bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2019‒10‒20
thirty-five papers selected by
Christian Frezza
University of Cambridge, MRC Cancer Unit


  1. Nature. 2019 Oct 16.
    Hoshino A, Wang WJ, Wada S, McDermott-Roe C, Evans CS, Gosis B, Morley MP, Rathi KS, Li J, Li K, Yang S, McMannus MJ, Bowman C, Potluri P, Levin M, Damrauer S, Wallace DC, Holzbaur ELF, Arany Z.
      Mitochondrial homeostasis vitally depends on mitophagy, the programmed degradation of mitochondria. The roster of proteins known to participate in mitophagy remains small. We devised here a multidimensional CRISPR/Cas9 genetic screen, using multiple mitophagy reporter systems and pro-mitophagy triggers, and uncover numerous new components of Parkin-dependent mitophagy1. Unexpectedly, we identify the adenine nucleotide translocator (ANT) complex as required for mitophagy in multiple cell types. While pharmacological inhibition of ANT-mediated ADP/ATP exchange promotes mitophagy, genetic ablation of ANT paradoxically suppresses mitophagy. Importantly, ANT promotes mitophagy independently of its nucleotide translocase catalytic activity. Instead, the ANT complex is required for inhibition of the presequence translocase TIM23, leading to PINK1 stabilization, in response to bioenergetic collapse. ANT modulates TIM23 indirectly via interaction with TIM44, known to regulate peptide import through TIM232. Mice lacking ANT1 reveal blunted mitophagy and consequent profound accumulation of aberrant mitochondria. Disease-causing human mutations in ANT1 abrogate binding to TIM44 and TIM23 and inhibit mitophagy. Together, these data identify a novel and essential function for ANT as a fundamental mediator of mitophagy in health and disease.
    DOI:  https://doi.org/10.1038/s41586-019-1667-4
  2. Traffic. 2019 Oct 17.
    Rahmani S, Defferrari MS, Wakarchuk WW, Antonescu CN.
      Endocytic membrane traffic controls the access of myriad cell surface proteins to the extracellular milieu, and thus gates nutrient uptake, ion homeostasis, signaling, adhesion and migration. Coordination of the regulation of endocytic membrane traffic with a cell's metabolic needs represents an important facet of maintenance of homeostasis under variable conditions of nutrient availability and metabolic demand. Many studies have revealed intimate regulation of endocytic membrane traffic by metabolic cues, from the specific control of certain receptors or transporters, to broader adaptation or remodeling of the endocytic membrane network. We examine how metabolic sensors such as AMP-activated protein kinase (AMPK), mechanistic target of rapamycin complex 1 (mTORC1) and hypoxia inducible factor 1 (HIF1) determine sufficiency of various metabolites, and in turn modulate cellular functions that includes control of endocytic membrane traffic. We also examine how certain metabolites can directly control endocytic traffic proteins, such as the regulation of specific protein glycosylation by limiting levels of uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) produced by the hexosamine biosynthetic pathway. From these ideas emerge a growing appreciation that endocytic membrane traffic is orchestrated by many intrinsic signals derived from cell metabolism, allowing alignment of the functions of cell surface proteins with cellular metabolic requirements. This article is protected by copyright. All rights reserved.
    Keywords:  AMP-Activated Protein Kinase (AMPK); Mgat5; N-glycan branching; O-linked β-N-acetylglucosamine (O-GlcNAc); clathrin; endocytosis; endosome; galectins; hexosamine biosynthetic pathway; hypoxia inducible factor (HIF); lysosome; mechanistic target of rapamycin complex 1 (mTORC1); uridine diphosphate N-acetylglucosamine (UDP-GlcNAc)
    DOI:  https://doi.org/10.1111/tra.12705
  3. Methods Enzymol. 2019 ;pii: S0076-6879(19)30293-9. [Epub ahead of print]626 1-21
    Trefely S, Doan MT, Snyder NW.
      Dynamic interplay between cellular metabolism and histone acetylation is a key mechanism underlying metabolic control of epigenetics. In particular, the central metabolite acetyl-coenzyme A (acetyl-CoA) acts as the acetyl-donor for histone acetylation in both an enzymatic and non-enzymatic manner. Since members of the family of histone acetyl transferases (HATs) that catalyze the acetylation of histone tails possess a Michaelis constant (Km) within the range of physiological cellular acetyl-CoA concentrations, changing concentrations of acetyl-CoA can restrict or promote enzymatic histone acetylation. Likewise, non-enzymatic histone acetylation occurs at physiological concentrations. These concepts implicate acetyl-CoA as a rheostat for nutrient availability acting, in part, by controlling histone acetylation. Histone acetylation is an important epigenetic modification that controls gene expression and acetyl-CoA dependent changes in both histone acetylation and gene expression have been shown in yeast and mammalian systems. However, quantifying the metabolic conditions required to achieve specific changes in histone acetylation is a major challenge. The relationship between acetyl-CoA and histone acetylation may be influenced by a variety of factors including sub-cellular location of metabolites and enzymes, relative quantities of metabolites, and substrate availability/preference. A diversity of substrates can contribute the two-carbon acyl-chain to acetyl-CoA, a number of pathways can create or degrade acetyl-CoA, and only a handful of potential mechanisms for the crosstalk between metabolism and histone acetylation have been explored. The centrality of acetyl-CoA in intermediary metabolism means that acetyl-CoA levels may change, or be resistant to change, in unexpected ways. Thus, quantification of relevant metabolites is critical evidence in understanding how the nutrient rheostat is set in normal and pathological contexts. Coupling metabolite quantitation with isotope tracing to examine fate of specific metabolites is critical to the crosstalk between metabolism and histone acetylation, including but not limited to acetyl-CoA provides necessary context. This chapter provides guidance on experimental design of quantification with isotope dilution and/or tracing of acetyl-CoA within a targeted or highly multiplexed multi-analyte workflow.
    Keywords:  Acetyl-coenzyme A; Acetylation; Liquid chromatography mass spectrometry; Metabolism
    DOI:  https://doi.org/10.1016/bs.mie.2019.07.013
  4. Enzymes. 2019 ;pii: S1874-6047(19)30010-1. [Epub ahead of print]45 311-341
    Zhao L.
