bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2019‒09‒01
forty papers selected by
Christian Frezza
University of Cambridge, MRC Cancer Unit


  1. Cell Metab. 2019 Aug 19. pii: S1550-4131(19)30385-7. [Epub ahead of print]
    Gouw AM, Margulis K, Liu NS, Raman SJ, Mancuso A, Toal GG, Tong L, Mosley A, Hsieh AL, Sullivan DK, Stine ZE, Altman BJ, Schulze A, Dang CV, Zare RN, Felsher DW.
      Lipid metabolism is frequently perturbed in cancers, but the underlying mechanism is unclear. We present comprehensive evidence that oncogene MYC, in collaboration with transcription factor sterol-regulated element-binding protein (SREBP1), regulates lipogenesis to promote tumorigenesis. We used human and mouse tumor-derived cell lines, tumor xenografts, and four conditional transgenic mouse models of MYC-induced tumors to show that MYC regulates lipogenesis genes, enzymes, and metabolites. We found that MYC induces SREBP1, and they collaborate to activate fatty acid (FA) synthesis and drive FA chain elongation from glucose and glutamine. Further, by employing desorption electrospray ionization mass spectrometry imaging (DESI-MSI), we observed in vivo lipidomic changes upon MYC induction across different cancers, for example, a global increase in glycerophosphoglycerols. After inhibition of FA synthesis, tumorigenesis was blocked, and tumors regressed in both xenograft and primary transgenic mouse models, revealing the vulnerability of MYC-induced tumors to the inhibition of lipogenesis.
    Keywords:  ChIP; MYC; MYC conditional transgenic mouse models; RNA-seq; SREBP1; acetyl-CoA carboxylase A inhibition; carbon tracing; fatty acid synthesis; glycerophosphoglycerols; mass spectrometry imaging; nuclear run-on
    DOI:  https://doi.org/10.1016/j.cmet.2019.07.012
  2. Cell Metab. 2019 Aug 19. pii: S1550-4131(19)30387-0. [Epub ahead of print]
    Labuschagne CF, Cheung EC, Blagih J, Domart MC, Vousden KH.
      Cancer metastasis depends on cell survival following loss of extracellular matrix attachment and dissemination through the circulation. The metastatic spread can be enhanced by the clustering of detached cancer cells and increased antioxidant defense. Here, we link these responses by describing how cell clustering limits reactive oxygen species (ROS). Loss of attachment causes mitochondrial perturbations and increased ROS production. The formation of cell clusters induces a hypoxic environment that drives hypoxia-inducible factor 1-alpha (Hif1α)-mediated mitophagy, clearing damaged mitochondria and limiting ROS. However, hypoxia and reduced mitochondrial capacity promote dependence on glycolysis for ATP production that is supported by cytosolic reductive metabolism. Preventing this metabolic adaptation or disruption of cell clusters results in ROS accumulation, cell death, and a reduction of metastatic capacity in vivo. Our results provide a mechanistic explanation for the role of cell clustering in supporting survival during extracellular matrix detachment and metastatic spread and may point to targetable vulnerabilities.
    Keywords:  ROS; hypoxia; metastasis; mitophagy; reductive metabolism
    DOI:  https://doi.org/10.1016/j.cmet.2019.07.014
  3. Oncogene. 2019 Aug 28.
    Rabinovich S, Silberman A, Adler L, Agron S, Levin-Zaidman S, Bahat A, Porat Z, Ben-Zeev E, Geva I, Itkin M, Malitsky S, Buchaklian A, Helbling D, Dimmock D, Erez A.
      Citrin, encoded by SLC25A13 gene, is an inner mitochondrial transporter that is part of the malate-aspartate shuttle, which regulates the NAD+/NADH ratio between the cytosol and mitochondria. Citrullinemia type II (CTLN-II) is an inherited disorder caused by germline mutations in SLC25A13, manifesting clinically in growth failure that can be alleviated by dietary restriction of carbohydrates. The association of citrin with glycolysis and NAD+/NADH ratio led us to hypothesize that it may play a role in carcinogenesis. Indeed, we find that citrin is upregulated in multiple cancer types and is essential for supplementing NAD+ for glycolysis and NADH for oxidative phosphorylation. Consequently, citrin deficiency associates with autophagy, whereas its overexpression in cancer cells increases energy production and cancer invasion. Furthermore, based on the human deleterious mutations in citrin, we found a potential inhibitor of citrin that restricts cancerous phenotypes in cells. Collectively, our findings suggest that targeting citrin may be of benefit for cancer therapy.
    DOI:  https://doi.org/10.1038/s41388-019-0976-2
  4. Int Rev Cell Mol Biol. 2019 ;pii: S1937-6448(19)30063-2. [Epub ahead of print]347 145-190
    Anderson CM, Macleod KF.
      Autophagy is an ancient catabolic process used by cells to clear excess or dysfunctional organelles and large subcellular structures and thus performs an important housekeeping role for the cell. Autophagy is acutely sensitive to nutrient availability and is upregulated at a transcriptional and posttranslational level in response to nutrient deprivation. This serves to promote turnover of cellular content and recycling of nutrients for continued growth and survival. While important for most normal tissues, tumor cells appear to be particularly dependent on autophagy for survival under ischemic or therapeutic stress, and in response to loss of matrix attachment; autophagy is upregulated markedly in cancers as they progress to malignancy. Ras-driven tumors appear to be particularly dependent on autophagy and thus inhibition of autophagy is being pursued as a productive clinical approach for such cancers. However, this enthusiasm needs to be offset against possible negative effects of autophagy inhibition on normal tissue function and on limiting antitumor immune responses. In addressing all of these topics, we focus in on understanding how autophagy is induced by nutrient stress, its role in recycling metabolites for growing tumors, how selective forms of autophagy, such as mitophagy and ribophagy contribute specifically to tumorigenesis, how autophagy in the tumor microenvironment and throughout the animal affects access of the tumor to nutrients, and finally how different oncogenic pathways may determine which tumors respond to autophagy inhibition and which ones will not.
    Keywords:  AMPK; ATF4; Amino acids; Autophagy; FoxO; Glycolysis; Lipophagy; MYC; Mitochondria; Mitophagy; RAS; Ribophagy; TFEB/MiTF; Therapeutic vulnerabilities; mTOR
    DOI:  https://doi.org/10.1016/bs.ircmb.2019.06.002
  5. Biochim Biophys Acta Mol Basis Dis. 2019 Aug 23. pii: S0925-4439(19)30261-3. [Epub ahead of print] 165538
    Anzmann AF, Pinto S, Busa V, Carlson J, McRitchie S, Sumner S, Pandey A, Vernon HJ.
      BACKGROUND: Methylmalonic acidemia (MMA) and propionic acidemia (PA) are related disorders of mitochondrial propionate metabolism, caused by defects in methylmalonyl-CoA mutase (MUT) and propionyl-CoA carboxylase (PCC), respectively. These biochemical defects lead to a complex cascade of downstream metabolic abnormalities, and identification of these abnormal pathways has important implications for understanding disease pathophysiology. Using a multi-omics approach in cellular models of MMA and PA, we identified serine and thiol metabolism as important areas of metabolic dysregulation.METHODS: We performed global proteomic analysis of fibroblasts and untargeted metabolomics analysis of plasma from individuals with MMA to identify novel pathways of dysfunction. We probed these novel pathways in CRISPR-edited, MUT and PCCA null HEK293 cell lines via targeted metabolomics, gene expression analysis, and flux metabolomics tracing utilization of 13C-glucose.
