in regulated cell death signalling in the absence of an apoptosome.
    DOI:  https://doi.org/10.1038/s41419-020-02920-0
  32. J Biol Chem. 2020 Sep 08. pii: jbc.RA119.012056. [Epub ahead of print]
    Exploitation of DHODH and p53 activation as therapeutic targets - a case study in polypharmacology.
    Marcus J G W Ladds, Gergana Popova, Andrés Pastor-Fernández, Srinivasaraghavan Kannan, Ingeborg M M van Leeuwen, Maria Håkansson, Björn Walse, Fredrik Tholander, Ravi Bhatia, Chandra S Verma, David P Lane, Sonia Laín.
      The tenovins are a frequently studied class of compounds capable of inhibiting sirtuin activity, which is thought to result in increased acetylation and protection of the tumor suppressor p53 from degradation. However, as we and other laboratories have shown previously, certain tenovins are also capable of inhibiting autophagic flux, demonstrating the ability of these compounds to engage with more than one target. In this study we present two additional mechanisms by which tenovins are able to activate p53 and kill tumor cells in culture. These mechanisms are the inhibition of a key enzyme of the de novo pyrimidine synthesis pathway, DHODH, and the blockage of uridine transport into cells. These findings hold a three-fold significance; firstly, we demonstrate that tenovins, and perhaps other compounds that activate p53, may activate p53 by more than one mechanism; secondly, that work previously conducted with certain tenovins as SirT1 inhibitors should additionally be viewed through the lens of DHODH inhibition as this is a major contributor to the mechanism of action of the most widely used tenovins; and finally, that small changes in the structure of a small molecule can lead to a dramatic change in the target profile of the molecule even when the phenotypic readout remains static.
    Keywords:  cell death; mitochondria; molecular modeling; molecular pharmacology; nucleoside/nucleotide biosynthesis; nucleoside/nucleotide transport; p53; tumor cell biology
    DOI:  https://doi.org/10.1074/jbc.RA119.012056
  33. Biochim Biophys Acta Bioenerg. 2020 Sep 08. pii: S0005-2728(20)30155-9. [Epub ahead of print] 148305
    Protein crowding in the inner mitochondrial membrane.
    Michael Schlame.
      The inner membrane of mitochondria is known for its low lipid-to-protein ratio. Calculations based on the size and the concentration of the principal membrane components, suggest about half of the hydrophobic volume of the membrane is occupied by proteins. Such high degree of crowding is expected to strain the hydrophobic coupling between proteins and lipids unless stabilizing mechanisms are in place. Both protein supercomplexes and cardiolipin are likely to be critical for the integrity of the inner mitochondrial membrane because they reduce the energy penalty of crowding.
    Keywords:  cardiolipin; lipids; membrane; mitochondria; protein
    DOI:  https://doi.org/10.1016/j.bbabio.2020.148305
  34. Nature. 2020 Sep 09.
    Adaptable haemodynamic endothelial cells for organogenesis and tumorigenesis.
    Brisa Palikuqi, Duc-Huy T Nguyen, Ge Li, Ryan Schreiner, Alessandro F Pellegata, Ying Liu, David Redmond, Fuqiang Geng, Yang Lin, Jesus M Gómez-Salinero, Masataka Yokoyama, Paul Zumbo, Tuo Zhang, Balvir Kunar, Mavee Witherspoon, Teng Han, Alfonso M Tedeschi, Federico Scottoni, Steven M Lipkin, Lukas Dow, Olivier Elemento, Jenny Z Xiang, Koji Shido, Jason R Spence, Qiao J Zhou, Robert E Schwartz, Paolo De Coppi, Sina Y Rabbany, Shahin Rafii.