      Mitochondria play a central role in bioenergetics, and fulfill a plethora of functions in cell signaling, programmed cell death, and biosynthesis of key protein cofactors. Mitochondria harbor their own genomic DNA, which encodes protein subunits of the electron transport chain and a full set of transfer and ribosomal RNAs. Mitochondrial DNA (mtDNA) is essential for cellular and organismal functions, and defects in mitochondrial genome maintenance have been implicated in common human diseases and mitochondrial disorders. mtDNA repair and degradation are known pathways to cope with mtDNA damage; however, molecular factors involved in this process have remained unclear. Such knowledge is fundamental to the understanding of mitochondrial genomic maintenance and pathology, because mtDNA degradation may contribute to the etiology of mtDNA depletion syndromes and to the activation of the innate immune response by fragmented mtDNA. This article reviews the current literature regarding the importance of mitochondrial DNA degradation in mtDNA maintenance and stress response, and the recent progress in uncovering molecular factors involved in mtDNA degradation. These factors include key components of the mtDNA replication machinery, such as DNA polymerase γ, helicase Twinkle, and exonuclease MGME1, as well as a major DNA-packaging protein, mitochondrial transcription factor A (TFAM).
    Keywords:  DNA damage; DNA repair; DNA turnover; Mitochondrial DNA; TFAM
    DOI:  https://doi.org/10.1016/bs.enz.2019.08.004
  5. Methods Appl Fluoresc. 2019 Oct 17.
    Lukina MM, Shimolina L, Nikolay K, Zagainov V, Komarov D, Zagaynova EV, Shirmanova M.
      Exploring metabolism in human tumors at the cellular level remains a challenge. The reduced form of metabolic cofactor NAD(P)H is one of the major intrinsic fluorescent components in tissues and a valuable indicator of cellular metabolic activity. Fluorescence lifetime imaging (FLIM) enables resolution of both the free and protein-bound fractions of this cofactor, and thus, high sensitivity detection of relative changes in the NAD(P)H-dependent metabolic pathways in real time. However, the clinical use of this technique is still very limited. The applications of metabolic FLIM could be usefully expanded by probing cellular metabolism in tissues ex vivo. For this, however, the development of appropriate tissue preservation protocols is required in order to maintain the optical metabolic characteristics in the ex vivo sample in a state similar to those of the tumor in vivo. Using mouse tumor models of different histological types - colorectal cancer, lung carcinoma and melanoma - we tested eight different methods of tissue handling by comparing NAD(P)H fluorescence decay parameters ex vivo and in vivo as measured with two-photon excited FLIM microscopy. It was found that the samples placed in 10% BSA on ice immediately after excision maintained the same fluorescence lifetimes and free/bound ratios as measured in vivo for at least 3 hours. This protocol was subsequently used for metabolic assessments in fresh postoperative samples from colorectal cancer patients. A high degree of inter- and intra-tumor heterogeneity with a trend to a more oxidative metabolism was detected in T3 colorectal tumors in comparison with normal tumor-distant colon samples. These results suggest that the methodology developed on the basis of FLIM of NAD(P)H in tissues ex vivo show promise for interrogating the metabolic state of patients' tumors.
    Keywords:  Colorectal cancer; FLIM; NAD(P)H; cancer metabolism; patients’ tumors; two-photon fluorescence microscopy
    DOI:  https://doi.org/10.1088/2050-6120/ab4ed8
  6. Cell Metab. 2019 Oct 03. pii: S1550-4131(19)30512-1. [Epub ahead of print]
    Zhu J, Berisa M, Schwörer S, Qin W, Cross JR, Thompson CB.
      Cysteine acts both as a building unit for protein translation and as the limiting substrate for glutathione synthesis to support the cellular antioxidant system. In addition to transporter-mediated uptake, cellular cysteine can also be synthesized from methionine through the transsulfuration pathway. Here, we investigate the regulation of transsulfuration and its role in sustaining cell proliferation upon extracellular cysteine limitation, a condition reported to occur in human tumors as they grow in size. We observed constitutive expression of transsulfuration enzymes in a subset of cancer cell lines, while in other cells, these enzymes are induced following cysteine deprivation. We show that both constitutive and inducible transsulfuration activities contribute to the cellular cysteine pool and redox homeostasis. The rate of transsulfuration is determined by the cellular capacity to conduct methylation reactions that convert S-adenosylmethionine to S-adenosylhomocysteine. Finally, our results demonstrate that transsulfuration-mediated cysteine synthesis is critical in promoting tumor growth in vivo.
    Keywords:  cancer; cysteine; glutathione; metabolism; methylation; redox homeostasis; transsulfuration; xCT
    DOI:  https://doi.org/10.1016/j.cmet.2019.09.009
  7. Cancer Res. 2019 Oct 16. pii: canres.1405.2019. [Epub ahead of print]
    Kanakkanthara A, Kurmi K, Ekstrom TL, Hou X, Purfeerst ER, Heinzen EP, Correia C, Huntoon CJ, O'Brien D, Wahner Hendrickson AE, Dowdy SC, Li H, Oberg AL, Hitosugi T, Kaufmann SH, Weroha SJ, Karnitz LM.
      BRCA1 plays a key role in homologous recombination (HR) DNA repair. Accordingly, changes that downregulate BRCA1, including BRCA1 mutations and reduced BRCA1 transcription, due to promoter hypermethylation or loss of the BRCA1 transcriptional regulator CDK12, disrupt HR in multiple cancers. In addition, BRCA1 has also been implicated in the regulation of metabolism. Here, we showed that reducing BRCA1 expression, either by CDK12 or BRCA1 depletion, led to metabolic reprogramming of ovarian cancer cells, causing decreased mitochondrial respiration and reduced ATP levels. BRCA1 depletion drove this reprogramming by upregulating NNMT (nicotinamide N-methyltransferase). Notably, the metabolic alterations caused by BRCA1 depletion and NNMT upregulation sensitized ovarian cancer cells to agents that inhibit mitochondrial metabolism (VLX600 and tigecycline) and to agents that inhibit glucose import (WZB117). These observations suggest that inhibition of energy metabolism may be a potential strategy to selectively target BRCA1-deficient high-grade serous ovarian cancer (HGSOC), which is characterized by frequent BRCA1 loss and NNMT overexpression.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-19-1405
  8. Front Physiol. 2019 ;10 1225
    Zhou L, Zhang L, Zhang Y, Yu X, Sun X, Zhu T, Li X, Liang W, Han Y, Qin C.
