bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2019–11–03
forty-nine papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit
  1. In vivo imaging of mitochondrial membrane potential in non-small-cell lung cancer.
  2. Exercise and mitochondrial health.
  3. Dysregulation of Mitochondrial Ca2+ Uptake and Sarcolemma Repair Underlie Muscle Weakness and Wasting in Patients and Mice Lacking MICU1.
  4. Causal roles of mitochondrial dynamics in longevity and healthy aging.
  5. Mitochondrial chaperone, TRAP1 as a potential pharmacological target to combat cancer metabolism.
  6. In silico simulation of reversible and irreversible swelling of mitochondria: the role of membrane rigidity.
  7. Adapt and conquer: Metabolic flexibility in cancer growth, invasion and evasion.
  8. Protein Kinase Cα Mediates Recovery of Renal and Mitochondrial Functions Following Acute Injury.
  9. Rhes, a striatal-enriched protein, promotes mitophagy via Nix.
  10. Increased 14C-acetate accumulation in IDH-mutated human glioblastoma: implications for detecting IDH-mutated glioblastoma with 11C-acetate PET imaging.
  11. The spatio-temporal organization of mitochondrial F1FO ATP synthase in cristae depends on its activity mode.
  12. The basic machineries for mitochondrial protein quality control.
  13. Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs.
  14. Multifaceted roles of porin in mitochondrial protein and lipid transport.
  15. Leucine-rich diet induces a shift in tumour metabolism from glycolytic towards oxidative phosphorylation, reducing glucose consumption and metastasis in Walker-256 tumour-bearing rats.
  16. The Effects of BCAAs on Insulin Resistance in Athletes.
  17. Maternal Lipid Metabolism Directs Fetal Liver Programming following Nutrient Stress.
  18. p53-dependent transcriptional suppression of BAG3 protects cells against metabolic stress via facilitation of p53 accumulation.
  19. Structural insights of human mitofusin-2 into mitochondrial fusion and CMT2A onset.
  20. Ironing the mitochondria: Relevance to its dynamics.
  21. The NADH Dehydrogenase Nde1 Executes Cell Death after Integrating Signals from Metabolism and Proteostasis on the Mitochondrial Surface.
  22. Glutamine Anabolism Plays a Critical Role in Pancreatic Cancer by Coupling Carbon and Nitrogen Metabolism.
  23. Folliculin Interacting Protein 1 Maintains Metabolic Homeostasis during B Cell Development by Modulating AMPK, mTORC1, and TFE3.
  24. A Shifty Target: Tumor-Initiating Cells and Their Metabolism.
  25. Hydralazine targets cAMP-dependent protein kinase leading to sirtuin1/5 activation and lifespan extension in C. elegans.
  26. Uncoupled turnover disrupts mitochondrial quality control in diabetic retinopathy.
  27. Structural mechanism of a Rag GTPase activation checkpoint by the lysosomal folliculin complex.
  28. Multiple mitochondrial thioesterases have distinct tissue and substrate specificity, and CoA regulation, suggesting unique functional roles.
  29. Deletion of Voltage-Dependent Anion Channel 1 knocks mitochondria down triggering metabolic rewiring in yeast.
  30. TFEB activation in macrophages attenuates postmyocardial infarction ventricular dysfunction independently of ATG5-mediated autophagy.
  31. Central metabolism of functionally heterogeneous mesenchymal stromal cells.
  32. METTL15 introduces N4-methylcytidine into human mitochondrial 12S rRNA and is required for mitoribosome biogenesis.
  33. Mitochondrial Protein Poldip2 Controls VSMC Differentiated Phenotype by O-Linked GlcNAc Transferase-Dependent Inhibition of a Ubiquitin Proteasome System.
  34. NAD+ homeostasis in renal health and disease.
  35. Human mitochondrial DNA is extensively methylated in a non-CpG context.
  36. MYCN-enhanced Oxidative and Glycolytic Metabolism Reveals Vulnerabilities for Targeting Neuroblastoma.
  37. FOXO1 inhibition prevents renal ischemia-reperfusion injury via promotion of CREB/PGC-1α-mediated mitochondrial biogenesis.
  38. Metabolic Reprogramming Associated with Aggressiveness Occurs in the G-CIMP-High Molecular Subtypes of IDH1mut Lower Grade Gliomas.
  39. Promoter demethylation of the asparagine synthetase gene is required for an ATF4-dependent adaptation to asparagine depletion.
  40. Mitochondrial Damage Causes Inflammation via cGAS-STING Signaling in Acute Kidney Injury.
  41. Dimethyl fumarate therapy reduces memory T cells and the CNS migration potential in patients with multiple sclerosis.
  42. Cellular Senescence: Defining a Path Forward.
  43. Cancer-Cell-Intrinsic cGAS Expression Mediates Tumor Immunogenicity.
  44. Branched chain amino acids impact health and lifespan indirectly via amino acid balance and appetite control.
  45. Lactate-mediated epigenetic reprogramming regulates formation of human pancreatic cancer-associated fibroblasts.
  46. The mitochondrial acyl-carrier protein interaction network highlights important roles for LYRM family members in complex I and mitoribosome assembly.
  47. Recognition of Histone Crotonylation by Taf14 Links Metabolic State to Gene Expression.
  48. Mitochondrial metabolic alterations in cancer cells and related therapeutic targets.
  49. Circulating glutamate level as a potential biomarker for abdominal obesity and metabolic risk.
  1. Nature. 2019 Oct 30.
    In vivo imaging of mitochondrial membrane potential in non-small-cell lung cancer.
    Milica Momcilovic, Anthony Jones, Sean T Bailey, Christopher M Waldmann, Rui Li, Jason T Lee, Gihad Abdelhady, Adrian Gomez, Travis Holloway, Ernst Schmid, David Stout, Michael C Fishbein, Linsey Stiles, Deepa V Dabir, Steven M Dubinett, Heather Christofk, Orian Shirihai, Carla M Koehler, Saman Sadeghi, David B Shackelford.
      Mitochondria are essential regulators of cellular energy and metabolism, and have a crucial role in sustaining the growth and survival of cancer cells. A central function of mitochondria is the synthesis of ATP by oxidative phosphorylation, known as mitochondrial bioenergetics. Mitochondria maintain oxidative phosphorylation by creating a membrane potential gradient that is generated by the electron transport chain to drive the synthesis of ATP1. Mitochondria are essential for tumour initiation and maintaining tumour cell growth in cell culture and xenografts2,3. However, our understanding of oxidative mitochondrial metabolism in cancer is limited because most studies have been performed in vitro in cell culture models. This highlights a need for in vivo studies to better understand how oxidative metabolism supports tumour growth. Here we measure mitochondrial membrane potential in non-small-cell lung cancer in vivo using a voltage-sensitive, positron emission tomography (PET) radiotracer known as 4-[18F]fluorobenzyl-triphenylphosphonium (18F-BnTP)4. By using PET imaging of 18F-BnTP, we profile mitochondrial membrane potential in autochthonous mouse models of lung cancer, and find distinct functional mitochondrial heterogeneity within subtypes of lung tumours. The use of 18F-BnTP PET imaging enabled us to functionally profile mitochondrial membrane potential in live tumours.
    DOI:  https://doi.org/10.1038/s41586-019-1715-0
  2. J Physiol. 2019 Nov 01.
    Exercise and mitochondrial health.
    Jonathan M Memme, Avigail T Erlich, Geetika Phukan, David A Hood.
      Mitochondrial health is an important mediator of cellular function across a range of tissues, and as a result contributes to whole-body vitality in health and disease. Our understanding of the regulation and function of these organelles is of great interest to scientists and clinicians across many disciplines within our healthcare system. Skeletal muscle is a useful model tissue for the study of mitochondrial adaptations because of its mass and contribution to whole body metabolism. The remarkable plasticity of mitochondria allows them to adjust their volume, structure, and capacity under conditions such as exercise, which is useful or improving metabolic health in individuals with various diseases and/or advancing age. Mitochondria exist within muscle as a functional reticulum which is maintained by dynamic processes of biogenesis and fusion, and is balanced by opposing processes of fission and mitophagy. The sophisticated coordination of these events is incompletely understood, but is imperative for organelle function and essential for the maintenance of an interconnected organelle network that is finely tuned to the metabolic needs of the cell. Further elucidation of the mechanisms of mitochondrial turnover in muscle could offer potential therapeutic targets for the advancement of health and longevity among our aging populations. As well, investigating exercise modalities that are both convenient and capable of inducing robust mitochondrial adaptations are useful in fostering more widespread global adherence. To this point, exercise remains the most potent behavioural therapeutic approach for the improvement of mitochondrial health, not only in muscle, but potentially also in other tissues. This article is protected by copyright. All rights reserved.
    Keywords:  Aging; Exercise training; Lysosomal biogenesis; Mitochondrial biogenesis; Mitochondrial quality control; Mitophagy; Skeletal muscle; UPRmt
    DOI:  https://doi.org/10.1113/JP278853
  3. Cell Rep. 2019 Oct 29. pii: S2211-1247(19)31260-4. [Epub ahead of print]29(5): 1274-1286.e6
    Dysregulation of Mitochondrial Ca2+ Uptake and Sarcolemma Repair Underlie Muscle Weakness and Wasting in Patients and Mice Lacking MICU1.
    Valentina Debattisti, Adam Horn, Raghavendra Singh, Erin L Seifert, Marshall W Hogarth, Davi A Mazala, Kai Ting Huang, Rita Horvath, Jyoti K Jaiswal, György Hajnóczky.
      Muscle function is regulated by Ca2+, which mediates excitation-contraction coupling, energy metabolism, adaptation to exercise, and sarcolemmal repair. Several of these actions rely on Ca2+ delivery to the mitochondrial matrix via the mitochondrial Ca2+ uniporter, the pore of which is formed by mitochondrial calcium uniporter (MCU). MCU's gatekeeping and cooperative activation are controlled by MICU1. Loss-of-protein mutation in MICU1 causes a neuromuscular disease. To determine the mechanisms underlying the muscle impairments, we used MICU1 patient cells and skeletal muscle-specific MICU1 knockout mice. Both these models show a lower threshold for MCU-mediated Ca2+ uptake. Lack of MICU1 is associated with impaired mitochondrial Ca2+ uptake during excitation-contraction, aerobic metabolism impairment, muscle weakness, fatigue, and myofiber damage during physical activity. MICU1 deficit compromises mitochondrial Ca2+ uptake during sarcolemmal injury, which causes ineffective repair of the damaged myofibers. Thus, dysregulation of mitochondrial Ca2+ uptake hampers myofiber contractile function, likely through energy metabolism and membrane repair.
    Keywords:  atrophy; autosomal recessive; calcium; injury; membrane; mitochondria; mitochondrial disease; muscle disease
    DOI:  https://doi.org/10.1016/j.celrep.2019.09.063
  4. EMBO Rep. 2019 Oct 31. e48395
    Causal roles of mitochondrial dynamics in longevity and healthy aging.
    Arpit Sharma, Hannah J Smith, Pallas Yao, William B Mair.