      Endothelial cells adopt tissue-specific characteristics to instruct organ development and regeneration1,2. This adaptability is lost in cultured adult endothelial cells, which do not vascularize tissues in an organotypic manner. Here, we show that transient reactivation of the embryonic-restricted ETS variant transcription factor 2 (ETV2)3 in mature human endothelial cells cultured in a serum-free three-dimensional matrix composed of a mixture of laminin, entactin and type-IV collagen (LEC matrix) 'resets' these endothelial cells to adaptable, vasculogenic cells, which form perfusable and plastic vascular plexi. Through chromatin remodelling, ETV2 induces tubulogenic pathways, including the activation of RAP1, which promotes the formation of durable lumens4,5. In three-dimensional matrices-which do not have the constraints of bioprinted scaffolds-the 'reset' vascular endothelial cells (R-VECs) self-assemble into stable, multilayered and branching vascular networks within scalable microfluidic chambers, which are capable of transporting human blood. In vivo, R-VECs implanted subcutaneously in mice self-organize into durable pericyte-coated vessels that functionally anastomose to the host circulation and exhibit long-lasting patterning, with no evidence of malformations or angiomas. R-VECs directly interact with cells within three-dimensional co-cultured organoids, removing the need for the restrictive synthetic semipermeable membranes that are required for organ-on-chip systems, therefore providing a physiological platform for vascularization, which we call 'Organ-On-VascularNet'. R-VECs enable perfusion of glucose-responsive insulin-secreting human pancreatic islets, vascularize decellularized rat intestines and arborize healthy or cancerous human colon organoids. Using single-cell RNA sequencing and epigenetic profiling, we demonstrate that R-VECs establish an adaptive vascular niche that differentially adjusts and conforms to organoids and tumoroids in a tissue-specific manner. Our Organ-On-VascularNet model will permit metabolic, immunological and physiochemical studies and screens to decipher the crosstalk between organotypic endothelial cells and parenchymal cells for identification of determinants of endothelial cell heterogeneity, and could lead to advances in therapeutic organ repair and tumour targeting.
    DOI:  https://doi.org/10.1038/s41586-020-2712-z
  35. Genes Dev. 2020 Sep 10.
    Yap/Taz promote the scavenging of extracellular nutrients through macropinocytosis.
    Bryan King, Jingwen Araki, Wilhelm Palm, Craig B Thompson.
      The uptake of macromolecules and cellular debris through macropinocytosis has emerged as an important nutrient acquisition strategy of cancer cells. Genetic alterations commonly found in human cancers (e.g. mutations in KRAS or loss of PTEN) have been shown to increase macropinocytosis. To identify additional effectors that enable cell growth dependent on the uptake of extracellular proteins, pancreatic ductal adenocarcinoma (PDA) cells were selected for growth in medium where extracellular albumin was the obligate source of the essential amino acid leucine. Analysis of global changes in chromatin availability and gene expression revealed that PDA cells selected under these conditions exhibited elevated activity of the transcriptional activators Yap/Taz. Knockout of Yap/Taz prevented growth of PDA cells in leucine-deficient medium, but not in complete medium. Furthermore, constitutively active forms of Yap or Taz were sufficient to stimulate macropinocytosis of extracellular protein. In addition to promoting the uptake of plasma proteins, Yap/Taz also promoted the scavenging of apoptotic cell bodies and necrotic debris by PDA cells. The Yap/Taz transcriptional target Axl was found to be essential for cell growth dependent on the uptake of dead cells and cell debris. Together, these studies suggest that the Hippo pathway effectors Yap and Taz are important transcriptional regulators of endocytic nutrient uptake.
    Keywords:  Yap; cancer metabolism; macropinocytosis
    DOI:  https://doi.org/10.1101/gad.340661.120
  36. Rev Physiol Biochem Pharmacol. 2020 Sep 08.
    Ion Channels in Cancer: Orchestrators of Electrical Signaling and Cellular Crosstalk.
    Jerry J Fan, Xi Huang.
      Ion channels are pore-forming transmembrane proteins that govern ion flux to regulate a myriad of biological processes in development, physiology, and disease. Across various types of cancer, ion channel expression and activity are often dysregulated. We review the contribution of ion channels to multiple stages of tumorigenesis based on data from in vivo model systems. As intertumoral and intratumoral heterogeneities are major obstacles in developing effective therapies, we provide perspectives on how ion channels in tumor cells and their microenvironment represent targetable vulnerabilities in the areas of tumor-stromal cell interactions, cancer neuroscience, and cancer mechanobiology.
    Keywords:  Bioelectrical signaling; Cancer; Ion channels; Mechanobiology; Membrane potential; Metastasis; Tumor heterogeneity; Tumor initiation; Tumor microenvironment; Tumor progression
    DOI:  https://doi.org/10.1007/112_2020_48
  37. JCSM Rapid Commun. 2020 Jul-Dec;3(2):3(2): 56-69
    The wasting-associated metabolite succinate disrupts myogenesis and impairs skeletal muscle regeneration.
