bims-camemi Biomed news
on Mitochondrial metabolism in cancer
Issue of 2019‒01‒06
forty-four papers selected by
Christian Frezza
University of Cambridge, MRC Cancer Unit

  1. Biochim Biophys Acta Mol Cell Res. 2018 Dec 27. pii: S0167-4889(18)30541-X. [Epub ahead of print]
    Sedlackova L, Korolchuk VI.
      Mitochondria are the energy producing dynamic double-membraned organelles essential for cellular and organismal survival. A multitude of intra- and extra-cellular signals involved in the regulation of energy metabolism and cell fate determination converge on mitochondria to promote or prevent cell survival by modulating mitochondrial function and structure. Mitochondrial fitness is maintained by mitophagy, a pathway of selective degradation of dysfunctional organelles. Mitophagy impairment and altered clearance results in increased levels of dysfunctional and structurally aberrant mitochondria, changes in energy production, loss of responsiveness to intra- and extra-cellular signals and ultimately cell death. The decline of mitochondrial function and homeostasis with age is reported to be central to age-related pathologies. Here we discuss the molecular mechanisms controlling mitochondrial dynamics, mitophagy and cell death signalling and how their perturbation may contribute to ageing and age-related illness.
    Keywords:  Ageing; BCL-2 family; Cell death; Mitochondria; Mitophagy; Ubiquitin
  2. J Mol Med (Berl). 2019 Jan 03.
    Antunes D, Chowdhury A, Aich A, Saladi S, Harpaz N, Stahl M, Schuldiner M, Herrmann JM, Rehling P, Rapaport D.
      The yeast protein Taz1 is the orthologue of human Tafazzin, a phospholipid acyltransferase involved in cardiolipin (CL) remodeling via a monolyso CL (MLCL) intermediate. Mutations in Tafazzin lead to Barth syndrome (BTHS), a metabolic and neuromuscular disorder that primarily affects the heart, muscles, and immune system. Similar to observations in fibroblasts and platelets from patients with BTHS or from animal models, abolishing yeast Taz1 results in decreased total CL amounts, increased levels of MLCL, and mitochondrial dysfunction. However, the biochemical mechanisms underlying the mitochondrial dysfunction in BTHS remain unclear. To better understand the pathomechanism of BTHS, we searched for multi-copy suppressors of the taz1Δ growth defect in yeast cells. We identified the branched-chain amino acid transaminases (BCATs) Bat1 and Bat2 as such suppressors. Similarly, overexpression of the mitochondrial isoform BCAT2 in mammalian cells lacking TAZ improves their growth. Elevated levels of Bat1 or Bat2 did not restore the reduced membrane potential, altered stability of respiratory complexes, or the defective accumulation of MLCL species in yeast taz1Δ cells. Importantly, supplying yeast or mammalian cells lacking TAZ1 with certain amino acids restored their growth behavior. Hence, our findings suggest that the metabolism of amino acids has an important and disease-relevant role in cells lacking Taz1 function. KEY MESSAGES: Bat1 and Bat2 are multi-copy suppressors of retarded growth of taz1Δ yeast cells. Overexpression of Bat1/2 in taz1Δ cells does not rescue known mitochondrial defects. Supplementation of amino acids enhances growth of cells lacking Taz1 or Tafazzin. Altered metabolism of amino acids might be involved in the pathomechanism of BTSH.
    Keywords:  Barth syndrome; Cardiolipin; Mitochondria; Tafazzin/TAZ1
  3. Wellcome Open Res. 2018 ;3 147
    Oakey LA, Fletcher RS, Elhassan YS, Cartwright DM, Doig CL, Garten A, Thakker A, Maddocks ODK, Zhang T, Tennant DA, Ludwig C, Lavery GG.
      Background: Skeletal muscle is central to whole body metabolic homeostasis, with age and disease impairing its ability to function appropriately to maintain health. Inadequate NAD + availability is proposed to contribute to pathophysiology by impairing metabolic energy pathway use. Despite the importance of NAD + as a vital redox cofactor in energy production pathways being well-established, the wider impact of disrupted NAD + homeostasis on these pathways is unknown. Methods: We utilised skeletal muscle myotube models to induce NAD + depletion, repletion and excess and conducted metabolic tracing to provide comprehensive and detailed analysis of the consequences of altered NAD + metabolism on central carbon metabolic pathways. We used stable isotope tracers, [1,2-13C] D-glucose and [U- 13C] glutamine, and conducted combined 2D-1H,13C-heteronuclear single quantum coherence (HSQC) NMR spectroscopy and GC-MS analysis. Results: NAD + excess driven by nicotinamide riboside (NR) supplementation within skeletal muscle cells results in enhanced nicotinamide clearance, but had no effect on energy homeostasis or central carbon metabolism. Nicotinamide phosphoribosyltransferase (NAMPT) inhibition induced NAD + depletion and resulted in equilibration of metabolites upstream of glyceraldehyde phosphate dehydrogenase (GAPDH). Aspartate production through glycolysis and TCA cycle activity is increased in response to low NAD +, which is rapidly reversed with repletion of the NAD + pool using NR. NAD + depletion reversibly inhibits cytosolic GAPDH activity, but retains mitochondrial oxidative metabolism, suggesting differential effects of this treatment on sub-cellular pyridine pools. When supplemented, NR efficiently reverses these metabolic consequences. However, the functional relevance of increased aspartate levels after NAD + depletion remains unclear, and requires further investigation. Conclusions: These data highlight the need to consider carbon metabolism and clearance pathways when investigating NAD + precursor usage in models of skeletal muscle physiology.
    Keywords:  NAD+; NAMPT; NR; aspartate; isotopic tracing; metabolism; skeletal muscle
  4. Crit Care. 2018 Dec 29. 22(1): 360
    Johansson PI, Nakahira K, Rogers AJ, McGeachie MJ, Baron RM, Fredenburgh LE, Harrington J, Choi AMK, Christopher KB.
      BACKGROUND: Cell-free plasma mitochondrial DNA (mtDNA) levels are associated with endothelial dysfunction and differential outcomes in critical illness. A substantial alteration in metabolic homeostasis is commonly observed in severe critical illness. We hypothesized that metabolic profiles significantly differ between critically ill patients relative to their level of plasma mtDNA.METHODS: We performed a metabolomic study with biorepository plasma samples collected from 73 adults with systemic inflammatory response syndrome or sepsis at a single academic medical center. Patients were treated in a 20-bed medical ICU between 2008 and 2010. To identify key metabolites and metabolic pathways related to plasma NADH dehydrogenase 1 (ND1) mtDNA levels in critical illness, we first generated metabolomic data using gas and liquid chromatography-mass spectroscopy. We performed fold change analysis and volcano plot visualization based on false discovery rate-adjusted p values to evaluate the distribution of individual metabolite concentrations relative to ND1 mtDNA levels. We followed this by performing orthogonal partial least squares discriminant analysis to identify individual metabolites that discriminated ND1 mtDNA groups. We then interrogated the entire metabolomic profile using pathway overrepresentation analysis to identify groups of metabolite pathways that were different relative to ND1 mtDNA levels.
    RESULTS: Metabolomic profiles significantly differed in critically ill patients with ND1 mtDNA levels ≥ 3200 copies/μl plasma relative to those with an ND1 mtDNA level < 3200 copies/μl plasma. Several analytical strategies showed that patients with ND1 mtDNA levels ≥ 3200 copies/μl plasma had significant decreases in glycerophosphocholines and increases in short-chain acylcarnitines.
    CONCLUSIONS: Differential metabolic profiles during critical illness are associated with cell-free plasma ND1 mtDNA levels that are indicative of cell damage. Elevated plasma ND1 mtDNA levels are associated with decreases in glycerophosphocholines and increases in short-chain acylcarnitines that reflect phospholipid metabolism dysregulation and decreased mitochondrial function, respectively.
    Keywords:  Acylcarnitine; Critical illness; Glycerophosphocholine; Homeostasis; Metabolite; Metabolomics; Mitochondrial DNA
  5. J Biol Chem. 2019 Jan 02. pii: jbc.RA118.006799. [Epub ahead of print]
    Mehta K, Chacko LA, Chug MK, Jhunjhunwala S, Ananthanarayanan V.