      Mitochondria are organized in the cell in the form of a dynamic, interconnected network. Mitochondrial dynamics, regulated by mitochondrial fission, fusion, and trafficking, ensure restructuring of this complex reticulum in response to nutrient availability, molecular signals, and cellular stress. Aberrant mitochondrial structures have long been observed in aging and age-related diseases indicating that mitochondrial dynamics are compromised as cells age. However, the specific mechanisms by which aging affects mitochondrial dynamics and whether these changes are causally or casually associated with cellular and organismal aging is not clear. Here, we review recent studies that show specifically how mitochondrial fission, fusion, and trafficking are altered with age. We discuss factors that change with age to directly or indirectly influence mitochondrial dynamics while examining causal roles for altered mitochondrial dynamics in healthy aging and underlying functional outputs that might affect longevity. Lastly, we propose that altered mitochondrial dynamics might not just be a passive consequence of aging but might constitute an adaptive mechanism to mitigate age-dependent cellular impairments and might be targeted to increase longevity and promote healthy aging.
    Keywords:  aging; fission; fusion; mitochondria; mitochondrial dynamics
    DOI:  https://doi.org/10.15252/embr.201948395
  5. Mitochondrion. 2019 Oct 25. pii: S1567-7249(19)30019-4. [Epub ahead of print]
    Mitochondrial chaperone, TRAP1 as a potential pharmacological target to combat cancer metabolism.
    Balaji Ramkumar, Shrikant P Dharaskar, Mounika Guntipally, Khanderao Paithankar, Amere Subbarao Sreedhar.
      The stress response forms the most ancient defense system in living cells. Heat shock proteins (Hsps) are highly conserved across species and play major roles in mounting the stress response. The emerging information now suggests that Hsp90 family of chaperones display additional cellular roles contributing to diseases like cancer. For this reason, pharmacological targeting of Hsp90 has emerged as a novel antitumor strategy. However, its mitochondrial homologue TRAP1 has not been implicated in cancer with conclusive mechanistic insights. Since understanding the mutational spectrum of cancer cells indicates the outcome of the disease as well as treatment response, we examined mutational spectrum of TRAP1. Our in silico analyses of TRAP1 SNPs and CNVs correlated with the aggressive cancer phenotypes, and are found to be predominant over Hsp90 itself. The increased CNVs have been correlated with increased expression of TRAP1 in metastatic cancer cells, increased ATP production, and decreased oxygen consumption rate of mitochondria. Examining TRAP1 knockdown as well as over expression in metastatic cancer cells furthered our understanding that TRAP1 likely to facilitate the altered energy metabolism in the functional compromise of mitochondrial OXPHOS. Interestingly, the increased ATP levels in the TRAP1 background are found to be independent of glucose oxidation. Our results suggest TRAP1 role in triggering the alternate energy metabolism in cancer cells. Since targeting tumor metabolism is considered as an alternate strategy to combat cancer, we propose pharmacological targeting of TRAP1 to target alternate energy metabolism.
    Keywords:  Hsp; TRAP1; cancer; metabolism; mitochondria
    DOI:  https://doi.org/10.1016/j.mito.2019.09.011
  6. Mitochondrion. 2019 Oct 25. pii: S1567-7249(19)30045-5. [Epub ahead of print]
    In silico simulation of reversible and irreversible swelling of mitochondria: the role of membrane rigidity.
    Vladimir I Makarov, Igor Khmelinskii, Zaza Khuchua, Sabzali Javadov.
      Mitochondria have been widely accepted as the main source of ATP in the cell. The inner mitochondrial membrane (IMM) is important for the maintenance of ATP production and other functions of mitochondria. The electron transport chain (ETC) generates an electrochemical gradient of protons known as the proton-motive force across the IMM and thus produces the mitochondrial membrane potential that is critical to ATP synthesis. One of the main factors regulating the structural and functional integrity of the IMM is the changes in the matrix volume. Mild (reversible) swelling regulates mitochondrial metabolism and function; however, excessive (irreversible) swelling causes mitochondrial dysfunction and cell death. The central mechanism of mitochondrial swelling includes the opening of non-selective channels known as permeability transition pores (PTPs) in the IMM by high mitochondrial Ca2+ and reactive oxygen species (ROS). The mechanisms of reversible and irreversible mitochondrial swelling and transition between these two states are still unknown. The present study elucidates an upgraded biophysical model of reversible and irreversible mitochondrial swelling dynamics. The model provides a description of the PTP regulation dynamics using an additional differential equation. The rigidity tensor was used in numerical simulations of the mitochondrial parameter dynamics with different initial conditions defined by Ca2+ concentration in the sarco/endoplasmic reticulum. We were able to estimate the values of the IMM rigidity tensor components by fitting the model to the previously reported experimental data. Overall, the model provides a better description of the reversible and irreversible mitochondrial swelling dynamics.
    Keywords:  calcium; ion transport; membrane rigidity; mitochondrial swelling; modeling analysis; permeability transition pore
    DOI:  https://doi.org/10.1016/j.mito.2019.09.006
  7. Mol Metab. 2019 Oct 10. pii: S2212-8778(19)30906-8. [Epub ahead of print]
    Adapt and conquer: Metabolic flexibility in cancer growth, invasion and evasion.
    Peter Kreuzaler, Yulia Panina, Joanna Segal, Mariia Yuneva.
       BACKGROUND: It has been known for close to a century that, on average, tumors have a metabolism that is different from those found in healthy tissues. Typically, tumors show a biosynthetic metabolism that distinguishes itself by engaging in large scale aerobic glycolysis, heightened flux through the pentose phosphate pathway, and increased glutaminolysis among other means. However, it is becoming equally clear that non tumorous tissues at times can engage in similar metabolism, while tumors show a high degree of metabolic flexibility reacting to cues, and stresses in their local environment.
    SCOPE OF THE REVIEW: In this review, we want to scrutinize historic and recent research on metabolism, comparing and contrasting oncogenic and physiological metabolic states. This will allow us to better define states of bona fide tumor metabolism. We will further contextualize the stress response and the metabolic evolutionary trajectory seen in tumors, and how these contribute to tumor progression. Lastly, we will analyze the implications of these characteristics with respect to therapy response.
    MAJOR CONCLUSIONS: In our review, we argue that there is not one single oncogenic state, but rather a diverse set of oncogenic states. These are grounded on a physiological proliferative/wound healing program but distinguish themselves due to their large scale of proliferation, mutations, and transcriptional changes in key metabolic pathways, and the adaptations to widespread stress signals within tumors. We find evidence for the necessity of metabolic flexibility and stress responses in tumor progression and how these responses in turn shape oncogenic progression. Lastly, we find evidence for the notion that the metabolic adaptability of tumors frequently frustrates therapeutic interventions.
    Keywords:  Central carbon metabolism; Metabolic flexibility; Tumour metabolism; Tumourigenesis
    DOI:  https://doi.org/10.1016/j.molmet.2019.08.021
  8. FEBS J. 2019 Oct 28.
    Protein Kinase Cα Mediates Recovery of Renal and Mitochondrial Functions Following Acute Injury.
    Grazyna Nowak, Judit Megyesi.
      Previously, we have shown that active PKCα promotes recovery of mitochondrial function after injury in vitro [24]. This study examined whether PKCα regulates recovery of mitochondrial and kidney functions after ischemia-induced acute injury (AKI) in vivo. Markers of kidney injury were increased after bilateral ischemia and returned to normal levels in wild-type (WT) mice. Maximum mitochondrial respiration and activities of respiratory complexes and Fo F1 -ATPase decreased after ischemia and recovered in WT mice. Reperfusion after ischemia was accompanied by translocation of active PKCα to mitochondria. PKCα deletion reduced mitochondrial respiration and activities of respiratory complex I and Fo F1 -ATPase in non-injured kidneys, indicating that PKCα is essential in developing fully functional renal mitochondria. These changes in PKCα-deficient mice were accompanied by lower levels of complex I subunits (NDUFA9 and NDUFS3) and the γ-subunit of Fo F1 -ATPase. Also, lack of PKCα exacerbated ischemia-induced decreases in respiration, complex I and Fo F1 -ATPase activities, and blocked their recovery after injury, indicating a crucial role of PKCα in promoting mitochondrial recovery after AKI. Further, PKCα deletion exacerbated acetylation and succinylation of key mitochondrial proteins of energy metabolism after ischemia due to decreases in deacetylase and desuccinylase (sirtuin3 and sirtuin5) levels in renal mitochondria. Thus, our data show a novel role for PKCα in regulating levels of mitochondrial sirtuins and acetylation and succinylation of key mitochondrial proteins. We conclude that PKCα deletion: 1) affects renal physiology by decreasing mitochondrial capacity for maximum respiration, 2) blocks recovery of mitochondrial functions, renal morphology and functions after AKI, and 3) decreases survival after AKI.
    Keywords:  ATP synthase; Acute kidney injury; Mitochondria; Protein kinase Cα Ischemia; Respiratory chain
    DOI:  https://doi.org/10.1111/febs.15110
  9. Proc Natl Acad Sci U S A. 2019 Nov 01. pii: 201912868. [Epub ahead of print]
    Rhes, a striatal-enriched protein, promotes mitophagy via Nix.
    Manish Sharma, Uri Nimrod Ramírez Jarquín, Oscar Rivera, Melissa Kazantzis, Mehdi Eshraghi, Neelam Shahani, Vishakha Sharma, Ricardo Tapia, Srinivasa Subramaniam.
      Elimination of dysfunctional mitochondria via mitophagy is essential for cell survival and neuronal functions. But, how impaired mitophagy participates in tissue-specific vulnerability in the brain remains unclear. Here, we find that striatal-enriched protein, Rhes, is a critical regulator of mitophagy and striatal vulnerability in brain. In vivo interactome and density fractionation reveal that Rhes coimmunoprecipitates and cosediments with mitochondrial and lysosomal proteins. Live-cell imaging of cultured striatal neuronal cell line shows Rhes surrounds globular mitochondria, recruits lysosomes, and ultimately degrades mitochondria. In the presence of 3-nitropropionic acid (3-NP), an inhibitor of succinate dehydrogenase, Rhes disrupts mitochondrial membrane potential (ΔΨ m ) and promotes excessive mitophagy and cell death. Ultrastructural analysis reveals that systemic injection of 3-NP in mice promotes globular mitochondria, accumulation of mitophagosomes, and striatal lesion only in the wild-type (WT), but not in the Rhes knockout (KO), striatum, suggesting that Rhes is critical for mitophagy and neuronal death in vivo. Mechanistically, Rhes requires Nix (BNIP3L), a known receptor of mitophagy, to disrupt ΔΨ m and promote mitophagy and cell death. Rhes interacts with Nix via SUMO E3-ligase domain, and Nix depletion totally abrogates Rhes-mediated mitophagy and cell death in the cultured striatal neuronal cell line. Finally, we find that Rhes, which travels from cell to cell via tunneling nanotube (TNT)-like cellular protrusions, interacts with dysfunctional mitochondria in the neighboring cell in a Nix-dependent manner. Collectively, Rhes is a major regulator of mitophagy via Nix, which may determine striatal vulnerability in the brain.