    Paige C Arneson, Kelly A Hogan, Alexandra M Shin, Adrienne Samani, Aminah Jatoi, Jason D Doles.
      Background: Muscle wasting is a debilitating co-morbidity affecting most advanced cancer patients. Alongside enhanced muscle catabolism, defects in muscle repair/regeneration contribute to cancer-associated wasting. Among the factors implicated in suppression of muscle regeneration are cytokines that interfere with myogenic signal transduction pathways. Less understood is how other cancer/wasting-associated cues, such as metabolites, contribute to muscle dysfunction. This study investigates how the metabolite succinate affects myogenesis and muscle regeneration.Methods: We leveraged an established ectopic metabolite treatment (cell permeable dimethyl-succinate) strategy to evaluate the ability of intracellular succinate elevation to 1) affect myoblast homeostasis (proliferation, apoptosis), 2) disrupt protein dynamics and induce wasting-associated atrophy, and 3) modulate in vitro myogenesis. In vivo succinate supplementation experiments (2% succinate, 1% sucrose vehicle) were used to corroborate and extend in vitro observations. Metabolic profiling and functional metabolic studies were then performed to investigate the impact of succinate elevation on mitochondria function.
    Results: We found that in vitro succinate supplementation elevated intracellular succinate about 2-fold, and did not have an impact on proliferation or apoptosis of C2C12 myoblasts. Elevated succinate had minor effects on protein homeostasis (~25% decrease in protein synthesis assessed by OPP staining), and no significant effect on myotube atrophy. Succinate elevation interfered with in vitro myoblast differentiation, characterized by significant decreases in late markers of myogenesis and fewer nuclei per myosin heavy chain positive structure (assessed by immunofluorescence staining). While mice orally administered succinate did not exhibit changes in overall body composition or whole muscle weights, these mice displayed smaller muscle myofiber diameters (~6% decrease in the mean of non-linear regression curves fit to the histograms of minimum feret diameter distribution), which was exacerbated when muscle regeneration was induced with barium chloride injury. Significant decreases in the mean of non-linear regression curves fit to the histograms of minimum feret diameter distributions were observed 7 days and 28 days post injury. Elevated numbers of myogenin positive cells (3-fold increase) supportive of the differentiation defects observed in vitro were observed 28 days post injury. Metabolic profiling and functional metabolic assessment of myoblasts revealed that succinate elevation caused both widespread metabolic changes and significantly lowered maximal cellular respiration (~35% decrease).
    Conclusions: This study broadens the repertoire of wasting-associated factors that can directly modulate muscle progenitor cell function and strengthens the hypothesis that metabolic derangements are significant contributors to impaired muscle regeneration, an important aspect of cancer-associated muscle wasting.
    Keywords:  Muscle wasting; myogenesis; skeletal muscle; succinate
    DOI:  https://doi.org/10.1002/rco2.14
  38. Nature. 2020 Sep 10.
    Structural mechanism of cGAS inhibition by the nucleosome.
    Ganesh R Pathare, Alexiane Decout, Selene Glück, Simone Cavadini, Kristina Makasheva, Ruud Hovius, Georg Kempf, Joscha Weiss, Zuzanna Kozicka, Baptiste Guey, Pauline Melenec, Beat Fierz, Nicolas H Thomä, Andrea Ablasser.
      The DNA sensor cGAS initiates innate immune responses following microbial infection, cellular stress, and cancer1. Upon activation by double-stranded DNA, cytosolic cGAS produces 2'3' cyclic GMP-AMP and triggers inflammatory cytokine and type I interferon (IFN) induction2-7. cGAS is also present inside the cell nucleus replete with genomic DNA8, where chromatin has been implicated in restricting its enzymatic activity9. However, the structural basis for cGAS inhibition by chromatin has remained unknown. Here we present the cryo-electron microscopy structure of human cGAS bound to nucleosomes at 3.1 Å resolution. cGAS makes extensive contacts with both the acidic patch of the histone H2A-H2B heterodimer and nucleosomal DNA. The structural and complementary biochemical analysis also finds cGAS engaged to a second nucleosome in trans. Mechanistically, nucleosome binding locks cGAS in a monomeric state, in which steric hindrance suppresses spurious activation by genomic DNA. We find that mutations to the cGAS-acidic patch interface are necessary and sufficient to abolish the inhibitory effect of nucleosomes in vitro and to unleash cGAS activity on genomic DNA in living cells. Our work uncovers the structural basis of cGAS interaction with chromatin and defines a compelling mechanism that permits self-nonself discrimination of genomic DNA by cGAS.
