bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2019‒05‒12
fifty-nine papers selected by
Christian Frezza
University of Cambridge, MRC Cancer Unit


  1. J Cell Sci. 2019 May 10. pii: jcs.224766. [Epub ahead of print]
    Tanaka H, Okazaki T, Aoyama S, Yokota M, Koike M, Okada Y, Fujiki Y, Gotoh Y.
      Peroxisomes cooperate with mitochondria in the performance of cellular metabolic functions such as fatty acid oxidation and maintenance of redox homeostasis. Whether peroxisomes also regulate mitochondrial fission-fusion dynamics or mitochondrion-dependent apoptosis has remained unclear, however. We now show that genetic ablation of the peroxins Pex3 or Pex5, which are essential for peroxisome biogenesis, resulted in mitochondrial fragmentation in MEFs in a manner dependent on Drp1. Conversely, treatment with 4-PBA, a peroxisome proliferator, resulted in mitochondrial elongation in wild-type MEFs, but not in Pex3-deficient MEFs. We further found that peroxisome deficiency increased the levels of cytosolic cytochrome c and caspase activity under basal conditions without inducing apoptosis. It also greatly enhanced etoposide-induced caspase activation and apoptosis, indicative of an enhanced cellular sensitivity to death signals. Together, our data unveil a previously unrecognized role of peroxisomes in the regulation of mitochondrial dynamics and mitochondrion-dependent apoptosis. Effects of peroxin genes mutations on mitochondrion-dependent apoptosis may contribute to pathogenesis of peroxisome biogenesis disorders.
    Keywords:  Apoptosis; Caspase; Drp1; Mitochondria; Organelles; Peroxisome
    DOI:  https://doi.org/10.1242/jcs.224766
  2. Proc Natl Acad Sci U S A. 2019 May 07. pii: 201903535. [Epub ahead of print]
    Boreikaite V, Wicky BIM, Watt IN, Clarke J, Walker JE.
      The endogenous inhibitor of ATP synthase in mitochondria, called IF1, conserves cellular energy when the proton-motive force collapses by inhibiting ATP hydrolysis. Around neutrality, the 84-amino-acid bovine IF1 is thought to self-assemble into active dimers and, under alkaline conditions, into inactive tetramers and higher oligomers. Dimerization is mediated by formation of an antiparallel α-helical coiled-coil involving residues 44-84. The inhibitory region of each monomer from residues 1-46 is largely α-helical in crystals, but disordered in solution. The formation of the inhibited enzyme complex requires the hydrolysis of two ATP molecules, and in the complex the disordered region from residues 8-13 is extended and is followed by an α-helix from residues 14-18 and a longer α-helix from residue 21, which continues unbroken into the coiled-coil region. From residues 21-46, the long α-helix binds to other α-helices in the C-terminal region of predominantly one of the β-subunits in the most closed of the three catalytic interfaces. The definition of the factors that influence the self-association of IF1 is a key to understanding the regulation of its inhibitory properties. Therefore, we investigated the influence of pH and salt-types on the self-association of bovine IF1 and the folding of its unfolded region. We identified the equilibrium between dimers and tetramers as a potential central factor in the in vivo modulation of the inhibitory activity and suggest that the intrinsically disordered region makes its inhibitory potency exquisitely sensitive and responsive to physiological changes that influence the capability of mitochondria to make ATP.
    Keywords:  ATP hydrolysis; inhibitor; intrinsically disordered protein; mitochondria; regulation
    DOI:  https://doi.org/10.1073/pnas.1903535116
  3. Autophagy. 2019 May 07. 1-10
    Soutar MPM, Kempthorne L, Annuario E, Luft C, Wray S, Ketteler R, Ludtmann MHR, Plun-Favreau H.
      Mitochondrial quality control is essential for maintaining a healthy population of mitochondria. Two proteins associated with Parkinson disease, the kinase PINK1 and the E3 ubiquitin ligase PRKN, play a central role in the selective degradation of heavily damaged mitochondria (mitophagy), thus avoiding their toxic accumulation. Most of the knowledge on PINK1-PRKN mitophagy comes from in vitro experiments involving the treatment of mammalian cells with high concentrations of mitochondrial uncouplers, such as CCCP. These chemicals have been shown to mediate off target effects, other than mitochondrial depolarization. A matter of controversy between mitochondrial physiologists and cell biologists is the discrepancy between concentrations of CCCP needed to activate mitophagy (usually >10 μM), when compared to the much lower concentrations used to depolarize mitochondria (<1 μM). Thus, there is an urgent need for optimizing the current methods to assess PINK1-PRKN mitophagy in vitro. In this study, we address the utilization of high CCCP concentrations commonly used to activate mitophagy. Combining live fluorescence microscopy and biochemistry, we show that the FBS/BSA in the cell culture medium reduces the ability of CCCP to induce PINK1 accumulation at depolarized mitochondria, subsequent PRKN recruitment and ubiquitin phosphorylation, and ultimately mitochondrial clearance. As a result, high concentrations of CCCP are required to induce mitophagy in FBS/BSA containing media. These data unite mitochondrial physiology and mitophagy studies and are a first step toward a consensus on optimal experimental conditions for PINK1-PRKN mitophagy and mitochondrial physiology investigations to be carried out in parallel. Abbreviations: BSA: bovine serum albumin; CCCP: carbonyl cyanide m-chlorophenylhydrazone; DMEM: dulbecco's Modified Eagle's Medium; DNP: 2,4-dinitrophenol; FBS: fetal bovine serum; FCCP: carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone; GSH: glutathione; HBSS: Hanks' balanced salt solution; mtKeima: mitochondria-targeted monomeric keima-red; PBS: phosphate buffered saline; PD: Parkinson disease; PINK1: PTEN induced kinase 1; POE SHSY5Ys: FLAG-PRKN over-expressing SHSY5Y cells; SDS-PAGE: sodium dodecyl sulfate polyacrylamide gel electrophoresis; TMRM: tetramethylrhodamine methyl ester; WB: western blot; WT: wild-type; ΔΨm: mitochondrial membrane potential.
    Keywords:  BSA; CCCP; PINK1; PRKN; mitophagy
    DOI:  https://doi.org/10.1080/15548627.2019.1603549
  4. Cell Metab. 2019 May 07. pii: S1550-4131(19)30191-3. [Epub ahead of print]29(5): 1015-1017
    Frankino PA, Moehle EA, Dillin A.
      Mitochondria are organelles descended from an endosymbiosed bacterium, and many bacterial toxins impair mitochondria, likely as an echo of ancient bacterial warfare. However, the signal transduction pathways that translate mitochondrial dysfunction into a transcriptional program for detoxification have not been well understood. In this issue of Cell Metabolism, Mao et al. (2019) provide insight into how mitochondrial perturbations can activate both the mitochondrial unfolded protein response (UPRmito) and detoxification response and, importantly, how these responses differentially affect organismal physiology under normal conditions or with pathogenic challenges.
    DOI:  https://doi.org/10.1016/j.cmet.2019.04.007
  5. Mol Cell Biol. 2019 May 06. pii: MCB.00109-19. [Epub ahead of print]
    Agarwal E, Altman BJ, Seo JH, Bertolini I, Ghosh JC, Kaur A, Kossenkov AV, Languino LR, Gabrilovich DI, Speicher DW, Dang CV, Altieri DC.
      Myc is a universal oncogene that promotes aggressive cancer, but its role in metastasis has remained elusive. Here, we show that Myc transcriptionally controls a gene network of subcellular mitochondrial trafficking that includes atypical mitochondrial GTPases RHOT1 and RHOT2, adapter protein TRAK2, anterograde motor Kif5B and effector of mitochondrial fission, Drp1. Interference with this pathway deregulates mitochondrial dynamics, shuts off subcellular organelle movements and prevents the recruitment of mitochondria to the cortical cytoskeleton of tumor cells. In turn, this inhibits tumor chemotaxis, blocks cell invasion and prevents metastatic spreading in preclinical models. Therefore, Myc regulation of mitochondrial trafficking enables tumor cell motility and metastasis.
    DOI:  https://doi.org/10.1128/MCB.00109-19
  6. Cancers (Basel). 2019 May 03. pii: E619. [Epub ahead of print]11(5):
    Sanford-Crane H, Abrego J, Sherman MH.
      Fibroblast activation is an accompanying feature of solid tumor progression, resembling a conserved host response to tissue damage. Cancer-associated fibroblasts (CAFs) comprise a heterogeneous and plastic population with increasingly appreciated roles in tumor growth, metastatic capacity, and response to therapy. Classical features of fibroblasts in a wound-healing response, including profound extracellular matrix production and cytokine release, are recapitulated in cancer. Emerging evidence suggests that fibroblastic cells in the microenvironments of solid tumors also critically modulate cellular metabolism in the neoplastic compartment through mechanisms including paracrine transfer of metabolites or non-cell-autonomous regulation of metabolic signaling pathways. These metabolic functions may represent common mechanisms by which fibroblasts stimulate growth of the regenerating epithelium during a wound-healing reaction, or may reflect unique co-evolution of cancer cells and surrounding stroma within the tumor microenvironment. Here we review the recent literature supporting an important role for CAFs in regulation of cancer cell metabolism, and relevant pathways that may serve as targets for therapeutic intervention.
    Keywords:  cancer metabolism; cancer-associated fibroblast; tumor-stroma crosstalk
    DOI:  https://doi.org/10.3390/cancers11050619
  7. Cell Metab. 2019 Apr 19. pii: S1550-4131(19)30187-1. [Epub ahead of print]
    Kumar S, Sharife H, Kreisel T, Mogilevsky M, Bar-Lev L, Grunewald M, Aizenshtein E, Karni R, Paldor I, Shlomi T, Keshet E.
      Differential exposure of tumor cells to blood-borne and angiocrine factors results in diverse metabolic microenvironments conducive for non-genetic tumor cell diversification. Here, we harnessed a methodology for retrospective sorting of fully functional, stroma-free cancer cells solely on the basis of their relative distance from blood vessels (BVs) to unveil the whole spectrum of genes, metabolites, and biological traits impacted by BV proximity. In both grafted mouse tumors and natural human glioblastoma (GBM), mTOR activity was confined to few cell layers from the nearest perfused vessel. Cancer cells within this perivascular tier are distinguished by intense anabolic metabolism and defy the Warburg principle through exercising extensive oxidative phosphorylation. Functional traits acquired by perivascular cancer cells, namely, enhanced tumorigenicity, superior migratory or invasive capabilities, and, unexpectedly, exceptional chemo- and radioresistance, are all mTOR dependent. Taken together, the study revealed a previously unappreciated graded metabolic zonation directly impacting the acquisition of multiple aggressive tumor traits.
    Keywords:  blood vessels; glioblastoma; mTOR pathway; metabolic compartmentalization; tumor heterogeneity; tumor microenvironment; tumor vasculature
    DOI:  https://doi.org/10.1016/j.cmet.2019.04.003
  8. Semin Cell Dev Biol. 2019 May 03. pii: S1084-9521(18)30203-9. [Epub ahead of print]
    Audrito V, Managò A, Gaudino F, Deaglio S.
