bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2019‒10‒13
33 papers selected by
Christian Frezza
University of Cambridge, MRC Cancer Unit


  1. Mol Cell. 2019 Sep 24. pii: S1097-2765(19)30693-8. [Epub ahead of print]
    Riscal R, Skuli N, Simon MC.
      Deregulated cell proliferation is an established feature of cancer, and altered tumor metabolism has witnessed renewed interest over the past decade, including the study of how cancer cells rewire metabolic pathways to renew energy sources and "building blocks" that sustain cell division. Microenvironmental oxygen, glucose, and glutamine are regarded as principal nutrients fueling tumor growth. However, hostile tumor microenvironments render O2/nutrient supplies chronically insufficient for increased proliferation rates, forcing cancer cells to develop strategies for opportunistic modes of nutrient acquisition. Recent work shows that cancer cells overcome this nutrient scarcity by scavenging other substrates, such as proteins and lipids, or utilizing adaptive metabolic pathways. As such, reprogramming lipid metabolism plays important roles in providing energy, macromolecules for membrane synthesis, and lipid-mediated signaling during cancer progression. In this review, we highlight more recently appreciated roles for lipids, particularly cholesterol and its derivatives, in cancer cell metabolism within intrinsically harsh tumor microenvironments.
    Keywords:  bile acids; cancer; cholesterol; lipids; metabolism; oxysterols
    DOI:  https://doi.org/10.1016/j.molcel.2019.09.008
  2. Nat Commun. 2019 Oct 11. 10(1): 4671
    Miklas JW, Clark E, Levy S, Detraux D, Leonard A, Beussman K, Showalter MR, Smith AT, Hofsteen P, Yang X, Macadangdang J, Manninen T, Raftery D, Madan A, Suomalainen A, Kim DH, Murry CE, Fiehn O, Sniadecki NJ, Wang Y, Ruohola-Baker H.
      Mitochondrial trifunctional protein deficiency, due to mutations in hydratase subunit A (HADHA), results in sudden infant death syndrome with no cure. To reveal the disease etiology, we generated stem cell-derived cardiomyocytes from HADHA-deficient hiPSCs and accelerated their maturation via an engineered microRNA maturation cocktail that upregulated the epigenetic regulator, HOPX.  Here we report, matured HADHA mutant cardiomyocytes treated with an endogenous mixture of fatty acids manifest the disease phenotype: defective calcium dynamics and repolarization kinetics which results in a pro-arrhythmic state. Single cell RNA-seq reveals a cardiomyocyte developmental intermediate, based on metabolic gene expression. This intermediate gives rise to mature-like cardiomyocytes in control cells but, mutant cells transition to a pathological state with reduced fatty acid beta-oxidation, reduced mitochondrial proton gradient, disrupted cristae structure and defective cardiolipin remodeling. This study reveals that HADHA (tri-functional protein alpha), a monolysocardiolipin acyltransferase-like enzyme, is required for fatty acid beta-oxidation and cardiolipin remodeling, essential for functional mitochondria in human cardiomyocytes.
    DOI:  https://doi.org/10.1038/s41467-019-12482-1
  3. EMBO Rep. 2019 Oct 10. e47728
    Koyano F, Yamano K, Kosako H, Kimura Y, Kimura M, Fujiki Y, Tanaka K, Matsuda N.
      Ubiquitylation of outer mitochondrial membrane (OMM) proteins is closely related to the onset of familial Parkinson's disease. Typically, a reduction in the mitochondrial membrane potential results in Parkin-mediated ubiquitylation of OMM proteins, which are then targeted for proteasomal and mitophagic degradation. The role of ubiquitylation of OMM proteins with non-degradative fates, however, remains poorly understood. In this study, we find that the mitochondrial E3 ubiquitin ligase MITOL/March5 translocates from depolarized mitochondria to peroxisomes following mitophagy stimulation. This unusual redistribution is mediated by peroxins (peroxisomal biogenesis factors) Pex3/16 and requires the E3 ligase activity of Parkin, which ubiquitylates K268 in the MITOL C-terminus, essential for p97/VCP-dependent mitochondrial extraction of MITOL. These findings imply that ubiquitylation directs peroxisomal translocation of MITOL upon mitophagy stimulation and reveal a novel role for ubiquitin as a sorting signal that allows certain specialized proteins to escape from damaged mitochondria.
    Keywords:   VCP ; March5; PINK1- and Parkin-mediated mitophagy; peroxin; ubiquitin
    DOI:  https://doi.org/10.15252/embr.201947728
  4. Cell Death Dis. 2019 Oct 07. 10(10): 755
    Wang TX, Liang JY, Zhang C, Xiong Y, Guan KL, Yuan HX.
      Ferroptosis is a non-apoptotic form of cell death characterized by the iron-dependent lipid peroxidation and is implicated in several human pathologies, such as tissue ischemia, neurodegeneration, and cancer. Ferroptosis appears to be high cell-context dependent and the regulation of ferroptosis by physiological or pathological conditions are unclear. Here, we report that tumor-derived IDH1 mutation sensitizes cells to ferroptosis. Deletion of the mutant IDH1 allele in IDH1 heterozygous tumor cells or pharmacological inhibition of mutant IDH1 to produce the oncometabolite D-2-hydroxyglutarate (D-2-HG) confers resistance to erastin-induced ferroptosis. Conversely, ectopic expression of mutant IDH1 or treatment of cells with cell-permeable D-2-HG promotes the accumulation of lipid reactive oxygen species (ROS) and subsequently ferroptosis. Mechanistically, mutant IDH1 reduces the protein level of the glutathione peroxidase 4 (GPX4), a key enzyme in removing lipid ROS and ferroptosis, and promotes depletion of glutathione. Our results uncover a new role of mutant IDH1 and 2-HG in ferroptosis.
    DOI:  https://doi.org/10.1038/s41419-019-1984-4
  5. Nat Commun. 2019 Oct 11. 10(1): 4624
    Moriyama M, Koshiba T, Ichinohe T.