    RESULTS: Proteomic analysis of fibroblasts identified upregulation of multiple proteins involved in serine synthesis and thiol metabolism including: phosphoserine amino transferase, cystathionine beta synthase and mercaptopyruvate sulfurtransferase. Metabolomics analysis of plasma revealed significantly increased levels of cystathionine and glutathione, central metabolites in thiol metabolism. CRISPR edited MUT and PCCA HEK293 cells recapitulate primary defects of MMA and PA and have upregulation of transcripts associated with serine and thiol metabolism including PSAT1. 13C-glucose flux metabolomics in MUT and PCCA null HEK293 cells identified increases in serine de novo biosynthesis, serine transport, and abnormal downstream TCA cycle utilization.
    CONCLUSION: We identified abnormal serine metabolism as a novel area of cellular dysfunction in MMA and PA, thus introducing a potential new target for therapeutic investigation.
    Keywords:  Methylmalonic acidemia; Propionic acidemia; Serine metabolism
    DOI:  https://doi.org/10.1016/j.bbadis.2019.165538
  6. Cancers (Basel). 2019 Aug 28. pii: E1264. [Epub ahead of print]11(9):
    de Castro GS, Simoes E, Lima JDCC, Ortiz-Silva M, Festuccia WT, Tokeshi F, Alcântara PS, Otoch JP, Coletti D, Seelaender M.
      Cachexia is a wasting syndrome characterized by the continuous loss of skeletal muscle mass due to imbalance between protein synthesis and degradation, which is related with poor prognosis and compromised quality of life. Dysfunctional mitochondria are associated with lower muscle strength and muscle atrophy in cancer patients, yet poorly described in human cachexia. We herein investigated mitochondrial morphology, autophagy and apoptosis in the skeletal muscle of patients with gastrointestinal cancer-associated cachexia (CC), as compared with a weight-stable cancer group (WSC). CC showed prominent weight loss and increased circulating levels of serum C-reactive protein, lower body mass index and decreased circulating hemoglobin, when compared to WSC. Electron microscopy analysis revealed an increase in intermyofibrillar mitochondrial area in CC, as compared to WSC. Relative gene expression of Fission 1, a protein related to mitochondrial fission, was increased in CC, as compared to WSC. LC3 II, autophagy-related (ATG) 5 and 7 essential proteins for autophagosome formation, presented higher content in the cachectic group. Protein levels of phosphorylated p53 (Ser46), activated caspase 8 (Asp384) and 9 (Asp315) were also increased in the skeletal muscle of CC. Overall, our results demonstrate that human cancer-associated cachexia leads to exacerbated muscle-stress response that may culminate in muscle loss, which is in part due to disruption of mitochondrial morphology, dysfunctional autophagy and increased apoptosis. To the best of our knowledge, this is the first report showing quantitative morphological alterations in skeletal muscle mitochondria in cachectic patients.
    Keywords:  apoptosis; autophagy; cancer cachexia; mitochondria; skeletal muscle
    DOI:  https://doi.org/10.3390/cancers11091264
  7. Proc Natl Acad Sci U S A. 2019 Aug 26. pii: 201904610. [Epub ahead of print]
    Chung CY, Posimo JM, Lee S, Tsang T, Davis JM, Brady DC, Chang CJ.
      Copper is essential for life, and beyond its well-established ability to serve as a tightly bound, redox-active active site cofactor for enzyme function, emerging data suggest that cellular copper also exists in labile pools, defined as loosely bound to low-molecular-weight ligands, which can regulate diverse transition metal signaling processes spanning neural communication and olfaction, lipolysis, rest-activity cycles, and kinase pathways critical for oncogenic signaling. To help decipher this growing biology, we report a first-generation ratiometric fluorescence resonance energy transfer (FRET) copper probe, FCP-1, for activity-based sensing of labile Cu(I) pools in live cells. FCP-1 links fluorescein and rhodamine dyes through a Tris[(2-pyridyl)methyl]amine bridge. Bioinspired Cu(I)-induced oxidative cleavage decreases FRET between fluorescein donor and rhodamine acceptor. FCP-1 responds to Cu(I) with high metal selectivity and oxidation-state specificity and facilitates ratiometric measurements that minimize potential interferences arising from variations in sample thickness, dye concentration, and light intensity. FCP-1 enables imaging of dynamic changes in labile Cu(I) pools in live cells in response to copper supplementation/depletion, differential expression of the copper importer CTR1, and redox stress induced by manipulating intracellular glutathione levels and reduced/oxidized glutathione (GSH/GSSG) ratios. FCP-1 imaging reveals a labile Cu(I) deficiency induced by oncogene-driven cellular transformation that promotes fluctuations in glutathione metabolism, where lower GSH/GSSG ratios decrease labile Cu(I) availability without affecting total copper levels. By connecting copper dysregulation and glutathione stress in cancer, this work provides a valuable starting point to study broader cross-talk between metal and redox pathways in health and disease with activity-based probes.
    Keywords:  activity-based sensing; cancer metabolism; fluorescent copper probe; oxidative stress; ratiometric imaging
    DOI:  https://doi.org/10.1073/pnas.1904610116
  8. Proc Natl Acad Sci U S A. 2019 Aug 26. pii: 201910574. [Epub ahead of print]
    Qian W, Kumar N, Roginskaya V, Fouquerel E, Opresko PL, Shiva S, Watkins SC, Kolodieznyi D, Bruchez MP, Van Houten B.
      Reactive oxygen species (ROS) play important roles in aging, inflammation, and cancer. Mitochondria are an important source of ROS; however, the spatiotemporal ROS events underlying oxidative cellular damage from dysfunctional mitochondria remain unresolved. To this end, we have developed and validated a chemoptogenetic approach that uses a mitochondrially targeted fluorogen-activating peptide (Mito-FAP) to deliver a photosensitizer MG-2I dye exclusively to this organelle. Light-mediated activation (660 nm) of the Mito-FAP-MG-2I complex led to a rapid loss of mitochondrial respiration, decreased electron transport chain complex activity, and mitochondrial fragmentation. Importantly, one round of singlet oxygen produced a persistent secondary wave of mitochondrial superoxide and hydrogen peroxide lasting for over 48 h after the initial insult. By following ROS intermediates, we were able to detect hydrogen peroxide in the nucleus through ratiometric analysis of the oxidation of nuclear cysteine residues. Despite mitochondrial DNA (mtDNA) damage and nuclear oxidative stress induced by dysfunctional mitochondria, there was a lack of gross nuclear DNA strand breaks and apoptosis. Targeted telomere analysis revealed fragile telomeres and telomere loss as well as 53BP1-positive telomere dysfunction-induced foci (TIFs), indicating that DNA double-strand breaks occurred exclusively in telomeres as a direct consequence of mitochondrial dysfunction. These telomere defects activated ataxia-telangiectasia mutated (ATM)-mediated DNA damage repair signaling. Furthermore, ATM inhibition exacerbated the Mito-FAP-induced mitochondrial dysfunction and sensitized cells to apoptotic cell death. This profound sensitivity of telomeres through hydrogen peroxide induced by dysregulated mitochondria reveals a crucial mechanism of telomere-mitochondria communication underlying the pathophysiological role of mitochondrial ROS in human diseases.
    Keywords:  ATM signaling; DNA damage response; mitochondria; singlet oxygen; telomere
    DOI:  https://doi.org/10.1073/pnas.1910574116
  9. Cell Rep. 2019 Aug 27. pii: S2211-1247(19)31013-7. [Epub ahead of print]28(9): 2306-2316.e5
    Aguilar E, Esteves P, Sancerni T, Lenoir V, Aparicio T, Bouillaud F, Dentin R, Prip-Buus C, Ricquier D, Pecqueur C, Guilmeau S, Alves-Guerra MC.