      Cancer cells rewire their metabolism to support proliferation, growth and survival. In metastatic melanoma the BRAF oncogenic pathway is a master regulator of this process, highlighting the importance of metabolic reprogramming in the pathogenesis of this tumor and offering potential therapeutic approaches. Metabolic adaptation of melanoma cells generally requires increased amounts of NAD+, an essential redox cofactor in cellular metabolism and a signaling molecule. Nicotinamide phosphoribosyltransferase (NAMPT) is the most important NAD+ biosynthetic enzyme in mammalian cells and a direct target of the BRAF oncogenic signaling pathway. These findings suggest that NAMPT is an attractive new therapeutic target, particularly in combination strategies with BRAF or MEK inhibitors. Here we review current knowledge on how oncogenic signaling reprograms metabolism in BRAF-mutated melanoma, and discuss how NAMPT/NAD+ axis contributes to these processes. Lastly, we present evidence supporting a role of NAMPT as a novel therapeutic target in metastatic melanoma.
    Keywords:  BRAF; Metabolic reprogramming; NAD(+)metabolism; NAMPT; combination therapy; melanoma
    DOI:  https://doi.org/10.1016/j.semcdb.2019.05.001
  9. Front Physiol. 2019 ;10 419
    Tezze C, Romanello V, Sandri M.
      Fibroblast growth factor 21 (FGF21) is a hormone that regulates important metabolic pathways. FGF21 is expressed in several metabolically active organs and interacts with different tissues. The FGF21 function is complicated and well debated due to its different sites of production and actions. Striated muscles are plastic tissues that undergo adaptive changes within their structural and functional properties in order to meet their different stresses, recently, they have been found to be an important source of FGF21. The FGF21 expression and secretion from skeletal muscles happen in both mouse and in humans during their different physiological and pathological conditions, including exercise and mitochondrial dysfunction. In this review, we will discuss the recent findings that identify FG21 as beneficial and/or detrimental cytokine interacting as an autocrine or endocrine in order to modulate cellular function, metabolism, and senescence.
    Keywords:  FGF21; cytokine; metabolism; mitochondria; myokine; regulation; skeletal muscle
    DOI:  https://doi.org/10.3389/fphys.2019.00419
  10. Sci Signal. 2019 May 07. pii: eaat7397. [Epub ahead of print]12(580):
    Kuo IY, Brill AL, Lemos FO, Jiang JY, Falcone JL, Kimmerling EP, Cai Y, Dong K, Kaplan DL, Wallace DP, Hofer AM, Ehrlich BE.
      Mitochondria and the endoplasmic reticulum (ER) have an intimate functional relationship due to tethering proteins that bring their membranes in close (~30 nm) apposition. One function of this interorganellar junction is to increase the efficiency of Ca2+ transfer into mitochondria, thus stimulating mitochondrial respiration. Here, we showed that the ER cation-permeant channel polycystin 2 (PC2) functions to reduce mitochondria-ER contacts. In cell culture models, PC2 knockdown led to a 50% increase in mitofusin 2 (MFN2) expression, an outer mitochondrial membrane GTPase. Live-cell super-resolution and electron microscopy analyses revealed enhanced MFN2-dependent tethering between the ER and mitochondria in PC2 knockdown cells. PC2 knockdown also led to increased ER-mediated mitochondrial Ca2+ signaling, bioenergetic activation, and mitochondrial density. Mutation or deletion of the gene encoding for PC2 results in autosomal dominant polycystic kidney disease (ADPKD), a condition characterized by numerous fluid-filled cysts. In cell culture models and mice with kidney-specific PC2 knockout, knockdown of MFN2 rescued defective mitochondrial Ca2+ transfer and diminished cell proliferation in kidney cysts. Consistent with these results, cyst-lining epithelial cells from human ADPKD kidneys had a twofold increase in mitochondria and MFN2 expression. Our data suggest that PC2 normally serves to limit key mitochondrial proteins at the ER-mitochondrial interface and acts as a checkpoint for mitochondrial biogenesis and bioenergetics. Loss of this regulation may contribute to the increased oxidative metabolism and aberrant cell proliferation typical of kidney cysts in ADPKD.
    DOI:  https://doi.org/10.1126/scisignal.aat7397
  11. Clin Exp Metastasis. 2019 May 09.
    Williams D, Fingleton B.
      Metabolic alterations are established as a hallmark of cancer. Such hallmark changes in cancer metabolism are characterized by reprogramming of energy-producing pathways and increases in the generation of biosynthetic intermediates to meet the needs of rapidly proliferating tumor cells. Various metabolic phenotypes such as aerobic glycolysis, increased glutamine consumption, and lipolysis have also been associated with the process of metastasis. However, in addition to the energy and biosynthetic alterations, a number of secondary functions of enzymes and metabolites are emerging that specifically contribute to metastasis. Here, we describe atypical intracellular roles of metabolic enzymes, extracellular functions of metabolic enzymes, roles of metabolites as signaling molecules, and epigenetic regulation mediated by altered metabolism, all of which can affect metastatic progression. We highlight how some of these mechanisms are already being exploited for therapeutic purposes, and discuss how others show similar potential.
    Keywords:  ATP citrate lyase; Epigenetic; Glutaminase; Mutant isocitrate dehydrogenase; Phosphohexose isomerase
    DOI:  https://doi.org/10.1007/s10585-019-09967-0
  12. J Clin Invest. 2019 May 07. pii: 127277. [Epub ahead of print]130
    Galvan DL, Long J, Green N, Chang BH, Lin JS, Schumacker PT, Truong LD, Overbeek P, Danesh FR.
      Phosphorylation of Dynamin-related protein1 (Drp1) represents an important regulatory mechanism for mitochondrial fission. Here we established the role of Drp1 Serine 600 (S600) phosphorylation on mitochondrial fission in vivo, and assessed the functional consequences of targeted elimination of the Drp1S600 phosphorylation site in progression of diabetic nephropathy (DN). We generated a knockin mouse in which S600 was mutated to alanine (Drp1S600A). We found that diabetic Drp1S600A mice exhibited improved biochemical and histological features of DN along with reduced mitochondrial fission and diminished mitochondrial ROS in vivo. Importantly, we observed that the effect of Drp1S600 phosphorylation on mitochondrial fission in the diabetic milieu was stimulus- but not cell type-dependent. Mechanistically, we showed that mitochondrial fission in high glucose conditions occurs through concomitant binding of phospho-Drp1S600 with mitochondrial fission factor (Mff) and actin-related protein 3 (Arp3), ultimately leading to accumulation of F-actin and Drp1 on the mitochondria. Taken together, these findings establish that a single phosphorylation site in Drp1 can regulate mitochondrial fission and progression of DN in vivo, and highlight the stimulus-specific consequences of Drp1S600 phosphorylation on mitochondrial dynamics.
    Keywords:  Cytoskeleton; Diabetes; Metabolism; Mitochondria; Nephrology
    DOI:  https://doi.org/10.1172/JCI127277
  13. Am J Physiol Regul Integr Comp Physiol. 2019 May 08.
    Mathers KE, Staples JF.
      During hibernation, small mammals, including the 13-lined ground squirrel (Ictidomys tridecemlineatus), cycle between two distinct metabolic states: torpor, where metabolic rate is suppressed by >95% and body temperature falls to ~5 °C, and interbout euthermia (IBE), where both metabolic rate and body temperature rapidly increase to euthermic levels. Suppression of whole-animal metabolism during torpor is paralleled by rapid, reversible suppression of mitochondrial respiration. We hypothesized that these changes in mitochondrial metabolism are regulated by post-translational modifications to mitochondrial proteins. Differential 2D gel electrophoresis and 2D Blue-Native PAGE revealed differences in the isoelectric point of several liver mitochondrial proteins between torpor and IBE. Q-TOF LC/MS and MALDI mass spectrometry identified these as proteins involved in β-oxidation, Krebs cycle, ROS detoxification and the electron transport system (ETS). Immunoblots revealed that subunit 1 of ETS complex IV was acetylated during torpor but not IBE. Phosphoprotein staining revealed significantly greater phosphorylation of succinyl-coA ligase and the flavoprotein subunit of ETS complex II in IBE compared to torpor. In addition, the 75 kDa subunit of ETS complex I was 1.5-fold more phosphorylated during torpor. In vitro treatment with alkaline phosphatase increased the maximal activity of complex I from liver mitochondria isolated from torpid animals but did not change complex I activity from IBE animals. By contrast, phosphatase treatment decreased complex II activity in IBE, but not torpor. These findings suggest that the rapid changes in mitochondrial metabolism in hibernators are mediated by post-translational modifications of key metabolic enzymes, perhaps by intramitochondrial kinases and deacetylases.
    Keywords:  Acetylation; Metabolic suppression; Mitochondrial metabolism; Phosphorylation; Succinate dehydrogenase
    DOI:  https://doi.org/10.1152/ajpregu.00052.2019
  14. Cancer Discov. 2019 May 08. pii: CD-18-1391. [Epub ahead of print]
    Loizou E, Banito A, Livshits G, Ho YJ, Koche RP, Sanchez-Rivera FJ, Mayle A, Chen CC, Kinalis S, Bagger FO, Kastenhuber ER, Durham BH, Lowe SW.
      Mutations in the TP53 tumor suppressor gene are common in many cancer types, including the acute myeloid leukemia (AML) subtype known as complex karyotype (CK) AML. Here, we identify a gain-of-function (GOF) p53 mutation that accelerates CK-AML initiation beyond p53 loss and, surprisingly, is required for disease maintenance. The p53R172H mutation (TP53R175H in humans) exhibits a neomorphic function by promoting aberrant self-renewal in leukemic cells, a phenotype that is present in hematopoietic stem and progenitor cells (HSPCs) even prior to their transformation. We identify the Forkhead box H1 transcription factor (Foxh1) as a critical mediator of mutant p53 function that binds to and regulates stem cell-associated genes and transcriptional programs. Our results identify a context where mutant p53 acts as a bona fide oncogene that contributes to the pathogenesis of CK-AML and suggests a common biological theme for TP53 gain-of-function in cancer.
    DOI:  https://doi.org/10.1158/2159-8290.CD-18-1391
  15. Redox Biol. 2019 Apr 16. pii: S2213-2317(19)30006-0. [Epub ahead of print] 101191
    Patel B, Zheleznova NN, Ray SC, Sun J, Cowley AW, O'Connor PM.
      Hv1 is a voltage-gated proton channel highly expressed in immune cells where, it acts to maintain NAD(P)H oxidase activity during the respiratory burst. We have recently reported that Hv1 is expressed in cells of the medullary thick ascending limb (mTAL) of the kidney and is critical to augment reactive oxygen species (ROS) production by this segment. While Hv1 is associated with NOX2 mediated ROS production in immune cells, the source of the Hv1 dependent ROS in mTAL remains unknown. In the current study, the rate of ROS formation was quantified in freshly isolated mTAL using dihydroethidium and ethidium fluorescence. Hv1 dependent ROS production was stimulated by increasing bath osmolality and ammonium chloride (NH4Cl) loading. Loss of either p67phox or NOX4 did not abolish the formation of ROS in mTAL. Hv1 was localized to mitochondria within mTAL, and the mitochondrial superoxide scavenger mitoTEMPOL reduced ROS formation. Rotenone significantly increased ROS formation and decreased mitochondrial membrane potential in mTAL from wild-type rats, while treatment with this inhibitor decreased ROS formation and increased mitochondrial membrane potential in mTAL from Hv1-/- mutant rats. These data indicate that NADPH oxidase is not the primary source of Hv1 dependent ROS production in mTAL. Rather Hv1 localizes to the mitochondria in mTAL and modulates the formation of ROS by complex I. These data provide a potential explanation for the effects of Hv1 on ROS production in cells independent of its contribution to maintenance of cell membrane potential and intracellular pH.