      Mitochondria are organized as tubular networks in the cell and undergo fission and fusion. Although several of the molecular players involved in mediating mitochondrial dynamics have been identified, the precise cellular cues that initiate mitochondrial fission or fusion remain largely unknown. In fission yeast (Schizosaccharomyces pombe), mitochondria are organized along microtubule bundles. Here, we employed deletions of kinesin-like proteins to perturb microtubule dynamics and used high-resolution and time-lapse fluorescence microscopy, revealing that mitochondrial lengths mimic microtubule lengths. Further, we determined that compared to wild-type cells, mutant cells with long microtubules exhibit fewer mitochondria, and mutant cells with short microtubules have an increased number of mitochondria, because of reduced mitochondrial fission in the former and elevated fission in the latter. Correspondingly, upon onset of closed mitosis in fission yeast, wherein interphase microtubules assemble to form the spindle within the nucleus, we observed increased mitochondrial fission. We found that the consequent rise in the mitochondrial copy number is necessary to reduce partitioning errors during independent segregation of mitochondria between daughter cells. We also discovered that the association of mitochondria with microtubules physically impedes the assembly of the fission protein Dnm1 around mitochondria, resulting in inhibition of mitochondrial fission. Taken together, we demonstrate a mechanism for the regulation of mitochondrial fission that is dictated by the interaction between mitochondria and the microtubule cytoskeleton.
    Keywords:  Dnm1; Mitochondrial dynamics; Schizosaccharomyces pombe; cell biology; cytoskeleton; in vivo imaging; microtubule; mitochondria; mitosis; molecular motor
  6. Mitochondrion. 2018 Dec 27. pii: S1567-7249(17)30028-4. [Epub ahead of print]
    Quintana DD, Garcia JA, Sarkar SN, Jun S, Engler-Chiurazzi EB, Russell AE, Cavendish JZ, Simpkins JW.
      Astrocytes serve to maintain proper neuronal function and support neuronal viability, but remain largely understudied in research of cerebral ischemia. Astrocytic mitochondria are core participants in the metabolic activity of astrocytes. The objective of this study is to assess astrocyte mitochondrial competence during hypoxia and post-hypoxia reoxygenation and to determine cellular adaptive and pathological changes in the mitochondrial network. We hypothesize that during metabolic distress in astrocytes; mitochondrial networks undergo a shift in fission-fusion dynamics that results in a change in the morphometric state of the entire mitochondrial network. This mitochondrial network shift may be protective during metabolic distress by priming mitochondrial size and facilitating mitophagy. We demonstrated that hypoxia and post-hypoxia reoxygenation of rat primary astrocytes results in a redistribution of mitochondria to smaller sizes evoked by increased mitochondrial fission. Excessive mitochondrial fission corresponded to Drp-1 dephosphorylation at Ser 637, which preceded mitophagy of relatively small mitochondria. Reoxygenation of astrocytes marked the initiation of elevated mitophagic activity primarily reserved to the perinuclear region where a large number of the smallest mitochondria occurred. Although, during hypoxia astrocytic ATP content was severely reduced, after reoxygenation ATP content returned to near normoxic values and these changes mirrored mitochondrial superoxide production. Concomitant with these changes in astrocytic mitochondria, the number of astrocytic extensions declined only after 10-hours post-hypoxic reoxygenation. Overall, we posit a drastic mitochondrial network change that is triggered by a metabolic crisis during hypoxia; these changes are followed by mitochondrial degradation and retraction of astrocytic extensions during reoxygenation.
    Keywords:  Astrocytes; Drp-1; Fission and fusion; LC3; Mitochondria; Mitophagy; Oxygen deprivation
  7. Am J Physiol Endocrinol Metab. 2019 Jan 02.
    Pinti MV, Fink GK, Hathaway QA, Durr AJ, Kunovac A, Hollander JM.
      Type 2 diabetes mellitus (T2DM) is a systemic disease characterized by hyperglycemia, hyperlipidemia, and organismic insulin resistance. This pathologic shift in both circulating fuel levels and in energy substrate utilization by central and peripheral tissues contributes to mitochondrial dysfunction across organ systems. The mitochondrion lies at the intersection of critical cellular pathways such as energy substrate metabolism, reactive oxygen species (ROS) generation, and apoptosis. It is the disequilibrium of these processes in T2DM that results in downstream deficits in vital functions including hepatocyte metabolism, cardiac output, skeletal muscle contraction, ß-cell insulin production, and neuronal health. While mitochondria are known to be susceptible to a variety of genetic and environmental insults, the accumulation of mitochondrial DNA (mtDNA) mutations and mtDNA copy number depletion is helping to explain the prevalence of mitochondrial-related diseases such as T2DM. Recent work has uncovered novel mitochondrial biology implicated in disease progression such as mtDNA heteroplasmy, non-coding RNA (ncRNA), epigenetic modification of the mitochondrial genome, and epitranscriptomic regulation of the mtDNA-encoded mitochondrial transcriptome. The goal of this review is to highlight mitochondrial dysfunction observed throughout major organ systems in the context of T2DM and to present new ideas for future research directions based on novel experimental and technological innovations in mitochondrial biology. Finally, the field of mitochondria targeted therapeutics is discussed with an emphasis on novel therapeutic strategies to restore mitochondrial homeostasis in the setting of T2DM.
    Keywords:  Diabetes Mellitus; Mitochondria Dysfunction
  8. Cell Rep. 2019 Jan 02. pii: S2211-1247(18)31969-7. [Epub ahead of print]26(1): 182-191.e5
    Battefeld A, Popovic MA, de Vries SI, Kole MHP.
      Ensheathment of axons by myelin is a highly complex and multi-cellular process. Cytosolic calcium (Ca2+) changes in the myelin sheath have been implicated in myelin synthesis, but the source of this Ca2+ and the role of neuronal activity is not well understood. Using one-photon Ca2+ imaging, we investigated myelin sheath formation in the mouse somatosensory cortex and found a high rate of spontaneous microdomain Ca2+ transients and large-amplitude Ca2+ waves propagating along the internode. The frequency of Ca2+ transients and waves rapidly declines with maturation and reactivates during remyelination. Unexpectedly, myelin microdomain Ca2+ transients occur independent of neuronal action potential generation or network activity but are nearly completely abolished when the mitochondrial permeability transition pores are blocked. These findings are supported by the discovery of mitochondria organelles in non-compacted myelin. Together, the results suggest that myelin microdomain Ca2+ signals are cell-autonomously driven by high activity of mitochondria during myelin remodeling.
    Keywords:  action potential; axon; calcium; development; mitochondria; mouse; myelin; permeability transition pore; pyramidal neuron; remyelination
  9. J Clin Invest. 2019 Jan 02. pii: 120848. [Epub ahead of print]129(1): 34-45
    Area-Gomez E, Guardia-Laguarta C, Schon EA, Przedborski S.
      Mitochondrial respiratory deficiencies have been observed in numerous neurodegenerative disorders, such as Alzheimer's and Parkinson's diseases. For decades, these reductions in oxidative phosphorylation (OxPhos) have been presumed to trigger an overall bioenergetic crisis in the neuron, resulting in cell death. While the connection between respiratory defects and neuronal death has never been proven, this hypothesis has been supported by the detection of nonspecific mitochondrial DNA mutations in these disorders. These findings led to the notion that mitochondrial respiratory defects could be initiators of these common neurodegenerative disorders, instead of being consequences of a prior insult, a theory we believe to be misconstrued. Herein, we review the roots of this mitochondrial hypothesis and offer a new perspective wherein mitochondria are analyzed not only from the OxPhos point of view, but also as a complex organelle residing at the epicenter of many metabolic pathways.
  10. Genes Cancer. 2018 May;9(5-6): 155-175
    Han CY, Patten DA, Richardson RB, Harper ME, Tsang BK.
      Elevated metabolism is a key hallmark of multiple cancers, serving to fulfill high anabolic demands. Ovarian cancer (OVCA) is the fifth leading cause of cancer deaths in women with a high mortality rate (45%). Chemoresistance is a major hurdle for OVCA treatment. Although substantial evidence suggests that metabolic reprogramming contributes to anti-apoptosis and the metastasis of multiple cancers, the link between tumor metabolism and chemoresistance in OVCA remains unknown. While clinical trials targeting metabolic reprogramming alone have been met with limited success, the synergistic effect of inhibiting tumor-specific metabolism with traditional chemotherapy warrants further examination, particularly in OVCA. This review summarizes the role of key glycolytic enzymes and other metabolic synthesis pathways in the progression of cancer and chemoresistance in OVCA. Within this context, mitochondrial dynamics (fission, fusion and cristae structure) are addressed regarding their roles in controlling metabolism and apoptosis, closely associated with chemosensitivity. The roles of multiple key oncogenes (Akt, HIF-1α) and tumor suppressors (p53, PTEN) in metabolic regulation are also described. Next, this review summarizes recent research of metabolism and future direction. Finally, we examine clinical drugs and inhibitors to target glycolytic metabolism, as well as the rationale for such strategies as potential therapeutics to overcome chemoresistant OVCA.
    Keywords:  chemoresistance; hexokinase 2; ovarian cancer; p53; tumor metabolism
  11. Methods Mol Biol. 2019 ;1880 621-642
    McWilliams TG, Ganley IG.