    Keywords:  SUMO-E3 ligase; mitophagosomes; mitophagy ligand; striatal neuronal vulnerability; tunneling nanotubes
    DOI:  https://doi.org/10.1073/pnas.1912868116
  10. J Neurooncol. 2019 Oct 30.
    Increased 14C-acetate accumulation in IDH-mutated human glioblastoma: implications for detecting IDH-mutated glioblastoma with 11C-acetate PET imaging.
    Sho Koyasu, Yoichi Shimizu, Akiyo Morinibu, Tsuneo Saga, Yuji Nakamoto, Kaori Togashi, Hiroshi Harada.
       PURPOSE: Recently, the potential value of isocitrate dehydrogenase (IDH) mutation as a prognostic marker in glioblastomas has been established. Glioblastomas are classified by their IDH mutation status under the 2016 WHO classification system. However, noninvasive diagnostic methods for the mutation status in glioblastoma patients have not been established so far. The purpose of this study was to evaluate the difference of acetate metabolism between in glioblastomas with wild-type IDH and in those with IDH mutation by comparing the uptake of 14C-acetate using genetically engineered glioblastoma cell lines in vitro and in vivo.
    METHODS: We established glioblastoma cells (U251) expressing IDH1 R132H and examined the cell uptake of [1-14C]acetate. Biodistribution studies and an autoradiographic study for U251 cell tumor-bearing mice (BALB/c-nu/nu) with or without the IDH1 mutation were performed 1 h after [1-14C]acetate administration.
    RESULTS: Significantly higher uptake of [1-14C]acetate was observed in U251/IDH1 R132H cells than in U251/IDH1 wild-type cells both in vitro (10.11 ± 0.94 vs. 4.26 ± 0.95%dose/mg, p = 0.0047) and in vivo (0.97 ± 0.14 vs. 0.66 ± 0.05%ID/g; p = 0.0037). Tumor-to-muscle ratios were also significantly higher in U251/IDH1 R132H tumors (3.36 ± 0.41 vs. 1.88 ± 0.59, p = 0.0030). The autoradiographic study shows the entirely higher radioactivity of the U251/IDH1 R132H tumor tissue section than that of the U251/IDH1 Wild-type tumor.
    CONCLUSIONS: In vitro and in vivo studies demonstrated that the uptake of radiolabeled acetate was significantly higher in IDH-mutated cells than in IDH-wild-type cells.
    Keywords:  2-Hydroxyglutarate; Acetate PET; Glioblastoma; Isocitrate dehydrogenase; Mutation
    DOI:  https://doi.org/10.1007/s11060-019-03322-9
  11. Biochim Biophys Acta Bioenerg. 2019 Oct 26. pii: S0005-2728(19)30138-0. [Epub ahead of print] 148091
    The spatio-temporal organization of mitochondrial F1FO ATP synthase in cristae depends on its activity mode.
    Kirill Salewskij, Bettina Rieger, Frances Hager, Tasnim Arroum, Patrick Duwe, Jimmy Villalta, Sara Colgiati, Christian P Richter, Olympia E Psathaki, José A Enriquez, Timo Dellmann, Karin B Busch.
      F1FO ATP synthase is a key enzyme of mitochondrial energy metabolism which works in two directions. It is not known whether ATP synthase and ATPase function are correlated with different spatio-temporal organization of the enzyme. To analyze this, we have tracked and localized individual ATP synthase/ATPase molecules in situ by live cell microscopy. Under normal conditions, ATP synthase is restricted mainly to cristae. A mobile fraction exist that displays orthogonal trajectories following the cristae membranes but also move in the IBM. By inhibiting glycolysis, we induced ATP hydrolysis in addition to ATP synthesis. The coexistence of two subpopulations was supported by data from single molecule localization and tracking analysis. We found that the spatial-temporal organization of ATP synthase was flexible and mirrored the physiological data. The clear cristae-related structuring of the ATP synthase/ATPase was obliterated when glycolysis was inhibited. At the same time, ATP synthase dimers decreased. The ratiometric change in dimeric/monomeric, respectively more mobile/less mobile ATP synthase was reversible. In IF1-KO cells, ATP synthase was more mobile, while inhibition of ATPase activity decreased the mobility. Together this data strongly supports the model of distinct subpopulations of ATP synthase and ATP hydrolase, the latter with higher mobility and likely present in the IBM compartment. Obviously, ATP synthase reacts quickly and reversibly to metabolic conditions, not only through functional but also through spatial and structural re-organization.
    Keywords:  ATP synthase dimers; F(1)F(O) ATP synthase; Metabolic adaptation; Mitochondria; OXPHOS; Reverse ATP synthase activity; Spatio-temporal organization; Superresolution microscopy; Tracking and localization microscopy (TALM); Ultrastructure
    DOI:  https://doi.org/10.1016/j.bbabio.2019.148091
  12. Mitochondrion. 2019 Oct 26. pii: S1567-7249(19)30149-7. [Epub ahead of print]
    The basic machineries for mitochondrial protein quality control.
    Carmela Vazquez-Calvo, Tamara Suhm, Sabrina Büttner, Martin Ott.
      Mitochondria play pivotal roles in cellular energy metabolism, the synthesis of essential biomolecules and the regulation of cell death and aging. The proper folding, unfolding and degradation of the many proteins active within mitochondria is surveyed by the mitochondrial quality control machineries. Here, we describe the principal components of the mitochondrial quality control system and recent developments in the elucidation of the molecular mechanisms maintaining a functional mitochondrial proteome.
    Keywords:  Aggregates; Chaperones; Mitochondria; Mitophagy; Proteases; Proteostasis; Quality control
    DOI:  https://doi.org/10.1016/j.mito.2019.10.003
  13. Nature. 2019 Oct 16.
    Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs.
    William A Flavahan, Yotam Drier, Sarah E Johnstone, Matthew L Hemming, Daniel R Tarjan, Esmat Hegazi, Sarah J Shareef, Nauman M Javed, Chandrajit P Raut, Benjamin K Eschle, Prafulla C Gokhale, Jason L Hornick, Ewa T Sicinska, George D Demetri, Bradley E Bernstein.
      Epigenetic aberrations are widespread in cancer, yet the underlying mechanisms and causality remain poorly understood1-3. A subset of gastrointestinal stromal tumours (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 between enhancer and oncogene, and strongly upregulated 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 tumour, including hypermethylation and insulator defects. This PDX model is highly sensitive to FGF receptor (FGFR) inhibition, 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
  14. Biochem Soc Trans. 2019 Oct 31. pii: BST20190153. [Epub ahead of print]
    Multifaceted roles of porin in mitochondrial protein and lipid transport.
    Toshiya Endo, Haruka Sakaue.
      Mitochondria are essential eukaryotic organelles responsible for primary cellular energy production. Biogenesis, maintenance, and functions of mitochondria require correct assembly of resident proteins and lipids, which require their transport into and within mitochondria. Mitochondrial normal functions also require an exchange of small metabolites between the cytosol and mitochondria, which is primarily mediated by a metabolite channel of the outer membrane (OM) called porin or voltage-dependent anion channel. Here, we describe recently revealed novel roles of porin in the mitochondrial protein and lipid transport. First, porin regulates the formation of the mitochondrial protein import gate in the OM, the translocase of the outer membrane (TOM) complex, and its dynamic exchange between the major form of a trimer and the minor form of a dimer. The TOM complex dimer lacks a core subunit Tom22 and mediates the import of a subset of mitochondrial proteins while the TOM complex trimer facilitates the import of most other mitochondrial proteins. Second, porin interacts with both a translocating inner membrane (IM) protein like a carrier protein accumulated at the small TIM chaperones in the intermembrane space and the TIM22 complex, a downstream translocator in the IM for the carrier protein import. Porin thereby facilitates the efficient transfer of carrier proteins to the IM during their import. Third, porin facilitates the transfer of lipids between the OM and IM and promotes a back-up pathway for the cardiolipin synthesis in mitochondria. Thus, porin has roles more than the metabolite transport in the protein and lipid transport into and within mitochondria, which is likely conserved from yeast to human.
    Keywords:  VDAC; mitochondria; phospholipid transport; porin; protein import; translocator
    DOI:  https://doi.org/10.1042/BST20190153
  15. Sci Rep. 2019 Oct 29. 9(1): 15529
    Leucine-rich diet induces a shift in tumour metabolism from glycolytic towards oxidative phosphorylation, reducing glucose consumption and metastasis in Walker-256 tumour-bearing rats.
    Laís Rosa Viana, Natália Tobar, Estela Natacha Brandt Busanello, Ana Carolina Marques, Andre Gustavo de Oliveira, Tanes I Lima, Gabrielly Machado, Bianca Gazieri Castelucci, Celso Dario Ramos, Sérgio Q Brunetto, Leonardo Reis Silveira, Anibal Eugenio Vercesi, Sílvio Roberto Consonni, Maria Cristina Cintra Gomes-Marcondes.
      Leucine can stimulate protein synthesis in skeletal muscle, and recent studies have shown an increase in leucine-related mitochondrial biogenesis and oxidative phosphorylation capacity in muscle cells. However, leucine-related effects in tumour tissues are still poorly understood. Thus, we described the effects of leucine in both in vivo and in vitro models of a Walker-256 tumour. Tumour-bearing Wistar rats were randomly distributed into a control group (W; normoprotein diet) and leucine group (LW; leucine-rich diet [normoprotein + 3% leucine]). After 20 days of tumour evolution, the animals underwent 18-fludeoxyglucose positron emission computed tomography (18F-FDG PET-CT) imaging, and after euthanasia, fresh tumour biopsy samples were taken for oxygen consumption rate measurements (Oroboros Oxygraph), electron microscopy analysis and RNA and protein extraction. Our main results from the LW group showed no tumour size change, lower tumour glucose (18F-FDG) uptake, and reduced metastatic sites. Furthermore, leucine stimulated a shift in tumour metabolism from glycolytic towards oxidative phosphorylation, higher mRNA and protein expression of oxidative phosphorylation components, and enhanced mitochondrial density/area even though the leucine-treated tumour had a higher number of apoptotic nuclei with increased oxidative stress. In summary, a leucine-rich diet directed Walker-256 tumour metabolism to a less glycolytic phenotype profile in which these metabolic alterations were associated with a decrease in tumour aggressiveness and reduction in the number of metastatic sites in rats fed a diet supplemented with this branched-chain amino acid.
    DOI:  https://doi.org/10.1038/s41598-019-52112-w
  16. J Nutr Sci Vitaminol (Tokyo). 2019 ;65(5): 383-389
    The Effects of BCAAs on Insulin Resistance in Athletes.
    Jian Shou, Pei-Jie Chen, Wei-Hua Xiao.