    DOI:  https://doi.org/10.1016/j.redox.2019.101191
  16. Front Immunol. 2019 ;10 775
    Wculek SK, Khouili SC, Priego E, Heras-Murillo I, Sancho D.
      Dendritic cells (DCs) control innate and adaptive immunity by patrolling tissues to gather antigens and danger signals derived from microbes and tissue. Subsequently, DCs integrate those environmental cues, orchestrate immunity or tolerance, and regulate tissue homeostasis. Recent advances in the field of immunometabolism highlight the notion that immune cells markedly alter cellular metabolic pathways during differentiation or upon activation, which has important implications on their functionality. Previous studies showed that active oxidative phosphorylation in mitochondria is associated with immature or tolerogenic DCs, while increased glycolysis upon pathogen sensing can promote immunogenic DC functions. However, new results in the last years suggest that regulation of DC metabolism in steady state, after immunogenic activation and during tolerance in different pathophysiological settings, may be more complex. Moreover, ontogenically distinct DC subsets show different functional specializations to control T cell responses. It is, thus, relevant how metabolism influences DC differentiation and plasticity, and what potential metabolic differences exist among DC subsets. Better understanding of the emerging connection between metabolic adaptions and functional DC specification will likely allow the development of therapeutic strategies to manipulate immune responses.
    Keywords:  AMP-activated protein kinase; DC subsets; dendritic cell; glycolysis; hypoxia-inducible factor; mammalian target of rapamycin; metabolism; mitochondria
    DOI:  https://doi.org/10.3389/fimmu.2019.00775
  17. Mol Metab. 2019 Apr 17. pii: S2212-8778(18)30958-X. [Epub ahead of print]
    Sebaa R, Johnson J, Pileggi C, Norgren M, Xuan J, Sai Y, Tong Q, Krystkowiak I, Bondy-Chorney E, Davey NE, Krogan N, Downey M, Harper ME.
      OBJECTIVE: Brown adipose tissue (BAT) is important for thermoregulation in many mammals. Uncoupling protein 1 (UCP1) is the critical regulator of thermogenesis in BAT. Here we aimed to investigate the deacetylation control of BAT and to investigate a possible functional connection between UCP1 and sirtuin 3 (SIRT3), the master mitochondrial lysine deacetylase.METHODS: We carried out physiological, molecular, and proteomic analyses of BAT from wild-type and Sirt3KO mice when BAT is activated. Mice were either cold exposed for 2 days or were injected with the β3-adrenergic agonist, CL316,243 (1 mg/kg; i.p.). Mutagenesis studies were conducted in a cellular model to assess the impact of acetylation lysine sites on UCP1 function. Cardiac punctures were collected for proteomic analysis of blood acylcarnitines. Isolated mitochondria were used for functional analysis of OXPHOS proteins.
    RESULTS: Our findings showed that SIRT3 absence in mice resulted in impaired BAT lipid use, whole body thermoregulation, and respiration in BAT mitochondria, without affecting UCP1 expression. Acetylome profiling of BAT mitochondria revealed that SIRT3 regulates acetylation status of many BAT mitochondrial proteins including UCP1 and crucial upstream proteins. Mutagenesis work in cells suggested that UCP1 activity was independent of direct SIRT3-regulated lysine acetylation. However, SIRT3 impacted BAT mitochondrial proteins activities of acylcarnitine metabolism and specific electron transport chain complexes, CI and CII.
    CONCLUSIONS: Our data highlight that SIRT3 likely controls BAT thermogenesis indirectly by targeting pathways upstream of UCP1.
    Keywords:  Acetylation; Acylcarnitines; Brown adipose tissue; Fatty acid oxidation; Mitochondria; Oxidative phosphorylation; Sirtuin 3; Thermogenesis; Thermoregulation; Uncoupling protein 1
    DOI:  https://doi.org/10.1016/j.molmet.2019.04.008
  18. Cell Metab. 2019 Apr 28. pii: S1550-4131(19)30188-3. [Epub ahead of print]
    Duman C, Yaqubi K, Hoffmann A, Acikgöz AA, Korshunov A, Bendszus M, Herold-Mende C, Liu HK, Alfonso J.
      Glioblastoma multiforme (GBM) undergoes metabolic reprogramming to meet the high ATP and anabolic demands of the tumor cells. However, the role of fatty acid oxidation (FAO) and its regulators in the GBM context has been largely unknown. Here, we show that the neural stem cell pro-proliferative factor acyl-CoA-binding protein (ACBP, also known as DBI) is highly expressed in GBM, and by binding to acyl-CoAs, it cell-autonomously maintains high proliferation rates, promoting tumor growth and poor survival in several preclinical models. Mechanistic experiments using ACBP-acyl-CoA binding affinity variants and pharmacological FAO modulators suggest that ACBP supports tumor growth by controlling the availability of long-chain fatty acyl-CoAs to mitochondria, promoting FAO in GBM. Thus, our findings uncover a critical link between lipid metabolism and GBM progression established by ACBP and offer a potential therapeutic strategy for an effective anti-proliferative metabolic management of GBM.
    Keywords:  ACBP; DBI; GABA(A) receptor; acyl-CoA; brain cancer; glioblastoma; lipid metabolism; mitochondrial respiration; senescence; β-oxidation
    DOI:  https://doi.org/10.1016/j.cmet.2019.04.004
  19. J Cachexia Sarcopenia Muscle. 2019 May 08.
    Goron A, Lamarche F, Blanchet S, Delangle P, Schlattner U, Fontaine E, Moinard C.
      BACKGROUND: Animal studies and clinical data support the interest of citrulline as a promising therapeutic for sarcopenia. Citrulline is known to stimulate muscle protein synthesis, but how it affects energy metabolism to support the highly energy-dependent protein synthesis machinery is poorly understood.METHODS: Here, we used myotubes derived from primary culture of mouse myoblasts to study the effect of citrulline on both energy metabolism and protein synthesis under different limiting conditions.
    RESULTS: When serum/amino acid deficiency or energy stress (mild uncoupling) were applied, citrulline stimulated muscle protein synthesis by +22% and +11%, respectively. Importantly, this increase was not associated with enhanced energy status (ATP/ADP ratio) or mitochondrial respiration. We further analysed the share of mitochondrial respiration and thus of generated ATP allocated to different metabolic pathways by using specific inhibitors. Our results indicate that addition of citrulline allocated an increased share of mitochondrially generated ATP to the protein synthesis machinery under conditions of both serum/amino acid deficiency (+28%) and energy stress (+21%). This reallocation was not because of reduced ATP supply to DNA synthesis or activities of sodium and calcium cycling ion pumps.
    CONCLUSIONS: Under certain stress conditions, citrulline increases muscle protein synthesis by specifically reallocating mitochondrial fuel to the protein synthesis machinery. Because ATP/ADP ratios and thus Gibbs free energy of ATP hydrolysis remained globally constant, this reallocation may be linked to decreased activation energies of one or several ATP (and GTP)-consuming reactions involved in muscle protein synthesis.
    Keywords:  Citrulline; Energy metabolism; Leucine; Mitochondria; Muscle; Protein metabolism
    DOI:  https://doi.org/10.1002/jcsm.12435
  20. J Immunol. 2019 May 10. pii: ji1801600. [Epub ahead of print]
    O'Brien A, Loftus RM, Pisarska MM, Tobin LM, Bergin R, Wood NAW, Foley C, Mat A, Tinley FC, Bannan C, Sommerville G, Veerapen N, Besra GS, Sinclair LV, Moynagh PN, Lynch L, Finlay DK, O'Shea D, Hogan AE.
      Obesity underpins the development of numerous chronic diseases, such as type II diabetes mellitus. It is well established that obesity negatively alters immune cell frequencies and functions. Mucosal-associated invariant T (MAIT) cells are a population of innate T cells, which we have previously reported are dysregulated in obesity, with altered circulating and adipose tissue frequencies and a reduction in their IFN-γ production, which is a critical effector function of MAIT cells in host defense. Hence, there is increased urgency to characterize the key molecular mechanisms that drive MAIT cell effector functions and to identify those which are impaired in the obesity setting. In this study, we found that MAIT cells significantly upregulate their rates of glycolysis upon activation in an mTORC1-dependent manner, and this is essential for MAIT cell IFN-γ production. Furthermore, we show that mTORC1 activation is dependent on amino acid transport via SLC7A5. In obese patients, using RNA sequencing, Seahorse analysis, and a series of in vitro experiments, we demonstrate that MAIT cells isolated from obese adults display defective glycolytic metabolism, mTORC1 signaling, and SLC7A5 aa transport. Collectively, our data detail the intrinsic metabolic pathways controlling MAIT cell cytokine production and highlight mTORC1 as an important metabolic regulator that is impaired in obesity, leading to altered MAIT cell responses.
    DOI:  https://doi.org/10.4049/jimmunol.1801600
  21. J Biol Chem. 2019 May 09. pii: jbc.RA118.007266. [Epub ahead of print]
    Bu P, Nagar S, Bhagwat M, Kaur P, Shah A, Zeng J, Vancurova I, Vancura A.
      The DNA damage response (DDR) is an evolutionarily conserved process essential for cell survival. Previously, we found that decreased histone expression induces mitochondrial respiration, raising the question whether the DDR also stimulates respiration. Here, using oxygen consumption and ATP assays, RT-qPCR and ChIP-qPCR methods, and dNTP analyses, we show that DDR activation in the budding yeast Saccharomyces cerevisiae, either via genetic manipulation or by growth in the presence of genotoxic chemicals, induces respiration. We observed that this induction is conferred by reduced transcription of histone genes and globally decreased DNA nucleosome occupancy. This globally altered chromatin structure increased the expression of genes encoding enzymes of tricarboxylic acid cycle (TCA), electron transport chain (ETC), and oxidative phosphorylation (OXPHOS) and elevated oxygen consumption and ATP synthesis. The elevated ATP levels resulting from DDR-stimulated respiration drove enlargement of dNTP pools; cells with a defect in respiration failed to increase dNTP synthesis and exhibited reduced fitness in the presence of DNA damage. Together, our results reveal an unexpected connection between respiration and the DDR and indicate that the benefit of increased dNTP synthesis in the face of DNA damage outweighs possible cellular damage due to increased oxygen metabolism.
    Keywords:  ATP; DNA damage response; cell stress; chromatin; dNTP; energy metabolism; histone; oxidative phosphorylation (OXPHOS); respiration; tricarboxylic acid cycle (TCA cycle) (Krebs cycle)
    DOI:  https://doi.org/10.1074/jbc.RA118.007266
  22. Nat Med. 2019 May;25(5): 825-837
    Wang Z, Yip LY, Lee JHJ, Wu Z, Chew HY, Chong PKW, Teo CC, Ang HY, Peh KLE, Yuan J, Ma S, Choo LSK, Basri N, Jiang X, Yu Q, Hillmer AM, Lim WT, Lim TKH, Takano A, Tan EH, Tan DSW, Ho YS, Lim B, Tam WL.