      Autophagy evolved as a mechanism to sustain cellular homeostasis during instances of nutrient deprivation. Mounting evidence has also clarified that under basal and stress conditions, selective autophagy pathways can target the destruction of specific organelles. Mitochondrial autophagy, or mitophagy, has emerged as a key quality control (QC) mechanism to sustain the integrity of eukaryotic mitochondrial networks. We recently reported the development of mito-QC, a novel reporter mouse model that enables the high-resolution study of mammalian mitophagy with precision, in fixed and live preparations. This model holds significant potential to transform our understanding of mammalian mitophagy pathways in vivo, in a variety of physiological contexts. We outline a detailed protocol for use of our recently described mito-QC mouse model, including tips and troubleshooting advice for those interested in monitoring mitophagy in vitro and in vivo.
    Keywords:  Autophagy; Cancer; Cardiology; Developmental biology; Histology; Immunology; Metabolism; Microscopy; Mitochondria; Mitophagy; Mouse models; Nephrology; Neurodegeneration; Vascular biology
  12. Cell Metab. 2018 Dec 20. pii: S1550-4131(18)30741-1. [Epub ahead of print]
    Zhang S, Weinberg S, DeBerge M, Gainullina A, Schipma M, Kinchen JM, Ben-Sahra I, Gius DR, Charvet LY, Chandel NS, Schumacker PT, Thorp EB.
      During wound injury, efferocytosis fills the macrophage with a metabolite load nearly equal to the phagocyte itself. A timely question pertains to how metabolic phagocytic signaling regulates the signature anti-inflammatory macrophage response. Here we report the metabolome of activated macrophages during efferocytosis to reveal an interleukin-10 (IL-10) cytokine escalation that was independent of glycolysis yet bolstered by apoptotic cell fatty acids and mitochondrial β-oxidation, the electron transport chain, and heightened coenzyme NAD+. Loss of IL-10 due to mitochondrial complex III defects was remarkably rescued by adding NAD+ precursors. This activated a SIRTUIN1 signaling cascade, largely independent of ATP, that culminated in activation of IL-10 transcription factor PBX1. Il-10 activation by the respiratory chain was also important in vivo, as efferocyte mitochondrial dysfunction led to cardiac rupture after myocardial injury. These findings highlight a new paradigm whereby macrophages leverage efferocytic metabolites and electron transport for anti-inflammatory reprogramming that culminates in organ repair.
    Keywords:  efferocytosis; immunometabolism; macrophage; wound healing
  13. Biochim Biophys Acta Mol Cell Res. 2019 Mar;pii: S0167-4889(18)30215-5. [Epub ahead of print]1866(3): 337-348
    Huber K, Hofer DC, Trefely S, Pelzmann HJ, Madreiter-Sokolowski C, Duta-Mare M, Schlager S, Trausinger G, Stryeck S, Graier WF, Kolb D, Magnes C, Snyder NW, Prokesch A, Kratky D, Madl T, Wellen KE, Bogner-Strauss JG.
      The discovery of significant amounts of metabolically active brown adipose tissue (BAT) in adult humans renders it a promising target for anti-obesity therapies by inducing weight loss through increased energy expenditure. The components of the N-acetylaspartate (NAA) pathway are highly abundant in BAT. Aspartate N-acetyltransferase (Asp-NAT, encoded by Nat8l) synthesizes NAA from acetyl-CoA and aspartate and increases energy expenditure in brown adipocytes. However, the exact mechanism how the NAA pathway contributes to accelerated mobilization and oxidation of lipids and the physiological regulation of the NAA pathway remained elusive. Here, we demonstrate that the expression of NAA pathway genes corresponds to nutrient availability and specifically responds to changes in exogenous glucose. NAA is preferentially produced from glucose-derived acetyl-CoA and aspartate and its concentration increases during adipogenesis. Overexpression of Nat8l drains glucose-derived acetyl-CoA into the NAA pool at the expense of cellular lipids and certain amino acids. Mechanistically, we elucidated that a combined activation of neutral and lysosomal (acid) lipolysis is responsible for the increased lipid degradation. Specifically, translocation of the transcription factor EB to the nucleus activates the biosynthesis of autophagosomes and lysosomes. Lipid degradation within lysosomes accompanied by adipose triglyceride lipase-mediated lipolysis delivers fatty acids for the support of elevated mitochondrial respiration. Together, our data suggest a crucial role of the NAA pathway in energy metabolism and metabolic adaptation in BAT.
    Keywords:  Asp-NAT; Aspartoacylase; Brown adipocytes; Energy expenditure; Fatty acid metabolism; Lipid metabolism; Lipophagy; N-acetylaspartate; N-acetyltransferase 8-like
  14. Methods Mol Biol. 2019 ;1880 601-610
    Moore AS, Holzbaur ELF.
      Investigating the precise spatiotemporal dynamics of mitophagy can provide insights into how mitochondrial quality control is regulated in different tissues and organisms. Here, we outline live imaging assays to quantitatively assess mitophagy dynamics in real time. This protocol describes both chemical and optogenetic techniques to induce mitochondrial damage with high spatial and temporal control. Using these assays, mitochondria can be tracked from before they sustain damage up to their engulfment by autophagosomes and acidification by lysosomes.
    Keywords:  Autophagy; LC3; Lysosome; Mitochondria; Mitophagy; OPTN; Parkin; Ubiquitin
  15. Plant J. 2019 Jan 02.
    Huang S, Braun HP, Gawryluk RMR, Millar AH.
      Complex II (succinate dehydrogenase [succinate-ubiquinone oxidoreductase]; EC; SDH) is the only enzyme shared by both the electron transport chain and the tricarboxylic acid (TCA) cycle in mitochondria. Complex II in plants is considered unusual due to its accessory subunits (SDH5-8) in addition to the catalytic subunits of SDH found in all eukaryotes (SDH1-4). Here we review compositional and phylogenetic analysis, and biochemical dissection studies to clarify the presence and to propose the role of these subunits. We also consider the wider functional and phylogenetic evidence for SDH assembly factors and the reports from plants on the control of SDH1 flavination and SDH1-SDH2 interaction. Plant Complex II has been shown to influence stomatal opening, the plant defence response and reactive oxygen species-dependent stress responses. Signalling molecules such as salicyclic acid (SA) and nitric oxide (NO) are also reported to interact with the UQ binding site of SDH, influencing signalling transduction in plants. Future directions for SDH research in plants and the specific roles of its different subunits and assembly factors are suggested, including the potential for reverse electron transport to explain succinate-dependent ROS production in plants and new avenues to explore plant mitochondrial Complex II evolution and its utility. This article is protected by copyright. All rights reserved.
    Keywords:  Assembly factors; Complex II; Plant mitochondria; Reactive Oxygen Species; Stress Signalling; Succinate Dehydrogenase
  16. Free Radic Biol Med. 2018 Dec 28. pii: S0891-5849(18)32256-1. [Epub ahead of print]
    Campbell MD, Duan J, Samuelson AT, Gaffrey MJ, Wang L, Bammler TK, Moore RJ, White CC, Kavanagh TJ, Voss JG, Szeto HH, Rabinovitch PS, Qian WJ, Marcinek DJ.
      Sarcopenia and exercise intolerance are major contributors to reduced quality of life in the elderly for which there are few effective treatments. We tested whether enhancing mitochondrial function and reducing mitochondrial oxidant production with SS-31 (elamipretide) could restore redox balance and improve skeletal muscle function in aged mice. Young (5 mo) and aged (26 mo) female C57BL/6Nia mice were treated for 8-weeks with 3mg/kg/day SS-31. Mitochondrial function was assessed in vivo using 31P and optical spectroscopy. SS-31 reversed age-related decline in maximum mitochondrial ATP production (ATPmax) and coupling of oxidative phosphorylation (P/O). Despite the increased in vivo mitochondrial capacity, mitochondrial protein expression was either unchanged or reduced in the treated aged mice and respiration in permeabilized gastrocnemius (GAS) fibers was not different between the aged and aged+SS-31 mice. Treatment with SS-31 also restored redox homeostasis in the aged skeletal muscle. The glutathione redox status was more reduced and thiol redox proteomics indicated a robust reversal of cysteine S-glutathionylation post-translational modifications across the skeletal muscle proteome. The gastrocnemius in the age+SS-31 mice was more fatigue resistant with significantly greater mass compared to aged controls. This contributed to a significant increase in treadmill endurance compared to both pretreatment and untreated control values. These results demonstrate that the shift of redox homeostasis due to mitochondrial oxidant production in aged muscle is a key factor in energetic defects and exercise intolerance. Treatment with SS-31 restores redox homeostasis, improves mitochondrial quality, and increases exercise tolerance without an increase in mitochondrial content. Since elamipretide is currently in clinical trials these results indicate it may have direct translational value for improving exercise tolerance and quality of life in the elderly.