    DOI:  https://doi.org/10.1038/s41586-020-2750-6
  39. PLoS One. 2020 ;15(9): e0237981
    Cancer proteome and metabolite changes linked to SHMT2.
    Jiefei Tong, Jonathan R Krieger, Paul Taylor, Rick Bagshaw, Jae Kang, Swathi Jeedigunta, Leanne E Wybenga-Groot, Wen Zhang, Heba Badr, Shideh Mirhadi, Nhu-An Pham, Étienne Coyaud, Man Yu, Ming Li, Michael Cabanero, Brian Raught, Jason T Maynes, Cynthia Hawkins, Ming Sound Tsao, Michael F Moran.
      Serine hydroxymethyltransferase 2 (SHMT2) converts serine plus tetrahydrofolate (THF) into glycine plus methylene-THF and is upregulated at the protein level in lung and other cancers. In order to better understand the role of SHMT2 in cancer a model system of HeLa cells engineered for inducible over-expression or knock-down of SHMT2 was characterized for cell proliferation and changes in metabolites and proteome as a function of SHMT2. Ectopic over-expression of SHMT2 increased cell proliferation in vitro and tumor growth in vivo. Knockdown of SHMT2 expression in vitro caused a state of glycine auxotrophy and accumulation of phosphoribosylaminoimidazolecarboxamide (AICAR), an intermediate of folate/1-carbon-pathway-dependent de novo purine nucleotide synthesis. Decreased glycine in the HeLa cell-based xenograft tumors with knocked down SHMT2 was potentiated by administration of the anti-hyperglycinemia agent benzoate. However, tumor growth was not affected by SHMT2 knockdown with or without benzoate treatment. Benzoate inhibited cell proliferation in vitro, but this was independent of SHMT2 modulation. The abundance of proteins of mitochondrial respiration complexes 1 and 3 was inversely correlated with SHMT2 levels. Proximity biotinylation in vivo (BioID) identified 48 mostly mitochondrial proteins associated with SHMT2 including the mitochondrial enzymes Acyl-CoA thioesterase (ACOT2) and glutamate dehydrogenase (GLUD1) along with more than 20 proteins from mitochondrial respiration complexes 1 and 3. These data provide insights into possible mechanisms through which elevated SHMT2 in cancers may be linked to changes in metabolism and mitochondrial function.
    DOI:  https://doi.org/10.1371/journal.pone.0237981
  40. Nature. 2020 Sep 10.
    Structural basis for sequestration and autoinhibition of cGAS by chromatin.
    Sebastian Michalski, Carina C de Oliveira Mann, Che Stafford, Gregor Witte, Joseph Bartho, Katja Lammens, Veit Hornung, Karl-Peter Hopfner.
      cGAS (cyclic GMP-AMP synthase) is an innate immune sensor for cytosolic microbial DNA1. Upon binding DNA, it synthesizes the messenger cGAMP (2'3' cyclic GMP-AMP)2-4, which triggers cell-autonomous defense and the production of type I interferons and pro-inflammatory cytokines via activation of STING5. Besides responding to cytosolic microbial DNA, cGAS also recognizes mis-localized cytosolic self-DNA and is implicated in autoimmunity and sterile inflammation6,7. Specificity towards pathogen or damage associated DNA was thought to be caused by cytosolic confinement. However, recent findings place cGAS robustly in the nucleus8-10, where tight chromatin tethering is even important to prevent autoreactivity to self-DNA8. Here we show how cGAS is sequestered and inhibited by chromatin. We provide a 3.1 Å cryo-electron microscopy structure of the cGAS catalytic domain bound to a nucleosome, which reveals that cGAS does not interact with the nucleosomal DNA, but rather histone 2A/2B, where it is tightly anchored to the "acidic patch". The interaction buries cGAS' DNA binding site B, blocking formation of active cGAS dimers. Acidic patch binding robustly outcompetes agonistic DNA, suggesting that nucleosome sequestration can efficiently inhibit cGAS, even when accessible DNA is nearby, such as in actively transcribed genomic regions. Altogether, our work shows how nuclear cGAS is sequestered by chromatin and provides a mechanism for preventing autoreactivity to nuclear self-DNA.
    DOI:  https://doi.org/10.1038/s41586-020-2748-0
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