      Understanding cellular metabolism holds immense potential for developing new classes of therapeutics that target metabolic pathways in cancer. Metabolic pathways are altered in bulk neoplastic cells in comparison to normal tissues. However, carcinoma cells within tumors are heterogeneous, and tumor-initiating cells (TICs) are important therapeutic targets that have remained metabolically uncharacterized. To understand their metabolic alterations, we performed metabolomics and metabolite tracing analyses, which revealed that TICs have highly elevated methionine cycle activity and transmethylation rates that are driven by MAT2A. High methionine cycle activity causes methionine consumption to far outstrip its regeneration, leading to addiction to exogenous methionine. Pharmacological inhibition of the methionine cycle, even transiently, is sufficient to cripple the tumor-initiating capability of these cells. Methionine cycle flux specifically influences the epigenetic state of cancer cells and drives tumor initiation. Methionine cycle enzymes are also enriched in other tumor types, and MAT2A expression impinges upon the sensitivity of certain cancer cells to therapeutic inhibition.
    DOI:  https://doi.org/10.1038/s41591-019-0423-5
  23. FEBS Lett. 2019 May 06.
    Fernandez-Sanz C, De la Fuente S, Sheu SS.
      Intracellular Ca2+ signaling controls numerous cellular functions. Mitochondria respond to cytosolic Ca2+ changes by adapting mitochondrial functions and, in some cell types, shaping the spatiotemporal properties of the cytosolic Ca2+ signal. Numerous methods have been developed to specifically and quantitatively measure the mitochondrial free Ca2+ concentrations ([Ca2+ ]m ), but there are still significant discrepancies in the calculated absolute values of [Ca2+ ]m in stimulated live cells. These discrepancies may be due to the distinct properties of the methods used to measure [Ca2+ ]m , the calcium-free/bound ratio, and the cell-type and stimulus-dependent Ca2+ dynamics. Critical processes happening in the mitochondria, such as ATP generation, ROS homeostasis, and mitochondrial permeability transition opening, depend directly on the [Ca2+ ]m values. Thus, precise determination of absolute [Ca2+ ]m values is imperative for understanding Ca2+ signaling. This review summarizes the reported calibrated [Ca2+ ]m values in many cell types and discusses the discrepancies among these values. Areas for future research are also proposed. This article is protected by copyright. All rights reserved.
    Keywords:  Fluorescent Ca2+ Indicators; Genetically Encoded Ca2+ Indicators; Live Cells; Mitochondrial Ca2+ Concentrations
    DOI:  https://doi.org/10.1002/1873-3468.13427
  24. MBio. 2019 May 07. pii: e00348-19. [Epub ahead of print]10(3):
    Bertolini MS, Chiurillo MA, Lander N, Vercesi AE, Docampo R.
      The mitochondrial Ca2+ uptake in trypanosomatids, which belong to the eukaryotic supergroup Excavata, shares biochemical characteristics with that of animals, which, together with fungi, belong to the supergroup Opisthokonta. However, the composition of the mitochondrial calcium uniporter (MCU) complex in trypanosomatids is quite peculiar, suggesting lineage-specific adaptations. In this work, we used Trypanosoma cruzi to study the role of orthologs for mitochondrial calcium uptake 1 (MICU1) and MICU2 in mitochondrial Ca2+ uptake. T. cruzi MICU1 (TcMICU1) and TcMICU2 have mitochondrial targeting signals, two canonical EF-hand calcium-binding domains, and localize to the mitochondria. Using the CRISPR/Cas9 system (i.e., clustered regularly interspaced short palindromic repeats with Cas9), we generated TcMICU1 and TcMICU2 knockout (-KO) cell lines. Ablation of either TcMICU1 or TcMICU2 showed a significantly reduced mitochondrial Ca2+ uptake in permeabilized epimastigotes without dissipation of the mitochondrial membrane potential or effects on the AMP/ATP ratio or citrate synthase activity. However, none of these proteins had a gatekeeper function at low cytosolic Ca2+ concentrations ([Ca2+]cyt), as occurs with their mammalian orthologs. TcMICU1-KO and TcMICU2-KO epimastigotes had a lower growth rate and impaired oxidative metabolism, while infective trypomastigotes have a reduced capacity to invade host cells and to replicate within them as amastigotes. The findings of this work, which is the first to study the role of MICU1 and MICU2 in organisms evolutionarily distant from animals, suggest that, although these components were probably present in the last eukaryotic common ancestor (LECA), they developed different roles during evolution of different eukaryotic supergroups. The work also provides new insights into the adaptations of trypanosomatids to their particular life styles.IMPORTANCE Trypanosoma cruzi is the etiologic agent of Chagas disease and belongs to the early-branching eukaryotic supergroup Excavata. Its mitochondrial calcium uniporter (MCU) subunit shares similarity with the animal ortholog that was important to discover its encoding gene. In animal cells, the MICU1 and MICU2 proteins act as Ca2+ sensors and gatekeepers of the MCU, preventing Ca2+ uptake under resting conditions and favoring it at high cytosolic Ca2+ concentrations ([Ca2+]cyt). Using the CRISPR/Cas9 technique, we generated TcMICU1 and TcMICU2 knockout cell lines and showed that MICU1 and -2 do not act as gatekeepers at low [Ca2+]cyt but are essential for normal growth, host cell invasion, and intracellular replication, revealing lineage-specific adaptations.
    Keywords:  MICU1; MICU2; Trypanosoma cruzi ; calcium signaling; calcium uniporter; mitochondria
    DOI:  https://doi.org/10.1128/mBio.00348-19
  25. Biol Open. 2019 May 09. pii: bio041467. [Epub ahead of print]8(5):
    Lau GY, Barts N, Hartley RC, Tobler M, Richards JG, Murphy MP, Arndt S.
      In this paper, we outline the use of a mitochondria-targeted ratiometric mass spectrometry probe, MitoA, to detect in vivo changes in mitochondrial hydrogen sulfide (H2S) in Poecilia mexicana (family Poeciliidae). MitoA is introduced via intraperitoneal injection into the animal and is taken up by mitochondria, where it reacts with H2S to form the product MitoN. The MitoN/MitoA ratio can be used to assess relative changes in the amounts of mitochondrial H2S produced over time. We describe the use of MitoA in the fish species P. mexicana to illustrate the steps for adopting the use of MitoA in a new organism, including extraction and purification of MitoA and MitoN from tissues followed by tandem mass spectrometry. In this proof-of-concept study we exposed H2S tolerant P. mexicana to 59 µM free H2S for 5 h, which resulted in increased MitoN/MitoA in brain and gills, but not in liver or muscle, demonstrating increased mitochondrial H2S levels in select tissues following whole-animal H2S exposure. This is the first time that accumulation of H2S has been observed in vivo during whole-animal exposure to free H2S using MitoA. This article has an associated First Person interview with the first author of the paper.
    Keywords:  Fish; Hydrogen sulfide; Mass spectrometry probe; MitoA; Mitochondria
    DOI:  https://doi.org/10.1242/bio.041467
  26. Dev Cell. 2019 May 06. pii: S1534-5807(19)30284-9. [Epub ahead of print]49(3): 425-443.e9
    White SM, Avantaggiati ML, Nemazanyy I, Di Poto C, Yang Y, Pende M, Gibney GT, Ressom HW, Field J, Atkins MB, Yi C.
      Merlin/NF2 is a bona fide tumor suppressor whose mutations underlie inherited tumor syndrome neurofibromatosis type 2 (NF2), as well as various sporadic cancers including kidney cancer. Multiple Merlin/NF2 effector pathways including the Hippo-YAP/TAZ pathway have been identified. However, the molecular mechanisms underpinning the growth and survival of NF2-mutant tumors remain poorly understood. Using an inducible orthotopic kidney tumor model, we demonstrate that YAP/TAZ silencing is sufficient to induce regression of pre-established NF2-deficient tumors. Mechanistically, YAP/TAZ depletion diminishes glycolysis-dependent growth and increases mitochondrial respiration and reactive oxygen species (ROS) buildup, resulting in oxidative-stress-induced cell death when challenged by nutrient stress. Furthermore, we identify lysosome-mediated cAMP-PKA/EPAC-dependent activation of RAF-MEK-ERK signaling as a resistance mechanism to YAP/TAZ inhibition. Finally, unbiased analysis of TCGA primary kidney tumor transcriptomes confirms a positive correlation of a YAP/TAZ signature with glycolysis and inverse correlations with oxidative phosphorylation and lysosomal gene expression, supporting the clinical relevance of our findings.
    Keywords:  Hippo pathway; NF2; RAF-MEK-ERK pathway; ROS; TAZ; YAP
    DOI:  https://doi.org/10.1016/j.devcel.2019.04.014
  27. Nat Commun. 2019 May 06. 10(1): 2071
    Malik N, Yan H, Moshkovich N, Palangat M, Yang H, Sanchez V, Cai Z, Peat TJ, Jiang S, Liu C, Lee M, Mock BA, Yuspa SH, Larson D, Wakefield LM, Huang J.
      Translation and transcription are frequently dysregulated in cancer. These two processes are generally regulated by distinct sets of factors. The CBFB gene, which encodes a transcription factor, has recently emerged as a highly mutated driver in a variety of human cancers including breast cancer. Here we report a noncanonical role of CBFB in translation regulation. RNA immunoprecipitation followed by deep sequencing (RIP-seq) reveals that cytoplasmic CBFB binds to hundreds of transcripts and regulates their translation. CBFB binds to mRNAs via hnRNPK and enhances translation through eIF4B, a general translation initiation factor. Interestingly, the RUNX1 mRNA, which encodes the transcriptional partner of CBFB, is bound and translationally regulated by CBFB. Furthermore, nuclear CBFB/RUNX1 complex transcriptionally represses the oncogenic NOTCH signaling pathway in breast cancer. Thus, our data reveal an unexpected function of CBFB in translation regulation and propose that breast cancer cells evade translation and transcription surveillance simultaneously through downregulating CBFB.
    DOI:  https://doi.org/10.1038/s41467-019-10102-6
  28. Methods Mol Biol. 2019 ;1967 211-227
    Bak DW, Weerapana E.
      Mitochondria are cellular sites of diverse redox biology, including ROS production, iron-sulfur biogenesis, and secondary metabolism, which all rely on proteogenic reactive cysteine residues. Mass spectrometry-based proteomic methods to monitor the reactivity and functionality of cysteine residues across complex proteomes have greatly expanded over the past decade. Here we describe a mitochondrial isolation procedure coupled with cysteine-reactive IA labeling that affords identification and characterization of functional mitochondrial cysteine residues that were heretofore inaccessible to whole-cell proteomic analysis.
    Keywords:  Activity-based proteomic profiling (ABPP); Cysteine reactivity; Mass spectrometry; Mitochondria; Proteomics
    DOI:  https://doi.org/10.1007/978-1-4939-9187-7_13
  29. Nat Commun. 2019 May 09. 10(1): 2123
    Kedia-Mehta N, Finlay DK.
      Changes in cellular metabolism are associated with the activation of diverse immune subsets. These changes are fuelled by nutrients including glucose, amino acids and fatty acids, and are closely linked to immune cell fate and function. An emerging concept is that nutrients are not equally available to all immune cells, suggesting that the regulation of nutrient utility through competitive uptake and use is important for controlling immune responses. This review considers immune microenvironments where nutrients become limiting, the signalling alterations caused by insufficient nutrients, and the importance of nutrient availability in the regulation of immune responses.