    Keywords:  Aging; Fatigue; Mitochondria; Oxidative stress; Skeletal muscle
  17. Neurogenetics. 2019 Jan 03.
    Borna NN, Kishita Y, Kohda M, Lim SC, Shimura M, Wu Y, Mogushi K, Yatsuka Y, Harashima H, Hisatomi Y, Fushimi T, Ichimoto K, Murayama K, Ohtake A, Okazaki Y.
      Pentatricopeptide repeat domain proteins are a large family of RNA-binding proteins involved in mitochondrial RNA editing, stability, and translation. Mitochondrial translation machinery defects are an expanding group of genetic diseases in humans. We describe a patient who presented with low birth weight, mental retardation, and optic atrophy. Brain MRI showed abnormal bilateral signals at the basal ganglia and brainstem, and the patient was diagnosed as Leigh syndrome. Exome sequencing revealed two potentially loss-of-function variants [c.415-2A>G, and c.1747_1748insCT (p.Phe583Serfs*3)] in PTCD3 (also known as MRPS39). PTCD3, a member of the pentatricopeptide repeat domain protein family, is a component of the small mitoribosomal subunit. The patient had marked decreases in mitochondrial complex I and IV levels and activities, oxygen consumption and ATP biosynthesis, and generalized mitochondrial translation defects in fibroblasts. Quantitative proteomic analysis revealed decreased levels of the small mitoribosomal subunits. Complementation experiments rescued oxidative phosphorylation complex I and IV levels and activities, ATP biosynthesis, and MT-RNR1 rRNA transcript level, providing functional validation of the pathogenicity of identified variants. This is the first report of an association of PTCD3 mutations with Leigh syndrome along with combined oxidative phosphorylation deficiencies caused by defects in the mitochondrial translation machinery.
    Keywords:  Leigh syndrome; Mitochondrial translation; Oxidative phosphorylation; PTCD3; Small mitoribosomal subunit
  18. J Cell Biol. 2018 Dec 31. pii: jcb.201806093. [Epub ahead of print]
    Richter F, Dennerlein S, Nikolov M, Jans DC, Naumenko N, Aich A, MacVicar T, Linden A, Jakobs S, Urlaub H, Langer T, Rehling P.
      The mitochondrial presequence translocation machinery (TIM23 complex) is conserved between the yeast Saccharomyces cerevisiae and humans; however, functional characterization has been mainly performed in yeast. Here, we define the constituents of the human TIM23 complex using mass spectrometry and identified ROMO1 as a new translocase constituent with an exceptionally short half-life. Analyses of a ROMO1 knockout cell line revealed aberrant inner membrane structure and altered processing of the GTPase OPA1. We show that in the absence of ROMO1, mitochondria lose the inner membrane YME1L protease, which participates in OPA1 processing and ROMO1 turnover. While ROMO1 is dispensable for general protein import along the presequence pathway, we show that it participates in the dynamics of TIM21 during respiratory chain biogenesis and is specifically required for import of YME1L. This selective import defect can be linked to charge distribution in the unusually long targeting sequence of YME1L. Our analyses establish an unexpected link between mitochondrial protein import and inner membrane protein quality control.
  19. Am J Hum Genet. 2019 Jan 03. pii: S0002-9297(18)30452-X. [Epub ahead of print]104(1): 112-138
    Kraja AT, Liu C, Fetterman JL, Graff M, Have CT, Gu C, Yanek LR, Feitosa MF, Arking DE, Chasman DI, Young K, Ligthart S, Hill WD, Weiss S, Luan J, Giulianini F, Li-Gao R, Hartwig FP, Lin SJ, Wang L, Richardson TG, Yao J, Fernandez EP, Ghanbari M, Wojczynski MK, Lee WJ, Argos M, Armasu SM, Barve RA, Ryan KA, An P, Baranski TJ, Bielinski SJ, Bowden DW, Broeckel U, Christensen K, Chu AY, Corley J, Cox SR, Uitterlinden AG, Rivadeneira F, Cropp CD, Daw EW, van Heemst D, de Las Fuentes L, Gao H, Tzoulaki I, Ahluwalia TS, de Mutsert R, Emery LS, Erzurumluoglu AM, Perry JA, Fu M, Forouhi NG, Gu Z, Hai Y, Harris SE, Hemani G, Hunt SC, Irvin MR, Jonsson AE, Justice AE, Kerrison ND, Larson NB, Lin KH, Love-Gregory LD, Mathias RA, Lee JH, Nauck M, Noordam R, Ong KK, Pankow J, Patki A, Pattie A, Petersmann A, Qi Q, Ribel-Madsen R, Rohde R, Sandow K, Schnurr TM, Sofer T, Starr JM, Taylor AM, Teumer A, Timpson NJ, de Haan HG, Wang Y, Weeke PE, Williams C, Wu H, Yang W, Zeng D, Witte DR, Weir BS, Wareham NJ, Vestergaard H, Turner ST, Torp-Pedersen C, Stergiakouli E, Sheu WH, Rosendaal FR, Ikram MA, Franco OH, Ridker PM, Perls TT, Pedersen O, Nohr EA, Newman AB, Linneberg A, Langenberg C, Kilpeläinen TO, Kardia SLR, Jørgensen ME, Jørgensen T, Sørensen TIA, Homuth G, Hansen T, Goodarzi MO, Deary IJ, Christensen C, Chen YI, Chakravarti A, Brandslund I, Bonnelykke K, Taylor KD, Wilson JG, Rodriguez S, Davies G, Horta BL, Thyagarajan B, Rao DC, Grarup N, Davila-Roman VG, Hudson G, Guo X, Arnett DK, Hayward C, Vaidya D, Mook-Kanamori DO, Tiwari HK, Levy D, Loos RJF, Dehghan A, Elliott P, Malik AN, Scott RA, Becker DM, de Andrade M, Province MA, Meigs JB, Rotter JI, North KE.
      Mitochondria (MT), the major site of cellular energy production, are under dual genetic control by 37 mitochondrial DNA (mtDNA) genes and numerous nuclear genes (MT-nDNA). In the CHARGEmtDNA+ Consortium, we studied genetic associations of mtDNA and MT-nDNA associations with body mass index (BMI), waist-hip-ratio (WHR), glucose, insulin, HOMA-B, HOMA-IR, and HbA1c. This 45-cohort collaboration comprised 70,775 (insulin) to 170,202 (BMI) pan-ancestry individuals. Validation and imputation of mtDNA variants was followed by single-variant and gene-based association testing. We report two significant common variants, one in MT-ATP6 associated (p ≤ 5E-04) with WHR and one in the D-loop with glucose. Five rare variants in MT-ATP6, MT-ND5, and MT-ND6 associated with BMI, WHR, or insulin. Gene-based meta-analysis identified MT-ND3 associated with BMI (p ≤ 1E-03). We considered 2,282 MT-nDNA candidate gene associations compiled from online summary results for our traits (20 unique studies with 31 dataset consortia's genome-wide associations [GWASs]). Of these, 109 genes associated (p ≤ 1E-06) with at least 1 of our 7 traits. We assessed regulatory features of variants in the 109 genes, cis- and trans-gene expression regulation, and performed enrichment and protein-protein interactions analyses. Of the identified mtDNA and MT-nDNA genes, 79 associated with adipose measures, 49 with glucose/insulin, 13 with risk for type 2 diabetes, and 18 with cardiovascular disease, indicating for pleiotropic effects with health implications. Additionally, 21 genes related to cholesterol, suggesting additional important roles for the genes identified. Our results suggest that mtDNA and MT-nDNA genes and variants reported make important contributions to glucose and insulin metabolism, adipocyte regulation, diabetes, and cardiovascular disease.
    Keywords:  BMI; HOMA-B; HOMA-IR; HbA1c; MT-nDNA candidate genes; glucose; insulin; mitochondria; mtDNA; waist-to-hip ratio
  20. Biosensors (Basel). 2018 Dec 28. pii: E5. [Epub ahead of print]9(1):
    Larion M, Dowdy T, Ruiz-Rodado V, Meyer MW, Song H, Zhang W, Davis D, Gilbert MR, Lita A.