      Mitophagy plays a key role in cleaning damaged and depolarized mitochondria to maintain cellular homeostasis and viability. Although it was originally found in neurodegenerative diseases, mitophagy is reported to play an important role in acute kidney injury. PINK1 and Parkin are key molecules in mitophagy pathway. Here, we used PINK1 knockout rats to examine the role of PINK1/Parkin-mediated mitophagy in cisplatin nephrotoxicity. After cisplatin treatment, PINK1 knockout rats showed lower plasma creatinine and less tubular damage when compared with wild-type rats. Meanwhile, mitophagy indicated by autophagosome formation and LC3B-II accumulation was also attenuated in PINK1 knockout rats. Renal expression of PINK1 and Parkin were down-regulated while BNIP3L was up-regulated by cisplatin treatment, indicating a major role of BNIP3/BNIP3L pathway in cisplatin-induced mitophagy. Transmission electron microscopy showed that PINK1 deficiency inhibited cisplatin-induced mitochondrial fragmentation indicating an involvement of mitochondrial fusion and fission. Renal expression of mitochondrial dynamics related proteins including Fis1, Drp1, Mfn1, Mfn2, and Opa1 were checked by real-time PCR and western blots. The results showed PINK1 deficiency distinctly prevented cisplatin-induced up-regulation of DRP1. Finally, PINK1 deficiency alleviated cisplatin-induced tubular apoptosis indicated by TUNEL assay as well as the expression of caspase3 and cleaved caspase3. Together, these results suggested PINK1 deficiency ameliorated cisplatin-induced acute kidney injury in rats, possibly via inhibiting DRP1-mediated mitochondrial fission and excessive mitophagy.
    Keywords:  DRP1; PINK1; mitochondrial dynamics; mitophagy; nephrotoxicity
    DOI:  https://doi.org/10.3389/fphys.2019.01225
  9. Semin Cell Dev Biol. 2019 Oct 11. pii: S1084-9521(19)30021-7. [Epub ahead of print]
    van den Ameele J, Li AYZ, Ma H, Chinnery PF.
      Inheritance of the mitochondrial genome does not follow the rules of conventional Mendelian genetics. The mitochondrial DNA (mtDNA) is present in many copies per cell and is inherited through the maternal germline. In addition, mutations in the mtDNA will give rise to heteroplasmy, the coexistence of different mtDNA variants within a single cell, whose levels can vary considerably between cells, organs or organisms. The inheritance and subsequent accumulation of deleterious variants are the cause of severe progressive mitochondrial disorders and play a role in many other conditions, including aging, cancer and neurodegenerative disorders. Here, we discuss the processes that give rise to cell-to-cell variability in mtDNA composition, focussing on somatic mtDNA segregation and on less conventional sources of heteroplasmy: non-maternal inheritance and mtDNA recombination. Understanding how mtDNA variants and mutations emerge and evolve within an organism is of crucial importance to prevent and cure mitochondrial disease and can potentially impact more common aging-associated conditions.
    Keywords:  Bottleneck; Heteroplasmy; Mitochondrial genome; Paternal leakage; Recombination; Somatic segregation
    DOI:  https://doi.org/10.1016/j.semcdb.2019.10.001
  10. J Biol Chem. 2019 Oct 18. pii: jbc.AW119.008146. [Epub ahead of print]
    Thompson CB, Bielska AA.
      How cells utilize nutrients to produce the ATP needed for bioenergetic homeostasis has been well characterized. What is less well studied is how resting cells metabolically shift from an ATP-producing catabolic metabolism to a metabolism that supports anabolic growth. In metazoan organisms, the discovery of growth factors and the ability of their receptors to induce new transcription and translation led to the hypothesis that the bioenergetic and synthetic demands of cell growth were primarily met through the replacement of nutrients consumed during net macromolecular synthesis, a demand-based system of nutrient uptake. Recent data have challenged this hypothesis. Instead there is increasing evidence that cellular nutrient uptake is a push system. Growth factor signaling has been linked to direct stimulation of nutrient uptake. The ability of growth factor signaling to increase the uptake of glucose, lipids, and amino acids to levels that exceed a cell's bioenergetic and synthetic needs has been documented in a wide variety of settings. In some tissues, this leads to the storage of the excess nutrients in the form of glycogen or fat. In others, the excess is secreted as lactate and certain non-essential amino acids. When growth factor signaling stimulates nutrient uptake to levels that exceed a cell's bioenergetic needs, adaptive changes in intermediate metabolism lead to the production of anabolic precursors that fuel the net synthesis of protein, lipids, and nucleic acids. Through the increased production of these precursors, growth factor signaling provides a supply side stimulation of cell growth and proliferation.
    Keywords:  bioenergetics; cell growth; cell metabolism; cell proliferation; growth factor
    DOI:  https://doi.org/10.1074/jbc.AW119.008146
  11. Circ Res. 2019 Oct 18.
    Chen Y, Yang M, Huang W, Chen W, Zhao Y, Schulte ML, Volberding PJ, Gerbec Z, Zimmermann MT, Zeighami A, Demos W, Zhang J, Knaack DA, Smith BC, Cui W, Malarkannan S, Sodhi K, Shapiro JI, Xie Z, Sahoo D, Silverstein RL.
      Rationale: A hallmark of chronic inflammatory disorders is persistence of pro-inflammatory macrophages in diseased tissues. In atherosclerosis this is associated with dyslipidemia and oxidative stress, but mechanisms linking these phenomena to macrophage activation remain incompletely understood. Objective: To investigate mechanisms linking dyslipidemia, oxidative stress and macrophage activation through modulation of immunemetabolism, and to explore therapeutic potential targeting specific metabolic pathways. Methods and Results: Using a combination of biochemical, immunological, and ex vivo cell metabolic studies, we report that CD36 mediates a mitochondrial metabolic switch from oxidative phosphorylation to superoxide production in response to its ligand, oxLDL. Mitochondrial-specific inhibition of superoxide inhibited oxLDL-induced NF-κB activation and inflammatory cytokine generation. RNAseq, flow cytometry, 3H-labeled palmitic acid uptake, lipidomic analysis, confocal and EM imaging, and functional energetics revealed that oxLDL upregulated effectors of long-chain fatty acid (FA) uptake and mitochondrial import, while downregulating FA oxidation and inhibiting ATP5A, an electron transport chain (ETC) component. The combined effect is long-chain FA accumulation, alteration of mitochondrial structure and function, repurposing of the ETC to superoxide production, and NF-κB activation. Apoe null mice challenged with high fat diet showed similar metabolic changes in circulating Ly6C+ monocytes and peritoneal macrophages, along with increased CD36 expression. Moreover, mitochondrial ROS was positively correlated with CD36 expression in aortic lesional macrophages. Conclusions: These findings reveal that oxLDL/CD36 signaling in macrophages links dys-regulated FA metabolism to oxidative stress from the mitochondria, which drives chronic inflammation. Thus, targeting to CD36 and its downstream effectors may serve as potential new strategies against chronic inflammatory diseases such as atherosclerosis.