      The toxic catabolic intermediates of branched chain amino acids can cause insulin resistance, and are involved in different mechanisms in different metabolic tissues. In skeletal muscle, 3-hydroxy-isobutyrate produced by valine promotes skeletal muscle fatty acid uptake, resulting in the accumulation of incompletely oxidized lipids in skeletal muscle, causing skeletal muscle insulin resistance. In the liver, branched-chain α-keto acids decompose in large amounts, promote hepatic gluconeogenesis, and lead to the accumulation of multiple acylcarnitines, which damages the mitochondrial tricarboxylic acid cycle, resulting in the accumulation of incomplete oxidation products, oxidative stress in mitochondria, and hepatic insulin resistance. In adipose tissue, the expression of branched-chain amino acid catabolic enzymes (branched-chain amino acid transaminase, branched-chain α-keto acid dehydrogenase) is reduced, resulting in an increased level of plasma branched-chain amino acids, thereby causing massive decomposition of branched-chain amino acids in tissues such as skeletal muscle and liver, and inducing insulin resistance. However, branched-chain amino acids, as a common nutritional supplement for athletes, do not induce insulin resistance. A possible explanation for this phenomenon is that exercise can enhance the mitochondrial oxidative potential of branched-chain amino acids, alleviate or even eliminate the accumulation of branched-chain amino acid catabolic intermediates, and promotes branched-chain amino acids catabolism into beta-aminoisobutyric acid, increasing plasma beta-aminoisobutyric acid concentration, improving insulin resistance. This article reveals the mechanism of BCAA-induced insulin resistance and the relationship between exercise and BCAAs metabolism, adds a guarantee for the use of BCAAs, and provides a new explanation for the occurrence of diabetes and how exercise improves diabetes.
    Keywords:  adipose; athletes metabolism; beta-aminoisobutyric acid; exercise; liver; skeletal muscle
    DOI:  https://doi.org/10.3177/jnsv.65.383
  17. Cell Rep. 2019 Oct 29. pii: S2211-1247(19)31241-0. [Epub ahead of print]29(5): 1299-1310.e3
    Maternal Lipid Metabolism Directs Fetal Liver Programming following Nutrient Stress.
    Caitlyn E Bowman, Ebru S Selen Alpergin, Kyle Cavagnini, Danielle M Smith, Susanna Scafidi, Michael J Wolfgang.
      The extreme metabolic demands of pregnancy require coordinated metabolic adaptations between mother and fetus to balance fetal growth and maternal health with nutrient availability. To determine maternal and fetal contributions to metabolic flexibility during gestation, pregnant mice with genetic impairments in mitochondrial carbohydrate and/or lipid metabolism were subjected to nutrient deprivation. The maternal fasting response initiates a fetal liver transcriptional program marked by upregulation of lipid- and peroxisome proliferator-activated receptor alpha (Pparα)-regulated genes. Impaired maternal lipid metabolism alters circulating lipid metabolite concentrations and enhances the fetal response to fasting, which is largely dependent on fetal Pparα. Maternal fasting also improves metabolic deficits in fetal carbohydrate metabolism by increasing the availability of alternative substrates. Impairment of both carbohydrate and lipid metabolism in pregnant dams further exacerbates the fetal liver transcriptional response to nutrient deprivation. Together, these data demonstrate a regulatory role for mitochondrial macronutrient metabolism in mediating maternal-fetal metabolic communication, particularly when nutrients are limited.
    Keywords:  Cpt2; PPARα; carnitine palmitoyltransferase 2; fatty acid oxidation; metabolism; mitochondria; mitochondrial pyruvate carrier. MPC; peroxisome proliferator-activated receptor alpha; pregnancy; pyruvate
    DOI:  https://doi.org/10.1016/j.celrep.2019.09.053
  18. J Cell Mol Med. 2019 Oct 28.
    p53-dependent transcriptional suppression of BAG3 protects cells against metabolic stress via facilitation of p53 accumulation.
    Jia-Mei Wang, Bao-Qin Liu, Zhen-Xian Du, Chao Li, Jia Sun, Jing Yan, Jing-Yi Jiang, Hua-Qin Wang.
      Solid tumour frequently undergoes metabolic stress during tumour development because of inadequate blood supply and the high nutrient expenditure. p53 is activated by glucose limitation and maintains cell survival via triggering metabolic checkpoint. However, the exact downstream contributors are not completely identified. BAG3 is a cochaperone with multiple cellular functions and is implicated in metabolic reprogramming of pancreatic cancer cells. The current study demonstrated that glucose limitation transcriptionally suppressed BAG3 expression in a p53-dependent manner. Importantly, hinderance of its down-regulation compromised cellular adaptation to metabolic stress triggered by glucose insufficiency, supporting that BAG3 might be one of p53 downstream contributors for cellular adaptation to metabolic stress. Our data showed that ectopic BAG3 expression suppressed p53 accumulation via direct interaction under metabolic stress. Thereby, the current study highlights the significance of p53-mediated BAG3 suppression in cellular adaptation to metabolic stress via facilitating p53 accumulation.
    Keywords:  BAG3; glucose insufficiency; metabolic stress; p53
    DOI:  https://doi.org/10.1111/jcmm.14764
  19. Nat Commun. 2019 Oct 29. 10(1): 4914
    Structural insights of human mitofusin-2 into mitochondrial fusion and CMT2A onset.
    Yu-Jie Li, Yu-Lu Cao, Jian-Xiong Feng, Yuanbo Qi, Shuxia Meng, Jie-Feng Yang, Ya-Ting Zhong, Sisi Kang, Xiaoxue Chen, Lan Lan, Li Luo, Bing Yu, Shoudeng Chen, David C Chan, Junjie Hu, Song Gao.
      Mitofusin-2 (MFN2) is a dynamin-like GTPase that plays a central role in regulating mitochondrial fusion and cell metabolism. Mutations in MFN2 cause the neurodegenerative disease Charcot-Marie-Tooth type 2A (CMT2A). The molecular basis underlying the physiological and pathological relevance of MFN2 is unclear. Here, we present crystal structures of truncated human MFN2 in different nucleotide-loading states. Unlike other dynamin superfamily members including MFN1, MFN2 forms sustained dimers even after GTP hydrolysis via the GTPase domain (G) interface, which accounts for its high membrane-tethering efficiency. The biochemical discrepancy between human MFN2 and MFN1 largely derives from a primate-only single amino acid variance. MFN2 and MFN1 can form heterodimers via the G interface in a nucleotide-dependent manner. CMT2A-related mutations, mapping to different functional zones of MFN2, lead to changes in GTP hydrolysis and homo/hetero-association ability. Our study provides fundamental insight into how mitofusins mediate mitochondrial fusion and the ways their disruptions cause disease.
    DOI:  https://doi.org/10.1038/s41467-019-12912-0
  20. Mitochondrion. 2019 Oct 25. pii: S1567-7249(19)30103-5. [Epub ahead of print]
    Ironing the mitochondria: Relevance to its dynamics.
    Mamta Upadhyay, Saloni Agarwal.
      The mitochondrion is "jack of many trades and master of one". Despite being a master in energy generation, it plays a significant role in other cellular processes, including calcium homeostasis, cell death, and iron metabolism. Since mitochondria employ the majority of cellular iron, it plays a central role in the iron homeostasis. Iron could be a major regulator of mitochondrial dynamics as the excess of iron leads to oxidative stress, which causes a disturbance in mitochondrial dynamics. Remarkably, abnormal iron accumulation has been observed in the brain regions of the neurodegenerative disorders patients. These neurodegenerative disorders are also often associated with the abnormal mitochondrial dynamics. Here in this article, we will mainly discuss the studies focused on unravelling the role of iron in mitochondrial dynamics.
    Keywords:  Mitochondrial dynamics; iron; iron chelator; iron homeostasis; neurodegenerative disorder
    DOI:  https://doi.org/10.1016/j.mito.2019.09.007
  21. Mol Cell. 2019 Oct 18. pii: S1097-2765(19)30732-4. [Epub ahead of print]
    The NADH Dehydrogenase Nde1 Executes Cell Death after Integrating Signals from Metabolism and Proteostasis on the Mitochondrial Surface.
    SreeDivya Saladi, Felix Boos, Michael Poglitsch, Hadar Meyer, Frederik Sommer, Timo Mühlhaus, Michael Schroda, Maya Schuldiner, Frank Madeo, Johannes M Herrmann.
      The proteolytic turnover of mitochondrial proteins is poorly understood. Here, we used a combination of dynamic isotope labeling and mass spectrometry to gain a global overview of mitochondrial protein turnover in yeast cells. Intriguingly, we found an exceptionally high turnover of the NADH dehydrogenase, Nde1. This homolog of the mammalian apoptosis inducing factor, AIF, forms two distinct topomers in mitochondria, one residing in the intermembrane space while the other spans the outer membrane and is exposed to the cytosol. The surface-exposed topomer triggers cell death in response to pro-apoptotic stimuli. The surface-exposed topomer is degraded by the cytosolic proteasome/Cdc48 system and the mitochondrial protease Yme1; however, it is strongly enriched in respiratory-deficient cells. Our data suggest that in addition to their role in electron transfer, mitochondrial NADH dehydrogenases such as Nde1 or AIF integrate signals from energy metabolism and cytosolic proteostasis to eliminate compromised cells from growing populations.
    Keywords:  NADH:ubiquinone dehydrogenase; apoptosis; apoptosis-inducing factor; mitochondria; protein import; respiration
    DOI:  https://doi.org/10.1016/j.molcel.2019.09.027
  22. Cell Rep. 2019 Oct 29. pii: S2211-1247(19)31244-6. [Epub ahead of print]29(5): 1287-1298.e6
    Glutamine Anabolism Plays a Critical Role in Pancreatic Cancer by Coupling Carbon and Nitrogen Metabolism.
    Alex J Bott, Jianliang Shen, Claudia Tonelli, Le Zhan, Nithya Sivaram, Ya-Ping Jiang, Xufen Yu, Vrushank Bhatt, Eric Chiles, Hua Zhong, Sara Maimouni, Weiwei Dai, Stephani Velasquez, Ji-An Pan, Nathiya Muthalagu, Jennifer Morton, Tracy G Anthony, Hui Feng, Wouter H Lamers, Daniel J Murphy, Jessie Yanxiang Guo, Jian Jin, Howard C Crawford, Lanjing Zhang, Eileen White, Richard Z Lin, Xiaoyang Su, David A Tuveson, Wei-Xing Zong.
      Glutamine is thought to play an important role in cancer cells by being deaminated via glutaminolysis to α-ketoglutarate (aKG) to fuel the tricarboxylic acid (TCA) cycle. Supporting this notion, aKG supplementation can restore growth/survival of glutamine-deprived cells. However, pancreatic cancers are often poorly vascularized and limited in glutamine supply, in alignment with recent concerns on the significance of glutaminolysis in pancreatic cancer. Here, we show that aKG-mediated rescue of glutamine-deprived pancreatic ductal carcinoma (PDAC) cells requires glutamate ammonia ligase (GLUL), the enzyme responsible for de novo glutamine synthesis. GLUL-deficient PDAC cells are capable of the TCA cycle but defective in aKG-coupled glutamine biosynthesis and subsequent nitrogen anabolic processes. Importantly, GLUL expression is elevated in pancreatic cancer patient samples and in mouse PDAC models. GLUL ablation suppresses the development of KrasG12D-driven murine PDAC. Therefore, GLUL-mediated glutamine biosynthesis couples the TCA cycle with nitrogen anabolism and plays a critical role in PDAC.
    Keywords:  K-Ras; glutamate ammonia ligase; glutamine; glutamine synthetase; hexosamine; nitrogen metabolism; nucleotide; pancreatic cancer; α-ketoglutarate
    DOI:  https://doi.org/10.1016/j.celrep.2019.09.056
  23. J Immunol. 2019 Nov 01. pii: ji1900395. [Epub ahead of print]
    Folliculin Interacting Protein 1 Maintains Metabolic Homeostasis during B Cell Development by Modulating AMPK, mTORC1, and TFE3.