      Colorectal cancer (CRC) is associated with metabolic and redox perturbation. The mitochondrial transporter uncoupling protein 2 (UCP2) controls cell proliferation in vitro through the modulation of cellular metabolism, but the underlying mechanism in tumors in vivo remains unexplored. Using murine intestinal cancer models and CRC patient samples, we find higher UCP2 protein levels in tumors compared to their non-tumoral counterparts. We reveal the tumor-suppressive role of UCP2 as its deletion enhances colon and small intestinal tumorigenesis in AOM/DSS-treated and ApcMin/+ mice, respectively, and correlates with poor survival in the latter model. Mechanistically, UCP2 loss increases levels of oxidized glutathione and proteins in tumors. UCP2 deficiency alters glycolytic pathways while promoting phospholipid synthesis, thereby limiting the availability of NADPH for buffering oxidative stress. We show that UCP2 loss renders colon cells more prone to malignant transformation through metabolic reprogramming and perturbation of redox homeostasis and could favor worse outcomes in CRC.
    Keywords:  colorectal cancer; lipid synthesis; mitochondria; mitochondrial carrier; oxidative stress; tumor metabolic reprogramming; tumor metabolism; uncoupling protein 2
    DOI:  https://doi.org/10.1016/j.celrep.2019.07.097
  10. FASEB J. 2019 Aug 30. fj201802655RR
    Al Khazal F, Holte MN, Bolon B, White TA, LeBrasseur N, Maher LJ.
      Leigh syndrome embodies degenerative disorders with a collection of symptoms secondary to inborn errors of metabolism. Combinations of hypomorphic and loss-of-function alleles in many genes have been shown to result in Leigh syndrome. Interestingly, deficiency for the tricarboxylic acid cycle enzyme succinate dehydrogenase (SDH) can lead to Leigh-like syndrome in some circumstances and to cancer (paraganglioma, renal cell carcinoma, gastrointestinal stromal tumor) in others. In our experiments originally intended to create an inducible whole-body SDH-loss mouse model of tumorigenesis, we generated a condition reminiscent of Leigh-like syndrome that is lethal to mice within 4 wk. Remarkably, as has been shown for other mitochondrial diseases, chronic hypoxia offers substantial protection to mice from this condition after systemic SDH loss, allowing survival in the context of profoundly impaired oxidative metabolism.-Al Khazal, F., Holte, M. N., Bolon, B., White, T. A., LeBrasseur, N., Maher III, L. J. A conditional mouse model of complex II deficiency manifesting as Leigh-like syndrome.
    Keywords:  familial paraganglioma; hypoxia; mitochondrial disease; succinate dehydrogenase
    DOI:  https://doi.org/10.1096/fj.201802655RR
  11. Mol Cell. 2019 Aug 06. pii: S1097-2765(19)30537-4. [Epub ahead of print]
    Wang X, Liu R, Qu X, Yu H, Chu H, Zhang Y, Zhu W, Wu X, Gao H, Tao B, Li W, Liang J, Li G, Yang W.
      The rapid proliferation of cancer cells and dysregulated vasculature within the tumor leads to limited nutrient accessibility. Cancer cells often rewire their metabolic pathways for adaption to nutrient stress, and the underlying mechanism remains largely unknown. Glutamate dehydrogenase 1 (GDH1) is a key enzyme in glutaminolysis that converts glutamate to α-ketoglutarate (α-KG). Here, we show that, under low glucose, GDH1 is phosphorylated at serine (S) 384 and interacts with RelA and IKKβ. GDH1-produced α-KG directly binds to and activates IKKβ and nuclear factor κB (NF-κB) signaling, which promotes glucose uptake and tumor cell survival by upregulating GLUT1, thereby accelerating gliomagenesis. In addition, GDH1 S384 phosphorylation correlates with the malignancy and prognosis of human glioblastoma. Our finding reveals a unique role of α-KG to directly regulate signal pathway, uncovers a distinct mechanism of metabolite-mediated NF-κB activation, and also establishes the critical role of α-KG-activated NF-κB in brain tumor development.
    Keywords:  GDH1; NF-κB; glucose deficiency; tumorigenesis; α-ketoglutarate
    DOI:  https://doi.org/10.1016/j.molcel.2019.07.007
  12. Sci Rep. 2019 Aug 30. 9(1): 12608
    Yetkin-Arik B, Vogels IMC, Nowak-Sliwinska P, Weiss A, Houtkooper RH, Van Noorden CJF, Klaassen I, Schlingemann RO.
      During sprouting angiogenesis, an individual endothelial tip cell grows out from a pre-existing vascular network and guides following and proliferating stalk cells to form a new vessel. Metabolic pathways such as glycolysis and mitochondrial respiration as the major sources of adenosine 5'-triphosphate (ATP) for energy production are differentially activated in these types of endothelial cells (ECs) during angiogenesis. Therefore, we studied energy metabolism during angiogenesis in more detail in tip cell and non-tip cell human umbilical vein ECs. Small interfering RNA was used to inhibit transcription of glycolytic enzymes PFKFB3 or LDHA and mitochondrial enzyme PDHA1 to test whether inhibition of these specific pathways affects tip cell differentiation and sprouting angiogenesis in vitro and in vivo. We show that glycolysis is essential for tip cell differentiation, whereas both glycolysis and mitochondrial respiration occur during proliferation of non-tip cells and in sprouting angiogenesis in vitro and in vivo. Finally, we demonstrate that inhibition of mitochondrial respiration causes adaptation of EC metabolism by increasing glycolysis and vice versa. In conclusion, our studies show a complex but flexible role of the different metabolic pathways to produce ATP in the regulation of tip cell and non-tip cell differentiation and functioning during sprouting angiogenesis.
    DOI:  https://doi.org/10.1038/s41598-019-48676-2
  13. Phys Biol. 2019 Aug 29.
    Shi X, You L, Luo R.
      The glycolytic enzyme pyruvate kinase M2 (PKM2) exists in both catalytically inactive dimeric and active tetrameric forms. In cancer cells, PKM2 dimer predominance contributes to tumor growth by triggering glycolytic reprogramming. However, the mechanism that promotes PKM2 dimer predominance over tetramer in cancer cells remains elusive. Here, we show that pulsatile phosphofructokinase (PFK-1) activity results in PKM2 dimer predominance. Mathematical simulations predict that pulsatile PFK-1 activity prevents the formation of PKM2 tetramer even under high levels of fructose-1,6-bisphosphate (FBP), a PKM2 tetramer-promoting metabolite produced by PFK-1. We experimentally confirm these predictions at the single-molecule level by providing evidence for pulsatile PFK-1 activity-induced synchronized dissociation of PKM2 tetramers and the subsequent accumulation of PKM2 dimers under high levels of FBP in HeLa cells. Moreover, we show that pulsatile PFK-1 activity-induced PKM2 dimer predominance also controls cell proliferation. Thus, our study reveals the significance of pulsatile PFK-1 activity in cancer cell metabolism.
    Keywords:  Cancer cell metabolism; Glycolytic reprogramming; Pulsatile PFK-1 activity; Quantitative Biology
    DOI:  https://doi.org/10.1088/1478-3975/ab3f5a
  14. Int Rev Cell Mol Biol. 2019 ;pii: S1937-6448(19)30059-0. [Epub ahead of print]347 39-103
    Ward NP, DeNicola GM.
      Metabolic dysregulation is an appreciated hallmark of cancer and a target for therapeutic intervention. Cellular metabolism involves a series of oxidation/reduction (redox) reactions that yield the energy and biomass required for tumor growth. Cells require diverse molecular species with constituent sulfur atoms to facilitate these processes. For humans, this sulfur is derived from the dietary consumption of the proteinogenic amino acids cysteine and methionine, as only lower organisms (e.g., bacteria, fungi, and plants) can synthesize them de novo. In addition to providing the sulfur required to sustain redox chemistry, the metabolism of these sulfur-containing amino acids yield intermediate metabolites that constitute the cellular antioxidant system, mediate inter- and intracellular signaling, and facilitate the epigenetic regulation of gene expression, all of which contribute to tumorigenesis.