    DOI:  https://doi.org/10.1161/CIRCRESAHA.119.315833
  12. Cell Metab. 2019 Oct 01. pii: S1550-4131(19)30513-3. [Epub ahead of print]
    Campbell C, Rudensky A.
      Regulatory T (Treg) cells expressing the X-chromosome-encoded transcription factor Foxp3 represent a specialized immunosuppressive lineage with a well-recognized, essential function in preventing fatal autoimmunity and inflammation. Recent studies revealed that Treg cells can also exert systemic effects on metabolism and partake in tissue repair, suggesting a dual role for these cells in serving and protecting tissues. Here, we review multiple means by which Treg cells support tissue function and organismal homeostasis.
    Keywords:  metabolism; regulatory T cells; tissue homeostasis
    DOI:  https://doi.org/10.1016/j.cmet.2019.09.010
  13. Cell Rep. 2019 Oct 15. pii: S2211-1247(19)31189-1. [Epub ahead of print]29(3): 685-696.e5
    Joshi DC, Zhang CL, Babujee L, Vevea JD, August BK, Sheng ZH, Chapman ER, Gomez TM, Chiu SY.
      Syntaphilin (SNPH) is a major mitochondrial anchoring protein targeted to axons and excluded from dendrites. In this study, we provide in vivo evidence that this spatial specificity is lost in Shiverer (Shi) mice, a model for progressive multiple sclerosis (MS), resulting in inappropriate intrusion of SNPH into dendrites of cerebellar Purkinje cells with neurodegenerative consequences. Thus, reconstituting dendritic SNPH intrusion in SNPH-KO mice by viral transduction greatly sensitizes Purkinje cells to excitotoxicity when the glutamatergic climbing fibers are stimulated. Finally, we demonstrate in vitro that overexpression of SNPH in dendrites compromises neuronal viability by inducing N-methyl-D-aspartate (NMDA) excitotoxicity, reducing mitochondrial calcium uptake, and interfering with quality control of mitochondria by blocking somal mitophagy. Collectively, we propose that inappropriate immobilization of dendritic mitochondria by SNPH intrusion produces excitotoxicity and suggest that interception of dendritic SNPH intrusion is a therapeutic strategy to combat neurodegeneration.
    Keywords:  excitotoxicity; mitochondria; multiple sclerosis; neurodegeneration; syntaphilin
    DOI:  https://doi.org/10.1016/j.celrep.2019.09.012
  14. Elife. 2019 Oct 15. pii: e49309. [Epub ahead of print]8
    Wang ZH, Liu Y, Chaitankar V, Pirooznia M, Xu H.
      Oogenesis features an enormous increase in mitochondrial mass and mtDNA copy number, which are required to furnish mature eggs with an adequate supply of mitochondria and to curb the transmission of deleterious mtDNA variants. Quiescent in dividing germ cells, mtDNA replication initiates upon oocyte determination in the Drosophila ovary, which necessitates active mitochondrial respiration. However, the underlying mechanism for this dynamic regulation remains unclear. Here, we show that an feedforward insulin-Myc loop promotes mitochondrial respiration and biogenesis by boosting the expression of electron transport chain subunits and of factors essential for mtDNA replication and expression, and for the import of mitochondrial proteins. We further reveal that transient activation of JNK enhances the expression of the insulin receptor and initiates the insulin-Myc signaling loop. This signaling relay promotes mitochondrial biogenesis in the ovary, and thereby plays a role in limiting the transmission of deleterious mtDNA mutations. Our study demonstrates cellular mechanisms that couple mitochondrial biogenesis and inheritance with oocyte development.
    Keywords:  D. melanogaster; developmental biology
    DOI:  https://doi.org/10.7554/eLife.49309
  15. Cell Metab. 2019 Oct 03. pii: S1550-4131(19)30517-0. [Epub ahead of print]
    Huang K, Liang Q, Zhou Y, Jiang LL, Gu WM, Luo MY, Tang YB, Wang Y, Lu W, Huang M, Zhang SZ, Zhuang GL, Dai Q, Shen QC, Zhang J, Lei HM, Zhu L, Ye DY, Chen HZ, Zhou L, Shen Y.
      Phosphoglycerate mutase 1 (PGAM1) plays a pivotal role in cancer metabolism and tumor progression via its metabolic activity and interaction with other proteins like α-smooth muscle actin (ACTA2). Allosteric regulation is considered to be an innovative strategy to discover a highly selective and potent inhibitor targeting PGAM1. Here, we identified a novel PGAM1 allosteric inhibitor, HKB99, via structure-based optimization. HKB99 acted to allosterically block conformational change of PGAM1 during catalytic process and PGAM1-ACTA2 interaction. HKB99 suppressed tumor growth and metastasis and overcame erlotinib resistance in non-small-cell lung cancer (NSCLC). Mechanistically, HKB99 enhanced the oxidative stress and altered multiple signaling pathways including the activation of JNK/c-Jun and suppression of AKT and ERK. Collectively, the study highlights the potential of PGAM1 as a therapeutic target in NSCLC and reveals a distinct mechanism by which HKB99 inhibits both metabolic activity and nonmetabolic function of PGAM1 by allosteric regulation.
    Keywords:  allosteric inhibitor; antitumor activity; metastasis; non-small-cell lung cancer; phosphoglycerate mutase 1
    DOI:  https://doi.org/10.1016/j.cmet.2019.09.014
  16. Nat Methods. 2019 Oct 14.
    Thiele C, Wunderling K, Leyendecker P.