    DOI:  https://doi.org/10.1038/s41467-019-10015-4
  30. Nat Med. 2019 May;25(5): 850-860
    Li H, Ning S, Ghandi M, Kryukov GV, Gopal S, Deik A, Souza A, Pierce K, Keskula P, Hernandez D, Ann J, Shkoza D, Apfel V, Zou Y, Vazquez F, Barretina J, Pagliarini RA, Galli GG, Root DE, Hahn WC, Tsherniak A, Giannakis M, Schreiber SL, Clish CB, Garraway LA, Sellers WR.
      Despite considerable efforts to identify cancer metabolic alterations that might unveil druggable vulnerabilities, systematic characterizations of metabolism as it relates to functional genomic features and associated dependencies remain uncommon. To further understand the metabolic diversity of cancer, we profiled 225 metabolites in 928 cell lines from more than 20 cancer types in the Cancer Cell Line Encyclopedia (CCLE) using liquid chromatography-mass spectrometry (LC-MS). This resource enables unbiased association analysis linking the cancer metabolome to genetic alterations, epigenetic features and gene dependencies. Additionally, by screening barcoded cell lines, we demonstrated that aberrant ASNS hypermethylation sensitizes subsets of gastric and hepatic cancers to asparaginase therapy. Finally, our analysis revealed distinct synthesis and secretion patterns of kynurenine, an immune-suppressive metabolite, in model cancer cell lines. Together, these findings and related methodology provide comprehensive resources that will help clarify the landscape of cancer metabolism.
    DOI:  https://doi.org/10.1038/s41591-019-0404-8
  31. Biochem Biophys Res Commun. 2019 May 03. pii: S0006-291X(19)30850-2. [Epub ahead of print]
    Steele HE, Guo Y, Li BY, Na S.
      The biophysical microenvironment of the tumor site has significant impact on breast cancer progression and metastasis. The importance of altered mechanotransduction in cancerous tissue has been documented, yet its role in the regulation of cellular metabolism and the potential link between cellular energy and cell migration remain poorly understood. In this study, we investigated the role of mechanotransduction in AMP-activated protein kinase (AMPK) activation in breast cancer cells in response to interstitial fluid flow (IFF). Additionally, we explored the involvement of AMPK in breast cancer cell migration. IFF was applied to the 3D cell-matrix construct. The subcellular signaling activity of Src, FAK, and AMPK was visualized in real-time using fluorescent resonance energy transfer (FRET). We observed that breast cancer cells (MDA-MB-231) are more sensitive to IFF than normal epithelial cells (MCF-10A). AMPK was activated at the mitochondria of MDA-MB-231 cells by IFF, but not in other subcellular compartments (i.e., cytosol, plasma membrane, and nucleus). The inhibition of FAK or Src abolished flow-induced AMPK activation in the mitochondria of MDA-MB-231 cells. We also observed that global AMPK activation reduced MDA-MB-231 cell migration. Interestingly, specific AMPK inhibition in the mitochondria reduced cell migration and blocked flow-induced cell migration. Our results suggest the linkage of FAK/Src and mitochondria-specific AMPK in mechanotransduction and the differential role of AMPK in breast cancer cell migration depending on its subcellular compartment-specific activation.
    Keywords:  AMPK; FAK; Mechanotransduction; Metabolic signaling; Src
    DOI:  https://doi.org/10.1016/j.bbrc.2019.04.191
  32. Plant Cell Rep. 2019 May 07.
    Armas AM, Balparda M, Turowski VR, Busi MV, Pagani MA, Gomez-Casati DF.
      KEY MESSAGE: The ISC Fe-S cluster biosynthetic pathway would play a key role in the regulation of iron and sulfur homeostasis in plants. The Arabidopsis thaliana mitochondrial cysteine desulfurase AtNFS1 has an essential role in cellular ISC Fe-S cluster assembly, and this pathway is one of the main sinks for iron (Fe) and sulfur (S) in the plant. In different plant species it has been reported a close relationship between Fe and S metabolisms; however, the regulation of both nutrient homeostasis is not fully understood. In this study, we have characterized AtNFS1 overexpressing and knockdown mutant Arabidopsis plants. Plants showed alterations in the ISC Fe-S biosynthetic pathway genes and in the activity of Fe-S enzymes. Genes involved in Fe and S uptakes, assimilation, and regulation were up-regulated in overexpressing plants and down-regulated in knockdown plants. Furthermore, the plant nutritional status in different tissues was in accordance with those gene activities: overexpressing lines accumulated increased amounts of Fe and S and mutant plant had lower contents of S. In summary, our results suggest that the ISC Fe-S cluster biosynthetic pathway plays a crucial role in the homeostasis of Fe and S in plants, and that it may be important in their regulation.
    Keywords:  Cysteine desulfurase; Fe–S clusters; Iron; Sulfur
    DOI:  https://doi.org/10.1007/s00299-019-02419-9
  33. Front Neurosci. 2019 ;13 329
    Gaudioso A, Garcia-Rozas P, Casarejos MJ, Pastor O, Rodriguez-Navarro JA.
      Mitochondrial quality control is important in neurological diseases, but in genetic Parkinson's disease caused by mutations in PINK and parkin mitochondrial degradation through autophagy is crucial. Reductions in autophagy and mitophagy are implicated in aging, age related diseases and Parkinson. The parkin null mice (PK-KO) show only a subtle phenotype, apparent with age or with stressors. We have studied the changes in the lipidomic composition of the mitochondrial membranes isolated from the brains of young and old PK-KO mice and compared them to wild type in order to determine possible implications for Parkinson's disease pathology. We observed an increase in the levels of phosphatidylethanolamine in the young PK-KO mice that is lost in the old and correlate to changes in the phosphatidylserine decarboxylase. PK-KO old mice mitochondria showed lower phosphatidylglicerol and phosphatidylinositol levels and higher levels of some forms of hydroxylated ceramides. Regarding cardiolipins there were changes in the degree of saturation mainly with age. The lipidomic composition discriminates between the study groups using partial least square discriminant analysis. We discuss the relevance of the lipid changes for the autophagic activity, the mitophagy, the mitochondrial activity and the Parkinson's disease pathology in absence of parkin.
    Keywords:  PARK2; Parkinson; aging; macroautophagy; mitochondrial membrane; mitophagy
    DOI:  https://doi.org/10.3389/fnins.2019.00329
  34. Cancer Res. 2019 May 07. pii: canres.2043.2018. [Epub ahead of print]
    Kaminski L, Torrino S, Dufies M, Djabari Z, Haider R, Roustan FR, Jaune E, Laurent K, Nottet N, Michiels JF, Gesson M, Rocchi S, Mazure NM, Durand M, Tanti JF, Ambrosetti D, Clavel S, Ben-Sahra I, Bost F.
      Although tumorigenesis is dependent on the reprogramming of cellular metabolism, the metabolic pathways engaged in the formation of metastases remain largely unknown. The transcriptional co-activator peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) plays a pleiotropic role in the control of cancer cell metabolism and has been associated with a good prognosis in prostate cancer (PCa). Here we show that PGC-1α represses the metastatic properties of PCa cells via modulation of the polyamine biosynthesis pathway. Mechanistically, PGC-1α inhibits the expression of c-MYC and ornithine decarboxylase 1 (ODC1), the rate limiting enzyme for polyamine synthesis. Analysis of in vivo metastases and clinical data from prostate cancer patients support the proposition that the PGC-1α/c-MYC/ODC1 axis regulates polyamine biosynthesis and prostate cancer aggressiveness. In conclusion, downregulation of PGC-1α renders PCa cells dependent on polyamine to promote metastasis.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-18-2043
  35. Metab Eng. 2019 May 06. pii: S1096-7176(19)30060-6. [Epub ahead of print]
    Yuzbasheva EY, Agrimi G, Yuzbashev TV, Scarcia P, Vinogradova EB, Palmieri L, Shutov AV, Kosikhina IM, Palmieri F, Sineoky SP.
      Mitochondrial citrate carrier plays a central role in exporting acetyl-CoA in the form of citrate from mitochondria to cytosol thereby connecting carbohydrate catabolism and lipogenesis. In this study, Yarrowia lipolytica mitochondrial citrate carrier was functionally defined and characterized. Firstly, deletion of Y. lipolytica YlCTP1 and YlYHM2 genes coding putative tricarboxylate mitochondrial carriers were performed. ΔYlctp1 strain did not differ significantly from wild type strain in terms of growth rate, organic acids and lipid production. In contrast, ΔYlyhm2 strain did not grow in liquid citrate-containing minimal medium. Moreover, in glucose-containing lipogenic medium YlYHM2 null mutant strain did not produce citric acid; the production of isocitric acid and lipids were decreased. Reintroduction of YlYHM2 gene as well as heterologous expression of Aspergillus niger gene AnYHM2 into ΔYlyhm2 strain restored the growth in minimal citrate medium and even enhanced citric acid production by 45% in both variants compared with wild type strain during test tube cultivation. Mitochondrial extracts isolated from YlYHM2 null mutant and wild type strain were incorporated into liposomes; citrate/citrate and α-ketoglutarate/α-ketoglutarate homoexchange activities were reduced by 87% and 40% in ΔYlyhm2 strain, respectively, compared with the wild type, whereas citratein/α-ketoglutarateout and α-ketoglutaratein/citrateout heteroexchanges were decreased by 87% and 95%, respectively. YlYhm2p was expressed in Escherichia coli, purified and reconstituted into liposomes. Besides high efficiency to citrate and α-ketoglutarate transport, YlYhm2p also transported oxaloacetate, succinate, fumarate, and to a much lesser extent, aconitate, malate, isocitrate, oxoadipate, and glutamate. The activity of reconstituted YlYhm2p was inhibited strongly by SH-blocking reagents, pyridoxal-5'-phosphate, and partly by N-ethylmaleimide. Co-expression of YlYHM2 and adenosine monophosphate deaminase YlAMPD genes resulted in the production of 49.7 g/L of citric acid during test tube cultivation, whereas wild type strain accumulated 30.1 g/L of citric acid. Large-scale cultivation in bioreactor of the engineered strain resulted in 97.1 g/L of citric acid production with a process selectivity of 94.2% and an overall citric acid yield of 0.5 g/g. The maximal specific rate of citric acid synthesis was 0.93 g/L/h. Therefore, the physiological role of YlYhm2p in glucose-containing medium is to catalyze both import of citrate into mitochondria for catabolic reactions and export of citrate as a source of acetyl-CoA from mitochondria. Possible shuttles for citrate exporting are discussed. Moreover, for the first time evidence has been given for the improvement of TCA cycle intermediate production by manipulation of a gene coding a mitochondrial carrier.
    Keywords:  Citric acid production; Mitochondrial citrate carrier; Yarrowia lipolytica; YlYhm2p
    DOI:  https://doi.org/10.1016/j.ymben.2019.05.002
  36. Comp Biochem Physiol A Mol Integr Physiol. 2019 May 06. pii: S1095-6433(19)30001-7. [Epub ahead of print]
    Robergs RA.