      Isocitrate dehydrogenase 1 (IDH1) mutations in gliomas, fibrosarcoma, and other cancers leads to a novel metabolite, D-2-hydroxyglutarate, which is proposed to cause tumorigenesis. The production of this metabolite also causes vulnerabilities in cellular metabolism, such as lowering NADPH levels. To exploit this vulnerability, we treated glioma and fibrosarcoma cells that harbor an IDH1 mutation with an inhibitor of nicotinamide adenine dinucleotide (NAD⁺) salvage pathway, FK866, and observed decreased viability in these cells. To understand the mechanism of action by which the inhibitor FK866 works, we used Raman imaging microscopy and identified that proteins and lipids are decreased upon treatment with the drug. Raman imaging showed a different distribution of lipids throughout the cell in the presence of the drug compared with the untreated cells. We employed nuclear magnetic resonance NMR spectroscopy and mass spectrometry to identify the classes of lipids altered. Our combined analyses point to a decrease in cell division due to loss of lipid content that contributes to membrane formation in the in vitro setting. However, the FK866 drug did not have the same potency in vivo. The use of Raman imaging microscopy indicated an opposite trend of lipid distribution in the tissue collected from treated versus untreated mice when compared with the cells. These results demonstrate the role of Raman imaging microscopy to identify and quantify metabolic changes in cancer cells and tissue.
    Keywords:  NAD+ synthesis; Raman spectrometry; fibrosarcoma IDH1; microscopy; single cell imaging; tissue imaging
  21. Cell Mol Life Sci. 2019 Jan 01.
    Magi S, Piccirillo S, Amoroso S.
      Glutamate is the major excitatory neurotransmitter in the central nervous system. Beyond this function, glutamate also plays a key role in intermediary metabolism in all organs and tissues, linking carbohydrate and amino acid metabolism via the tricarboxylic acid cycle. Under both physiological and pathological conditions, we have recently found that the ability of glutamate to fuel cell metabolism selectively relies on the activity of two main transporters: the sodium-calcium exchanger (NCX) and the sodium-dependent excitatory amino-acid transporters (EAATs). In ischemic settings, when glutamate is administered at the onset of the reoxygenation phase, the coordinate activity of EAAT and NCX allows glutamate to improve cell viability by stimulating ATP production. So far, this phenomenon has been observed in both cardiac and neuronal models. In this review, we focus on the most recent findings exploring the unusual activity of glutamate as a potential survival factor in different settings.
    Keywords:  ATP; Amino-acid transporters; Cell viability; Ischemia/reperfusion; Sodium–calcium exchanger
  22. Cytometry A. 2019 Jan 02.
    Cao R, Wallrabe H, Siller K, Rehman Alam S, Periasamy A.
      Redox changes in live HeLa cervical cancer cells after doxorubicin treatment can either be analyzed by a novel fluorescence lifetime microscopy (FLIM)-based redox ratio NAD(P)H-a2%/FAD-a1%, called fluorescence lifetime redox ratio or one of its components (NAD(P)H-a2%), which is actually driving that ratio and offering a simpler and alternative metric and are both compared. Auto-fluorescent NAD(P)H, FAD lifetime is acquired by 2- photon excitation and Tryptophan by 3-photon, at 4 time points after treatment up to 60 min demonstrating early drug response to doxorubicin. Identical Fields-of-view (FoV) at each interval allows single-cell analysis, showing heterogeneous responses to treatment, largely based on their initial control redox state. Based on a discrete ROI selection method, mitochondrial OXPHOS and cytosolic glycolysis are discriminated. Furthermore, putative FRET interaction and energy transfer between tryptophan residue carrying enzymes and NAD(P)H correlate with NAD(P)H-a2%, as does the NADPH/NADH ratio, highlighting a multi-parametric assay to track metabolic changes in live specimens. © 2019 International Society for Advancement of Cytometry.
    Keywords:  FAD; Fluorescence Lifetime Imaging Microscopy (FLIM); NAD(P)H; NAD(P)H-a2%, redox: reduction/oxidation states; NADPH/NADH ratio; fluorescence lifetime redox ratio (FLIRR); single-cell analysis
  23. Cell Metab. 2018 Dec 19. pii: S1550-4131(18)30740-X. [Epub ahead of print]
    Ying W, Lee YS, Dong Y, Seidman JS, Yang M, Isaac R, Seo JB, Yang BH, Wollam J, Riopel M, McNelis J, Glass CK, Olefsky JM, Fu W.
      The nature of obesity-associated islet inflammation and its impact on β cell abnormalities remains poorly defined. Here, we explore immune cell components of islet inflammation and define their roles in regulating β cell function and proliferation. Islet inflammation in obese mice is dominated by macrophages. We identify two islet-resident macrophage populations, characterized by their anatomical distributions, distinct phenotypes, and functional properties. Obesity induces the local expansion of resident intra-islet macrophages, independent of recruitment from circulating monocytes. Functionally, intra-islet macrophages impair β cell function in a cell-cell contact-dependent manner. Increased engulfment of β cell insulin secretory granules by intra-islet macrophages in obese mice may contribute to restricting insulin secretion. In contrast, both intra- and peri-islet macrophage populations from obese mice promote β cell proliferation in a PDGFR signaling-dependent manner. Together, these data define distinct roles and mechanisms for islet macrophages in the regulation of islet β cells.
    Keywords:  islet inflammation; local macrophages proliferation; macrophages; obesity; β cell function; β cell proliferation
  24. Am J Respir Cell Mol Biol. 2019 Jan 04.
    Waters DW, Blokland KEC, Pathinayake PS, Wei L, Schuliga M, Jaffar J, Westall GP, Hansbro PM, Prele CM, Mutsaers SE, Bartlett NW, Burgess JK, Grainge CL, Knight DA.
      Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease of unknown cause with a median survival of only 3 years. We and others have shown that fibroblasts derived from IPF-lungs display characteristics of senescent cells and that dysregulated activation of the transcription factor signal transducer and activator of transcription 3 (STAT3) correlates with IPF progression. The question of whether STAT3 activation is involved in fibroblast senescence remains unanswered. We hypothesized that inhibiting STAT3 activation after oxidant-induced senescence would attenuate characteristics of the senescent phenotype. We aimed to characterize a model of oxidant induced senescence in human lung fibroblasts and to determine the effect of inhibiting STAT3 activity on the development of senescence. Exposing human lung fibroblasts to 150µM hydrogen peroxide (H2O2) resulted in increased senescence-associated-β-galactosidase (SA-β-Gal) content, expression of p21 and interleukin (IL)-6, all of which are features of senescence. The shift into senescence was accompanied by an increase of STAT3 translocation to the nucleus and mitochondria. Additionally, Seahorse analysis provided evidence of increased mitochondrial respiration characterized by increased basal respiration, proton leak and an associated increase in superoxide (O2-) production in senescent fibroblasts. Targeting STAT3 activity using the small molecule inhibitor STA-21 attenuated IL-6 production, reduced p21 levels, decreased SA-β-Gal accumulation and restored normal mitochondrial function. The results of this study illustrate that stress-induced senescence in lung fibroblasts involves the activation of STAT3 which can be pharmacologically modulated.
    Keywords:  Senescence; Signal transducer and activator of transcription 3; cell cycle; fibroblast; mitochondrial dysfunction
  25. Exp Cell Res. 2018 Dec 28. pii: S0014-4827(18)31186-8. [Epub ahead of print]
    Neethling A, Engelbrecht L, Loos B, Kinnear C, Theart R, Abrahams S, Niesler T, Mellick GD, Williams M, Bardien S.
      Leucine-rich repeat kinase 2 (LRRK2) is important in various cellular processes including mitochondrial homeostasis and mutations in this gene lead to Parkinson's disease (PD). However, the full spectrum of LRRK2's functions remain to be elucidated. The translocase of outer mitochondrial membrane (TOM) complex is essential for the import of almost all nuclear-encoded mitochondrial proteins and is fundamental for cellular survival. Using co-immunoprecipitation, super-resolution structured illumination microscopy (SR-SIM), and 3D virtual reality (VR) assisted co-localization analysis techniques we show that wild-type and mutant (G2019S) LRRK2 associate and co-localize with subunits of the TOM complex, either under basal (dimethyl sulfoxide, DMSO) or stress-induced (carbonyl cyanide m-chlorophenyl hydrazine, CCCP) conditions. Interestingly, LRRK2 interacted with TOM40 under both DMSO and CCCP conditions, and when the PD causing mutation, G2019S was introduced, the association was not altered. Moreover, overexpression of G2019S LRRK2 resulted in the formation of large, perinuclear aggregates that co-localized with the TOM complex. Taken together, this is the first study to show that both WT and mutant LRRK2 associate with the TOM complex subunits. These findings provide additional evidence for LRRK2's role in mitochondrial function which has important implications for its role in PD pathogenesis.
    Keywords:  LRRK2; Parkinson's disease; TOM complex; TOM40; co-immunoprecipitation; co-localization
  26. PLoS Genet. 2019 Jan;15(1): e1007781
    Posse V, Al-Behadili A, Uhler JP, Clausen AR, Reyes A, Zeviani M, Falkenberg M, Gustafsson CM.