      Cytosolic mitochondrial DNA (mtDNA) activates cGAS-mediated antiviral immune responses, but the mechanism by which RNA viruses stimulate mtDNA release remains unknown. Here we show that viroporin activity of influenza virus M2 or encephalomyocarditis virus (EMCV) 2B protein triggers translocation of mtDNA into the cytosol in a MAVS-dependent manner. Although influenza virus-induced cytosolic mtDNA stimulates cGAS- and DDX41-dependent innate immune responses, the nonstructural protein 1 (NS1) of influenza virus associates with mtDNA to evade the STING-dependent antiviral immunity. The STING-dependent antiviral signaling is amplified in neighboring cells through gap junctions. In addition, we find that STING-dependent recognition of influenza virus is essential for limiting virus replication in vivo. Our results show a mechanism by which influenza virus stimulates mtDNA release and highlight the importance of DNA sensing pathway in limiting influenza virus replication.
    DOI:  https://doi.org/10.1038/s41467-019-12632-5
  6. Elife. 2019 Oct 09. pii: e51601. [Epub ahead of print]8
    Varuzhanyan G, Rojansky R, Sweredoski MJ, Graham RL, Hess S, Ladinsky MS, Chan DC.
      Differentiating cells tailor their metabolism to fulfill their specialized functions. We examined whether mitochondrial fusion is important for metabolic tailoring during spermatogenesis. Acutely after depletion of mitofusins Mfn1 and Mfn2, spermatogenesis arrests due to failure to accomplish a metabolic shift during meiosis. This metabolic shift includes increased mitochondrial content, mitochondrial elongation, and upregulation of oxidative phosphorylation (OXPHOS). With long-term mitofusin loss, all differentiating germ cell types are depleted, but proliferation of stem-like undifferentiated spermatogonia remains unaffected. Thus, compared with undifferentiated spermatogonia, differentiating spermatogonia and meiotic spermatocytes have cell physiologies that require high levels of mitochondrial fusion. Proteomics in fibroblasts reveals that mitofusin-null cells downregulate respiratory chain complexes and mitochondrial ribosomal subunits. Similarly, mitofusin depletion in immortalized spermatocytes or germ cells in vivo results in reduced OXPHOS subunits and activity. We reveal that by promoting OXPHOS, mitofusins enable spermatogonial differentiation and a metabolic shift during meiosis.
    Keywords:  cell biology; developmental biology; mouse
    DOI:  https://doi.org/10.7554/eLife.51601
  7. Invest Ophthalmol Vis Sci. 2019 Oct 01. 60(13): 4187-4195
    Chattopadhyay C, Oba J, Roszik J, Marszalek JR, Chen K, Qi Y, Eterovic K, Robertson AG, Burks JK, McCannel TA, Grimm EA, Woodman SE.
      Purpose: Metastatic uveal melanoma (UM) has a very poor prognosis and no effective therapy. Despite remarkable advances in treatment of cutaneous melanoma, UM remains recalcitrant to chemotherapy, small-molecule kinase inhibitors, and immune-based therapy.Methods: We assessed two sets of oxidative phosphorylation (OxPhos) genes within 9858 tumors across 31 cancer types. An OxPhos inhibitor was used to characterize differential metabolic programming of highly metastatic monosomy 3 (M3) UM. Seahorse analysis and global metabolomics profiling were done to identify metabolic vulnerabilities. Analyses of UM TCGA data set were performed to determine expressions of key OxPhos effectors in M3 and non-M3 UM. We used targeted knockdown of succinate dehydrogenase A (SDHA) to determine the role of SDHA in M3 UM in conferring resistance to OxPhos inhibition.
    Results: We identified UM to have among the highest median OxPhos levels and showed that M3 UM exhibits a distinct metabolic profile. M3 UM shows markedly low succinate levels and has highly increased levels of SDHA, the enzyme that couples the tricarboxylic acid cycle with OxPhos by oxidizing (lowering) succinate. We showed that SDHA-high M3 UM have elevated expression of key OxPhos molecules, exhibit abundant mitochondrial reserve respiratory capacity, and are resistant to OxPhos antagonism, which can be reversed by SDHA knockdown.
    Conclusions: Our study has identified a critical metabolic program within poor prognostic M3 UM. In addition to the heightened mitochondrial functional capacity due to elevated SDHA, M3 UM SDHA-high mediate resistance to therapy that is reversible with targeted treatment.
    DOI:  https://doi.org/10.1167/iovs.19-28082
  8. Cell Metab. 2019 Oct 03. pii: S1550-4131(19)30510-8. [Epub ahead of print]
    Latorre-Pellicer A, Lechuga-Vieco AV, Johnston IG, Hämäläinen RH, Pellico J, Justo-Méndez R, Fernández-Toro JM, Clavería C, Guaras A, Sierra R, Llop J, Torres M, Criado LM, Suomalainen A, Jones NS, Ruíz-Cabello J, Enríquez JA.
      mtDNA is present in multiple copies in each cell derived from the expansions of those in the oocyte. Heteroplasmy, more than one mtDNA variant, may be generated by mutagenesis, paternal mtDNA leakage, and novel medical technologies aiming to prevent inheritance of mtDNA-linked diseases. Heteroplasmy phenotypic impact remains poorly understood. Mouse studies led to contradictory models of random drift or haplotype selection for mother-to-offspring transmission of mtDNA heteroplasmy. Here, we show that mtDNA heteroplasmy affects embryo metabolism, cell fitness, and induced pluripotent stem cell (iPSC) generation. Thus, genetic and pharmacological interventions affecting oxidative phosphorylation (OXPHOS) modify competition among mtDNA haplotypes during oocyte development and/or at early embryonic stages. We show that heteroplasmy behavior can fall on a spectrum from random drift to strong selection, depending on mito-nuclear interactions and metabolic factors. Understanding heteroplasmy dynamics and its mechanisms provide novel knowledge of a fundamental biological process and enhance our ability to mitigate risks in clinical applications affecting mtDNA transmission.
    Keywords:  embryo; germline selection; heteroplasmy; mitochondria; mitochondrial replacement; mtDNA competition; mtDNA inheritance
    DOI:  https://doi.org/10.1016/j.cmet.2019.09.007
  9. Curr Opin Syst Biol. 2018 Apr;8 32-38
    Locasale JW.