      Given that the chemistry of lactate production disproves the existence of a lactic acidosis, there is a need to further reveal and explain the importance of the organic and computational chemistry of pH dependent competitive cation fractional (~) proton (H+) exchange (~H+e). An additional importance of this knowledge is that it could potentially contradict the assumption of the Stewart approach to the physico-chemical theory of acid-base balance. For example, Stewart proposed that chemical reaction and pH dependent H+ dissociation and association do not directly influence the pH of cellular and systemic body fluids. Yet at the time of Stewart's work, there were no data that quantified the H+ exchange during chemical reactions, or from pH dependent metabolite H+ association or dissociation. Consequently, the purpose of this review and commentary was three-fold; 1) to provide explanation of pH dependent competitive cation ~H+e exchange; 2) develop a model of and calculate new data of substrate flux in skeletal muscle during intense exercise; and 3) then combine substrate flux data with the now known ~H+e from chemical reactions of non-mitochondrial energy catabolism to quantify chemical reaction and metabolic pathway ~H+e. The results of purpose 3 were that ~H+ release for the totality of cytosolic energy catabolism = -187.2 mmol·L-1, where total glycolytic ~H+te = -85.0 mmol·L-1. ATP hydrolysis had a ~H+te = -43.1 mmol·L-1. Lactate production provided the largest metabolic ~H+ buffering with a ~H+te = 44.5 mmol·L-1. The total ~H+ release to La ratio = 4.25. The review content and research results of this manuscript should direct science towards new approaches to understanding the cause and source of H+e during metabolic acidosis and alkalosis.
    Keywords:  ATP turnover; Cations; Creatine phosphate; Dissociation constant; Glycolysis
    DOI:  https://doi.org/10.1016/j.cbpa.2019.04.024
  37. J Extracell Vesicles. 2019 ;8(1): 1609206
    Witwer KW, Van Balkom BWM, Bruno S, Choo A, Dominici M, Gimona M, Hill AF, De Kleijn D, Koh M, Lai RC, Mitsialis SA, Ortiz LA, Rohde E, Asada T, Toh WS, Weiss DJ, Zheng L, Giebel B, Lim SK.
      Small extracellular vesicles (sEVs) from mesenchymal stromal/stem cells (MSCs) are transiting rapidly towards clinical applications. However, discrepancies and controversies about the biology, functions, and potency of MSC-sEVs have arisen due to several factors: the diversity of MSCs and their preparation; various methods of sEV production and separation; a lack of standardized quality assurance assays; and limited reproducibility of in vitro and in vivo functional assays. To address these issues, members of four societies (SOCRATES, ISEV, ISCT and ISBT) propose specific harmonization criteria for MSC-sEVs to facilitate data sharing and comparison, which should help to advance the field towards clinical applications. Specifically, MSC-sEVs should be defined by quantifiable metrics to identify the cellular origin of the sEVs in a preparation, presence of lipid-membrane vesicles, and the degree of physical and biochemical integrity of the vesicles. For practical purposes, new MSC-sEV preparations might also be measured against a well-characterized MSC-sEV biological reference. The ultimate goal of developing these metrics is to map aspects of MSC-sEV biology and therapeutic potency onto quantifiable features of each preparation.
    Keywords:  Definition; MSC; Please check whether the inserted Keywords are correct; Therapeutics; sEV
    DOI:  https://doi.org/10.1080/20013078.2019.1609206
  38. J Cell Physiol. 2019 May 06.
    Huang D, Liu M, Jiang Y.
      Mitochondrial dysfunction has been found to be associated with neuronal inflammation; however, no effective drug is available to attenuate neuroinflammation via sustaining mitochondrial function. In the current study, experiments were performed to understand the beneficial effects of mitochonic acid 5 (MA-5) on tumor necrosis factor-α (TNF-α)-mediated neuronal injury and mitochondrial damage. Our data illustrated that MA-5 pretreatment reduced inflammation response induced by TNF-α in CATH.a cells. Molecular investigations demonstrated that MA-5 pretreatment repressed oxidative stress, inhibited endoplasmic reticulum stress, sustained cellular energy metabolism, and blocked cell apoptosis induced by TNF-α stress. Further, we found that MA-5 treatment elevated the expression of Sirtuin 3 (Sirt3) and this effect was dependent on the activation of AMP-activated protein kinase (AMPK) pathway. Blockade of AMPK abolished the promotive action of MA-5 on Sirt3 and thus mediated mitochondrial damage and cell death. Besides, we also found that MA-5 treatment augmented Parkin-related mitophagy and increased mitophagy promoted CATH.a cells survival via improving mitochondrial function. Knockdown of Parkin abolished the beneficial action of MA-5 on mitochondrial homeostasis and CATH.a cell survival. Altogether, our results confirm that MA-5 is an effective drug to attenuate neuroinflammation via sustaining mitochondrial damage and promoting CATH.a cell survival. The protective action of MA-5 on neuronal damage is associated with Parkin-related mitophagy and the activation of AMPK-Sirt3 pathways.
    Keywords:  AMPK-Sirt3 pathway; MA-5; Parkin-related mitophagy; TNF-α
    DOI:  https://doi.org/10.1002/jcp.28783
  39. Nephron. 2019 May 03. 1-4
    Parikh SM.
      Acute kidney injury (AKI) is estimated to affect 3-10% of all hospitalized adults in the United States, making it one of the most common inpatient diagnoses. Despite this staggering incidence, most individuals exposed to AKI stressors, such as intravenous radiocontrast or cardiopulmonary bypass, do not develop AKI. In fact, whereas animal models of ischemia, sepsis, or nephrotoxicity suggest near-uniform responses to stressors, the natural history of stressed patients is highly heterogeneous. Recent studies of mitochondrial perturbations underlying experimental and human AKI suggest a conserved metabolic contribution to this variance. The renal tubule is only second to the heart in terms of mitochondrial abundance, reflecting the exquisite need for fuel combustion to generate the energy for active solute transport. The homeostasis of nicotinamide adenine dinucleotide (NAD+), a requisite coenzyme in oxidative metabolism, may be an important determinant of the renal response to AKI stressors. This mini-review highlights recent studies implicating NAD+ dysregulation in experimental and human AKI and summarizes findings from a pilot randomized trial to augment NAD+ among at-risk individuals.
    Keywords:   Tubule; Acute kidney injury; Acute renal failure; Mitochondria ; Niacinamide; Nicotinamide; Nicotinamide adenine dinucleotide; Quinolinate; Vitamin B3
    DOI:  https://doi.org/10.1159/000500168
  40. Cell Metab. 2019 May 07. pii: S1550-4131(19)30194-9. [Epub ahead of print]29(5): 1019-1021
    Prouteau M, Loewith R.
      Recently in Cell, Kato et al. (2019) and Yang et al. (2019) report that reversible oxidation of multiple methionines in a region of Pbp1, the yeast paralog of ataxin-2 protein, couples metabolic redox status to phase separation of Pbp1 into liquid-like condensates. In turn, Pbp1 condensates inhibit target of rapamycin complex 1 (TORC1) signaling and thereby induce autophagy and restore metabolic homeostasis.
    DOI:  https://doi.org/10.1016/j.cmet.2019.04.010
  41. Cell Rep. 2019 May 07. pii: S2211-1247(19)30507-8. [Epub ahead of print]27(6): 1920-1933.e7
    Soday L, Lu Y, Albarnaz JD, Davies CTR, Antrobus R, Smith GL, Weekes MP.
      Vaccinia virus (VACV) has numerous immune evasion strategies, including multiple mechanisms of inhibition of interferon regulatory factor 3 (IRF-3), nuclear factor κB (NF-κB), and type I interferon (IFN) signaling. Here, we use highly multiplexed proteomics to quantify ∼9,000 cellular proteins and ∼80% of viral proteins at seven time points throughout VACV infection. A total of 265 cellular proteins are downregulated >2-fold by VACV, including putative natural killer cell ligands and IFN-stimulated genes. Two-thirds of these viral targets, including class II histone deacetylase 5 (HDAC5), are degraded proteolytically during infection. In follow-up analysis, we demonstrate that HDAC5 restricts replication of both VACV and herpes simplex virus type 1. By generating a protein-based temporal classification of VACV gene expression, we identify protein C6, a multifunctional IFN antagonist, as being necessary and sufficient for proteasomal degradation of HDAC5. Our approach thus identifies both a host antiviral factor and a viral mechanism of innate immune evasion.
    Keywords:  histone deacetylase; host-pathogen interaction; immune evasion; innate immunity; interferon; poxvirus; quantitative proteomics; restriction factor; systems virology; tandem mass tag
    DOI:  https://doi.org/10.1016/j.celrep.2019.04.042
  42. Cancer Metastasis Rev. 2019 May 10.
    Pastorekova S, Gillies RJ.
      Cancer development is a complex process that follows an intricate scenario with a dynamic interplay of selective and adaptive steps and an extensive cast of molecules and signaling pathways. Solid tumor initially grows as an avascular bulk of cells carrying oncogenic mutations until diffusion distances from the nearest functional blood vessels limit delivery of nutrients and oxygen on the one hand and removal of metabolic waste on the other one. These restrictions result in regional hypoxia and acidosis that select for adaptable tumor cells able to promote aberrant angiogenesis, remodel metabolism, acquire invasiveness and metastatic propensity, and gain therapeutic resistance. Tumor cells are thereby endowed with capability to survive and proliferate in hostile microenvironment, communicate with stroma, enter circulation, colonize secondary sites, and generate metastases. While the role of oncogenic mutations initializing and driving these processes is well established, a key contribution of non-genomic, landscaping molecular players is still less appreciated despite they can equally serve as viable targets of anticancer therapies. Carbonic anhydrase IX (CA IX) is one of these players: it is induced by hypoxia, functionally linked to acidosis, implicated in invasiveness, and correlated with therapeutic resistance. Here, we summarize the available experimental evidence supported by accumulating preclinical and clinical data that CA IX can contribute virtually to each step of cancer progression path via its enzyme activity and/or non-catalytic mechanisms. We also propose that targeting tumor cells that express CA IX may provide therapeutic benefits in various settings and combinations with both conventional and newly developed treatments.
    Keywords:  Acidosis; Cancer progression; Carbonic anhydrase IX; Hypoxia; Tumor microenvironment; pH regulation
    DOI:  https://doi.org/10.1007/s10555-019-09799-0
  43. Biochim Biophys Acta Proteins Proteom. 2019 May 02. pii: S1570-9639(19)30080-9. [Epub ahead of print]
    Nasir I, Onuchic PL, Labra SR, Deniz AA.
      Intrinsically disordered proteins (IDPs) are ubiquitous in proteomes and serve in a range of cellular functions including signaling, regulation, transport and enzyme function. IDP misfunction and aggregation are also associated with several diseases including neurodegenerative diseases and cancer. During the past decade, single-molecule methods have become popular for detailed biophysical and structural studies of these complex proteins. This work has included recent applications to cellular liquid-liquid phase separation (LLPS), relevant for functional dynamics of membraneless organelles such as the nucleolus and stress granules. In this concise review, we cover the conceptual motivations for development and application of single-molecule fluorescence methods for such IDP studies. We follow with a few key examples of systems and biophysical problems that have been addressed, and conclude with thoughts for emerging and future directions.
    Keywords:  Intrinsically disordered proteins; Liquid-liquid phase separation; Single-molecule FRET; Single-molecule biophysics
    DOI:  https://doi.org/10.1016/j.bbapap.2019.04.007
  44. Br J Pharmacol. 2019 May 11.
    Desai R, Campanella M.