      Human mitochondrial DNA (mtDNA) replication is first initiated at the origin of H-strand replication. The initiation depends on RNA primers generated by transcription from an upstream promoter (LSP). Here we reconstitute this process in vitro using purified transcription and replication factors. The majority of all transcription events from LSP are prematurely terminated after ~120 nucleotides, forming stable R-loops. These nascent R-loops cannot directly prime mtDNA synthesis, but must first be processed by RNase H1 to generate 3'-ends that can be used by DNA polymerase γ to initiate DNA synthesis. Our findings are consistent with recent studies of a knockout mouse model, which demonstrated that RNase H1 is required for R-loop processing and mtDNA maintenance in vivo. Both R-loop formation and DNA replication initiation are stimulated by the mitochondrial single-stranded DNA binding protein. In an RNase H1 deficient patient cell line, the precise initiation of mtDNA replication is lost and DNA synthesis is initiated from multiple sites throughout the mitochondrial control region. In combination with previously published in vivo data, the findings presented here suggest a model, in which R-loop processing by RNase H1 directs origin-specific initiation of DNA replication in human mitochondria.
  27. J Biol Chem. 2018 Dec 31. pii: jbc.RA118.006741. [Epub ahead of print]
    Aggarwal S, Gabrovsek L, Langeberg LK, Golkowski M, Ong SE, Smith FD, Scott JD.
      Breast cancer screening and new precision therapies have improved patient outcomes. Yet, a positive prognosis is less certain when primary tumors metastasize. Metastasis requires a coordinated program of cellular changes that promote increased survival, migration, and energy consumption. These pathways converge on mitochondrial function, where distinct signaling networks of kinases, phosphatases, and metabolic enzymes regulate these processes. The A-kinase anchoring protein dAKAP1 compartmentalizes protein kinase A (PKA) and other signaling enzymes at the outer mitochondrial membrane and thereby controls mitochondrial function and dynamics. Modulation of these processes occurs in part through regulation of dynamin-related protein 1 (Drp1). Here, we report an inverse relationship between the expression of dAKAP1 and mesenchymal markers in breast cancer. Molecular, cellular, and in silico analyses of breast cancer cell lines confirmed that dAKAP1 depletion is associated with impaired mitochondrial function and dynamics, as well as with increased glycolytic potential and invasiveness. Furthermore, disruption of dAKAP1-PKA complexes affected cell motility and mitochondrial movement toward the leading edge in invasive breast cancer cells. We therefore propose that depletion of dAKAP1-PKA "signaling islands" from the outer mitochondrial membrane augments progression toward metastatic breast cancer.
    Keywords:  A-kinase anchoring protein (AKAP); Signaling islands.; breast cancer; cancer biology; cell migration; cell signaling; mitochondria; protein kinase A (PKA); signal transduction
  28. J Biol Chem. 2019 Jan 03. pii: jbc.RA118.004726. [Epub ahead of print]
    Hada K, Hirota K, Inanobe A, Kako K, Miyata M, Araoi S, Matsumoto M, Ohta R, Arisawa M, Daitoku H, Hanada T, Fukamizu A.
      The tricarboxylic acid (TCA) cycle (or citric acid cycle) is responsible for the complete oxidation of acetyl-CoA and formation of intermediates required for ATP production and other anabolic pathways, such as amino acid synthesis. Here, we uncovered an additional mechanism that may help explain the essential role of the TCA cycle in the early embryogenesis of Caenorhabditis elegans We found that knockdown of citrate synthase (cts-1), the initial and rate-limiting enzyme of the TCA cycle, results in early embryonic arrest, but that this phenotype is not due to ATP and amino acids depletion. As a possible alternative mechanism explaining this developmental deficiency, we observed that cts-1-RNAi embryos had elevated levels of intracellular acetyl-CoA, the starting metabolite of the TCA cycle. Of note, we further discovered that these embryos exhibit hyperacetylation of mitochondrial proteins. We found that supplementation with acetylase-inhibiting polyamines, including spermidine and putrescine, counteracted the protein hyperacetylation and developmental arrest in the cts-1 RNAi embryos. Contrary to the hypothesis that spermidine acts as an acetyl sink for elevated acetyl-CoA, the levels of three forms of acetylspermidine, N1 -acetylspermidine, N8 -acetylspermidine, and N1 ,N8 -diasecylspermidine, were not significantly increased in embryos treated with exogenous spermidine. Instead, we demonstrated that the mitochondrial deacetylase sirtuin 4 (encoded by the sir-2.2 gene) is required for spermidine's suppression of protein hyperacetylation and developmental arrest in the cts-1-RNAi embryos. Taken together, these results suggest the possibility that during early embryogenesis, acetyl-CoA consumption by the TCA cycle in C. elegans prevents protein hyperacetylation and thereby protects mitochondrial function.
    Keywords:  Caenorhabditis elegans (C. elegans); acetyl coenzyme A (acetyl-CoA); citrate synthase; deacetylase; early embryogenesis; mitochondrial protein acetylation; polyamine; post-translational modification (PTM); tricarboxylic acid cycle (TCA cycle) (Krebs cycle)
  29. PLoS Comput Biol. 2019 Jan 02. 15(1): e1006663
    Zhang SY, Zhang SW, Fan XN, Meng J, Chen Y, Gao SJ, Huang Y.
      N6-methyladenosine (m6A) is the most abundant methylation, existing in >25% of human mRNAs. Exciting recent discoveries indicate the close involvement of m6A in regulating many different aspects of mRNA metabolism and diseases like cancer. However, our current knowledge about how m6A levels are controlled and whether and how regulation of m6A levels of a specific gene can play a role in cancer and other diseases is mostly elusive. We propose in this paper a computational scheme for predicting m6A-regulated genes and m6A-associated disease, which includes Deep-m6A, the first model for detecting condition-specific m6A sites from MeRIP-Seq data with a single base resolution using deep learning and Hot-m6A, a new network-based pipeline that prioritizes functional significant m6A genes and its associated diseases using the Protein-Protein Interaction (PPI) and gene-disease heterogeneous networks. We applied Deep-m6A and this pipeline to 75 MeRIP-seq human samples, which produced a compact set of 709 functionally significant m6A-regulated genes and nine functionally enriched subnetworks. The functional enrichment analysis of these genes and networks reveal that m6A targets key genes of many critical biological processes including transcription, cell organization and transport, and cell proliferation and cancer-related pathways such as Wnt pathway. The m6A-associated disease analysis prioritized five significantly associated diseases including leukemia and renal cell carcinoma. These results demonstrate the power of our proposed computational scheme and provide new leads for understanding m6A regulatory functions and its roles in diseases.
  30. Anal Biochem. 2018 Dec 31. pii: S0003-2697(18)31107-2. [Epub ahead of print]
    Kuskovsky R, Buj R, Xu P, Hofbauer S, Doan MT, Jiang H, Bostwick A, Mesaros C, Aird KM, Snyder NW.
      Quantification of cellular deoxyribonucleoside mono- (dNMP), di- (dNDP), triphosphates (dNTPs) and related nucleoside metabolites are difficult due to their physiochemical properties and widely varying abundance. Involvement of dNTP metabolism in cellular processes including senescence and pathophysiological processes including cancer and viral infection make dNTP metabolism an important bioanalytical target. We modified a previously developed ion pairing reversed phase chromatography-mass spectrometry method for the simultaneous quantification and 13C isotope tracing of dNTP metabolites. dNMPs, dNDPs, and dNTPs were chromatographically resolved to avoid mis-annotation of in-source fragmentation. We used commercially available 13C15N-stable isotope labeled analogs as internal standards and show that this isotope dilution approach improves analytical figures of merit. At sufficiently high mass resolution achievable on an Orbitrap mass analyzer, stable isotope resolved metabolomics allows simultaneous isotope dilution quantification and 13C isotope tracing from major substrates including 13C-glucose. As a proof of principle, we quantified dNMP, dNDP and dNTP pools from multiple cell lines. We also identified isotopologue enrichment from glucose corresponding to ribose from the pentose-phosphate pathway in dNTP metabolites.
    Keywords:  High resolution mass spectrometry; Metabolism; Nucleotide; dNTP
  31. Metabolites. 2019 Jan 02. pii: E7. [Epub ahead of print]9(1):
    Warth B, Palermo A, Rattray NJW, Lee NV, Zhu Z, Hoang LT, Cai Y, Mazurek A, Dann S, VanArsdale T, Fantin VR, Shields D, Siuzdak G, Johnson CH.