      Cellular lipid metabolism is a complex network process comprising dozens of enzymes, multiple organelles and more than a thousand lipid species. Tracing metabolic reactions in this network is a major technological and scientific challenge. Using a click-chemistry mass spectrometry reporter strategy, we have developed a specific, highly sensitive and robust tracing procedure for alkyne-labeled lipids. The method enables sample multiplexing, which improves sample comparison. We demonstrate this by a time-resolved analysis of hepatocyte glycerolipid metabolism with parallel quantitative monitoring of 120 labeled lipid species. The subfemtomole sensitivity enabled a single cell analysis of fatty acid incorporation into neutral and membrane lipids. The results demonstrate the robustness of lipid homeostasis at the single cell level.
    DOI:  https://doi.org/10.1038/s41592-019-0593-6
  17. Cell Rep. 2019 Oct 15. pii: S2211-1247(19)31169-6. [Epub ahead of print]29(3): 560-572.e4
    Hazan I, Monin J, Bouwman BAM, Crosetto N, Aqeilan RI.
      DNA double-strand breaks (DSBs) are deleterious and tumorigenic but could also be essential for DNA-based processes. Yet the landscape of physiological DSBs and their role and repair are still elusive. Here, we mapped DSBs at high resolution in cancer and non-tumorigenic cells and found a transcription-coupled repair mechanism at oncogenic super-enhancers. At these super-enhancers the transcription factor TEAD4, together with various transcription factors and co-factors, co-localizes with the repair factor RAD51 of the homologous recombination pathway. Depletion of TEAD4 or RAD51 increases DSBs at RAD51/TEAD4 common binding sites within super-enhancers and decreases expression of related genes, which are mostly oncogenes. Co-localization of RAD51 with transcription factors at super-enhancers occurs in various cell types, suggesting a broad phenomenon. Together, our findings uncover a coupling between transcription and repair mechanisms at oncogenic super-enhancers, to control the hyper-transcription of multiple cancer drivers.
    Keywords:  AP-1 complex (JUN/FOS); BLISS; DSBs; RAD51; TEAD4; super-enhancer; transcription
    DOI:  https://doi.org/10.1016/j.celrep.2019.09.001
  18. Hum Mol Genet. 2019 Oct 18. pii: ddz232. [Epub ahead of print]
    Conduit SE, Davies EM, Ooms LM, Gurung R, McGrath MJ, Hakim S, Cottle DL, Smyth IM, Dyson JM, Mitchell CA.
      Polycystic kidney disease (PKD) results in the formation of renal cysts that can impair function leading to renal failure. DNA damage accumulates in renal epithelial cells in PKD but the molecular mechanisms are unclear and are investigated here. Phosphoinositide 3- kinase (PI3K)/AKT signaling activates mammalian target of rapamycin complex 1 (mTORC1) and hyperactivation of mTORC1 is a common event in PKD, however, mTORC1 inhibitors have yielded disappointing results in clinical trials. Here we demonstrate AKT and mTORC1 hyperactivation in two representative murine PKD models (renal epithelial-specific Inpp5e knockout and collecting duct-specific Pkd1 deletion) and identify a downstream signaling network that contributes to DNA damage accumulation. Inpp5e- and Pkd1-null renal epithelial cells showed DNA damage including double-stranded DNA breaks associated with increased replication fork numbers, multinucleation and centrosome amplification. mTORC1 activated CAD, which promotes de novo pyrimidine synthesis, to sustain cell proliferation. AKT, but not mTORC1, inhibited the DNA repair/replication fork origin firing regulator TOPBP1, which impacts on DNA damage and cell proliferation. Notably, Inpp5e- and Pkd1-null renal epithelial cell spheroid formation defects were rescued by AKT inhibition. These data reveal that AKT hyperactivation contributes to DNA damage accumulation in multiple forms of PKD and cooperates with mTORC1 to promote cell proliferation. Hyperactivation of AKT may play a causal role in PKD by regulating DNA damage and cell proliferation, independent of mTORC1, and AKT inhibition may be a novel therapeutic approach for PKD.
    DOI:  https://doi.org/10.1093/hmg/ddz232
  19. Elife. 2019 10 15. pii: e50069. [Epub ahead of print]8
    Teo E, Ravi S, Barardo D, Kim HS, Fong S, Cazenave-Gassiot A, Tan TY, Ching J, Kovalik JP, Wenk MR, Gunawan R, Moore PK, Halliwell B, Tolwinski N, Gruber J.
      Alzheimer's disease (AD) is the most common neurodegenerative disease affecting the elderly worldwide. Mitochondrial dysfunction has been proposed as a key event in the etiology of AD. We have previously modeled amyloid-beta (Aβ)-induced mitochondrial dysfunction in a transgenic Caenorhabditis elegans strain by expressing human Aβ peptide specifically in neurons (GRU102). Here, we focus on the deeper metabolic changes associated with this Aβ-induced mitochondrial dysfunction. Integrating metabolomics, transcriptomics and computational modeling, we identify alterations in Tricarboxylic Acid (TCA) cycle metabolism following even low-level Aβ expression. In particular, GRU102 showed reduced activity of a rate-limiting TCA cycle enzyme, alpha-ketoglutarate dehydrogenase. These defects were associated with elevation of protein carbonyl content specifically in mitochondria. Importantly, metabolic failure occurred before any significant increase in global protein aggregate was detectable. Treatment with an anti-diabetes drug, Metformin, reversed Aβ-induced metabolic defects, reduced protein aggregation and normalized lifespan of GRU102. Our results point to metabolic dysfunction as an early and causative event in Aβ-induced pathology and a promising target for intervention.
    Keywords:  C. elegans; TCA cycle; amyloid beta; metabolism; metformin; mitochondria; neuroscience
    DOI:  https://doi.org/10.7554/eLife.50069
  20. Nature. 2019 Oct;574(7778): 337-338
    Solanas G, Benitah SA.
      
    Keywords:  Brain; Cancer; Metabolism
    DOI:  https://doi.org/10.1038/d41586-019-03042-0
  21. iScience. 2019 Oct 01. pii: S2589-0042(19)30379-7. [Epub ahead of print]20 434-448
    Almacellas E, Pelletier J, Manzano A, Gentilella A, Ambrosio S, Mauvezin C, Tauler A.