      The pharmacological targeting of cholesterol levels continues to draw interest due to the vast success of therapeutics such as statins in extending life expectancy by modifying the prognosis of diseases associated with the impairment of the lipid metabolism. Advances in our understanding of mitochondrial dysfunction in chronic age-related diseases of the brain have unveiled an emerging role for mitochondrial cholesterol (mChol) in their pathophysiology, thus delineating an opportunity to provide mechanistic insights and explore strategies of intervention. This review draws attention to novel signalling mechanisms in conditions linked with impaired metabolism associated with impaired handling of cholesterol and its oxided forms (oxysterols) by mitochondria. By emphasising the role of mChol in neurological diseases we here call for novel approaches as well as new means of assessment.
    Keywords:  Mitochondria; Neurodegeneration; cholesterol; oxysterol
    DOI:  https://doi.org/10.1111/bph.14697
  45. Autophagy. 2019 May 08.
    Livingston MJ, Wang J, Zhou J, Wu G, Ganley IG, Hill JA, Yin XM, Dong Z.
      Ischemic preconditioning (IPC) affords tissue protection in organs including kidneys; however, the underlying mechanism remains unclear. Here we demonstrates an important role of macroautophagy/autophagy (especially mitophagy) in the protective effect of IPC in kidneys. IPC induced autophagy in renal tubular cells in mice and suppressed subsequent renal ischemia-reperfusion injury (IRI). The protective effect of IPC was abolished by pharmacological inhibitors of autophagy and by the ablation of Atg7 from kidney proximal tubules. Pretreatment with BECN1/Beclin1 peptide induced autophagy and protected against IRI. These results suggest the dependence of IPC protection on renal autophagy. During IPC, the mitophagy regulator PINK1 (PTEN induced putative kinase 1) was activated. Both IPC and BECN1 peptide enhanced mitolysosome formation during renal IRI in mitophagy reporter mice, suggesting that IPC may protect kidneys by activating mitophagy. We further established an in vitro model of IPC by inducing "chemical ischemia" in kidney proximal tubular cells with carbonyl cyanide 3-chlorophenylhydrazone (CCCP). Brief treatment with CCCP protected against subsequent injury in these cells and the protective effect was abrogated by autophagy inhibition. In vitro IPC increased mitophagosome formation, enhanced the delivery of mitophagosomes to lysosomes, and promoted the clearance of damaged mitochondria during subsequent CCCP treatment. IPC also suppressed mitochondrial depolarization, improved ATP production, and inhibited the generation of reactive oxygen species. Knockdown of Pink1 suppressed mitophagy and reduced the cytoprotective effect of IPC. Together, these results suggest that autophagy, especially mitophagy, plays an important role in the protective effect of IPC.
    Keywords:  acute kidney injury; autophagy; ischemic preconditioning; mitophagy; proximal tubule; renal ischemia-reperfusion
    DOI:  https://doi.org/10.1080/15548627.2019.1615822
  46. Methods Mol Biol. 2019 ;1975 305-320
    Shen F, Cheek C, Chandrasekaran S.
      Stem cell metabolism is intrinsically tied to stem cell pluripotency and function. Yet, understanding metabolic rewiring in stem cells has been challenging due to the complex and highly interconnected nature of the metabolic network. Genome-scale metabolic network models are increasingly used to holistically model the metabolic behavior of various cells and tissues using transcriptomics data. However, these powerful approaches that model steady-state behavior have limited utility for studying dynamic stem cell state transitions. To address this complexity, we recently developed the dynamic flux activity (DFA) approach; DFA is a genome-scale modeling approach that uses time-course metabolic data to predict metabolic flux rewiring. This protocol outlines the steps for modeling steady-state and dynamic metabolic behavior using transcriptomics and time-course metabolomics data, respectively. Using data from naive and primed pluripotent stem cells, we demonstrate how we can use genome-scale modeling and DFA to comprehensively characterize the metabolic differences between these states.
    Keywords:  Constraint-based modeling; Dynamic network modeling; Flux balance analysis (FBA); Genome-scale metabolic models (GEMs); Metabolism; Metabolomics; Stem cells
    DOI:  https://doi.org/10.1007/978-1-4939-9224-9_14
  47. Front Cell Infect Microbiol. 2019 ;9 95
    Moreno-Altamirano MMB, Kolstoe SE, Sánchez-García FJ.
      Over the last decade, there has been significant advances in the understanding of the cross-talk between metabolism and immune responses. It is now evident that immune cell effector function strongly depends on the metabolic pathway in which cells are engaged in at a particular point in time, the activation conditions, and the cell microenvironment. It is also clear that some metabolic intermediates have signaling as well as effector properties and, hence, topics such as immunometabolism, metabolic reprograming, and metabolic symbiosis (among others) have emerged. Viruses completely rely on their host's cell energy and molecular machinery to enter, multiply, and exit for a new round of infection. This review explores how viruses mimic, exploit or interfere with host cell metabolic pathways and how, in doing so, they may evade immune responses. It offers a brief outline of key metabolic pathways, mitochondrial function and metabolism-related signaling pathways, followed by examples of the mechanisms by which several viral proteins regulate host cell metabolic activity.
    Keywords:  cell metabolism; immune response; mitochondria; viral evasion; viruses
    DOI:  https://doi.org/10.3389/fcimb.2019.00095
  48. Sci Rep. 2019 May 06. 9(1): 6913
    Sajic T, Ciuffa R, Lemos V, Xu P, Leone V, Li C, Williams EG, Makris G, Banaei-Esfahani A, Heikenwalder M, Schoonjans K, Aebersold R.
      To-date, most proteomic studies aimed at discovering tissue-based cancer biomarkers have compared the quantity of selected proteins between case and control groups. However, proteins generally function in association with other proteins to form modules localized in particular subcellular compartments in specialized cell types and tissues. Sub-cellular mislocalization of proteins has in fact been detected as a key feature in a variety of cancer cells. Here, we describe a strategy for tissue-biomarker detection based on a mitochondrial fold enrichment (mtFE) score, which is sensitive to protein abundance changes as well as changes in subcellular distribution between mitochondria and cytosol. The mtFE score integrates protein abundance data from total cellular lysates and mitochondria-enriched fractions, and provides novel information for the classification of cancer samples that is not necessarily apparent from conventional abundance measurements alone. We apply this new strategy to a panel of wild-type and mutant mice with a liver-specific gene deletion of Liver receptor homolog 1 (Lrh-1hep-/-), with both lines containing control individuals as well as individuals with liver cancer induced by diethylnitrosamine (DEN). Lrh-1 gene deletion attenuates cancer cell metabolism in hepatocytes through mitochondrial glutamine processing. We show that proteome changes based on mtFE scores outperform protein abundance measurements in discriminating DEN-induced liver cancer from healthy liver tissue, and are uniquely robust against genetic perturbation. We validate the capacity of selected proteins with informative mtFE scores to indicate hepatic malignant changes in two independent mouse models of hepatocellular carcinoma (HCC), thus demonstrating the robustness of this new approach to biomarker research. Overall, the method provides a novel, sensitive approach to cancer biomarker discovery that considers contextual information of tested proteins.
    DOI:  https://doi.org/10.1038/s41598-019-43091-z
  49. J Genet Genomics. 2019 Apr 23. pii: S1673-8527(19)30067-0. [Epub ahead of print]
    Chen Z, Zhang F, Xu H.
      Mutations that disrupt the mitochondrial genome cause a number of human diseases whose phenotypic presentation varies widely among tissues and individuals. This variability owes in part to the unconventional genetics of mitochondrial DNA (mtDNA), which includes polyploidy, maternal inheritance and dependence on nuclear-encoded factors. The recent development of genetic tools for manipulating mitochondrial genome in Drosophila melanogaster renders this powerful model organism an attractive alternative to mammalian systems for understanding mtDNA-related diseases. In this review, we summarize mtDNA genetics and human mtDNA-related diseases. We highlight existing Drosophila models of mtDNA mutations and discuss their potential use in advancing our knowledge of mitochondrial biology and in modeling human mitochondrial disorders. We also discuss the potential and present challenges of gene therapy for the future treatment of mtDNA diseases.
    Keywords:  Drosophila model; Mitochondrial DNA; mtDNA disease; mtDNA genetics
    DOI:  https://doi.org/10.1016/j.jgg.2019.03.009
  50. Aging (Albany NY). 2019 May 10.
    Marcheggiani F, Cirilli I, Orlando P, Silvestri S, Vogelsang A, Knott A, Blatt T, Weise JM, Tiano L.
      Coenzyme Q10 (CoQ10) is an endogenous lipophilic quinone, ubiquitous in biological membranes and endowed with antioxidant and bioenergetic properties, both crucial to the aging process. In fact, coenzyme Q10 synthesis is known to decrease with age in different tissues including skin. Moreover, synthesis can be inhibited by 3-hydroxy-3-methyl-glutaryl-coenzyme A (HMG-CoA) reductase inhibitors such as statins, that are widely used hypocholesterolemic drugs. They target a key enzymatic step along the mevalonate pathway, involved in the synthesis of both cholesterol and isoprenylated compounds including CoQ10.In the present study, we show that pharmacological CoQ10 deprivation at concentrations of statins > 10000 nM triggers intracellular oxidative stress, mitochondrial dysfunction and generates cell death in human dermal fibroblasts (HDF). On the contrary, at lower statin concentrations, cells and mainly mitochondria, are able to partially adapt and prevent oxidative imbalance and overt mitochondrial toxicity. Importantly, our data demonstrate that CoQ10 decrease promotes mitochondrial permeability transition and bioenergetic dysfunction leading to premature aging of human dermal fibroblasts in vitro.
    Keywords:  Coenzyme Q 10; aging; mitochondria; oxidative stress; senescence; skin
    DOI:  https://doi.org/10.18632/aging.101926
  51. Front Physiol. 2019 ;10 461
    Dakik P, Medkour Y, Mohammad K, Titorenko VI.
      Recent studies have revealed that some low-molecular weight molecules produced in mitochondria are essential contributing factors to aging and aging-associated pathologies in evolutionarily distant eukaryotes. These molecules are intermediates or products of certain metabolic reactions that are activated in mitochondria in response to specific changes in the nutrient, stress, proliferation, or age status of the cell. After being released from mitochondria, these metabolites directly or indirectly change activities of a distinct set of protein sensors that reside in various cellular locations outside of mitochondria. Because these protein sensors control the efficiencies of some pro- or anti-aging cellular processes, such changes in their activities allow to create a pro- or anti-aging cellular pattern. Thus, mitochondria can function as signaling platforms that respond to certain changes in cell stress and physiology by remodeling their metabolism and releasing a specific set of metabolites known as "mitobolites." These mitobolites then define the pace of cellular and organismal aging because they regulate some longevity-defining processes taking place outside of mitochondria. In this review, we discuss recent progress in understanding mechanisms underlying the ability of mitochondria to function as such signaling platforms in aging and aging-associated diseases.
    Keywords:  aging; hormetic stress response; interorganellar communications; longevity; metabolism; mitochondria; redox homeostasis; signaling
    DOI:  https://doi.org/10.3389/fphys.2019.00461
  52. Nat Metab. 2019 Mar;1 404-415
    Chen L, Zhang Z, Hoshino A, Zheng HD, Morley M, Arany Z, Rabinowitz JD.