      Glycolysis, the breakdown of glucose, is one of the most conserved and extensively studied biochemical pathways. Designing principles from chemistry and thermodynamics allow for energy production, biosynthesis and cellular communication. However, the kinetics or metabolic flux through the pathway also determines its function. Recently, there have been numerous developments that establish new allosteric interactions of glycolytic enzymes with small molecule metabolites and other mechanisms that may cooperate to allow for addition complex regulation of glycolysis. This review surveys these newfound sources of glycolysis regulation and discusses their possible roles in establishing kinetic design principles of glycolysis.
    Keywords:  Kinetics; feedback regulation; feedforward regulation; glucose metabolism; network design principles
    DOI:  https://doi.org/10.1016/j.coisb.2017.11.005
  10. Clin Genet. 2019 Oct 10.
    Sommerville EW, Dalla Rosa I, Rosenberg MM, Bruni F, Thompson K, Rocha M, Blakely EL, He L, Falkous G, Schaefer AM, Yu-Wai-Man P, Chinnery PF, Hedstrom L, Spinazzola A, Taylor RW, Gorman GS.
      Autosomal dominant progressive external ophthalmoplegia (adPEO) is a late-onset, Mendelian mitochondrial disorder characterised by paresis of the extraocular muscles, ptosis and skeletal-muscle restricted multiple mitochondrial DNA (mtDNA) deletions. While dominantly-inherited, pathogenic variants in POLG, TWNK and RRM2B are among the most common genetic defects of adPEO, identification of novel candidate genes and the underlying pathomechanisms remain challenging. We report the clinical, genetic and molecular investigations of a patient who presented in the seventh decade of life with PEO. Oxidative histochemistry revealed cytochrome c oxidase deficient fibres and occasional ragged red fibres showing subsarcolemmal mitochondrial accumulation in skeletal muscle, while molecular studies identified the presence of multiple mtDNA deletions. Negative candidate screening of known nuclear genes associated with PEO prompted diagnostic exome sequencing, leading to the prioritisation of a novel heterozygous c.547G > C variant in GMPR (NM_006877.3) encoding guanosine monophosphate reductase, a cytosolic enzyme required for maintaining the cellular balance of adenine and guanine nucleotides. We show that the novel c.547G > C variant causes aberrant splicing, decreased GMPR protein levels in patient skeletal muscle, proliferating and quiescent cells and is associated with subtle changes in nucleotide homeostasis protein levels and evidence of disturbed mtDNA maintenance in skeletal muscle. Despite confirmation of GMPR deficiency, demonstrating marked defects of mtDNA replication or nucleotide homeostasis in patient cells proved challenging. Our study proposes that GMPR is the nineteenth (19th) locus for PEO and highlights the complexities of uncovering disease mechanisms in late-onset PEO phenotypes. This article is protected by copyright. All rights reserved.
    Keywords:  GMPR; PEO; mitochondrial DNA maintenance; multiple mtDNA deletions; whole exome sequencing
    DOI:  https://doi.org/10.1111/cge.13652
  11. Cell Commun Signal. 2019 Oct 10. 17(1): 124
    Dai Z, Yang S, Xu L, Hu H, Liao K, Wang J, Wang Q, Gao S, Li B, Lai L.
      BACKGROUND: Cancer cells undergo global reprogramming of cellular metabolism to satisfy demands of energy and biomass during proliferation and metastasis. Computational modeling of genome-scale metabolic models is an effective approach for designing new therapeutics targeting dysregulated cancer metabolism by identifying metabolic enzymes crucial for satisfying metabolic goals of cancer cells, but nearly all previous studies neglect the existence of metabolic demands other than biomass synthesis and trade-offs between these contradicting metabolic demands. It is thus necessary to develop computational models covering multiple metabolic objectives to study cancer metabolism and identify novel metabolic targets.METHODS: We developed a multi-objective optimization model for cancer cell metabolism at genome-scale and an integrated, data-driven workflow for analyzing the Pareto optimality of this model in achieving multiple metabolic goals and identifying metabolic enzymes crucial for maintaining cancer-associated metabolic phenotypes. Using this workflow, we constructed cell line-specific models for a panel of cancer cell lines and identified lists of metabolic targets promoting or suppressing cancer cell proliferation or the Warburg Effect. The targets were then validated using knockdown and over-expression experiments in cultured cancer cell lines.
    RESULTS: We found that the multi-objective optimization model correctly predicted phenotypes including cell growth rates, essentiality of metabolic genes and cell line specific sensitivities to metabolic perturbations. To our surprise, metabolic enzymes promoting proliferation substantially overlapped with those suppressing the Warburg Effect, suggesting that simply targeting the overlapping enzymes may lead to complicated outcomes. We also identified lists of metabolic enzymes important for maintaining rapid proliferation or high Warburg Effect while having little effect on the other. The importance of these enzymes in cancer metabolism predicted by the model was validated by their association with cancer patient survival and knockdown and overexpression experiments in a variety of cancer cell lines.
    CONCLUSIONS: These results confirm this multi-objective optimization model as a novel and effective approach for studying trade-off between metabolic demands of cancer cells and identifying cancer-associated metabolic vulnerabilities, and suggest novel metabolic targets for cancer treatment.
    Keywords:  Cancer metabolism; Drug discovery; Flux balance analysis; Genome-scale metabolic model; Pareto optimality
    DOI:  https://doi.org/10.1186/s12964-019-0439-y
  12. Mol Cell. 2019 Sep 27. pii: S1097-2765(19)30695-1. [Epub ahead of print]
    Nicholls TJ, Spåhr H, Jiang S, Siira SJ, Koolmeister C, Sharma S, Kauppila JHK, Jiang M, Kaever V, Rackham O, Chabes A, Falkenberg M, Filipovska A, Larsson NG, Gustafsson CM.