      Cancer cells rely on mTORC1 activity to coordinate mitogenic signaling with nutrients availability for growth. Based on the metabolic function of E2F1, we hypothesize that glucose catabolism driven by E2F1 could participate on mTORC1 activation. Here, we demonstrate that glucose potentiates E2F1-induced mTORC1 activation by promoting mTORC1 translocation to lysosomes, a process that occurs independently of AMPK activation. We showed that E2F1 regulates glucose metabolism by increasing aerobic glycolysis and identified the PFKFB3 regulatory enzyme as an E2F1-regulated gene important for mTORC1 activation. Furthermore, PFKFB3 and PFK1 were found associated to lysosomes and we demonstrated that modulation of PFKFB3 activity, either by substrate accessibility or expression, regulates the translocation of mTORC1 to lysosomes by direct interaction with Rag B and subsequent mTORC1 activity. Our results support a model whereby a glycolytic metabolon containing phosphofructokinases transiently interacts with the lysosome acting as a sensor platform for glucose catabolism toward mTORC1 activity.
    Keywords:  Cell Biology; Molecular Genetics
    DOI:  https://doi.org/10.1016/j.isci.2019.09.040
  22. Biochemistry. 2019 Oct 18.
    Walter LA, Lin YH, Halbrook CJ, Chuh KN, He L, Pedowitz NJ, Batt AR, Brennan CK, Stiles BL, Lyssiotis CA, Pratt MR.
      The amounts of the intracellular glycosylation, O-GlcNAc modification, are increased in essentially all tumors when compared to healthy tissue, and lowering O-GlcNAcylation levels results in reduced tumorigenesis and increased cancer cell death. Therefore, the pharmacological reduction of O-GlcNAc may represent a therapeutic vulnerability. The most direct approach to this goal is the inhibition of O-GlcNAc transferase (OGT), the enzyme that directly adds the modification to proteins. However, despite some recent success, this enzyme has proven difficult to inhibit. An alternative strategy involves starving OGT of its sugar substrate UDP-GlcNAc by targeting enzymes of the hexosamine biosynthetic pathway (HBP). Here, we explore the potential of the rate determining enzyme of this pathway, glutamine fructose-6-phosphate amidotransferase (GFAT). We first show that CRISPR-mediated knockout of GFAT results in inhibition of cancer cell growth in vitro and a xenograft model that correlates with O-GlcNAcylation levels. We then demonstrate that pharmacological inhibition of GFAT sensitizes a small panel of cancer cells to undergo apoptosis in response to diamide-induced oxidative stress. Finally, we find that GFAT expression and O-GlcNAc levels are increased in a spontaneous mouse model of liver cancer. Together these experiments support the further development of inhibitors of the HBP as an indirect approach to lowering O-GlcNAcylation levels in cancer.
    DOI:  https://doi.org/10.1021/acs.biochem.9b00560
  23. Proc Natl Acad Sci U S A. 2019 Oct 14. pii: 201908353. [Epub ahead of print]
    Rabara D, Tran TH, Dharmaiah S, Stephens RM, McCormick F, Simanshu DK, Holderfield M.
      KRAS mutations occur in ∼35% of colorectal cancers and promote tumor growth by constitutively activating the mitogen-activated protein kinase (MAPK) pathway. KRAS mutations at codons 12, 13, or 61 are thought to prevent GAP protein-stimulated GTP hydrolysis and render KRAS-mutated colorectal cancers unresponsive to epidermal growth factor receptor (EGFR) inhibitors. We report here that KRAS G13-mutated cancer cells are frequently comutated with NF1 GAP but NF1 is rarely mutated in cancers with KRAS codon 12 or 61 mutations. Neurofibromin protein (encoded by the NF1 gene) hydrolyzes GTP directly in complex with KRAS G13D, and KRAS G13D-mutated cells can respond to EGFR inhibitors in a neurofibromin-dependent manner. Structures of the wild type and G13D mutant of KRAS in complex with neurofibromin (RasGAP domain) provide the structural basis for neurofibromin-mediated GTP hydrolysis. These results reveal that KRAS G13D is responsive to neurofibromin-stimulated hydrolysis and suggest that a subset of KRAS G13-mutated colorectal cancers that are neurofibromin-competent may respond to EGFR therapies.
    Keywords:  EGFR; G13D; GTPase; KRAS; NF1
    DOI:  https://doi.org/10.1073/pnas.1908353116
  24. Redox Biol. 2019 Oct 05. pii: S2213-2317(19)31117-6. [Epub ahead of print]28 101339
    Young A, Oldford C, Mailloux RJ.
      Research over the past seventy years has established that mitochondrial-l-lactate dehydrogenase (m-L-LDH) is vital for mitochondrial bioenergetics. However, in recent report, Fulghum et al. concluded that lactate is a poor fuel for mitochondrial respiration [1]. In the present study, we have followed up on these findings and conducted an independent investigation to determine if lactate can support mitochondrial bioenergetics. We demonstrate herein that lactate can fuel the bioenergetics of heart, muscle, and liver mitochondria. Lactate was just as effective as pyruvate at stimulating mitochondrial coupling efficiency. Inclusion of LDH (sodium oxamate or GSK 2837808A) and pyruvate dehydrogenase (PDH; CPI-613) inhibitors abolished respiration in mitochondria energized with lactate. Lactate also fueled mitochondrial ROS generation and was just as effective as pyruvate at stimulating H2O2 production. Additionally, lactate-induced ROS production was inhibited by both LDH and PDH inhibitors. Enzyme activity measurements conducted on permeabilized mitochondria revealed that LDH is localized in mitochondria. In aggregate, we can conclude that mitochondrial LDH fuels bioenergetics in several tissues by oxidizing lactate.
    DOI:  https://doi.org/10.1016/j.redox.2019.101339
  25. Cell Calcium. 2019 Oct 10. pii: S0143-4160(19)30168-X. [Epub ahead of print]84 102101
    Filadi R, Pizzo P.
      Inter-organelle communication represents a booming topic in cell biology research, with endoplasmic reticulum (ER)-mitochondria coupling playing the lion's share. In a recent work, Bartok and colleagues found that inositol trisphosphates receptors (IP3Rs), in addition to their well-known involvement in ER-mitochondria Ca2+ transfer, are endowed with structural properties at organelles' interface.
    DOI:  https://doi.org/10.1016/j.ceca.2019.102101
  26. Enzymes. 2019 ;pii: S1874-6047(19)30002-2. [Epub ahead of print]45 257-287
    Alencar RR, Batalha CMPF, Freire TS, de Souza-Pinto NC.