    Julita A Ramírez, Terri Iwata, Heon Park, Mark Tsang, Janella Kang, Katy Cui, Winnie Kwong, Richard G James, Masaya Baba, Laura S Schmidt, Brian M Iritani.
      Folliculin interacting protein 1 (Fnip1) is a cytoplasmic protein originally discovered through its interaction with the master metabolic sensor 5' AMP-activated protein kinase (AMPK) and Folliculin, a protein mutated in individuals with Birt-Hogg-Dubé Syndrome. In response to low energy, AMPK stimulates catabolic pathways such as autophagy to enhance energy production while inhibiting anabolic pathways regulated by the mechanistic target of rapamycin complex 1 (mTORC1). We previously found that constitutive disruption of Fnip1 in mice resulted in a lack of peripheral B cells because of a block in B cell development at the pre-B cell stage. Both AMPK and mTORC1 were activated in Fnip1-deficient B cell progenitors. In this study, we found inappropriate mTOR localization at the lysosome under nutrient-depleted conditions. Ex vivo lysine or arginine depletion resulted in increased apoptosis. Genetic inhibition of AMPK, inhibition of mTORC1, or restoration of cell viability with a Bcl-xL transgene failed to rescue B cell development in Fnip1-deficient mice. Fnip1-deficient B cell progenitors exhibited increased nuclear localization of transcription factor binding to IgHM enhancer 3 (TFE3) in developing B cells, which correlated with an increased expression of TFE3-target genes, increased lysosome numbers and function, and increased autophagic flux. These results indicate that Fnip1 modulates autophagy and energy response pathways in part through the regulation of AMPK, mTORC1, and TFE3 in B cell progenitors.
    DOI:  https://doi.org/10.4049/jimmunol.1900395
  24. Int J Mol Sci. 2019 Oct 28. pii: E5370. [Epub ahead of print]20(21):
    A Shifty Target: Tumor-Initiating Cells and Their Metabolism.
    Nicole Bezuidenhout, Maria Shoshan.
      Tumor-initiating cells (TICs), or cancer stem cells, constitute highly chemoresistant, asymmetrically dividing, and tumor-initiating populations in cancer and are thought to play a key role in metastatic and chemoresistant disease. Tumor-initiating cells are isolated from cell lines and clinical samples based on features such as sphere formation in stem cell medium and expression of TIC markers, typically a set of outer membrane proteins and certain transcription factors. Although both bulk tumor cells and TICs show an adaptive metabolic plasticity, TIC metabolism is thought to differ and likely in a tumor-specific and growth condition-dependent pattern. In the context of some common solid tumor diseases, we here review reports on how TIC isolation methods and markers associate with metabolic features, with some focus on oxidative metabolism, including fatty acid and lipid metabolism. These have emerged as significant factors in TIC phenotypes, and in tumor biology as a whole. Other sections address mitochondrial biogenesis and dynamics in TICs, and the influence of the tumor microenvironment. Further elucidation of the complex biology of TICs and their metabolism will require advanced methodologies.
    Keywords:  cancer; cellular metabolism; mitochondria; stem cell markers; tumor-initiating cells
    DOI:  https://doi.org/10.3390/ijms20215370
  25. Nat Commun. 2019 Oct 28. 10(1): 4905
    Hydralazine targets cAMP-dependent protein kinase leading to sirtuin1/5 activation and lifespan extension in C. elegans.
    Esmaeil Dehghan, Mohammad Goodarzi, Bahar Saremi, Rueyling Lin, Hamid Mirzaei.
      Therapeutic activation of mitochondrial function has been suggested as an effective strategy to combat aging. Hydralazine is an FDA-approved drug used in the treatment of hypertension, heart failure and cancer. Hydralazine has been recently shown to promote lifespan in C. elegans, rotifer and yeast through a mechanism which has remained elusive. Here we report cAMP-dependent protein kinase (PKA) as the direct target of hydralazine. Using in vitro and in vivo models, we demonstrate a mechanism in which binding and stabilization of a catalytic subunit of PKA by hydralazine lead to improved mitochondrial function and metabolic homeostasis via the SIRT1/SIRT5 axis, which underlies hydralazine's prolongevity and stress resistance benefits. Hydralazine also protects mitochondrial metabolism and function resulting in restoration of health and lifespan in C. elegans under high glucose and other stress conditions. Our data also provide new insights into the mechanism(s) that explain various other known beneficial effects of hydralazine.
    DOI:  https://doi.org/10.1038/s41467-019-12425-w
  26. JCI Insight. 2019 Oct 29. pii: 129760. [Epub ahead of print]
    Uncoupled turnover disrupts mitochondrial quality control in diabetic retinopathy.
    Jose R Hombrebueno, Lauren Cairns, Louise R Dutton, Timothy J Lyons, Derek P Brazil, Paul Moynagh, Tim M Curtis, Heping Xu.
      Mitochondrial quality control (MQC) is crucial for regulating central nervous system homeostasis and its disruption has been implicated in the pathogenesis of some of the most common neurodegenerative diseases. In healthy tissues, the maintenance of MQC depends upon an exquisite balance between mitophagy (removal of damaged mitochondria by autophagy) and biogenesis (de-novo synthesis of mitochondria). Here, we show that mitophagy is disrupted in diabetic retinopathy (DR) and decoupled from mitochondrial biogenesis during the progression of the disease. Diabetic retinas from human post-mortem donors and experimental mice exhibit a net loss of mitochondrial contents during the early stages of the disease process. Using novel diabetic mitophagy-reporter mice (mitoQC-Ins2Akita) alongside pMitoTimer (a molecular clock to address mitochondrial-age dynamics), we demonstrate that mitochondrial loss arose due to an inability of mitochondrial biogenesis to compensate for diabetes-exacerbated mitophagy. However, as diabetes duration increases, Pink1-dependent mitophagy deteriorates, leading to the build-up of mitochondria primed for degradation in DR. Impairment of mitophagy during prolonged diabetes is linked with the development of retinal senescence, a phenotype that blunted hyperglycaemia-induced mitophagy in mitoQC primary Müller cells. Our findings suggest that normalizing mitochondrial turnover may preserve MQC and provide novel therapeutic options for the management of DR-associated complications.
    Keywords:  Autophagy; Mitochondria; Neuroscience; Ophthalmology; Retinopathy
    DOI:  https://doi.org/10.1172/jci.insight.129760
  27. Science. 2019 Oct 31. pii: eaax0364. [Epub ahead of print]
    Structural mechanism of a Rag GTPase activation checkpoint by the lysosomal folliculin complex.
    Rosalie E Lawrence, Simon A Fromm, Yangxue Fu, Adam L Yokom, Do Jin Kim, Ashley M Thelen, Lindsey N Young, Chun-Yan Lim, Avi J Samelson, James H Hurley, Roberto Zoncu.
      The tumor suppressor folliculin (FLCN) enables nutrient-dependent activation of the mechanistic target of rapamycin complex 1 (mTORC1) protein kinase via its guanosine triphosphatase (GTPase) Activating Protein (GAP) activity toward the GTPase RagC. Concomitant with mTORC1 inactivation by starvation, FLCN relocalizes from the cytosol to lysosomes. To determine the lysosomal function of FLCN, we reconstituted the lysosomal FLCN complex (LFC) containing FLCN, its partner FLCN-interacting protein 2 (FNIP2), the RagAGDP:RagCGTP GTPases as they exist in the starved state with their lysosomal anchor Ragulator complex, and determined its cryo-EM structure to 3.6 Å. The RagC-GAP activity of FLCN was inhibited within LFC, due to displacement of a catalytically required Arginine in FLCN from the RagC nucleotide. Disassembly of the LFC and release of the RagC-GAP activity of FLCN enabled mTORC1-dependent regulation of the master regulator of lysosomal biogenesis, transcription factor E3, implicating the LFC as a checkpoint in mTORC1 signaling.
    DOI:  https://doi.org/10.1126/science.aax0364
  28. J Biol Chem. 2019 Nov 01. pii: jbc.RA119.010901. [Epub ahead of print]
    Multiple mitochondrial thioesterases have distinct tissue and substrate specificity, and CoA regulation, suggesting unique functional roles.
    Carmen Bekeova, Lauren Anderson-Pullinger, Kevin Boye, Felix Boos, Yana Sharpadskaya, Johannes M Herrmann, Erin L Seifert.
      Acyl-CoA thioesterases (Acots) hydrolyze fatty acyl-CoA esters. Acots in the mitochondrial matrix are poised to mitigate β-oxidation overload and maintain CoA availability. Several Acots associate with mitochondria, but whether they all localize to the matrix, are redundant, or have different roles is unresolved. Here, we compared the suborganellar localization, activity, expression, and regulation among mitochondrial Acots (Acot2, 7, 9, and 13) in mitochondria from multiple mouse tissues and from a model of Acot2 depletion. Acot7, 9, and 13 localized to the matrix, joining Acot2 that was previously shown to localize there. Mitochondria from heart, skeletal muscle, brown adipose tissue, and kidney robustly expressed Acot2, 9, and 13; Acot9 levels were substantially higher in brown adipose tissue and kidney mitochondria, as was activity for C4:0-CoA, a unique Acot9 substrate. In all tissues, Acot2 accounted for about half of the thioesterase activity for C14:0-CoA and C16:0-CoA. In contrast, liver mitochondria from fed and fasted mice expressed little Acot activity, which was confined to long-chain CoAs and due mainly to Acot7 and Acot13 activities. Matrix Acots occupied different functional niches, based on substrate specificity (Acot9 vs. Acot2 and 13) and strong CoA inhibition (Acot7, 9, and 13, but not Acot2). Interpreted in the context of β-oxidation, CoA inhibition would prevent Acot-mediated suppression of β-oxidation, while providing a release valve when CoA is limiting. In contrast, CoA-insensitive Acot2 could provide a constitutive syphon for long-chain fatty acyl-CoAs. These results reveal how the family of matrix Acots can mitigate β-oxidation overload and prevent CoA limitation.
    Keywords:  acyl-CoA thioesterase; allosteric regulation; coenzyme A (CoA); enzyme compartmentalization; fatty acid oxidation; lipid hydrolase; lipid metabolism; long-chain acyl-CoA regulation; mitochondria; mitochondrial metabolism; mouse; subcellular localization
    DOI:  https://doi.org/10.1074/jbc.RA119.010901
  29. Cell Mol Life Sci. 2019 Oct 26.
    Deletion of Voltage-Dependent Anion Channel 1 knocks mitochondria down triggering metabolic rewiring in yeast.
    Andrea Magrì, Maria Carmela Di Rosa, Ivan Orlandi, Francesca Guarino, Simona Reina, Maria Guarnaccia, Giovanna Morello, Antonio Spampinato, Sebastiano Cavallaro, Angela Messina, Marina Vai, Vito De Pinto.