      Oligoribonucleases are conserved enzymes that degrade short RNA molecules of up to 5 nt in length and are assumed to constitute the final stage of RNA turnover. Here we demonstrate that REXO2 is a specialized dinucleotide-degrading enzyme that shows no preference between RNA and DNA dinucleotide substrates. A heart- and skeletal-muscle-specific knockout mouse displays elevated dinucleotide levels and alterations in gene expression patterns indicative of aberrant dinucleotide-primed transcription initiation. We find that dinucleotides act as potent stimulators of mitochondrial transcription initiation in vitro. Our data demonstrate that increased levels of dinucleotides can be used to initiate transcription, leading to an increase in transcription levels from both mitochondrial promoters and other, nonspecific sequence elements in mitochondrial DNA. Efficient RNA turnover by REXO2 is thus required to maintain promoter specificity and proper regulation of transcription in mammalian mitochondria.
    Keywords:  POLRMT; REXO2; RNA turnover; degradosome; mitochondria; mtDNA; oligoribonuclease; transcription
    DOI:  https://doi.org/10.1016/j.molcel.2019.09.010
  13. Cell Chem Biol. 2019 Sep 30. pii: S2451-9456(19)30314-9. [Epub ahead of print]
    Kim JT, Li VL, Terrell SM, Fischer CR, Long JZ.
      Enzymes catalyze fundamental biochemical reactions that control cellular and organismal homeostasis. Here we present an approach for de novo biochemical pathway discovery across entire mammalian enzyme families using parallel viral transduction in mice and untargeted liquid chromatography-mass spectrometry. Applying this method to the M20 peptidases uncovers both known pathways of amino acid metabolism as well as a previously unknown CNDP2-regulated pathway for threonyl dipeptide catabolism. Ablation of CNDP2 in mice elevates threonyl dipeptides across multiple tissues, establishing the physiologic relevance of our biochemical assignments. Taken together, these data underscore the utility of parallel in vivo metabolomics for the family-wide discovery of enzymatic pathways.
    Keywords:  acid; acy1; amino; cndp2; enzyme; in vivo; metabolomics; peptidase; pm20d1
    DOI:  https://doi.org/10.1016/j.chembiol.2019.09.009
  14. Methods Mol Biol. 2019 ;2049 263-282
    Campbell K, Correia-Melo C, Ralser M.
      All biosynthetically active cells are able to export and import metabolites, the small molecule intermediaries of metabolism. In dense cell populations, this hallmark of cells results in the intercellular exchange of a wide spectrum of metabolites. Such metabolite exchange enables metabolic specialization of individual cells, leading to far reaching biological implications, as a consequence of the intrinsic connection between metabolism and cell physiology. In this chapter, we discuss methods on how to study metabolite exchange interactions by using self-establishing metabolically cooperating communities (SeMeCos) in the budding yeast Saccharomyces cerevisiae. SeMeCos exploit the stochastic segregation of episomes to progressively increase the number of essential metabolic interdependencies in a community that grows out from an initially prototrophic cell. By coupling genotype to metabotype, SeMeCos allow for the tracking of cells while they specialize metabolically and hence the opportunity to study their progressive change in physiology.
    Keywords:  Metabolic cooperation; Metabolic specialization; Yeast communities
    DOI:  https://doi.org/10.1007/978-1-4939-9736-7_16
  15. Nat Metab. 2019 Sep;1(9): 861-867
    Diehl FF, Lewis CA, Fiske BP, Vander Heiden MG.
      The de novo serine synthesis pathway is upregulated in many cancers. However, even cancer cells with increased serine synthesis take up large amounts of serine from the environment1 and we confirm that exogenous serine is needed for maximal proliferation of these cells. Here we show that even when enzymes in the serine synthesis pathway are genetically upregulated, the demand for oxidized NAD+ constrains serine synthesis, rendering serine-deprived cells sensitive to conditions that decrease the cellular NAD+/NADH ratio. Further, purine depletion is a major consequence of reduced intracellular serine availability, particularly when NAD+ regeneration is impaired. Thus, cells rely on exogenous serine consumption to maintain purine biosynthesis. In support of this explanation, providing exogenous purine nucleobases, or increasing NAD+ availability to facilitate de novo serine and purine synthesis, both rescue maximal proliferation even in the absence of extracellular serine. Together, these data indicate that NAD+ is an endogenous limitation for cancer cells to synthesize the serine needed for purine production to support rapid proliferation.
    DOI:  https://doi.org/10.1038/s42255-019-0108-x
  16. Nat Commun. 2019 Oct 11. 10(1): 4623
    Henríquez-Olguin C, Knudsen JR, Raun SH, Li Z, Dalbram E, Treebak JT, Sylow L, Holmdahl R, Richter EA, Jaimovich E, Jensen TE.
      Reactive oxygen species (ROS) act as intracellular compartmentalized second messengers, mediating metabolic stress-adaptation. In skeletal muscle fibers, ROS have been suggested to stimulate glucose transporter 4 (GLUT4)-dependent glucose transport during artificially evoked contraction ex vivo, but whether myocellular ROS production is stimulated by in vivo exercise to control metabolism is unclear. Here, we combined exercise in humans and mice with fluorescent dyes, genetically-encoded biosensors, and NADPH oxidase 2 (NOX2) loss-of-function models to demonstrate that NOX2 is the main source of cytosolic ROS during moderate-intensity exercise in skeletal muscle. Furthermore, two NOX2 loss-of-function mouse models lacking either p47phox or Rac1 presented striking phenotypic similarities, including greatly reduced exercise-stimulated glucose uptake and GLUT4 translocation. These findings indicate that NOX2 is a major myocellular ROS source, regulating glucose transport capacity during moderate-intensity exercise.
    DOI:  https://doi.org/10.1038/s41467-019-12523-9
  17. Mol Cell. 2019 Sep 27. pii: S1097-2765(19)30692-6. [Epub ahead of print]
    Gao X, Zhao L, Liu S, Li Y, Xia S, Chen D, Wang M, Wu S, Dai Q, Vu H, Zacharias L, DeBerardinis R, Lim E, Metallo C, Boggon TJ, Lonial S, Lin R, Mao H, Pan Y, Shan C, Chen J.