    Keywords:  Cancer metabolism; Cysteine; Glutathione; Hydrogen sulfide; Methionine; S-Adenosylmethionine; Sulfur
    DOI:  https://doi.org/10.1016/bs.ircmb.2019.05.001
  15. Trends Endocrinol Metab. 2019 Aug 24. pii: S1043-2760(19)30159-6. [Epub ahead of print]
    Quintana-Cabrera R, Soriano ME.
      Assembly factors are necessary for the formation of mitochondrial supercomplexes (SCs) and in making cellular respiration more efficient. In a recent study, Balsa et al. (Mol. Cell, 2019) report that nutrient-induced endoplasmic reticulum (ER) stress engages PERK-eIF2α-mediated transcription of the SCs assembly factor SCAF1, events that coordinate ER stress and SCs formation to improve bioenergetics.
    Keywords:  ER stress; SCAF1; glucose deprivation; mitochondrial cristae; supercomplexes
    DOI:  https://doi.org/10.1016/j.tem.2019.08.003
  16. PLoS One. 2019 ;14(8): e0221886
    Haraux F, Lombès A.
      BACKGROUND: ATP synthase, the mitochondrial complex V, plays a major role in bioenergetics and its defects lead to severe diseases. Lack of a consensual protocol for the assay of complex V activity probably explains the under-representation of complex V defect among mitochondrial diseases. The aim of this work was to elaborate a fast, simple and reliable method to check the maximal complex V capacity in samples relevant to clinical diagnosis.METHODS: Using homogenates from four different murine organs, we tested the use of dodecylmaltoside, stability of the activity, linearity with protein amount, sensitivity to oligomycin and to exogenous inhibitory factor 1 (IF1), influence of freezing, and impact of mitochondrial purification.
    RESULTS: We obtained organ-dependent, reproducible and stable complex V specific activities, similar with fresh and frozen organs. Similar inhibition by oligomycin and exogenous IF1 demonstrated tight coupling between F1 and F0 domains. The Michaelis constant for MgATP had close values for all organs, in the 150-220 μM range. Complex V catalytic turnover rate, as measured in preparations solubilized in detergent using immunotitration and activity measurements, was more than three times higher in extracts from brain or muscle than in extracts from heart or liver. This tissue specificity suggested post-translational modifications. Concomitant measurement of respiratory activities showed only slightly different complex II/complex V ratio in the four organs. In contrast, complex I/complex V ratio differed in brain as compared to the three other organs because of a high complex I activity in brain. Mitochondria purification preserved these ratios, except for brain where selective degradation of complex I occurred. Therefore, mitochondrial purification could introduce a biased enzymatic evaluation.
    CONCLUSION: Altogether, this work demonstrates that a reliable assay of complex V activity is perfectly possible with very small samples from frozen biopsies, which was confirmed using control and deficient human muscles.
    DOI:  https://doi.org/10.1371/journal.pone.0221886
  17. Cell Rep. 2019 Aug 27. pii: S2211-1247(19)31001-0. [Epub ahead of print]28(9): 2386-2396.e5
    Song N, Qi Q, Cao R, Qin B, Wang B, Wang Y, Zhao L, Li W, Du X, Liu F, Yan Y, Yi W, Jiang H, Li T, Zhou T, Li HY, Xia Q, Zhang XM, Zhong W, Li AL, Duan X.
      It is known that lethal viruses profoundly manipulate host metabolism, but how the metabolism alternation affects the immediate host antiviral immunity remains elusive. Here, we report that the O-GlcNAcylation of mitochondrial antiviral-signaling protein (MAVS), a key mediator of interferon signaling, is a critical regulation to activate the host innate immunity against RNA viruses. We show that O-GlcNAcylation depletion in myeloid cells renders the host more susceptible to virus infection both in vitro and in vivo. Mechanistically, we demonstrate that MAVS O-GlcNAcylation is required for virus-induced MAVS K63-linked ubiquitination, thereby facilitating IRF3 activation and IFNβ production. We further demonstrate that D-glucosamine, a commonly used dietary supplement, effectively protects mice against a range of lethal RNA viruses, including human influenza virus. Our study highlights a critical role of O-GlcNAcylation in regulating host antiviral immunity and validates D-glucosamine as a potential therapeutic for virus infections.
    Keywords:  MAVS; O-GlcNAcylation; RNA virus; antiviral immunity; glucosamine; influenza; interferon
    DOI:  https://doi.org/10.1016/j.celrep.2019.07.085
  18. Mol Cell Neurosci. 2019 Aug 21. pii: S1044-7431(19)30106-X. [Epub ahead of print]100 103396
    Gao J, Wang L, Yan T, Perry G, Wang X.
      Genetic mutations in TAR DNA-binding protein 43 (TDP-43) cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Importantly, TDP-43 proteinopathy, characterized by aberrant phosphorylation, ubiquitination, cleavage or nuclear depletion of TDP-43 in neurons and glial cells, is a common prominent pathological feature of various major neurodegenerative diseases including ALS, FTD, and Alzheimer's disease (AD). Although the pathomechanisms underlying TDP-43 proteinopathy remain elusive, pathologically relevant TDP-43 has been repeatedly shown to be present in either the inside or outside of mitochondria, and functionally involved in the regulation of mitochondrial morphology, trafficking, and function, suggesting mitochondria as likely targets of TDP-43 proteinopathy. In this review, we first describe the current knowledge of the association of TDP-43 with mitochondria. We then review in detail multiple mitochondrial pathways perturbed by pathological TDP-43, including mitochondrial fission and fusion dynamics, mitochondrial trafficking, bioenergetics, and mitochondrial quality control. Lastly, we briefly discuss how the study of TDP-43 proteinopathy and mitochondrial abnormalities may provide new avenues for neurodegeneration therapeutics.
    Keywords:  Alzheimer's disease; Amyotrophic lateral sclerosis; Frontotemporal dementia; Mitochondria; Neurodegeneration; Neurodegenerative diseases; TDP-43; TDP-43 proteinopathy
    DOI:  https://doi.org/10.1016/j.mcn.2019.103396
  19. Adv Exp Med Biol. 2019 ;1158 197-216
    Mailloux RJ.
      Mitochondria are dynamic organelles that perform a number of interconnected tasks that are elegantly intertwined with the regulation of cell functions. This includes the provision of ATP, reactive oxygen species (ROS), and building blocks for the biosynthesis of macromolecules while also serving as signaling platforms for the cell. Although the functions executed by mitochondria are complex, at its core these roles are, to a certain degree, fulfilled by electron transfer reactions and the establishment of a protonmotive force (PMF). Indeed, mitochondria are energy conserving organelles that extract electrons from nutrients to establish a PMF, which is then used to drive ATP and NADPH production, solute import, and many other functions including the propagation of cell signals. These same electrons extracted from nutrients are also used to produce ROS, pro-oxidants that can have potentially damaging effects at high levels, but also serve as secondary messengers at low amounts. Mitochondria are also enriched with antioxidant defenses, which are required to buffer cellular ROS. These same redox buffering networks also fulfill another important role; regulation of proteins through the reversible oxidation of cysteine switches. The modification of cysteine switches with the antioxidant glutathione, a process called protein S-glutathionylation, has been found to play an integral role in controlling various mitochondrial functions. In addition, recent findings have demonstrated that disrupting mitochondrial protein S-glutathionylation reactions can have some dire pathological consequences. Accordingly, this chapter focuses on the role of mitochondrial cysteine switches in the modulation of different physiological functions and how defects in these pathways contribute to the development of disease.