      The Voltage-Dependent Anion-selective Channel (VDAC) is the pore-forming protein of mitochondrial outer membrane, allowing metabolites and ions exchanges. In Saccharomyces cerevisiae, inactivation of POR1, encoding VDAC1, produces defective growth in the presence of non-fermentable carbon source. Here, we characterized the whole-genome expression pattern of a VDAC1-null strain (Δpor1) by microarray analysis, discovering that the expression of mitochondrial genes was completely abolished, as consequence of the dramatic reduction of mtDNA. To overcome organelle dysfunction, Δpor1 cells do not activate the rescue signaling retrograde response, as ρ0 cells, and rather carry out complete metabolic rewiring. The TCA cycle works in a "branched" fashion, shunting intermediates towards mitochondrial pyruvate generation via malic enzyme, and the glycolysis-derived pyruvate is pushed towards cytosolic utilization by PDH bypass rather than the canonical mitochondrial uptake. Overall, Δpor1 cells enhance phospholipid biosynthesis, accumulate lipid droplets, increase vacuoles and cell size, overproduce and excrete inositol. Such unexpected re-arrangement of whole metabolism suggests a regulatory role of VDAC1 in cell bioenergetics.
    Keywords:  Fatty acids; Inositol; Mitochondrial DNA; PDH bypass; Porin; Retrograde signaling; Warburg effect
    DOI:  https://doi.org/10.1007/s00018-019-03342-8
  30. JCI Insight. 2019 Nov 01. pii: 127312. [Epub ahead of print]4(21):
    TFEB activation in macrophages attenuates postmyocardial infarction ventricular dysfunction independently of ATG5-mediated autophagy.
    Ali Javaheri, Geetika Bajpai, Antonino Picataggi, Smrithi Mani, Layla Foroughi, Hosannah Evie, Attila Kovacs, Carla J Weinheimer, Krzystztof Hyrc, Qingli Xiao, Andrea Ballabio, Jin-Moo Lee, Scot J Matkovich, Babak Razani, Joel D Schilling, Kory J Lavine, Abhinav Diwan.
      Lysosomes are at the epicenter of cellular processes critical for inflammasome activation in macrophages. Inflammasome activation and IL-1β secretion are implicated in myocardial infarction (MI) and resultant heart failure; however, little is known about how macrophage lysosomes regulate these processes. In mice subjected to cardiac ischemia/reperfusion (IR) injury and humans with ischemic cardiomyopathy, we observed evidence of lysosomal impairment in macrophages. Inducible macrophage-specific overexpression of transcription factor EB (TFEB), a master regulator of lysosome biogenesis (Mϕ-TFEB), attenuated postinfarction remodeling, decreased abundance of proinflammatory macrophages, and reduced levels of myocardial IL-1β compared with controls. Surprisingly, neither inflammasome suppression nor Mϕ-TFEB-mediated attenuation of postinfarction myocardial dysfunction required intact ATG5-dependent macroautophagy (hereafter termed "autophagy"). RNA-seq of flow-sorted macrophages postinfarction revealed that Mϕ-TFEB upregulated key targets involved in lysosomal lipid metabolism. Specifically, inhibition of the TFEB target, lysosomal acid lipase, in vivo abrogated the beneficial effect of Mϕ-TFEB on postinfarction ventricular function. Thus, TFEB reprograms macrophage lysosomal lipid metabolism to attenuate remodeling after IR, suggesting an alternative paradigm whereby lysosome function affects inflammation.
    Keywords:  Autophagy; Cardiology; Inflammation; Lysosomes; Macrophages
    DOI:  https://doi.org/10.1172/jci.insight.127312
  31. Sci Rep. 2019 Oct 28. 9(1): 15420
    Central metabolism of functionally heterogeneous mesenchymal stromal cells.
    Mario Barilani, Roberta Palorini, Giuseppina Votta, Roberta Piras, Giuseppe Buono, Michela Grassi, Valentina Bollati, Ferdinando Chiaradonna, Lorenza Lazzari.
      Metabolism and mitochondrial biology have gained a prominent role as determinants of stem cell fate and function. In the context of regenerative medicine, innovative parameters predictive of therapeutic efficacy could be drawn from the association of metabolic or mitochondrial parameters to different degrees of stemness and differentiation potentials. Herein, this possibility was addressed in human mesenchymal stromal/stem cells (hMSC) previously shown to differ in lifespan and telomere length. First, these hMSC were shown to possess significantly distinct proliferation rate, senescence status and differentiation capacity. More potential hMSC were associated to higher mitochondrial (mt) DNA copy number and lower mtDNA methylation. In addition, they showed higher expression levels of oxidative phosphorylation subunits. Consistently, they exhibited higher coupled oxygen consumption rate and lower transcription of glycolysis-related genes, glucose consumption and lactate production. All these data pointed at oxidative phosphorylation-based central metabolism as a feature of higher stemness-associated hMSC phenotypes. Consistently, reduction of mitochondrial activity by complex I and III inhibitors in higher stemness-associated hMSC triggered senescence. Finally, functionally higher stemness-associated hMSC showed metabolic plasticity when challenged by glucose or glutamine shortage, which mimic bioenergetics switches that hMSC must undergo after transplantation or during self-renewal and differentiation. Altogether, these results hint at metabolic and mitochondrial parameters that could be implemented to identify stem cells endowed with superior growth and differentiation potential.
    DOI:  https://doi.org/10.1038/s41598-019-51937-9
  32. Nucleic Acids Res. 2019 Nov 04. 47(19): 10267-10281
    METTL15 introduces N4-methylcytidine into human mitochondrial 12S rRNA and is required for mitoribosome biogenesis.
    Lindsey Van Haute, Alan G Hendrick, Aaron R D'Souza, Christopher A Powell, Pedro Rebelo-Guiomar, Michael E Harbour, Shujing Ding, Ian M Fearnley, Byron Andrews, Michal Minczuk.
      Post-transcriptional RNA modifications, the epitranscriptome, play important roles in modulating the functions of RNA species. Modifications of rRNA are key for ribosome production and function. Identification and characterization of enzymes involved in epitranscriptome shaping is instrumental for the elucidation of the functional roles of specific RNA modifications. Ten modified sites have been thus far identified in the mammalian mitochondrial rRNA. Enzymes responsible for two of these modifications have not been characterized. Here, we identify METTL15, show that it is the main N4-methylcytidine (m4C) methyltransferase in human cells and demonstrate that it is responsible for the methylation of position C839 in mitochondrial 12S rRNA. We show that the lack of METTL15 results in a reduction of the mitochondrial de novo protein synthesis and decreased steady-state levels of protein components of the oxidative phosphorylation system. Without functional METTL15, the assembly of the mitochondrial ribosome is decreased, with the late assembly components being unable to be incorporated efficiently into the small subunit. We speculate that m4C839 is involved in the stabilization of 12S rRNA folding, therefore facilitating the assembly of the mitochondrial small ribosomal subunits. Taken together our data show that METTL15 is a novel protein necessary for efficient translation in human mitochondria.
    DOI:  https://doi.org/10.1093/nar/gkz735
  33. Circ Res. 2019 Oct 28.
    Mitochondrial Protein Poldip2 Controls VSMC Differentiated Phenotype by O-Linked GlcNAc Transferase-Dependent Inhibition of a Ubiquitin Proteasome System.
    Felipe Paredes, Holly C Williams, Raymundo A Quintana, Alejandra San Martin.
      Rationale: The mitochondrial protein polymerase interacting protein 2 (Poldip2) is required for the activity of the tricarboxylic acid (TCA) cycle. As a consequence, Poldip2 deficiency induces metabolic reprograming with repressed mitochondrial respiration and increased glycolytic activity. Though homozygous deletion of Poldip2 is lethal, heterozygous mice are viable and show protection against aneurysm and injury-induced neointimal hyperplasia, diseases linked to loss of VSMC differentiation. Thus, we hypothesize that the metabolic reprograming induced by Poldip2 deficiency controls VSMC differentiation. Objective: To determine the role of Poldip2-mediated metabolic reprograming in phenotypic modulation of VSMC. Methods and Results: We show that Poldip2 deficiency in vascular smooth muscle in vitro and in vivo induces the expression of the serum response factor (SRF), Myocardin, and MRTFA and dramatically represses KLF4. Consequently, Poldip2-deficient VSMC and mouse aorta express high levels of contractile proteins and, more significantly, these cells do not dedifferentiate nor acquire macrophage-like characteristics when exposed to Cholesterol or PDGF. Regarding the mechanism, we found that Poldip2 deficiency upregulates the hexosamine biosynthetic pathway and OGT-mediated protein O-GlcNAcylation. Increased protein glycosylation causes the inhibition of a nuclear UPS responsible for SRF stabilization and KLF4 repression and is required for the establishment of the differentiated phenotype in Poldip2-deficient cells. Conclusions: Our data show that Poldip2 deficiency induces a highly differentiated phenotype in VSMCs through a mechanism that involves regulation of metabolism and proteostasis. Additionally, our study positions mitochondria-initiated signaling as key element of the VSMC differentiation programs that can be targeted to modulate VSMC phenotype during vascular diseases.
    Keywords:  OGT; Poldip2
    DOI:  https://doi.org/10.1161/CIRCRESAHA.119.315932
  34. Nat Rev Nephrol. 2019 Oct 31.
    NAD+ homeostasis in renal health and disease.
    Kenneth M Ralto, Eugene P Rhee, Samir M Parikh.
      The mammalian kidney relies on abundant mitochondria in the renal tubule to generate sufficient ATP to provide the energy required for constant reclamation of solutes from crude blood filtrate. The highly metabolically active cells of the renal tubule also pair their energetic needs to the regulation of diverse cellular processes, including energy generation, antioxidant responses, autophagy and mitochondrial quality control. Nicotinamide adenine dinucleotide (NAD+) is essential not only for the harvesting of energy from substrates but also for an array of regulatory reactions that determine cellular health. In acute kidney injury (AKI), substantial decreases in the levels of NAD+ impair energy generation and, ultimately, the core kidney function of selective solute transport. Conversely, augmentation of NAD+ may protect the kidney tubule against diverse acute stressors. For example, NAD+ augmentation can ameliorate experimental AKI triggered by ischaemia-reperfusion, toxic injury and systemic inflammation. NAD+-dependent maintenance of renal tubular metabolic health may also attenuate long-term profibrotic responses that could lead to chronic kidney disease. Further understanding of the genetic, environmental and nutritional factors that influence NAD+ biosynthesis and renal resilience may lead to novel approaches for the prevention and treatment of kidney disease.
    DOI:  https://doi.org/10.1038/s41581-019-0216-6
  35. Nucleic Acids Res. 2019 Nov 04. 47(19): 10072-10085
    Human mitochondrial DNA is extensively methylated in a non-CpG context.
    Vibha Patil, Cyrille Cuenin, Felicia Chung, Jesus R Rodriguez Aguilera, Nora Fernandez-Jimenez, Irati Romero-Garmendia, Jose Ramon Bilbao, Vincent Cahais, Joseph Rothwell, Zdenko Herceg.