      The oxidative pentose phosphate pathway (oxiPPP) contributes to cell metabolism through not only the production of metabolic intermediates and reductive NADPH but also inhibition of LKB1-AMPK signaling by ribulose-5-phosphate (Ru-5-P), the product of the third oxiPPP enzyme 6-phosphogluconate dehydrogenase (6PGD). However, we found that knockdown of glucose-6-phosphate dehydrogenase (G6PD), the first oxiPPP enzyme, did not affect AMPK activation despite decreased Ru-5-P and subsequent LKB1 activation, due to enhanced activity of PP2A, the upstream phosphatase of AMPK. In contrast, knockdown of 6PGD or 6-phosphogluconolactonase (PGLS), the second oxiPPP enzyme, reduced PP2A activity. Mechanistically, knockdown of G6PD or PGLS decreased or increased 6-phosphogluconolactone level, respectively, which enhanced the inhibitory phosphorylation of PP2A by Src. Furthermore, γ-6-phosphogluconolactone, an oxiPPP byproduct with unknown function generated through intramolecular rearrangement of δ-6-phosphogluconolactone, the only substrate of PGLS, bound to Src and enhanced PP2A recruitment. Together, oxiPPP regulates AMPK homeostasis by balancing the opposing LKB1 and PP2A.
    Keywords:  ▪▪▪
    DOI:  https://doi.org/10.1016/j.molcel.2019.09.007
  18. Int J Mol Sci. 2019 Oct 08. pii: E4966. [Epub ahead of print]20(19):
    Tedesco S, Scattolini V, Albiero M, Bortolozzi M, Avogaro A, Cignarella A, Fadini GP.
      Macrophages are highly plastic and dynamic cells that exert much of their function through phagocytosis. Phagocytosis depends on a coordinated, finely tuned, and compartmentalized regulation of calcium concentrations. We examined the role of mitochondrial calcium uptake and mitochondrial calcium uniporter (MCU) in macrophage polarization and function. In primary cultures of human monocyte-derived macrophages, calcium uptake in mitochondria was instrumental for alternative (M2) macrophage polarization. Mitochondrial calcium uniporter inhibition with KB-R7943 or MCU knockdown, which prevented mitochondrial calcium uptake, reduced M2 polarization, while not affecting classical (M1) polarization. Challenging macrophages with E. coli fragments induced spikes of mitochondrial calcium concentrations, which were prevented by MCU inhibition or silencing. In addition, mitochondria remodelled in M2 macrophages during phagocytosis, especially close to sites of E. coli internalization. Remarkably, inhibition or knockdown of MCU significantly reduced the phagocytic capacity of M2 macrophages. KB-R7943, which also inhibits the membrane sodium/calcium exchanger and Complex I, reduced mitochondria energization and cellular ATP levels, but such effects were not observed with MCU silencing. Therefore, phagocytosis inhibition by MCU knockdown depended on the impaired mitochondrial calcium buffering rather than changes in mitochondrial and cellular energy status. These data uncover a new role for MCU in alternative macrophage polarization and phagocytic activity.
    Keywords:  calcium; innate immunity; macrophage; mitochondria; phagocytosis; second messenger
    DOI:  https://doi.org/10.3390/ijms20194966
  19. Biosens Bioelectron. 2019 Oct 01. pii: S0956-5663(19)30832-2. [Epub ahead of print]146 111753
    Roshanzadeh A, Kang H, You SH, Park J, Khoa ND, Lee DH, Kim GJ, Kim ES.
      Nicotinamide adenine nucleotide phosphate (NADPH) has been known to be involved in the multiple pathways of cell metabolism. However, conventional quantification assays for NADPH have required breaking down the cell membranes of around one million cells per assay, and monitoring NADPH flux in living cells has been limited by a few available tools. Here, we visualized NADPH levels in human cervical cancer cells HeLa using metagenome-derived blue fluorescent protein (mBFP), which specifically binds to NADPH and enhances the intrinsic fluorescence of NADPH up to 10-fold when imaged by two-photon microscopy to reduce photodamage. Adding an oxidizing agent such as diamide to HeLa cells that expressed mBFP led to an immediate decrease of intracellular NADPH depending on glucose availability in culture media. Furthermore, inhibiting glucose-6-phosphate dehydrogenase (G6PD) in the pentose phosphate pathway with dehydroandrosterone (DHEA) and knockdown of G6PD transcripts gradually decreased NADPH when diamide was added to living cells. These results demonstrate that introducing a bacterial mBFP gene into mammalian cells is a straightforward approach to monitoring intracellular NADPH flux in real time at the single-cell level. Moreover, this strategy can be expanded to tracking the spatio-temporal changes in NADPH even in single-cell organelles such as mitochondria and chloroplasts, which will allow us to more precisely assess the efficacy of biochemically or biophysically metabolic perturbations in animal and plant cells.
    Keywords:  Cell metabolism; Chemical inhibitors; Fluorescence enhancement; Metagenomic-blue fluorescent protein (mBFP); NADPH-mBFP complex; Real-time imaging; Two-photon microscopy
    DOI:  https://doi.org/10.1016/j.bios.2019.111753
  20. J Biol Chem. 2019 Oct 11. pii: jbc.RA119.010243. [Epub ahead of print]
    Bartel K, Müller R, von Schwarzenberg K.
      The cellular energy sensor AMP-activated protein kinase (AMPK) is a metabolic hub regulating various pathways involved in tumor metabolism. Here, we report that vacuolar H+-ATPase (V-ATPase) inhibition differentially affects regulation of AMPK in tumor and non-tumor cells and that this differential regulation contributes to the selectivity of V-ATPase inhibitors for tumor cells. In non-malignant cells, the V-ATPase inhibitor archazolid increased phosphorylation and lysosomal localization of AMPK. We noted that AMPK localization has a pro-survival role, as AMPK silencing decreased cellular growth rates. In contrast, in cancer cells, we found that AMPK is constitutively active and that archazolid does not affect its phosphorylation and localization. Moreover, V-ATPase-independent AMPK induction in the tumor cells protected them from archazolid-induced cytotoxicity, further underlining the role of AMPK as a pro-survival mediator. These observations indicate that AMPK regulation is uncoupled from V-ATPase activity in cancer cells and that this makes them more susceptible to cell death induction by V-ATPase inhibitors. In both tumor and healthy cells, V-ATPase inhibition induced a distinct metabolic regulatory cascade downstream of AMPK, affecting ATP and NADPH levels, glucose uptake, and reactive oxygen species (ROS) production. We could attribute the pro-survival effects to AMPK's ability to maintain redox homeostasis by inhibiting ROS production and maintaining NADPH levels. In summary, the results of our work indicate that V-ATPase inhibition has differential effects on AMPK-mediated metabolic regulation in cancer and healthy cells and explain the tumor-specific cytotoxicity of V-ATPase inhibition.