      The aims of this study were to determine whether combination chemotherapeutics exhibit a synergistic effect on breast cancer cell metabolism. Palbociclib, is a selective inhibitor of cyclin-dependent kinases 4 and 6, and when patients are treated in combination with fulvestrant, an estrogen receptor antagonist, they have improved progression-free survival. The mechanisms for this survival advantage are not known. Therefore, we analyzed metabolic and transcriptomic changes in MCF-7 cells following single and combination chemotherapy to determine whether selective metabolic pathways are targeted during these different modes of treatment. Individually, the drugs caused metabolic disruption to the same metabolic pathways, however fulvestrant additionally attenuated the pentose phosphate pathway and the production of important coenzymes. A comprehensive effect was observed when the drugs were applied together, confirming the combinatory therapy's synergism in the cell model. This study also highlights the power of merging high-dimensional datasets to unravel mechanisms involved in cancer metabolism and therapy.
    Keywords:  RNA-seq; XCMS Online; breast cancer; combination drug therapy; metabolomics; multi-omics
  32. Nat Protoc. 2019 Jan 04.
    Hidalgo San Jose L, Signer RAJ.
      Although protein synthesis is a conserved and essential cellular function, it is often regulated in a cell-type-specific manner to influence cell fate, growth and homeostasis. Most methods used to measure protein synthesis depend on metabolically labeling large numbers of cells with radiolabeled amino acids or amino acid analogs. Because these methods typically depend on specialized growth conditions, they have been largely restricted to yeast, bacteria and cell lines. Application of these techniques to investigating protein synthesis within mammalian systems in vivo has been challenging. The synthesis of O-propargyl-puromycin (OP-Puro), an analog of puromycin that contains a terminal alkyne group, has facilitated the quantification of protein synthesis within individual cells in vivo. OP-Puro enters the acceptor site of ribosomes and incorporates into nascent polypeptide chains. Incorporated OP-Puro can be detected through a click-chemistry reaction that links it to a fluorescently tagged azide molecule. In this protocol, we describe how to administer OP-Puro to mice, obtain cells of interest (here, we use bone marrow cells) just 1 h later, and quantify the amount of protein synthesized per hour by flow cytometry on the basis of OP-Puro incorporation. We have used this approach to show that hematopoietic stem cells (HSCs) exhibit an unusually low rate of protein synthesis relative to other hematopoietic cells, and it can be easily adapted to quantify cell-type-specific rates of protein synthesis across diverse mammalian tissues in vivo. Measurement of protein synthesis within bone marrow cells in a cohort of six mice can be achieved in 8-10 h.
  33. Methods Mol Biol. 2019 ;1880 655-668
    Palikaras K, Lionaki E, Tavernarakis N.
      Mitochondrial selective autophagy (mitophagy) is a critical cellular process for mitochondrial homeostasis and survival both under basal and stress conditions. Distinct cell types display different requirements for mitochondrial turnover depending on their metabolic status, differentiation state, and environmental cues. This points to the necessity of developing novel tools for real-time, tissue-specific assessment of mitophagy. Caenorhabditis elegans is an invaluable model organism for this kind of analysis providing a platform for simultaneous monitoring of mitophagy in vivo in different tissues and cell types, during development, stress conditions, and/or throughout life span. In this chapter we describe three versatile, noninvasive methods, developed for monitoring in vivo early and late mitophagic events in body wall muscles and neuronal cells of C. elegans. These procedures can be readily used and/or provide insights into the generation of novel imaging methods to investigate further the role of mitophagy at the organismal level under normal and pathological conditions.
    Keywords:  Aging; Autophagosome; Autophagy; Caenorhabditis elegans; DsRed; Fluorescent microscopy; Green fluorescent protein (GFP); Lysosomes; Mitochondria; Mitophagy; mtRosella
  34. Nat Cell Biol. 2019 Jan 02.
    Lawrence RE, Zoncu R.
      Long known as terminal degradation stations, lysosomes have emerged as sophisticated signalling centres that govern cell growth, division and differentiation. Lysosomes interface physically and functionally with other organelles, and the master regulator mechanistic target of rapamycin complex 1 kinase is activated on lysosomes in response to nutrient and growth factor inputs. Lysosomes also enable autophagy, a 'self-eating' process essential for quality control and stress adaptation. Faulty execution of lysosomal growth and catabolic programmes drives cancer, neurodegeneration and age-related diseases.
  35. Mol Cell. 2018 Dec 28. pii: S1097-2765(18)30980-8. [Epub ahead of print]
    Liccardi G, Ramos Garcia L, Tenev T, Annibaldi A, Legrand AJ, Robertson D, Feltham R, Anderton H, Darding M, Peltzer N, Dannappel M, Schünke H, Fava LL, Haschka MD, Glatter T, Nesvizhskii A, Schmidt A, Harris PA, Bertin J, Gough PJ, Villunger A, Silke J, Pasparakis M, Bianchi K, Meier P.
      Receptor-interacting protein kinase (RIPK) 1 functions as a key mediator of tissue homeostasis via formation of Caspase-8 activating ripoptosome complexes, positively and negatively regulating apoptosis, necroptosis, and inflammation. Here, we report an unanticipated cell-death- and inflammation-independent function of RIPK1 and Caspase-8, promoting faithful chromosome alignment in mitosis and thereby ensuring genome stability. We find that ripoptosome complexes progressively form as cells enter mitosis, peaking at metaphase and disassembling as cells exit mitosis. Genetic deletion and mitosis-specific inhibition of Ripk1 or Caspase-8 results in chromosome alignment defects independently of MLKL. We found that Polo-like kinase 1 (PLK1) is recruited into mitotic ripoptosomes, where PLK1's activity is controlled via RIPK1-dependent recruitment and Caspase-8-mediated cleavage. A fine balance of ripoptosome assembly is required as deregulated ripoptosome activity modulates PLK1-dependent phosphorylation of downstream effectors, such as BUBR1. Our data suggest that ripoptosome-mediated regulation of PLK1 contributes to faithful chromosome segregation during mitosis.
    Keywords:  BUBR1; PLK1; RIPK1; cancer; caspase-8; cell cycle; cell death; chromosomal instability; mitosis; ripoptosome
  36. Cell Rep. 2019 Jan 02. pii: S2211-1247(18)31963-6. [Epub ahead of print]26(1): 11-17.e2
    Neginskaya MA, Solesio ME, Berezhnaya EV, Amodeo GF, Mnatsakanyan N, Jonas EA, Pavlov EV.
      Permeability transition (PT) is an increase in mitochondrial inner membrane permeability that can lead to a disruption of mitochondrial function and cell death. PT is responsible for tissue damage in stroke and myocardial infarction. It is caused by the opening of a large conductance (∼1.5 nS) channel, the mitochondrial PT pore (mPTP). We directly tested the role of the c-subunit of ATP synthase in mPTP formation by measuring channel activity in c-subunit knockout mitochondria. We found that the classic mPTP conductance was lacking in c-subunit knockout mitochondria, but channels sensitive to the PT inhibitor cyclosporine A could be recorded. These channels had a significantly lower conductance compared with the cyclosporine A-sensitive channels detected in parental cells and were sensitive to the ATP/ADP translocase inhibitor bongkrekic acid. We propose that, in the absence of the c-subunit, mPTP cannot be formed, and a distinct cyclosporine A-sensitive low-conductance channel emerges.
    Keywords:  ATP synthase c-subunit; HAP1-A12 cells; cyclosporine A-sensitive channel; patch-clamp; permeability transition pore
  37. Nat Cell Biol. 2019 Jan;21(1): 85-93
    Jung J, Zeng H, Horng T.
      Recent studies indicate that cellular metabolism plays a key role in supporting immune cell maintenance and development. Here, we review how metabolism guides immune cell activation and differentiation to distinct cellular states, and how differential regulation of metabolism allows for context-dependent support during activation and lineage commitment. We discuss emerging principles of metabolic support of immune cell function in physiology and disease, as well as their general relevance to the field of cell biology.
  38. Redox Biol. 2018 Dec 13. pii: S2213-2317(18)30908-X. [Epub ahead of print] 101073
    Lee M, Hirpara JL, Eu JQ, Sethi G, Wang L, Goh BC, Wong AL.
      Drug resistance invariably limits the response of oncogene-addicted cancer cells to targeted therapy. The upregulation of signal transducer and activator of transcription 3 (STAT3) has been implicated as a mechanism of drug resistance in a range of oncogene-addicted cancers. However, the development of inhibitors against STAT3 has been fraught with challenges such as poor delivery or lack of specificity. Clinical experience with small molecule STAT3 inhibitors has seen efficacy signals, but this success has been tempered by drug limiting toxicities from off-target adverse events. It has emerged in recent years that, contrary to the Warburg theory, certain tumor types undergo metabolic reprogramming towards oxidative phosphorylation (OXPHOS) to satisfy their energy production. In particular, certain drug-resistant oncogene-addicted tumors have been found to rely on OXPHOS as a mechanism of survival. Multiple cellular signaling pathways converge on STAT3, hence the localization of STAT3 to the mitochondria may provide the link between oncogene-induced signaling pathways and cancer cell metabolism. In this article, we review the role of STAT3 and OXPHOS as targets of novel therapeutic strategies aimed at restoring drug sensitivity in treatment-resistant oncogene-addicted tumor types. Apart from drugs which have been re-purposed as OXPHOS inhibitors for-anti-cancer therapy (e.g., metformin and phenformin), several novel compounds in the drug-development pipeline have demonstrated promising pre-clinical and clinical activity. However, the clinical development of OXPHOS inhibitors remains in its infancy. The further identification of compounds with acceptable toxicity profiles, alongside the discovery of robust companion biomarkers of OXPHOS inhibition, would represent tangible early steps in transforming the therapeutic landscape of cancer cell metabolism.