      Mitochondrial dysfunction plays critical roles in cancer development and related therapeutic response; however, exact molecular mechanisms remain unclear. Recently, alongside the discovery of mitochondrial-specific DNA methyltransferases, global and site-specific methylation of the mitochondrial genome has been described. Investigation of any functional consequences however remains unclear and debated due to insufficient evidence of the quantitative degree and frequency of mitochondrial DNA (mtDNA) methylation. This study uses WGBS to provide the first quantitative report of mtDNA methylation at single base pair resolution. The data show that mitochondrial genomes are extensively methylated predominantly at non-CpG sites. Importantly, these methylation patterns display notable differences between normal and cancer cells. Furthermore, knockdown of DNA methyltransferase enzymes resulted in a marked global reduction of mtDNA methylation levels, indicating these enzymes may be associated with the establishment and/or maintenance of mtDNA methylation. DNMT3B knockdown cells displayed a comparatively pronounced global reduction in mtDNA methylation with concomitant increases in gene expression, suggesting a potential functional link between methylation and gene expression. Together these results demonstrate reproducible, non-random methylation patterns of mtDNA and challenge the notion that mtDNA is lowly methylated. This study discusses key differences in methodology that suggest future investigations must allow for techniques that assess both CpG and non-CpG methylation.
    DOI:  https://doi.org/10.1093/nar/gkz762
  36. iScience. 2019 Oct 11. pii: S2589-0042(19)30399-2. [Epub ahead of print]21 188-204
    MYCN-enhanced Oxidative and Glycolytic Metabolism Reveals Vulnerabilities for Targeting Neuroblastoma.
    Ganna Oliynyk, María Victoria Ruiz-Pérez, Lourdes Sainero-Alcolado, Johanna Dzieran, Hanna Zirath, Héctor Gallart-Ayala, Craig Wheelock, Henrik J Johansson, Roland Nilsson, Janne Lehtiö, Marie Arsenian-Henriksson.
      In pediatric neuroblastoma, MYCN-amplification correlates to poor clinical outcome and new treatment options are needed for these patients. Identifying the metabolic adaptations crucial for tumor progression may be a promising strategy to discover novel therapeutic targets. Here, we have combined proteomics, gene expression profiling, functional analysis, and metabolic tracing to decipher the impact of MYCN on neuroblastoma cell metabolism. We found that high MYCN levels are correlated with altered expression of proteins involved in multiple metabolic processes, including enhanced glycolysis and increased oxidative phosphorylation. Unexpectedly, we discovered that MYCN-amplified cells showed de novo glutamine synthesis. Furthermore, inhibition of β-oxidation reduced the viability of MYCN-amplified cells in vitro and decreased tumor burden in vivo, while not affecting non-MYCN-amplified tumors. Our data provide information on metabolic processes in MYCN expressing tumors, which could be exploited for the development of novel targeted therapies.
    Keywords:  Biological Sciences; Cancer; Cell Biology
    DOI:  https://doi.org/10.1016/j.isci.2019.10.020
  37. Br J Pharmacol. 2019 Oct 26.
    FOXO1 inhibition prevents renal ischemia-reperfusion injury via promotion of CREB/PGC-1α-mediated mitochondrial biogenesis.
    Di Wang, Yanqing Wang, Xiantong Zou, Yundi Shi, Qian Liu, Tianru Huyan, Jing Su, Qi Wang, Fengxue Zhang, Xuejun Li, Lu Tie.
      Background And Purpose Growing evidence indicates targeting mitochondrial dynamics and biogenesis could accelerate recovery from renal ischemia-reperfusion (I/R) injury, but the underlying mechanisms remain elusive. Transcription factor forkhead box O1 (FOXO1) is a key regulator of mitochondrial homeostasis and plays a pathologic role in the progression of renal disease. Experimental Approach A mouse model of renal I/R injury and a hypoxia/reoxygenation (H/R) injury model for human renal tubular epithelial cells (HK2s) were used. Key Results I/R injury up-regulated renal expression of FOXO1, and treatment with FOXO1-selective inhibitor AS1842856 prior to I/R injury decreased serum urea nitrogen, serum creatinine and the tubular damage score after injury. Post-I/R injury AS1842856 treatment could also ameliorate renal function and improve the survival rate of mice following injury. AS1842856 administration reduced mitochondrial mediated apoptosis, suppressed the overproduction of mitochondrial reactive oxygen species (mtROS) and accelerated recovery of ATP both in vivo and in vitro. Additionally, FOXO1 inhibition improved mitochondrial biogenesis and suppressed mitophagy. Expression of peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α), a master regulator of mitochondrial biogenesis, was down-regulated in both I/R and H/R injury, which could be abrogated by FOXO1 inhibition. Experiments using integrated bioinformatics analysis and coimmunoprecipitation established that FOXO1 inhibited PGC-1α transcription by competing with CREB for its binding to transcriptional coactivators CREBBP/EP300 (CBP/P300). Conclusion And Implications These findings suggested that FOXO1 was critical to maintain mitochondrial function in renal tubular epithelial cells and FOXO1 may serve as a therapeutic target for pharmacologic intervention in renal.
    Keywords:  FOXO1; PGC-1α; apoptosis; ischemia-reperfusion injury; mitochondria
    DOI:  https://doi.org/10.1111/bph.14878
  38. Neuro Oncol. 2019 Oct 30. pii: noz207. [Epub ahead of print]
    Metabolic Reprogramming Associated with Aggressiveness Occurs in the G-CIMP-High Molecular Subtypes of IDH1mut Lower Grade Gliomas.
    Ruiz-Rodado Victor, Tathiane M Malta, Tomohiro Seki, Adrian Lita, Tyrone Dowdy, Orieta Celiku, Alejandra Cavazos-Saldana, Aiguo Li, Yang Liu, Sue Han, Wei Zhang, Hua Song, Dionne Davis, Sunmin Lee, Jane B Trepel, Thais S Sabedot, Jeeva Munasinghe, Chunzhang Yang, Christel Herold-Mende, Mark R Gilbert, Murali Krishna Cherukuri, Houtan Noushmehr, Mioara Larion.
       BACKGROUND: Early detection of increased aggressiveness of brain tumors is a major challenge in the field of neuro-oncology because of the inability of traditional imaging to uncover it. IDH-mutant gliomas represent an ideal model system to study the molecular mechanisms associated with tumorigenicity because they appear indolent and non-glycolytic initially, but eventually a subset progresses towards secondary glioblastoma with a Warburg-like phenotype. The mechanisms and molecular features associated with this transformation are poorly understood.
    METHODS: We employed model systems for IDH1 mutant gliomas with different growth and proliferation rates in vivo and in vitro. We described the metabolome, transcriptome and epigenome of these models in order to understand the link between their metabolism and the tumor biology. To verify whether this metabolic reprogramming occurs in the clinic we analyzed TCGA data.
    RESULTS: We reveal that the aggressive glioma models have lost DNA methylation in the promoters of glycolytic enzymes, especially LDHA, and have increased mRNA and metabolite levels compared to the indolent model. We find that the acquisition of the high glycolytic phenotype occurs at the G-CIMP-high molecular subtype in patients and is associated with the worst outcome.
    CONCLUSION: We propose very early monitoring of lactate levels as a biomarker of metabolic reprogramming and tumor aggressiveness.
    Keywords:  13C-hyperpolarized MRSI; IDH1-mutant; epigenetics; glioma; metabolism
    DOI:  https://doi.org/10.1093/neuonc/noz207
  39. J Biol Chem. 2019 Oct 28. pii: jbc.RA119.010447. [Epub ahead of print]
    Promoter demethylation of the asparagine synthetase gene is required for an ATF4-dependent adaptation to asparagine depletion.
    Jie Jiang, Sankalp Srivastava, Gretchen Seim, Natalya N Pavlova, Bryan King, Lihua Zou, Chi Zhang, Minghua Zhong, Hui Feng, Reuben Kapur, Ronald C Wek, Jing Fan, Ji Zhang.
      Tumor cells adapt to nutrient-limiting environments by inducing gene expression that ensures adequate nutrients to sustain metabolic demands. For example, during amino acid limitations, ATF4 in the amino acid response induces expression of asparagine synthetase (ASNS), which provides for asparagine biosynthesis. Acute lymphoblastic leukemia (ALL) cells are sensitive to asparagine depletion, and administration of the asparagine-depletion enzyme L-asparaginase is an important therapy option. ASNS expression can counterbalance L-asparaginase treatment by mitigating nutrient stress. Therefore understanding the mechanisms regulating ASNS expression is important to define the adaptive processes underlying tumor progression and treatment. Here, we show that DNA hypermethylation at the ASNS promoter prevents its transcriptional expression following asparagine depletion. Insufficient expression of ASNS leads to asparagine deficiency, which facilitates an ATF4-independent induction of C/EBP homologous protein (CHOP) that triggers apoptosis. We conclude that chromatin accessibility is critical for ATF4 activity at the ASNS promoter, which can switch ALL cells from an ATF4-dependent adaptive response to ATF4-independent apoptosis during asparagine depletion.  This work may also help explain why ALL cells are most sensitive to L-asparaginase treatment when compared to other cancers.
    Keywords:  ATF4; CHOP; DNA methylation; acute lymphoblastic leukemia; amino acid; asparagine synthetase; cell metabolism; chromatin modification; stress response; tumor metabolism
    DOI:  https://doi.org/10.1074/jbc.RA119.010447
  40. Cell Rep. 2019 Oct 29. pii: S2211-1247(19)31238-0. [Epub ahead of print]29(5): 1261-1273.e6
    Mitochondrial Damage Causes Inflammation via cGAS-STING Signaling in Acute Kidney Injury.
    Hiroshi Maekawa, Tsuyoshi Inoue, Haruki Ouchi, Tzu-Ming Jao, Reiko Inoue, Hiroshi Nishi, Rie Fujii, Fumiyoshi Ishidate, Tetsuhiro Tanaka, Yosuke Tanaka, Nobutaka Hirokawa, Masaomi Nangaku, Reiko Inagi.
      Acute kidney injury (AKI) is characterized by mitochondrial dysfunction and activation of the innate immune system. The cyclic GMP-AMP synthase (cGAS) stimulator of interferon genes (STING) pathway detects cytosolic DNA and induces innate immunity. Here, we investigate the role of mitochondrial damage and subsequent activation of the cGAS-STING pathway using a genetically engineered animal model of cisplatin-induced AKI and cultured tubular cells. Cisplatin induced mtDNA leakage into the cytosol-probably through BCL-2-like protein 4 (BAX) pores in the mitochondrial outer membrane-in tubules, with subsequent activation of the cGAS-STING pathway, thereby triggering inflammation and AKI progression, which is improved in STING-deficient mice. STING knockdown in cultured tubular cells ameliorates inflammatory responses induced by cisplatin. mtDNA depletion and repletion studies support tubular inflammatory responses via the cGAS-STING signal activation by cytosolic mtDNA. Therefore, we conclude that mitochondrial dysfunction and subsequent activation of the mtDNA-cGAS-STING pathway is a critical regulator of kidney injury.
    Keywords:  acute kidney injury; cGAS-STING pathway; cisplatin nephrotoxicity; inflammation; mitochondrial DNA; tubular cells
    DOI:  https://doi.org/10.1016/j.celrep.2019.09.050
  41. Mult Scler Relat Disord. 2019 Oct 16. pii: S2211-0348(19)30439-0. [Epub ahead of print]37 101451
    Dimethyl fumarate therapy reduces memory T cells and the CNS migration potential in patients with multiple sclerosis.