    Keywords:  AMP-activated kinase (AMPK); apoptosis; archazolid; cancer; glucose starvation; metabolism; pH homeostasis; reactive oxygen species (ROS); tumor suppressor; vacuolar ATPase
    DOI:  https://doi.org/10.1074/jbc.RA119.010243
  21. Trends Endocrinol Metab. 2019 Oct 07. pii: S1043-2760(19)30176-6. [Epub ahead of print]
    Wang Y, Hekimi S.
      Ubiquinone (UQ, coenzyme Q) is an essential electron transfer lipid in the mitochondrial respiratory chain. It is a main source of mitochondrial reactive oxygen species (ROS) but also has antioxidant properties. This mix of characteristics is why ubiquinone supplementation is considered a potential therapy for many diseases involving mitochondrial dysfunction. Mutations in the ubiquinone biosynthetic pathway are increasingly being identified in patients. Furthermore, secondary ubiquinone deficiency is a common finding associated with mitochondrial disorders and might exacerbate these conditions. Recent developments have suggested that ubiquinone biosynthesis occurs in discrete domains of the mitochondrial inner membrane close to ER-mitochondria contact sites. This spatial requirement for ubiquinone biosynthesis could be the link between secondary ubiquinone deficiency and mitochondrial dysfunction, which commonly results in loss of mitochondrial structural integrity.
    Keywords:  ER–mitochondria contact sites; coenzyme Q; mitochondrial dysfunction; ubiquinone; ubiquinone biosynthesis
    DOI:  https://doi.org/10.1016/j.tem.2019.08.009
  22. EMBO Mol Med. 2019 Oct 10. e10698
    Wu H, Han Y, Rodriguez Sillke Y, Deng H, Siddiqui S, Treese C, Schmidt F, Friedrich M, Keye J, Wan J, Qin Y, Kühl AA, Qin Z, Siegmund B, Glauben R.
      Tumor-associated macrophages (TAMs) promote tumor growth and metastasis by suppressing tumor immune surveillance. Herein, we provide evidence that the immunosuppressive phenotype of TAMs is controlled by long-chain fatty acid metabolism, specifically unsaturated fatty acids, here exemplified by oleate. Consequently, en-route enriched lipid droplets were identified as essential organelles, which represent effective targets for chemical inhibitors to block in vitro polarization of TAMs and tumor growth in vivo. In line, analysis of human tumors revealed that myeloid cells infiltrating colon cancer but not gastric cancer tissue indeed accumulate lipid droplets. Mechanistically, our data indicate that oleate-induced polarization of myeloid cells depends on the mammalian target of the rapamycin pathway. Thus, our findings reveal an alternative therapeutic strategy by targeting the pro-tumoral myeloid cells on a metabolic level.
    Keywords:  cancer immunotherapy; lipid droplets; lipid metabolism; tumor microenvironment; tumor-associated macrophage
    DOI:  https://doi.org/10.15252/emmm.201910698
  23. Antioxidants (Basel). 2019 Oct 06. pii: E454. [Epub ahead of print]8(10):
    Kuznetsov AV, Javadov S, Margreiter R, Grimm M, Hagenbuchner J, Ausserlechner MJ.
      Mitochondria play a critical role in maintaining cellular function by ATP production. They are also a source of reactive oxygen species (ROS) and proapoptotic factors. The role of mitochondria has been established in many aspects of cell physiology/pathophysiology, including cell signaling. Mitochondria may deteriorate under various pathological conditions, including ischemia-reperfusion (IR) injury. Mitochondrial injury can be one of the main causes for cardiac and other tissue injuries by energy stress and overproduction of toxic reactive oxygen species, leading to oxidative stress, elevated calcium and apoptotic and necrotic cell death. However, the interplay among these processes in normal and pathological conditions is still poorly understood. Mitochondria play a critical role in cardiac IR injury, where they are directly involved in several pathophysiological mechanisms. We also discuss the role of mitochondria in the context of mitochondrial dynamics, specializations and heterogeneity. Also, we wanted to stress the existence of morphologically and functionally different mitochondrial subpopulations in the heart that may have different sensitivities to diseases and IR injury. Therefore, various cardioprotective interventions that modulate mitochondrial stability, dynamics and turnover, including various pharmacologic agents, specific mitochondrial antioxidants and uncouplers, and ischemic preconditioning can be considered as the main strategies to protect mitochondrial and cardiovascular function and thus enhance longevity.
    Keywords:  cytoskeleton; energy metabolism; heart; ischemia-reperfusion; mitochondria; mitochondrial heterogeneity; preconditioning; reactive oxygen species; signaling
    DOI:  https://doi.org/10.3390/antiox8100454
  24. Science. 2019 Oct 11. 366(6462): 203-210
    Anandapadamanaban M, Masson GR, Perisic O, Berndt A, Kaufman J, Johnson CM, Santhanam B, Rogala KB, Sabatini DM, Williams RL.
      The Rag guanosine triphosphatases (GTPases) recruit the master kinase mTORC1 to lysosomes to regulate cell growth and proliferation in response to amino acid availability. The nucleotide state of Rag heterodimers is critical for their association with mTORC1. Our cryo-electron microscopy structure of RagA/RagC in complex with mTORC1 shows the details of RagA/RagC binding to the RAPTOR subunit of mTORC1 and explains why only the RagAGTP/RagCGDP nucleotide state binds mTORC1. Previous kinetic studies suggested that GTP binding to one Rag locks the heterodimer to prevent GTP binding to the other. Our crystal structures and dynamics of RagA/RagC show the mechanism for this locking and explain how oncogenic hotspot mutations disrupt this process. In contrast to allosteric activation by RHEB, Rag heterodimer binding does not change mTORC1 conformation and activates mTORC1 by targeting it to lysosomes.