    Keywords:  Antioxidant defenses; Bioenergetics; Cysteine switches; Mitochondria; Protein S-glutathionylation; Reactive oxygen species; Redox signaling
    DOI:  https://doi.org/10.1007/978-981-13-8367-0_11
  20. EMBO Mol Med. 2019 Aug 29. e10769
    Nguyen TTT, Ishida CT, Shang E, Shu C, Torrini C, Zhang Y, Bianchetti E, Sanchez-Quintero MJ, Kleiner G, Quinzii CM, Westhoff MA, Karpel-Massler G, Canoll P, Siegelin MD.
      Liver-X-receptor (LXR) agonists are known to bear anti-tumor activity. However, their efficacy is limited and additional insights regarding the underlying mechanism are necessary. By performing transcriptome analysis coupled with global polar metabolite screening, we show that LXR agonists, LXR623 and GW3965, enhance synergistically the anti-proliferative effect of BH3 mimetics in solid tumor malignancies, which is predominantly mediated by cell death with features of apoptosis and is rescued by exogenous cholesterol. Extracellular flux analysis and carbon tracing experiments (U-13 C-glucose and U-13 C-glutamine) reveal that within 5 h, activation of LXRβ results in reprogramming of tumor cell metabolism, leading to suppression of mitochondrial respiration, a phenomenon not observed in normal human astrocytes. LXR activation elicits a suppression of respiratory complexes at the protein level by reducing their stability. In turn, energy starvation drives an integrated stress response (ISR) that up-regulates pro-apoptotic Noxa in an ATF4-dependent manner. Cholesterol and nucleotides rescue from the ISR elicited by LXR agonists and from cell death induced by LXR agonists and BH3 mimetics. In conventional and patient-derived xenograft models of colon carcinoma, melanoma, and glioblastoma, the combination treatment of ABT263 and LXR agonists reduces tumor sizes significantly stronger than single treatments. Therefore, the combination treatment of LXR agonists and BH3 mimetics might be a viable efficacious treatment approach for solid malignancies.
    Keywords:  BH3 mimetics; LXR agonist; colon adenocarcinoma; electron transport chain; glioblastoma
    DOI:  https://doi.org/10.15252/emmm.201910769
  21. Aging Cell. 2019 Aug 28. e13034
    Parkhitko AA, Jouandin P, Mohr SE, Perrimon N.
      Methionine restriction (MetR) extends lifespan across different species and exerts beneficial effects on metabolic health and inflammatory responses. In contrast, certain cancer cells exhibit methionine auxotrophy that can be exploited for therapeutic treatment, as decreasing dietary methionine selectively suppresses tumor growth. Thus, MetR represents an intervention that can extend lifespan with a complementary effect of delaying tumor growth. Beyond its function in protein synthesis, methionine feeds into complex metabolic pathways including the methionine cycle, the transsulfuration pathway, and polyamine biosynthesis. Manipulation of each of these branches extends lifespan; however, the interplay between MetR and these branches during regulation of lifespan is not well understood. In addition, a potential mechanism linking the activity of methionine metabolism and lifespan is regulation of production of the methyl donor S-adenosylmethionine, which, after transferring its methyl group, is converted to S-adenosylhomocysteine. Methylation regulates a wide range of processes, including those thought to be responsible for lifespan extension by MetR. Although the exact mechanisms of lifespan extension by MetR or methionine metabolism reprogramming are unknown, it may act via reducing the rate of translation, modifying gene expression, inducing a hormetic response, modulating autophagy, or inducing mitochondrial function, antioxidant defense, or other metabolic processes. Here, we review the mechanisms of lifespan extension by MetR and different branches of methionine metabolism in different species and the potential for exploiting the regulation of methyltransferases to delay aging.
    Keywords:  S-adenosylmethionine; aging; lifespan; methionine restriction; methylation; methyltransferases
    DOI:  https://doi.org/10.1111/acel.13034
  22. Methods Mol Biol. 2019 ;2037 169-186
    Pichumani K.
      Altered metabolism is considered one of the hallmarks of cancer. The findings that malignant brain tumors and brain metastases utilize acetate as an alternative nutrient are relatively recent and offer new avenues for investigation of altered metabolism in human cancers. Here, we describe comprehensively the details of the 13C NMR-based isotopomer methodology to measure in vivo acetate utilization in brain tumor patients, including the contribution from acetate metabolism of peripheral tissues. Methods described in this chapter can be readily extended to other cancer types.
    Keywords:  13C NMR; 13C–13C spin–spin coupling; Acetyl-CoA; Citric acid cycle; Isotopomer; Pyruvate recycling; [1,2-13C]acetate
    DOI:  https://doi.org/10.1007/978-1-4939-9690-2_10
  23. Int Rev Cell Mol Biol. 2019 ;pii: S1937-6448(19)30065-6. [Epub ahead of print]347 27-37
    Sica V, Bravo-San Pedro JM, Kroemer G.
      The combination of inhibitor of oxidative phosphorylation (OXPHOS) with dimethyl-α-ketoglutarate, a cell-permeable precursor of α-ketoglutarate, is highly efficient in killing human cancer cells in vitro or in vivo, in xenotransplanted mice. This effect involves excessive anaplerosis, as demonstrated by the fact that inhibition of isocitrate dehydrogenase-1, IDH1, reduced the efficacy of cancer cell killing by the combination treatment. However, the signal transduction pathway leading to cell death turned out to be complex because it involved numerous atypical cell death effectors (such as AIF, APEX, MDM2, PARP1), as well as a profound remodeling of the transcriptome resulting in reduced expression of glycolytic enzymes. The combined inhibition of OXPHOS and glycolytic ATP generation culminated in a lethal bioenergetic catastrophe.
    Keywords:  Anaplerosis; Cancer; Cell death; Metabolism; Mitochondria
    DOI:  https://doi.org/10.1016/bs.ircmb.2019.07.002
  24. Elife. 2019 Aug 27. pii: e47084. [Epub ahead of print]8
    Shemorry A, Harnoss JM, Guttman O, Marsters SA, Kőműves LG, Lawrence DA, Ashkenazi A.
      Upon detecting endoplasmic reticulum (ER) stress, the unfolded protein response (UPR) orchestrates adaptive cellular changes to reestablish homeostasis. If stress resolution fails, the UPR commits the cell to apoptotic death. Here we show that in hematopoietic cells, including multiple myeloma (MM), lymphoma, and leukemia cell lines, ER stress leads to caspase-mediated cleavage of the key UPR sensor IRE1 within its cytoplasmic linker region, generating a stable IRE1 fragment comprising the ER-lumenal domain and transmembrane segment (LDTM). This cleavage uncouples the stress-sensing and signaling domains of IRE1, attenuating its activation upon ER perturbation. Surprisingly, LDTM exerts negative feedback over apoptotic signaling by inhibiting recruitment of the key proapoptotic protein BAX to mitochondria. Furthermore, ectopic LDTM expression enhances xenograft growth of MM tumors in mice. These results uncover an unexpected mechanism of cross-regulation between the apoptotic caspase machinery and the UPR, which has biologically significant consequences for cell survival under ER stress.
    Keywords:  BAX; XBP1; apoptosis; cancer; cancer biology; cell biology; hematopoietic; human; mouse; myeloma
    DOI:  https://doi.org/10.7554/eLife.47084
  25. EMBO Rep. 2019 Aug 26. e47734
    Fraser J, Simpson J, Fontana R, Kishi-Itakura C, Ktistakis NT, Gammoh N.