      The mitochondrial genome encodes proteins essential for the oxidative phosphorylation and, consequently, for proper mitochondrial function. Its localization and, possibly, structural organization contribute to higher DNA damage accumulation, when compared to the nuclear genome. In addition, the mitochondrial genome mutates at rates several times higher than the nuclear, although the causal relationship between these events are not clearly established. Maintaining mitochondrial DNA stability is critical for cellular function and organismal fitness, and several pathways contribute to that, including damage tolerance and bypass, degradation of damaged genomes and DNA repair. Despite initial evidence suggesting that mitochondria lack DNA repair activities, most DNA repair pathways have been at least partially characterized in mitochondria from several model organisms, including humans. In this chapter, we review what is currently known about how the main DNA repair pathways operate in mitochondria and contribute to mitochondrial DNA stability, with focus on the enzymology of mitochondrial DNA repair.
    Keywords:  BER; DNA repair; DSBR; MMR; Mitochondrial DNA; NER
    DOI:  https://doi.org/10.1016/bs.enz.2019.06.002
  27. Nat Commun. 2019 Oct 16. 10(1): 4695
    Chen RX, Chen X, Xia LP, Zhang JX, Pan ZZ, Ma XD, Han K, Chen JW, Judde JG, Deas O, Wang F, Ma NF, Guan X, Yun JP, Wang FW, Xu RH, Dan Xie .
      Circular RNAs (circRNAs) have been implicated in cancer progression through largely unknown mechanisms. Herein, we identify an N6-methyladenosine (m6A) modified circRNA, circNSUN2, frequently upregulated in tumor tissues and serum samples from colorectal carcinoma (CRC) patients with liver metastasis (LM) and predicts poorer patient survival. The upregulated expression of circNSUN2 promotes LM in PDX metastasis models in vivo and accelerates cancer cells invasion in vitro. Importantly, N6-methyladenosine modification of circNSUN2 increases export to the cytoplasm. By forming a circNSUN2/IGF2BP2/HMGA2 RNA-protein ternary complex in the cytoplasm, circNSUN2 enhances the stability of HMGA2 mRNA to promote CRC metastasis progression. Clinically, the upregulated expressions of circNSUN2 and HMGA2 are more prevalent in LM tissues than in primary CRC tissues. These findings elucidate that N6-methyladenosine modification of circNSUN2 modulates cytoplasmic export and stabilizes HMGA2 to promote CRC LM, and suggest that circNSUN2 could represent a critical prognostic marker and/or therapeutic target for the disease.
    DOI:  https://doi.org/10.1038/s41467-019-12651-2
  28. EMBO J. 2019 Oct 14. e101056
    Wolf DM, Segawa M, Kondadi AK, Anand R, Bailey ST, Reichert AS, van der Bliek AM, Shackelford DB, Liesa M, Shirihai OS.
      The mitochondrial membrane potential (ΔΨm ) is the main driver of oxidative phosphorylation (OXPHOS). The inner mitochondrial membrane (IMM), consisting of cristae and inner boundary membranes (IBM), is considered to carry a uniform ΔΨm . However, sequestration of OXPHOS components in cristae membranes necessitates a re-examination of the equipotential representation of the IMM. We developed an approach to monitor ΔΨm at the resolution of individual cristae. We found that the IMM was divided into segments with distinct ΔΨm , corresponding to cristae and IBM. ΔΨm was higher at cristae compared to IBM. Treatment with oligomycin increased, whereas FCCP decreased, ΔΨm heterogeneity along the IMM. Impairment of cristae structure through deletion of MICOS-complex components or Opa1 diminished this intramitochondrial heterogeneity of ΔΨm . Lastly, we determined that different cristae within the individual mitochondrion can have disparate membrane potentials and that interventions causing acute depolarization may affect some cristae while sparing others. Altogether, our data support a new model in which cristae within the same mitochondrion behave as independent bioenergetic units, preventing the failure of specific cristae from spreading dysfunction to the rest.
    Keywords:  MICOS complex; Opa1; crista junction; cristae; membrane potential
    DOI:  https://doi.org/10.15252/embj.2018101056
  29. Nature. 2019 Oct 16.
    Flavahan WA, Drier Y, Johnstone SE, Hemming ML, Tarjan DR, Hegazi E, Shareef SJ, Javed NM, Raut CP, Eschle BK, Gokhale PC, Hornick JL, Sicinska ET, Demetri GD, Bernstein BE.
      Epigenetic aberrations are widespread in cancer, yet the underlying mechanisms and causality remain poorly understood1-3. A subset of gastrointestinal stromal tumors (GISTs) lack canonical kinase mutations but instead have succinate dehydrogenase (SDH)-deficiency and global DNA hyper-methylation4,5. Here we associate this hyper-methylation with changes in genome topology that activate oncogenic programs. To investigate epigenetic alterations systematically, we mapped DNA methylation, CTCF insulators, enhancers, and chromosome topology in KIT-mutant, PDGFRA-mutant, and SDH-deficient GISTs. Although these respective subtypes shared similar enhancer landscapes, we identified hundreds of putative insulators where DNA methylation replaced CTCF binding in SDH-deficient GISTs. We focused on a disrupted insulator that normally partitions a core GIST super-enhancer from the FGF4 oncogene. Recurrent loss of this insulator alters locus topology in SDH-deficient GISTs, allowing aberrant physical interaction between enhancer and oncogene. CRISPR-mediated excision of the corresponding CTCF motifs in an SDH-intact GIST model disrupted the boundary and strongly up-regulated FGF4 expression. We also identified a second recurrent insulator loss event near the KIT oncogene, which is also highly expressed across SDH-deficient GISTs. Finally, we established a patient-derived xenograft (PDX) from an SDH-deficient GIST that faithfully maintains the epigenetics of the parental tumor, including hyper-methylation and insulator defects. This PDX model is highly sensitive to FGF receptor (FGFR) inhibitor, and more so to combined FGFR and KIT inhibition, validating the functional significance of the underlying epigenetic lesions. Our study reveals how epigenetic alterations can drive oncogenic programs in the absence of canonical kinase mutations, with implications for mechanistic targeting of aberrant pathways in cancers.