    DOI:  https://doi.org/10.1126/science.aax3939
  25. Nat Immunol. 2019 Oct 07.
    Howden AJM, Hukelmann JL, Brenes A, Spinelli L, Sinclair LV, Lamond AI, Cantrell DA.
      Quantitative mass spectrometry reveals how CD4+ and CD8+ T cells restructure proteomes in response to antigen and mammalian target of rapamycin complex 1 (mTORC1). Analysis of copy numbers per cell of >9,000 proteins provides new understanding of T cell phenotypes, exposing the metabolic and protein synthesis machinery and environmental sensors that shape T cell fate. We reveal that lymphocyte environment sensing is controlled by immune activation, and that CD4+ and CD8+ T cells differ in their intrinsic nutrient transport and biosynthetic capacity. Our data also reveal shared and divergent outcomes of mTORC1 inhibition in naïve versus effector T cells: mTORC1 inhibition impaired cell cycle progression in activated naïve cells, but not effector cells, whereas metabolism was consistently impacted in both populations. This study provides a comprehensive map of naïve and effector T cell proteomes, and a resource for exploring and understanding T cell phenotypes and cell context effects of mTORC1.
    DOI:  https://doi.org/10.1038/s41590-019-0495-x
  26. J Neuromuscul Dis. 2019 Sep 24.
    Diane Shelton G, Minor KM, Li K, Naviaux JC, Monk J, Wang L, Guzik E, Guo LT, Porcelli V, Gorgoglione R, Lasorsa M, Leegwater PJ, Persico AM, Mickelson JR, Palmieri L, Naviaux RK.
      BACKGROUND: Inflammatory myopathies are characterized by infiltration of inflammatory cells into muscle. Typically, immune-mediated disorders such as polymyositis, dermatomyositis and inclusion body myositis are diagnosed.OBJECTIVE: A small family of dogs with early onset muscle weakness and inflammatory muscle biopsies were investigated for an underlying genetic cause.
    METHODS: Following the histopathological diagnosis of inflammatory myopathy, mutational analysis including whole genome sequencing, functional transport studies of the mutated and wild-type proteins, and metabolomic analysis were performed.
    RESULTS: Whole genome resequencing identified a pathological variant in the SLC25A12 gene, resulting in a leucine to proline substitution at amino acid 349 in the mitochondrial aspartate-glutamate transporter known as the neuron and muscle specific aspartate glutamate carrier 1 (AGC1). Functionally reconstituting recombinant wild-type and mutant AGC1 into liposomes demonstrated a dramatic decrease in AGC1 transport activity and inability to transfer reducing equivalents from the cytosol into mitochondria. Targeted, broad-spectrum metabolomic analysis from affected and control muscles demonstrated a proinflammatory milieu and strong support for oxidative stress.
    CONCLUSIONS: This study provides the first description of a metabolic mechanism in which ablated mitochondrial glutamate transport markedly reduced the import of reducing equivalents into mitochondria and produced a highly oxidizing and proinflammatory muscle environment and an inflammatory myopathy.
    Keywords:  Canine; SLC25A12; metabolomics; mitochondrial transporter; myopathy
    DOI:  https://doi.org/10.3233/JND-190421
  27. Annu Rev Cell Dev Biol. 2019 Oct 06. 35 85-109
    Balla T, Kim YJ, Alvarez-Prats A, Pemberton J.
      Phospholipids are synthesized primarily within the endoplasmic reticulum and are subsequently distributed to various subcellular membranes to maintain the unique lipid composition of specific organelles. As a result, in most cases, the steady-state localization of membrane phospholipids does not match their site of synthesis. This raises the question of how diverse lipid species reach their final membrane destinations and what molecular processes provide the energy to maintain the lipid gradients that exist between various membrane compartments. Recent studies have highlighted the role of inositol phospholipids in the nonvesicular transport of lipids at membrane contact sites. This review attempts to summarize our current understanding of these complex lipid dynamics and highlights their implications for defining future research directions.
    Keywords:  endoplasmic reticulum; lipid metabolism; lipid transfer protein; membrane contact sites; nonvesicular lipid transport
    DOI:  https://doi.org/10.1146/annurev-cellbio-100818-125251
  28. Nat Chem Biol. 2019 Oct 07.
    van Delft MF, Chappaz S, Khakham Y, Bui CT, Debrincat MA, Lowes KN, Brouwer JM, Grohmann C, Sharp PP, Dagley LF, Li L, McArthur K, Luo MX, Chin HS, Fairlie WD, Lee EF, Segal D, Duflocq S, Lessene R, Bernard S, Peilleron L, Nguyen T, Miles C, Wan SS, Lane RM, Wardak A, Lackovic K, Colman PM, Sandow JJ, Webb AI, Czabotar PE, Dewson G, Watson KG, Huang DCS, Lessene G, Kile BT.
      Activating the intrinsic apoptosis pathway with small molecules is now a clinically validated approach to cancer therapy. In contrast, blocking apoptosis to prevent the death of healthy cells in disease settings has not been achieved. Caspases have been favored, but they act too late in apoptosis to provide long-term protection. The critical step in committing a cell to death is activation of BAK or BAX, pro-death BCL-2 proteins mediating mitochondrial damage. Apoptosis cannot proceed in their absence. Here we show that WEHI-9625, a novel tricyclic sulfone small molecule, binds to VDAC2 and promotes its ability to inhibit apoptosis driven by mouse BAK. In contrast to caspase inhibitors, WEHI-9625 blocks apoptosis before mitochondrial damage, preserving cellular function and long-term clonogenic potential. Our findings expand on the key role of VDAC2 in regulating apoptosis and demonstrate that blocking apoptosis at an early stage is both advantageous and pharmacologically tractable.