      Despite recently uncovered connections between autophagy and the endocytic pathway, the role of autophagy in regulating endosomal function remains incompletely understood. Here, we find that the ablation of autophagy-essential players disrupts EGF-induced endocytic trafficking of EGFR. Cells lacking ATG7 or ATG16L1 exhibit increased levels of phosphatidylinositol-3-phosphate (PI(3)P), a key determinant of early endosome maturation. Increased PI(3)P levels are associated with an accumulation of EEA1-positive endosomes where EGFR trafficking is stalled. Aberrant early endosomes are recognised by the autophagy machinery in a TBK1- and Gal8-dependent manner and are delivered to LAMP2-positive lysosomes. Preventing this homeostatic regulation of early endosomes by autophagy reduces EGFR recycling to the plasma membrane and compromises downstream signalling and cell survival. Our findings uncover a novel role for the autophagy machinery in maintaining early endosome function and growth factor sensing.
    Keywords:  EGFR; autophagy; early endosomes; galectin; signalling
    DOI:  https://doi.org/10.15252/embr.201947734
  26. Nat Cell Biol. 2019 Aug 26.
    Wallroth A, Koch PA, Marat AL, Krause E, Haucke V.
      Mechanistic target of rapamycin (mTOR) kinase functions in two multiprotein complexes: lysosomal mTOR complex 1 (mTORC1) and mTORC2 at the plasma membrane. mTORC1 modulates the cell response to growth factors and nutrients by increasing protein synthesis and cell growth, and repressing the autophagy-lysosomal pathway1-4; however, dysfunction in mTORC1 is implicated in various diseases3,5,6. mTORC1 activity is regulated by phosphoinositide lipids7-10. Class I phosphatidylinositol-3-kinase (PI3K)-mediated production of phosphatidylinositol-3,4,5-trisphosphate6,11 at the plasma membrane stimulates mTORC1 signalling, while local synthesis of phosphatidylinositol-3,4-bisphosphate by starvation-induced recruitment of class II PI3K-β (PI3KC2-β) to lysosomes represses mTORC1 activity12. How the localization and activity of PI3KC2-β are regulated by mitogens is unknown. We demonstrate that protein kinase N (PKN) facilitates mTORC1 signalling by repressing PI3KC2-β-mediated phosphatidylinositol-3,4-bisphosphate synthesis downstream of mTORC2. Active PKN2 phosphorylates PI3KC2-β to trigger PI3KC2-β complex formation with inhibitory 14-3-3 proteins. Conversely, loss of PKN2 or inactivation of its target phosphorylation site in PI3KC2-β represses nutrient signalling via mTORC1. These results uncover a mechanism that couples mTORC2-dependent activation of PKN2 to the regulation of mTORC1-mediated nutrient signalling by local lipid signals.
    DOI:  https://doi.org/10.1038/s41556-019-0377-3
  27. Antioxid Redox Signal. 2019 Aug 28.
    Gaudino F, Manfredonia I, Managò A, Audrito V, Raffaelli N, Vaisitti T, Deaglio S.
      AIM: NAD+ plays central roles in a wide array of normal and pathological conditions. Inhibition of NAD+ biosynthesis can be exploited therapeutically in cancer, including melanoma. To obtain quantitation of NAD+ levels in live cells and to address the issue of the compartmentalization of NAD+ biosynthesis, we exploited a recently described, genetically-encoded NAD+ biosensor (LigA-cpVENUS), which was targeted to the cytosol, mitochondria and nuclei of BRAF-V600E A375 melanoma cells, a model of metastatic melanoma (MM).RESULTS: FK866, a specific inhibitor of nicotinamide phosphoribosyltransferase (NAMPT), the main NAD+-producing enzyme in MM cells, was used to monitor NAD+ depletion kinetics at the subcellular level in biosensor-transduced A375 cells. In addition, we treated FK866-blocked A375 cells with NAD+ precursors, including nicotinamide, nicotinic acid, nicotinamide riboside and quinolinic acid, highlighting an organelle-specific capacity of each substrate to rescue from NAMPT block. Expression patterns of NAD+ biosynthetic enzymes were then biochemically studied in isolated organelles, revealing expression of NAMPT in all three cellular compartments, while NAPRT was predominantly cytosolic and mitochondrial, and NRK mitochondrial and nuclear. In keeping with biosensor data, QPRT was expressed at extremely low levels. Innovation & Conclusions: Throughout this work, we validated the use of genetically encoded NAD+ biosensors to characterize subcellular distribution of NAD+ production routes in MM. The chance of real time monitoring of NAD+ fluctuations after chemical perturbations, together with a deeper comprehension of the cofactor biosynthesis compartmentalization, strengthens the foundation for a targeted strategy of NAD+ pool manipulation in cancer and metabolic diseases.
    DOI:  https://doi.org/10.1089/ars.2019.7799
  28. Sci Rep. 2019 Aug 27. 9(1): 12419
    Stephan T, Roesch A, Riedel D, Jakobs S.
      Mitochondria are highly dynamic organelles that exhibit a complex inner architecture. They exhibit a smooth outer membrane and a highly convoluted inner membrane that forms invaginations called cristae. Imaging cristae in living cells poses a formidable challenge for super-resolution light microscopy. Relying on a cell line stably expressing the mitochondrial protein COX8A fused to the SNAP-tag and using STED (stimulated emission depletion) nanoscopy, we demonstrate the visualization of cristae dynamics in cultivated human cells. We show that in human HeLa cells lamellar cristae are often arranged in groups separated by voids that are generally occupied by mitochondrial nucleoids.
    DOI:  https://doi.org/10.1038/s41598-019-48838-2
  29. Int Rev Cell Mol Biol. 2019 ;pii: S1937-6448(19)30070-X. [Epub ahead of print]347 1-26
    Montrose DC, Galluzzi L.
      As compared to their normal counterparts, neoplastic cells exhibit a variety of metabolic changes that reflect not only genetic and epigenetic defects underlying malignant transformation, but also the nutritional and immunobiological conditions of the tumor microenvironment. Such alterations, including the so-called Warburg effect (an increase in glucose uptake largely feeding anabolic and antioxidant metabolism), have attracted considerable attention as potential targets for the development of novel anticancer therapeutics. However, very few drugs specifically conceived to target bioenergetic cancer metabolism are currently approved by regulatory agencies for use in humans. This reflects the elevated degree of heterogeneity and redundancy in the metabolic circuitries exploited by neoplastic cells from different tumors (even of the same type), as well as the resemblance of such metabolic pathways to those employed by highly proliferating normal cells. Here, we summarize the major metabolic alterations that accompany oncogenesis, the potential of targeting bioenergetic metabolism for cancer therapy, and the obstacles that still prevent the clinical translation of such a promising therapeutic paradigm.
    Keywords:  Glutamine; Krebs cycle; Oxidative phosphorylation; Pentose phosphate pathway; Reductive carboxylation; Serine
    DOI:  https://doi.org/10.1016/bs.ircmb.2019.07.007
  30. Cell Metab. 2019 Aug 19. pii: S1550-4131(19)30428-0. [Epub ahead of print]
    Bieniasz-Krzywiec P, Martín-Pérez R, Ehling M, García-Caballero M, Pinioti S, Pretto S, Kroes R, Aldeni C, Di Matteo M, Prenen H, Tribulatti MV, Campetella O, Smeets A, Noel A, Floris G, Van Ginderachter JA, Mazzone M.
      Among mammary tumor-infiltrating immune cells, the highest expression of podoplanin (PDPN) is found in a subset of tumor-associated macrophages (TAMs). We hereby demonstrate that PDPN is involved in the attachment of this TAM subset to lymphatic endothelial cells (LECs). Mechanistically, the binding of PDPN to LEC-derived galectin 8 (GAL8) in a glycosylation-dependent manner promotes the activation of pro-migratory integrin β1. When proximal to lymphatics, PDPN-expressing macrophages (PoEMs) stimulate local matrix remodeling and promote vessel growth and lymphoinvasion. Anti-integrin β1 blockade, macrophage-specific Pdpn knockout, or GAL8 inhibition impairs TAM adhesion to LECs, restraining lymphangiogenesis and reducing lymphatic cancer spread. In breast cancer patients, association of PoEMs with tumor lymphatic vessels correlates with incidences of lymph node and distant organ metastasis.