    DOI:  https://doi.org/10.1038/s41586-019-1668-3
  30. Elife. 2019 Oct 14. pii: e50414. [Epub ahead of print]8
    Krejčová G, Danielová A, Nedbalová P, Kazek M, Strych L, Chawla G, Tennessen JM, Lieskovská J, Jindra M, Doležal T, Bajgar A.
      Macrophage-mediated phagocytosis and cytokine production represent the front lines of resistance to bacterial invaders. A key feature of this pro-inflammatory response in mammals is the complex remodeling of cellular metabolism towards aerobic glycolysis. Although, the function of bactericidal macrophages is highly conserved, the metabolic remodeling of insect macrophages remains poorly understood. Here we used the adult fruit fly Drosophila melanogaster to investigate the metabolic changes that occur in macrophages during the acute and resolution phases of Streptococcus-induced sepsis. Our studies revealed that orthologs of the Hypoxia inducible factor 1α (HIF1α) and Lactate dehydrogenase (LDH) are required for macrophage activation, their bactericidal function, and resistance to infection, thus documenting conservation of this cellular response between insect and mammals. Further, we show that macrophages employing aerobic glycolysis induce changes in systemic metabolism that are necessary to meet the biosynthetic and energetic demands of their function and resistance to bacterial infection.
    Keywords:  D. melanogaster; immunology; inflammation
    DOI:  https://doi.org/10.7554/eLife.50414
  31. Front Immunol. 2019 ;10 2278
    Terrén I, Orrantia A, Vitallé J, Zenarruzabeitia O, Borrego F.
      Natural Killer (NK) cells are characterized by their potential to kill tumor cells by different means without previous sensitization and have, therefore, become a valuable tool in cancer immunotherapy. However, their efficacy against solid tumors is still poor and further studies are required to improve it. One of the major restrictions for NK cell activity is the immunosuppressive tumor microenvironment (TME). There, tumor and other immune cells create the appropriate conditions for tumor proliferation while, among others, preventing NK cell activation. Furthermore, NK cell metabolism is impaired in the TME, presumably due to nutrient and oxygen deprivation, and the higher concentration of tumor-derived metabolic end products, such as lactate. This metabolic restriction of NK cells limits their effector functions, and it could represent a potential target to focus on to improve the efficacy of NK cell-based therapies against solid tumors. In this review, we discuss the potential effect of TME into NK cell metabolism and its influence in NK cell effector functions.
    Keywords:  NK cell; TME; amino acid; glucose; glycolysis; hypoxia; metabolism; tumor microenvironment
    DOI:  https://doi.org/10.3389/fimmu.2019.02278
  32. EMBO J. 2019 Oct 16. e103472
    Schlame M.
      The mitochondrial inner membrane consists of the inner boundary membrane and invaginations called cristae, which differ in protein composition and likely have distinct functions. In this issue of The EMBO Journal, Wolf et al (2019) report that the cristae carry a higher membrane potential than the intervening boundary membranes. Their data suggest electro-chemical discontinuity among segments of the inner membrane, implying that individual cristae may operate with some degree of independence.
    DOI:  https://doi.org/10.15252/embj.2019103472
  33. Nat Commun. 2019 Oct 18. 10(1): 4766
    Powers RK, Culp-Hill R, Ludwig MP, Smith KP, Waugh KA, Minter R, Tuttle KD, Lewis HC, Rachubinski AL, Granrath RE, Carmona-Iragui M, Wilkerson RB, Kahn DE, Joshi M, Lleó A, Blesa R, Fortea J, D'Alessandro A, Costello JC, Sullivan KD, Espinosa JM.
      Trisomy 21 (T21) causes Down syndrome (DS), affecting immune and neurological function by ill-defined mechanisms. Here we report a large metabolomics study of plasma and cerebrospinal fluid, showing in independent cohorts that people with DS produce elevated levels of kynurenine and quinolinic acid, two tryptophan catabolites with potent immunosuppressive and neurotoxic properties, respectively. Immune cells of people with DS overexpress IDO1, the rate-limiting enzyme in the kynurenine pathway (KP) and a known interferon (IFN)-stimulated gene. Furthermore, the levels of IFN-inducible cytokines positively correlate with KP dysregulation. Using metabolic tracing assays, we show that overexpression of IFN receptors encoded on chromosome 21 contribute to enhanced IFN stimulation, thereby causing IDO1 overexpression and kynurenine overproduction in cells with T21. Finally, a mouse model of DS carrying triplication of IFN receptors exhibits KP dysregulation. Together, our results reveal a mechanism by which T21 could drive immunosuppression and neurotoxicity in DS.
    DOI:  https://doi.org/10.1038/s41467-019-12739-9
  34. Proc Natl Acad Sci U S A. 2019 Oct 14. pii: 201903485. [Epub ahead of print]
    Kreuzaler P, Clarke MA, Brown EJ, Wilson CH, Kortlever RM, Piterman N, Littlewood T, Evan GI, Fisher J.
      Cells with higher levels of Myc proliferate more rapidly and supercompetitively eliminate neighboring cells. Nonetheless, tumor cells in aggressive breast cancers typically exhibit significant and stable heterogeneity in their Myc levels, which correlates with refractoriness to therapy and poor prognosis. This suggests that Myc heterogeneity confers some selective advantage on breast tumor growth and progression. To investigate this, we created a traceable MMTV-Wnt1-driven in vivo chimeric mammary tumor model comprising an admixture of low-Myc- and reversibly switchable high-Myc-expressing clones. We show that such tumors exhibit interclonal mutualism wherein cells with high-Myc expression facilitate tumor growth by promoting protumorigenic stroma yet concomitantly suppress Wnt expression, which renders them dependent for survival on paracrine Wnt provided by low-Myc-expressing clones. To identify any therapeutic vulnerabilities arising from such interdependency, we modeled Myc/Ras/p53/Wnt signaling cross talk as an executable network for low-Myc, for high-Myc clones, and for the 2 together. This executable mechanistic model replicated the observed interdependence of high-Myc and low-Myc clones and predicted a pharmacological vulnerability to coinhibition of COX2 and MEK. This was confirmed experimentally. Our study illustrates the power of executable models in elucidating mechanisms driving tumor heterogeneity and offers an innovative strategy for identifying combination therapies tailored to the oligoclonal landscape of heterogenous tumors.
    Keywords:  Myc; breast cancer; cancer heterogeneity; computational modeling; oncogenic signaling
    DOI:  https://doi.org/10.1073/pnas.1903485116