    Keywords:  Cancer cell metabolism; OXPHOS inhibitors; Oxidative phosphorylation (OXPHOS); STAT inhibitors; STAT3 signaling pathways
  39. Biochem Biophys Res Commun. 2018 Dec 26. pii: S0006-291X(18)32817-1. [Epub ahead of print]
    Zhao M, Chen J, Mao K, She H, Ren Y, Gui C, Wu X, Zou F, Li W.
      Parkinson's disease (PD) is a progressive neurodegenerative disease characterized by the loss of dopaminergic neurons in the substantia nigra. Prevailing evidence suggests that abnormal autophagy and mitochondrial dysfunction participate in the process of PD. However, many damages of neuronal functions are regulated by intracellular Ca2+ signaling and the contribution of mitochondrial Ca2+ to the process of neurodegeneration is still unclear. MPP+, the metabolite of a neurotoxin MPTP, causes symptom of PD in animal models by selectively destroying dopaminergic neurons in substantia nigra. Here we report that mitochondrial Ca2+ uniporter (MCU) participated in MPP+-induced autophagic cell death in SH-SY5Y cells. Pharmacological agonist of MCU or exogenous expressed MCU can partially reduce MPP+-induced autophagic cell death. Down-regulation of MCU enhanced autophagic cell death via AMPK activation, which was independent of Beclin1 and PI3K. These findings show that the mitochondrial calcium dyshomeostasis contributes to MPP+-induced neuronal degeneration, and MCU may be a potential therapeutic target of PD through the prevention of pathological autophagy.
    Keywords:  AMPK; Autophagy; Calcium; MCU; MPP(+)
  40. Nat Cell Biol. 2019 Jan;21(1): 63-71
    Kim J, Guan KL.
      The highly conserved protein kinase mechanistic target of rapamycin (mTOR; originally known as mammalian target of rapamycin) is a central cell growth regulator connecting cellular metabolism and growth with a wide range of environmental inputs as part of mTOR complex 1 (mTORC1) and mTORC2. In this Review, we introduce the landmark discoveries in the mTOR field, starting from the isolation of rapamycin to the molecular characterizations of key components of the mTORC signalling network with an emphasis on amino acid sensing, and discuss the perspectives of mTORC inhibitors in therapeutic applications.
  41. Nat Commun. 2019 Jan 03. 10(1): 15
    Qian Y, Lynch JH, Guo L, Rhodes D, Morgan JA, Dudareva N.
      In addition to being a vital component of proteins, phenylalanine is also a precursor of numerous aromatic primary and secondary metabolites with broad physiological functions. In plants phenylalanine is synthesized predominantly via the arogenate pathway in plastids. Here, we describe the structure, molecular players and subcellular localization of a microbial-like phenylpyruvate pathway for phenylalanine biosynthesis in plants. Using a reverse genetic approach and metabolic flux analysis, we provide evidence that the cytosolic chorismate mutase is responsible for directing carbon flux towards cytosolic phenylalanine production via the phenylpyruvate pathway. We also show that an alternative transcription start site of a known plastidial enzyme produces a functional cytosolic prephenate dehydratase that catalyzes the conversion of prephenate to phenylpyruvate, the intermediate step between chorismate mutase and phenylpyruvate aminotransferase. Thus, our results complete elucidation of phenylalanine biosynthesis via phenylpyruvate in plants, showing that this pathway splits from the known plastidial arogenate pathway at chorismate, instead of prephenate as previously thought, and the complete pathway is localized in the cytosol.
  42. Sci Signal. 2019 Jan 01. pii: eaau9048. [Epub ahead of print]12(562):
    Schneditz G, Elias JE, Pagano E, Zaeem Cader M, Saveljeva S, Long K, Mukhopadhyay S, Arasteh M, Lawley TD, Dougan G, Bassett A, Karlsen TH, Kaser A, Kaneider NC.
      The sodium potassium pump (Na/K-ATPase) ensures the electrochemical gradient of a cell through an energy-dependent process that consumes about one-third of regenerated ATP. We report that the G protein-coupled receptor GPR35 interacted with the α chain of Na/K-ATPase and promotes its ion transport and Src signaling activity in a ligand-independent manner. Deletion of Gpr35 increased baseline Ca2+ to maximal levels and reduced Src activation and overall metabolic activity in macrophages and intestinal epithelial cells (IECs). In contrast, a common T108M polymorphism in GPR35 was hypermorphic and had the opposite effects to Gpr35 deletion on Src activation and metabolic activity. The T108M polymorphism is associated with ulcerative colitis and primary sclerosing cholangitis, inflammatory diseases with a high cancer risk. GPR35 promoted homeostatic IEC turnover, whereas Gpr35 deletion or inhibition by a selective pepducin prevented inflammation-associated and spontaneous intestinal tumorigenesis in mice. Thus, GPR35 acts as a central signaling and metabolic pacesetter, which reveals an unexpected role of Na/K-ATPase in macrophage and IEC biology.
  43. Adv Med Sci. 2018 Dec 31. pii: S1896-1126(18)30346-8. [Epub ahead of print]64(1): 104-110
    Szefel J, Danielak A, Kruszewski WJ.
      Difference in the metabolism of normal and cancer cells inspires to search for new, more specific and less toxic therapies than those currently used. The development of tumors is conditioned by genetic changes in cancer-transformed cells, immunological tolerance and immunosuppression. At the initial stages of carcinogenesis, the immune system shows anti-tumor activity, however later, cancer disrupts the function of Th1/Th17/Th2 lymphocytes by regulatory T (Treg) cells, tumor-associated macrophages (TAMs), and myeloid-derived suppressor cells (MDSCs) and finally causes immunosuppression. Recently, much attention has been devoted to the influence of l-arginine metabolism disorders on both carcinogenesis and the immune system. l-Arginine is essential for the maturation of the T cell receptor zeta (TCRζ), and its absence deprives T-cells of the ability to interact with tumor antigens. MDSCs deplete l-arginine due to a high expression of arginase 1 (ARG1) and their number increases 4-10 times depending on the type of the cancer. L-Arginine has been shown to be essential for the survival and progression of arginine auxotrophic tumors. However, the progression of arginine non-auxotrophic tumors is independent of exogenous l-arginine, because these tumors have arginine-succinate synthetase (ASS1) activity and are available to produce l-arginine from citrulline. Clinical studies have confirmed the high efficacy of arginine auxotrophic tumors therapy based on the elimination of l-arginine. However, l-arginine supplementation may improve the results of treatment of patients with arginine non-auxotrophic cancer. This review is an attempt to explain the seemingly contradictory results of oncological therapies based on the deprivation or supplementation of l-arginine.
    Keywords:  Auxotrophy; Cancer; Immune system; L-Arginine; Myeloid-derived suppressor cells
  44. Cell Rep. 2019 Jan 02. pii: S2211-1247(18)31966-1. [Epub ahead of print]26(1): 192-208.e6
    Garcia D, Hellberg K, Chaix A, Wallace M, Herzig S, Badur MG, Lin T, Shokhirev MN, Pinto AFM, Ross DS, Saghatelian A, Panda S, Dow LE, Metallo CM, Shaw RJ.
      The AMP-activated protein kinase (AMPK) is a highly conserved master regulator of metabolism, whose activation has been proposed to be therapeutically beneficial for the treatment of several metabolic diseases, including nonalcoholic fatty liver disease (NAFLD). NAFLD, characterized by excessive accumulation of hepatic lipids, is the most common chronic liver disease and a major risk factor for development of nonalcoholic steatohepatitis, type 2 diabetes, and other metabolic conditions. To assess the therapeutic potential of AMPK activation, we have generated a genetically engineered mouse model, termed iAMPKCA, where AMPK can be inducibly activated in vivo in mice in a spatially and temporally restricted manner. Using this model, we show that liver-specific AMPK activation reprograms lipid metabolism, reduces liver steatosis, decreases expression of inflammation and fibrosis genes, and leads to significant therapeutic benefits in the context of diet-induced obesity. These findings further support AMPK as a target for the prevention and treatment of NAFLD.
    Keywords:  AMPK; GEMM; NAFLD; lipid metabolism; liver steatosis; obesity