    Keywords:  breast cancer; lymph nodes; lymphangiogenesis; lymphoinvasion; metastasis; podoplanin; tumor-associated macrophages
    DOI:  https://doi.org/10.1016/j.cmet.2019.07.015
  31. Leukemia. 2019 Aug 28.
    Ray A, Song Y, Du T, Tai YT, Chauhan D, Anderson KC.
      Our prior studies showed that dysfunctional plasmacytoid dendritic cells (pDCs) contribute to multiple myeloma (MM) pathogenesis. Specifically, pDC interactions with tumor and T/NK effector cells in the bone marrow (BM) milieu induce immune suppression and MM cell proliferation. Delineation of the mechanism(s) mediating pDC-MM-T-NK cell interactions will identify novel therapeutic targets to both enhance cytotoxicity and anti-MM immunity. Here, we utilized gene expression profiling (GEP) to show that pDC-MM interactions trigger upregulation of immunosuppressive tryptophan catabolic kynurenine (Kyn) pathway. In particular, we show that Kyn pathway enzyme kynurenine-3-monooxygenase (KMO) is upregulated during pDC-MM interactions. Using our coculture models of patient autologous pDC-T-NK-MM cells, we show that pharmacological blockade of KMO activates pDCs and triggers both MM-specific cytotoxic T-cell lymphocytes (CTL) and NK cells cytolytic activity against tumor cells. Furthermore, we show that simultaneous inhibition of Kyn pathway and immune checkpoint PD-L1 enhances antitumor immunity and cytotoxicity in MM. Our preclinical data therefore provide the basis for novel immune-based therapeutic approaches targeting Kyn metabolic pathway enzyme KMO, alone or in combination with anti-PD-L1 Ab, to restore anti-MM immune responses in MM.
    DOI:  https://doi.org/10.1038/s41375-019-0558-x
  32. Proc Natl Acad Sci U S A. 2019 Aug 26. pii: 201908755. [Epub ahead of print]
    Monit C, Morris ER, Ruis C, Szafran B, Thiltgen G, Tsai MC, Mitchison NA, Bishop KN, Stoye JP, Taylor IA, Fassati A, Goldstein RA.
      The vertebrate protein SAMHD1 is highly unusual in having roles in cellular metabolic regulation, antiviral restriction, and regulation of innate immunity. Its deoxynucleoside triphosphohydrolase activity regulates cellular dNTP concentration, reducing levels below those required by lentiviruses and other viruses to replicate. To counter this threat, some primate lentiviruses encode accessory proteins that bind SAMHD1 and induce its degradation; in turn, positive diversifying selection has been observed in regions bound by these lentiviral proteins, suggesting that primate SAMHD1 has coevolved to evade these countermeasures. Moreover, deleterious polymorphisms in human SAMHD1 are associated with autoimmune disease linked to uncontrolled DNA synthesis of endogenous retroelements. Little is known about how evolutionary pressures affect these different SAMHD1 functions. Here, we examine the deeper history of these interactions by testing whether evolutionary signatures in SAMHD1 extend to other mammalian groups and exploring the molecular basis of this coevolution. Using codon-based likelihood models, we find positive selection in SAMHD1 within each mammal lineage for which sequence data are available. We observe positive selection at sites clustered around T592, a residue that is phosphorylated to regulate SAMHD1 activity. We verify experimentally that mutations within this cluster affect catalytic rate and lentiviral restriction, suggesting that virus-host coevolution has required adaptations of enzymatic function. Thus, persistent positive selection may have involved the adaptation of SAMHD1 regulation to balance antiviral, metabolic, and innate immunity functions.
    Keywords:  HIV-1; SAMHD1; evolution; mammals; restriction
    DOI:  https://doi.org/10.1073/pnas.1908755116
  33. Nat Commun. 2019 Aug 26. 10(1): 3856
    Li Z, Wang Z, Tang Y, Lu X, Chen J, Dong Y, Wu B, Wang C, Yang L, Guo Z, Xue M, Lu S, Wei W, Shi Q.
      Accurate prediction of chemo- or targeted therapy responses for patients with similar driver oncogenes through a simple and least-invasive assay represents an unmet need in the clinical diagnosis of non-small cell lung cancer. Using a single-cell on-chip metabolic cytometry and fluorescent metabolic probes, we show metabolic phenotyping on the rare disseminated tumor cells in pleural effusions across a panel of 32 lung adenocarcinoma patients. Our results reveal extensive metabolic heterogeneity of tumor cells that differentially engage in glycolysis and mitochondrial oxidation. The cell number ratio of the two metabolic phenotypes is found to be predictive for patient therapy response, physiological performance, and survival. Transcriptome analysis reveals that the glycolytic phenotype is associated with mesenchymal-like cell state with elevated expression of the resistant-leading receptor tyrosine kinase AXL and immune checkpoint ligands. Drug targeting AXL induces a significant cell killing in the glycolytic cells without affecting the cells with active mitochondrial oxidation.
    DOI:  https://doi.org/10.1038/s41467-019-11808-3
  34. Cell Syst. 2019 Aug 28. pii: S2405-4712(19)30234-0. [Epub ahead of print]9(2): 109-127
    Suhail Y, Cain MP, Vanaja K, Kurywchak PA, Levchenko A, Kalluri R, Kshitiz .
      Cancer metastasis is no longer viewed as a linear cascade of events but rather as a series of concurrent, partially overlapping processes, as successfully metastasizing cells assume new phenotypes while jettisoning older behaviors. The lack of a systemic understanding of this complex phenomenon has limited progress in developing treatments for metastatic disease. Because metastasis has traditionally been investigated in distinct physiological compartments, the integration of these complex and interlinked aspects remains a challenge for both systems-level experimental and computational modeling of metastasis. Here, we present some of the current perspectives on the complexity of cancer metastasis, the multiscale nature of its progression, and a systems-level view of the processes underlying the invasive spread of cancer cells. We also highlight the gaps in our current understanding of cancer metastasis as well as insights emerging from interdisciplinary systems biology approaches to understand this complex phenomenon.
    Keywords:  ▪▪
    DOI:  https://doi.org/10.1016/j.cels.2019.07.003
  35. Nature. 2019 Aug;572(7771): 603-608
    Ombrato L, Nolan E, Kurelac I, Mavousian A, Bridgeman VL, Heinze I, Chakravarty P, Horswell S, Gonzalez-Gualda E, Matacchione G, Weston A, Kirkpatrick J, Husain E, Speirs V, Collinson L, Ori A, Lee JH, Malanchi I.
      Direct investigation of the early cellular changes induced by metastatic cells within the surrounding tissue remains a challenge. Here we present a system in which metastatic cancer cells release a cell-penetrating fluorescent protein, which is taken up by neighbouring cells and enables spatial identification of the local metastatic cellular environment. Using this system, tissue cells with low representation in the metastatic niche can be identified and characterized within the bulk tissue. To highlight its potential, we applied this strategy to study the cellular environment of metastatic breast cancer cells in the lung. We report the presence of cancer-associated parenchymal cells, which exhibit stem-cell-like features, expression of lung progenitor markers, multi-lineage differentiation potential and self-renewal activity. In ex vivo assays, lung epithelial cells acquire a cancer-associated parenchymal-cell-like phenotype when co-cultured with cancer cells and support their growth. These results highlight the potential of this method as a platform for new discoveries.