      NADPH donates high energy electrons for antioxidant defense and reductive biosynthesis. Cytosolic NADP is recycled to NADPH by the oxidative pentose phosphate pathway (oxPPP), malic enzyme 1 (ME1) and isocitrate dehydrogenase 1 (IDH1). Here we show that any one of these routes can support cell growth, but the oxPPP is uniquely required to maintain a normal NADPH/NADP ratio, mammalian dihydrofolate reductase (DHFR) activity and folate metabolism. These findings are based on CRISPR deletions of glucose-6-phosphate dehydrogenase (G6PD, the committed oxPPP enzyme), ME1, IDH1, and combinations thereof in HCT116 colon cancer cells. Loss of G6PD results in high NADP, which induces compensatory increases in ME1 and IDH1 flux. But the high NADP inhibits dihydrofolate reductase (DHFR), resulting in impaired folate-mediated biosynthesis, which is reversed by recombinant expression of E. coli DHFR. Across different cancer cell lines, G6PD deletion produced consistent changes in folate-related metabolites, suggesting a general requirement for the oxPPP to support folate metabolism.
  53. Proc Natl Acad Sci U S A. 2019 May 09. pii: 201821332. [Epub ahead of print]
    Fanibunda SE, Deb S, Maniyadath B, Tiwari P, Ghai U, Gupta S, Figueiredo D, Weisstaub N, Gingrich JA, Vaidya ADB, Kolthur-Seetharam U, Vaidya VA.
      Mitochondria in neurons, in addition to their primary role in bioenergetics, also contribute to specialized functions, including regulation of synaptic transmission, Ca2+ homeostasis, neuronal excitability, and stress adaptation. However, the factors that influence mitochondrial biogenesis and function in neurons remain poorly elucidated. Here, we identify an important role for serotonin (5-HT) as a regulator of mitochondrial biogenesis and function in rodent cortical neurons, via a 5-HT2A receptor-mediated recruitment of the SIRT1-PGC-1α axis, which is relevant to the neuroprotective action of 5-HT. We found that 5-HT increased mitochondrial biogenesis, reflected through enhanced mtDNA levels, mitotracker staining, and expression of mitochondrial components. This resulted in higher mitochondrial respiratory capacity, oxidative phosphorylation (OXPHOS) efficiency, and a consequential increase in cellular ATP levels. Mechanistically, the effects of 5-HT were mediated via the 5-HT2A receptor and master modulators of mitochondrial biogenesis, SIRT1 and PGC-1α. SIRT1 was required to mediate the effects of 5-HT on mitochondrial biogenesis and function in cortical neurons. In vivo studies revealed that 5-HT2A receptor stimulation increased cortical mtDNA and ATP levels in a SIRT1-dependent manner. Direct infusion of 5-HT into the neocortex and chemogenetic activation of 5-HT neurons also resulted in enhanced mitochondrial biogenesis and function in vivo. In cortical neurons, 5-HT enhanced expression of antioxidant enzymes, decreased cellular reactive oxygen species, and exhibited neuroprotection against excitotoxic and oxidative stress, an effect that required SIRT1. These findings identify 5-HT as an upstream regulator of mitochondrial biogenesis and function in cortical neurons and implicate the mitochondrial effects of 5-HT in its neuroprotective action.
    Keywords:  5-HT; 5-HT2A receptor; mitochondria; neuronal survival; sirtuin 1
    DOI:  https://doi.org/10.1073/pnas.1821332116
  54. Mol Cancer Res. 2019 May 08. pii: molcanres.0020.2019. [Epub ahead of print]
    Gonthier K, Poluri RTK, Weidmann C, Tadros M, Audet-Walsh E.
      Mutations of the isocitrate dehydrogenase genes IDH1 and IDH2, key enzymes involved in citrate metabolism, are important oncogenic events in several cancer types, including in 1-3% of all prostate cancer (PCa) cases. However, if IDH1 and other IDH isoforms are associated with PCa progression, as well as the regulatory factors controlling their expression and activity, remain mostly unknown. Using publicly available datasets, we showed that PCa harbors the highest IDH1 expression across the human cancer spectrum and that IDH1 expression is altered during PCa progression. We showed that the androgen receptor (AR), a key oncogene in PCa, controls multiple IDH isoforms in both in vitro and in vivo models, predominantly positively regulating IDH1. Chromatin immunoprecipitation experiments confirmed the recruitment of AR at several regulatory regions of IDH1 and enzymatic assays demonstrated that AR significantly induces IDH activity. Genetic blockade of IDH1 significantly impaired PCa cell proliferation, consistent with IDH1 having a key function in these cancer cells. Importantly, knockdown of IDH1 blocked the AR-mediated induction in IDH activity, indicating that AR promotes a mitochondrial to cytoplasmic reprogramming of IDH activity. Overall, our study demonstrates that IDH1 expression is associated with PCa progression, that AR signaling integrates one of the first transcriptional mechanisms shown to regulate IDH1, and that AR reprograms PCa cell metabolism by selectively inducing extra-mitochondrial IDH activity. Implications: The discovery that AR reprograms IDH activity highlights a novel metabolic reprogramming necessary for PCa growth and suggests targeting IDH activity as a new therapeutic approach for PCa treatment.
    DOI:  https://doi.org/10.1158/1541-7786.MCR-19-0020
  55. Cell Rep. 2019 May 07. pii: S2211-1247(19)30502-9. [Epub ahead of print]27(6): 1858-1874.e6
    Myers DR, Norlin E, Vercoulen Y, Roose JP.
      Naive CD4+ T cells are an example of dynamic cell homeostasis: T cells need to avoid autoreactivity while constantly seeing self-peptides, yet they must be primed to react to foreign antigens during infection. The instructive signals that balance this primed yet quiescent state are unknown. Interactions with self-peptides result in membrane-proximal, tonic signals in resting T cells. Here we reveal selective and robust tonic mTORC1 signals in CD4+ T cells that influence T cell fate decisions. We find that the Ras exchange factor Rasgrp1 is necessary to generate tonic mTORC1 signals. Genome-wide ribosome profiling of resting, primary CD4+ T cells uncovers a baseline translational landscape rich in mTOR targets linked to mitochondria, oxidative phosphorylation, and splicing. Aberrantly increased tonic mTORC1 signals from a Rasgrp1Anaef allele result in immunopathology with spontaneous appearance of T peripheral helper cells, follicular helper T cells, and anti-nuclear antibodies that are preceded by subtle alterations in the translational landscape.
    Keywords:  Anaef; CD44; CD5; Rasgrp1; autoimmunity; mRNA translation; mTOR; naive T cell; ribosome profiling; tonic signaling
    DOI:  https://doi.org/10.1016/j.celrep.2019.04.037
  56. Trends Biochem Sci. 2019 May 07. pii: S0968-0004(19)30089-1. [Epub ahead of print]
    Bonora M, Pinton P.
      Mitochondrial F1/FO ATP synthase participation in the mitochondrial permeability transition pore complex (PTPC) remains controversial. Neginskaya et al. (Cell Rep. 2019;26:11-17) reported an unexpected current with PTPC-like properties in F1/FO ATP synthase C subunit knockout cells that could explain part of the conflictual literature.
    DOI:  https://doi.org/10.1016/j.tibs.2019.04.009
  57. Nat Commun. 2019 May 06. 10(1): 2065
    Lin X, Chai G, Wu Y, Li J, Chen F, Liu J, Luo G, Tauler J, Du J, Lin S, He C, Wang H.
      N6-Methyladenosine (m6A) modification has been implicated in the progression of several cancers. We reveal that during epithelial-mesenchymal transition (EMT), one important step for cancer cell metastasis, m6A modification of mRNAs increases in cancer cells. Deletion of methyltransferase-like 3 (METTL3) down-regulates m6A, impairs the migration, invasion and EMT of cancer cells both in vitro and in vivo. m6A-sequencing and functional studies confirm that Snail, a key transcription factor of EMT, is involved in m6A-regulated EMT. m6A in Snail CDS, but not 3'UTR, triggers polysome-mediated translation of Snail mRNA in cancer cells. Loss and gain functional studies confirm that YTHDF1 mediates m6A-increased translation of Snail mRNA. Moreover, the upregulation of METTL3 and YTHDF1 act as adverse prognosis factors for overall survival (OS) rate of liver cancer patients. Our study highlights the critical roles of m6A on regulation of EMT in cancer cells and translation of Snail during this process.
    DOI:  https://doi.org/10.1038/s41467-019-09865-9
  58. Cell. 2019 Apr 26. pii: S0092-8674(19)30327-7. [Epub ahead of print]
    Alim I, Caulfield JT, Chen Y, Swarup V, Geschwind DH, Ivanova E, Seravalli J, Ai Y, Sansing LH, Ste Marie EJ, Hondal RJ, Mukherjee S, Cave JW, Sagdullaev BT, Karuppagounder SS, Ratan RR.
      Ferroptosis, a non-apoptotic form of programmed cell death, is triggered by oxidative stress in cancer, heat stress in plants, and hemorrhagic stroke. A homeostatic transcriptional response to ferroptotic stimuli is unknown. We show that neurons respond to ferroptotic stimuli by induction of selenoproteins, including antioxidant glutathione peroxidase 4 (GPX4). Pharmacological selenium (Se) augments GPX4 and other genes in this transcriptional program, the selenome, via coordinated activation of the transcription factors TFAP2c and Sp1 to protect neurons. Remarkably, a single dose of Se delivered into the brain drives antioxidant GPX4 expression, protects neurons, and improves behavior in a hemorrhagic stroke model. Altogether, we show that pharmacological Se supplementation effectively inhibits GPX4-dependent ferroptotic death as well as cell death induced by excitotoxicity or ER stress, which are GPX4 independent. Systemic administration of a brain-penetrant selenopeptide activates homeostatic transcription to inhibit cell death and improves function when delivered after hemorrhagic or ischemic stroke.
    Keywords:  GPX4; adaptation; cell death; ferroptosis; intracerebral hemorrhage; selenium; selenoprotein; stroke; therapeutic peptides; transcription
    DOI:  https://doi.org/10.1016/j.cell.2019.03.032
  59. Nat Commun. 2019 May 08. 10(1): 2110
    Prakash V, Carson BB, Feenstra JM, Dass RA, Sekyrova P, Hoshino A, Petersen J, Guo Y, Parks MM, Kurylo CM, Batchelder JE, Haller K, Hashimoto A, Rundqivst H, Condeelis JS, Allis CD, Drygin D, Nieto MA, Andäng M, Percipalle P, Bergh J, Adameyko I, Farrants AÖ, Hartman J, Lyden D, Pietras K, Blanchard SC, Vincent CT.
      Ribosome biogenesis is a canonical hallmark of cell growth and proliferation. Here we show that execution of Epithelial-to-Mesenchymal Transition (EMT), a migratory cellular program associated with development and tumor metastasis, is fueled by upregulation of ribosome biogenesis during G1/S arrest. This unexpected EMT feature is independent of species and initiating signal, and is accompanied by release of the repressive nucleolar chromatin remodeling complex (NoRC) from rDNA, together with recruitment of the EMT-driving transcription factor Snai1 (Snail1), RNA Polymerase I (Pol I) and the Upstream Binding Factor (UBF). EMT-associated ribosome biogenesis is also coincident with increased nucleolar recruitment of Rictor, an essential component of the EMT-promoting mammalian target of rapamycin complex 2 (mTORC2). Inhibition of rRNA synthesis in vivo differentiates primary tumors to a benign, Estrogen Receptor-alpha (ERα) positive, Rictor-negative phenotype and reduces metastasis. These findings implicate the EMT-associated ribosome biogenesis program with cellular plasticity, de-differentiation, cancer progression and metastatic disease.
    DOI:  https://doi.org/10.1038/s41467-019-10100-8