    DOI:  https://doi.org/10.1038/s41589-019-0365-8
  29. Nat Med. 2019 Oct 07.
    Ganesh K, Wu C, O'Rourke KP, Szeglin BC, Zheng Y, Sauvé CG, Adileh M, Wasserman I, Marco MR, Kim AS, Shady M, Sanchez-Vega F, Karthaus WR, Won HH, Choi SH, Pelossof R, Barlas A, Ntiamoah P, Pappou E, Elghouayel A, Strong JS, Chen CT, Harris JW, Weiser MR, Nash GM, Guillem JG, Wei IH, Kolesnick RN, Veeraraghavan H, Ortiz EJ, Petkovska I, Cercek A, Manova-Todorova KO, Saltz LB, Lavery JA, DeMatteo RP, Massagué J, Paty PB, Yaeger R, Chen X, Patil S, Clevers H, Berger MF, Lowe SW, Shia J, Romesser PB, Dow LE, Garcia-Aguilar J, Sawyers CL, Smith JJ.
      Rectal cancer (RC) is a challenging disease to treat that requires chemotherapy, radiation and surgery to optimize outcomes for individual patients. No accurate model of RC exists to answer fundamental research questions relevant to patients. We established a biorepository of 65 patient-derived RC organoid cultures (tumoroids) from patients with primary, metastatic or recurrent disease. RC tumoroids retained molecular features of the tumors from which they were derived, and their ex vivo responses to clinically relevant chemotherapy and radiation treatment correlated with the clinical responses noted in individual patients' tumors. Upon engraftment into murine rectal mucosa, human RC tumoroids gave rise to invasive RC followed by metastasis to lung and liver. Importantly, engrafted tumors displayed the heterogenous sensitivity to chemotherapy observed clinically. Thus, the biology and drug sensitivity of RC clinical isolates can be efficiently interrogated using an organoid-based, ex vivo platform coupled with in vivo endoluminal propagation in animals.
    DOI:  https://doi.org/10.1038/s41591-019-0584-2
  30. Annu Rev Physiol. 2019 Oct 07.
    Zhang J, Chatham J, Young ME.
      On Earth, all life is exposed to dramatic changes in the environment over the course of the day; consequently, organisms have evolved strategies to both adapt to and anticipate these 24-h oscillations. As a result, time of day is major regulator of mammalian physiology and processes, including transcription, signaling, metabolism, and muscle contraction, all of which oscillate over the course of the day. In particular, the heart is subject to wide fluctuations in energetic demand throughout the day as a result of waking, physical activity, and food intake patterns. Daily rhythms in cardiovascular function ensure that increased delivery of oxygen, nutrients, and endocrine factors to organs during the active period and the removal of metabolic by-products are in balance. Failure to maintain these physiologic rhythms invariably has pathologic consequences. This review highlights rhythms that underpin cardiac physiology. More specifically, we summarize the key aspects of cardiac physiology that oscillate over the course of the day and discuss potential mechanisms that regulate these 24-h rhythms. Expected final online publication date for the Annual Review of Physiology, Volume 82 is February 10, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-physiol-020518-114349
  31. Immunometabolism. 2019 ;1 e190014
    Kedia-Mehta N, Choi C, McCrudden A, Littwitz-Salomon E, Fox PG, Gardiner CM, Finlay DK.
      Natural Killer (NK) cells are lymphocytes with an important role in anti-tumour responses. NK cells bridge the innate and adaptive arms of the immune system; they are primed for immediate anti-tumour function but can also have prolonged actions alongside the adaptive T cell response. However, the key signals and cellular processes that are required for extended NK cell responses are not fully known. Herein we show that murine NK cell interaction with tumour cells induces the expression of CD25, the high affinity IL2 receptor, rendering these NK cells highly sensitive to the T cell-derived cytokine IL2. In response to IL2, CD25high NK cells show robust increases in metabolic signalling pathways (mTORC1, cMyc), nutrient transporter expression (CD71, CD98), cellular growth and in NK cell effector functions (IFNγ, granzyme B). Specific ligation of an individual activating NK cell receptor, NK1.1, showed similar increases in CD25 expression and IL2-induced responses. NK cell receptor ligation and IL2 collaborate to induce mTORC1/cMyc signalling leading to high rates of glycolysis and oxidative phosphorylation (OXPHOS) and prolonged NK cell survival. Disrupting mTORC1 and cMyc signalling in CD25high tumour interacting NK cells prevents IL2-induced cell growth and function and compromises NK cell viability. This study reveals that tumour cell interactions and T cell-derived IL2 cooperate to promote robust and prolonged NK cell anti-tumour metabolic responses.
    Keywords:  CD25; IL2; NK1.1; OXPHOS; Slc7a5; cMyc; cancer; glycolysis; mTORC1; metabolism; natural killer cell; receptor; tumour
    DOI:  https://doi.org/10.20900/immunometab20190014
  32. Nature. 2019 Oct;574(7777): 161-162
    Ledford H, Callaway E.
      
    Keywords:  Cell biology; Medical research; Physiology
    DOI:  https://doi.org/10.1038/d41586-019-02963-0
  33. Science. 2019 Oct 10. pii: eaay0166. [Epub ahead of print]
    Rogala KB, Gu X, Kedir JF, Abu-Remaileh M, Bianchi LF, Bottino AMS, Dueholm R, Niehaus A, Overwijn D, Fils AP, Zhou SX, Leary D, Laqtom NN, Brignole EJ, Sabatini DM.
      The mTORC1 protein kinase regulates growth in response to nutrients and growth factors. Nutrients promote its translocation to the lysosomal surface, where its Raptor subunit interacts with the Rag GTPase-Ragulator complex. Nutrients switch the heterodimeric Rag GTPases between four different nucleotide binding states, only one of which (RagA/B•GTP-RagC/D•GDP) permits mTORC1 association. We determined the structure of the supercomplex of Raptor with Rag-Ragulator to 3.2 Å resolution by cryo-electron microscopy. The Raptor α-solenoid directly detects the nucleotide state of RagA, while the Raptor "claw" threads between the GTPase domains to detect that of RagC. Mutations that disrupt Rag-Raptor binding inhibit mTORC1 lysosomal localization and signaling. By comparison with a structure of mTORC1 bound to its activator Rheb, we develop a model of active mTORC1 docked on the lysosome.
    DOI:  https://doi.org/10.1126/science.aay0166