    DOI:  https://doi.org/10.1038/s41586-019-1487-6
  36. Nat Commun. 2019 Aug 29. 10(1): 3885
    Jadiya P, Kolmetzky DW, Tomar D, Di Meco A, Lombardi AA, Lambert JP, Luongo TS, Ludtmann MH, Praticò D, Elrod JW.
      Impairments in neuronal intracellular calcium (iCa2+) handling may contribute to Alzheimer's disease (AD) development. Metabolic dysfunction and progressive neuronal loss are associated with AD progression, and mitochondrial calcium (mCa2+) signaling is a key regulator of both of these processes. Here, we report remodeling of the mCa2+ exchange machinery in the prefrontal cortex of individuals with AD. In the 3xTg-AD mouse model impaired mCa2+ efflux capacity precedes neuropathology. Neuronal deletion of the mitochondrial Na+/Ca2+ exchanger (NCLX, Slc8b1 gene) accelerated memory decline and increased amyloidosis and tau pathology. Further, genetic rescue of neuronal NCLX in 3xTg-AD mice is sufficient to impede AD-associated pathology and memory loss. We show that mCa2+ overload contributes to AD progression by promoting superoxide generation, metabolic dysfunction and neuronal cell death. These results provide a link between the calcium dysregulation and metabolic dysfunction hypotheses of AD and suggest mCa2+ exchange as potential therapeutic target in AD.
    DOI:  https://doi.org/10.1038/s41467-019-11813-6
  37. Cancer Discov. 2019 Aug 27. pii: CD-19-0215. [Epub ahead of print]
    Dong Z, Zhang G, Qu M, Gimple RC, Wu Q, Qiu Z, Prager BC, Wang X, Kim LJY, Morton AR, Dixit D, Zhou W, Huang H, Li B, Zhu Z, Bao S, Mack SC, Chavez L, Kay SA, Rich JN.
      Glioblastomas are highly lethal cancers, containing self-renewing glioblastoma stem cells (GSCs). Here, we show that GSCs, differentiated glioblastoma cells (DGCs), and non-malignant brain cultures all displayed robust circadian rhythms, yet GSCs alone displayed exquisite dependence on core clock transcription factors, BMAL1 and CLOCK, for optimal cell growth. Downregulation of BMAL1 or CLOCK in GSCs induced cell cycle arrest and apoptosis. Chromatin immunoprecipitation revealed BMAL1 preferentially bound at metabolic genes in GSCs, associated with differences in active chromatin regions compared to NSCs. Targeting BMAL1 or CLOCK attenuated mitochondrial metabolic function and reduced expression of the tricarboxylic acid (TCA) cycle enzymes. Small molecule agonists of two independent BMAL1::CLOCK negative regulators, the Cryptochromes and REV-ERBs, downregulated stem cell factors and reduced GSC growth. Combination of Cryptochrome and REV-ERB agonists induced synergistic anti-tumor efficacy. Collectively, GSCs coopt circadian regulators beyond canonical circadian circuitry to promote stemness maintenance and metabolism, offering novel therapeutic paradigms.
    DOI:  https://doi.org/10.1158/2159-8290.CD-19-0215
  38. Nature. 2019 Aug 28.
    Kampjut D, Sazanov LA.
      Proton-translocating transhydrogenase (also known as nicotinamide nucleotide transhydrogenase (NNT)) is found in the plasma membranes of bacteria and the inner mitochondrial membranes of eukaryotes. NNT catalyses the transfer of a hydride between NADH and NADP+, coupled to the translocation of one proton across the membrane. Its main physiological function is the generation of NADPH, which is a substrate in anabolic reactions and a regulator of oxidative status; however, NNT may also fine-tune the Krebs cycle1,2. NNT deficiency causes familial glucocorticoid deficiency in humans and metabolic abnormalities in mice, similar to those observed in type II diabetes3,4. The catalytic mechanism of NNT has been proposed to involve a rotation of around 180° of the entire NADP(H)-binding domain that alternately participates in hydride transfer and proton-channel gating. However, owing to the lack of high-resolution structures of intact NNT, the details of this process remain unclear5,6. Here we present the cryo-electron microscopy structure of intact mammalian NNT in different conformational states. We show how the NADP(H)-binding domain opens the proton channel to the opposite sides of the membrane, and we provide structures of these two states. We also describe the catalytically important interfaces and linkers between the membrane and the soluble domains and their roles in nucleotide exchange. These structures enable us to propose a revised mechanism for a coupling process in NNT that is consistent with a large body of previous biochemical work. Our results are relevant to the development of currently unavailable NNT inhibitors, which may have therapeutic potential in ischaemia reperfusion injury, metabolic syndrome and some cancers7-9.
    DOI:  https://doi.org/10.1038/s41586-019-1519-2
  39. Cell Rep. 2019 Aug 27. pii: S2211-1247(19)30967-2. [Epub ahead of print]28(9): 2317-2330.e8
    Chatterjee N, Pazarentzos E, Mayekar MK, Gui P, Allegakoen DV, Hrustanovic G, Olivas V, Lin L, Verschueren E, Johnson JR, Hofree M, Yan JJ, Newton BW, Dollen JV, Earnshaw CH, Flanagan J, Chan E, Asthana S, Ideker T, Wu W, Suzuki J, Barad BA, Kirichok Y, Fraser JS, Weiss WA, Krogan NJ, Tulpule A, Sabnis AJ, Bivona TG.
      Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) is a tumor suppressor and bi-functional lipid and protein phosphatase. We report that the metabolic regulator pyruvate dehydrogenase kinase1 (PDHK1) is a synthetic-essential gene in PTEN-deficient cancer and normal cells. The PTEN protein phosphatase dephosphorylates nuclear factor κB (NF-κB)-activating protein (NKAP) and limits NFκB activation to suppress expression of PDHK1, a NF-κB target gene. Loss of the PTEN protein phosphatase upregulates PDHK1 to induce aerobic glycolysis and PDHK1 cellular dependence. PTEN-deficient human tumors harbor increased PDHK1, a biomarker of decreased patient survival. This study uncovers a PTEN-regulated signaling pathway and reveals PDHK1 as a potential target in PTEN-deficient cancers.
    Keywords:  NF-κB; NKAP; PDHK1; PTEN; cancer; metabolism; protein phosphatase; signaling; synthetic lethality
    DOI:  https://doi.org/10.1016/j.celrep.2019.07.063
  40. Nat Microbiol. 2019 Aug 26.
    Lopatkin AJ, Stokes JM, Zheng EJ, Yang JH, Takahashi MK, You L, Collins JJ.
      Growth rate and metabolic state of bacteria have been separately shown to affect antibiotic efficacy1-3. However, the two are interrelated as bacterial growth inherently imposes a metabolic burden4; thus, determining individual contributions from each is challenging5,6. Indeed, faster growth is often correlated with increased antibiotic efficacy7,8; however, the concurrent role of metabolism in that relationship has not been well characterized. As a result, a clear understanding of the interdependence between growth and metabolism, and their implications for antibiotic efficacy, are lacking9. Here, we measured growth and metabolism in parallel across a broad range of coupled and uncoupled conditions to determine their relative contribution to antibiotic lethality. We show that when growth and metabolism are uncoupled, antibiotic lethality uniformly depends on the bacterial metabolic state at the time of treatment, rather than growth rate. We further reveal a critical metabolic threshold below which antibiotic lethality is negligible. These findings were general for a wide range of conditions, including nine representative bactericidal drugs and a diverse range of Gram-positive and Gram-negative species (Escherichia coli, Acinetobacter baumannii and Staphylococcus aureus). This study provides a cohesive metabolic-dependent basis for antibiotic-mediated cell death, with implications for current treatment strategies and future drug development.
    DOI:  https://doi.org/10.1038/s41564-019-0536-0