    Rikke Holm Hansen, Helene Højsgaard Chow, Jeppe Romme Christensen, Finn Sellebjerg, Marina Rode von Essen.
       BACKGROUND: Dimethyl fumarate (DMF) is a disease-modifying therapy for patients with relapsing-remitting multiple sclerosis (RRMS). T cells are major contributors to the pathogenesis of RRMS, where they regulate the pathogenic immune response and participate in CNS lesion development.
    OBJECTIVES: In this study we evaluate the therapeutic effects of DMF on T cell subpopulations, their CNS migration potential and effector functions.
    METHODS: Blood and CSF from untreated and DMF-treated patients with RRMS and healthy donors were analyzed by flow cytometry.
    RESULTS: DMF reduced the prevalence of circulating proinflammatory CD4+ and CD8+ memory T cells, whereas regulatory T cells were unaffected. Furthermore, DMF reduced the frequency of CD4+ T cells expressing CNS-homing markers. In coherence, we found a reduced recruitment of CD4+ but not CD8+ T cells to CSF. We also found that monomethyl fumarate dampened T cell proliferation and reduced the frequency of TNF-α, IL-17 and IFN-γ producing T cells.
    CONCLUSION: DMF influences the balance between proinflammatory and regulatory T cells, presumably favoring a less proinflammatory environment. DMF also reduces the CNS migratory potential of CD4+ T cells whereas CD8+ T cells are less affected. Altogether, our study suggests an anti-inflammatory effect of DMF mainly on the CD4+ T cell compartment.
    DOI:  https://doi.org/10.1016/j.msard.2019.101451
  42. Cell. 2019 Oct 31. pii: S0092-8674(19)31121-3. [Epub ahead of print]179(4): 813-827
    Cellular Senescence: Defining a Path Forward.
    Vassilis Gorgoulis, Peter D Adams, Andrea Alimonti, Dorothy C Bennett, Oliver Bischof, Cleo Bishop, Judith Campisi, Manuel Collado, Konstantinos Evangelou, Gerardo Ferbeyre, Jesús Gil, Eiji Hara, Valery Krizhanovsky, Diana Jurk, Andrea B Maier, Masashi Narita, Laura Niedernhofer, João F Passos, Paul D Robbins, Clemens A Schmitt, John Sedivy, Konstantinos Vougas, Thomas von Zglinicki, Daohong Zhou, Manuel Serrano, Marco Demaria.
      Cellular senescence is a cell state implicated in various physiological processes and a wide spectrum of age-related diseases. Recently, interest in therapeutically targeting senescence to improve healthy aging and age-related disease, otherwise known as senotherapy, has been growing rapidly. Thus, the accurate detection of senescent cells, especially in vivo, is essential. Here, we present a consensus from the International Cell Senescence Association (ICSA), defining and discussing key cellular and molecular features of senescence and offering recommendations on how to use them as biomarkers. We also present a resource tool to facilitate the identification of genes linked with senescence, SeneQuest (available at http://Senequest.net). Lastly, we propose an algorithm to accurately assess and quantify senescence, both in cultured cells and in vivo.
    DOI:  https://doi.org/10.1016/j.cell.2019.10.005
  43. Cell Rep. 2019 Oct 29. pii: S2211-1247(19)31262-8. [Epub ahead of print]29(5): 1236-1248.e7
    Cancer-Cell-Intrinsic cGAS Expression Mediates Tumor Immunogenicity.
    Linda Schadt, Colin Sparano, Nicole Angelika Schweiger, Karina Silina, Virginia Cecconi, Giulia Lucchiari, Hideo Yagita, Emilien Guggisberg, Sascha Saba, Zuzana Nascakova, Winfried Barchet, Maries van den Broek.
      Sensing of cytoplasmic DNA by cyclic guanosine monophosphate-adenosine monophosphate (cGAMP) synthase (cGAS) results in production of the dinucleotide cGAMP and consecutive activation of stimulator of interferon genes (STING) followed by production of type I interferon (IFN). Although cancer cells contain supra-normal concentrations of cytoplasmic DNA, they rarely produce type I IFN spontaneously. This suggests that defects in the DNA-sensing pathway may serve as an immune escape mechanism. We find that cancer cells produce cGAMP that is transferred via gap junctions to tumor-associated dendritic cells (DCs) and macrophages, which respond by producing type I IFN in situ. Cancer-cell-intrinsic expression of cGAS, but not STING, promotes infiltration by effector CD8+ T cells and consequently results in prolonged survival. Furthermore, cGAS-expressing cancers respond better to genotoxic treatments and immunotherapy. Thus, cancer-cell-derived cGAMP is crucial to protective anti-tumor CD8+ T cell immunity. Consequently, cancer-cell-intrinsic expression of cGAS determines tumor immunogenicity and makes tumors hot. These findings are relevant for genotoxic and immune therapies for cancer.
    Keywords:  CD8(+) T cells; STING; cGAMP; cGAS; cancer; chemotherapy; gap junctions; immunotherapy; radiotherapy; type I IFN
    DOI:  https://doi.org/10.1016/j.celrep.2019.09.065
  44. Nat Metab. 2019 May;1(5): 532-545
    Branched chain amino acids impact health and lifespan indirectly via amino acid balance and appetite control.
    Samantha M Solon-Biet, Victoria C Cogger, Tamara Pulpitel, Devin Wahl, Ximonie Clark, Elena Bagley, Gabrielle C Gregoriou, Alistair M Senior, Qiao-Ping Wang, Amanda E Brandon, Ruth Perks, John O'Sullivan, Yen Chin Koay, Kim Bell-Anderson, Melkam Kebede, Belinda Yau, Clare Atkinson, Gunbjorg Svineng, Timothy Dodgson, Jibran A Wali, Matthew D W Piper, Paula Juricic, Linda Partridge, Adam J Rose, David Raubenheimer, Gregory J Cooney, David G Le Couteur, Stephen J Simpson.
      Elevated branched chain amino acids (BCAAs) are associated with obesity and insulin resistance. How long-term dietary BCAAs impact late-life health and lifespan is unknown. Here, we show that when dietary BCAAs are varied against a fixed, isocaloric macronutrient background, long-term exposure to high BCAA diets leads to hyperphagia, obesity and reduced lifespan. These effects are not due to elevated BCAA per se or hepatic mTOR activation, but rather due to a shift in the relative quantity of dietary BCAAs and other AAs, notably tryptophan and threonine. Increasing the ratio of BCAAs to these AAs resulted in hyperphagia and is associated with central serotonin depletion. Preventing hyperphagia by calorie restriction or pair-feeding averts the health costs of a high BCAA diet. Our data highlight a role for amino acid quality in energy balance and show that health costs of chronic high BCAA intakes need not be due to intrinsic toxicity but, rather, a consequence of hyperphagia driven by AA imbalance.
    Keywords:  Nutrition; aging; appetite; branched chain amino acids; dietary balance; dietary restriction; lifespan; metabolic health; obesity; serotonin
    DOI:  https://doi.org/10.1038/s42255-019-0059-2
  45. Elife. 2019 Oct 30. pii: e50663. [Epub ahead of print]8
    Lactate-mediated epigenetic reprogramming regulates formation of human pancreatic cancer-associated fibroblasts.
    Tushar D Bhagat, Dagny Von Ahrens, Meelad Dawlaty, Yiyu Zou, Joelle Baddour, Abhinav Achreja, Hongyun Zhao, Lifeng Yang, Brijesh Patel, Changsoo Kwak, Gaurav S Choudhary, Shanisha Gordon-Mitchell, Srinivas Aluri, Sanchari Bhattacharyya, Srabani Sahu, Yiting Yu, Matthias Bartenstein, Orsi Giricz, Masako Suzuki, Davendra Sohal, Sonal Gupta, Paola A Guerrero, Surinder Batra, Michael Goggins, Ulrich Steidl, John Greally, Beamon Agarwal, Kith Pradhan, Debabrata Banerjee, Deepak Nagrath, Anirban Maitra, Amit Verma.
      Even though pancreatic ductal adenocarcinoma (PDAC) is associated with fibrotic stroma, the molecular pathways regulating the formation of cancer associated fibroblasts (CAFs) are not well elucidated. An epigenomic analysis of patient-derived and de-novo generated CAFs demonstrated widespread loss of cytosine methylation that was associated with overexpression of various inflammatory transcripts including CXCR4. Co-culture of neoplastic cells with CAFs led to increased invasiveness that was abrogated by inhibition of CXCR4. Metabolite tracing revealed that lactate produced by neoplastic cells leads to increased production of alpha-ketoglutarate (aKG) within mesenchymal stem cells (MSCs). In turn, aKG mediated activation of the demethylase TET enzyme led to decreased cytosine methylation and increased hydroxymethylation during de novo differentiation of MSCs to CAF. Co-injection of neoplastic cells with TET-deficient MSCs inhibited tumor growth in vivo. Thus, in PDAC, a tumor-mediated lactate flux is associated with widespread epigenomic reprogramming that is seen during CAF formation.
    Keywords:  cancer biology; mouse
    DOI:  https://doi.org/10.7554/eLife.50663
  46. Mol Cell Proteomics. 2019 Oct 30. pii: mcp.RA119.001784. [Epub ahead of print]
    The mitochondrial acyl-carrier protein interaction network highlights important roles for LYRM family members in complex I and mitoribosome assembly.
    Marris G Dibley, Luke E Formosa, Baobei Lyu, Boris Reljic, Dylan McGann, Linden Muellner-Wong, Felix Kraus, Alice J Sharpe, David A Stroud, Michael T Ryan.
      NDUFAB1 is the mitochondrial acyl carrier protein (ACP) essential for cell viability. Through its pantetheine-4'-phosphate post-translational modification, NDUFAB1 interacts with members of the leucine-tyrosine-arginine motif (LYRM) protein family. Although a number of LYRM proteins have been described to participate in a variety of defined processes, the functions of others remain either partially or entirely unknown. We profiled the interaction network of NDUFAB1 to reveal associations with 9 known LYRM proteins as well as more than 20 other proteins involved in mitochondrial respiratory chain complex and mitochondrial ribosome assembly. Subsequent knockout and interaction network studies in human cells revealed the LYRM member AltMiD51 to be important for optimal assembly of the large mitoribosome subunit, consistent with recent structural studies. In addition, we used proteomics coupled with topographical heat-mapping to reveal that knockout of LYRM2 impairs assembly of the NADH-dehydrogenase module of complex I, leading to defects in cellular respiration. Together, this work adds to the catalogue of functions executed by LYRM family of proteins in building mitochondrial complexes and emphasises the common and essential role of NDUFAB1 as a protagonist in mitochondrial metabolism.
    Keywords:  Acyl-Carrier Protein; Affinity proteomics; Blue Native Polyacrylamide Gel Electrophoresis; Complex I; Mitochondria function or biology; Protein complex analysis; Protein structure*; Protein-Protein Interactions*
    DOI:  https://doi.org/10.1074/mcp.RA119.001784
  47. Mol Cell. 2019 Oct 23. pii: S1097-2765(19)30734-8. [Epub ahead of print]
    Recognition of Histone Crotonylation by Taf14 Links Metabolic State to Gene Expression.
    Graeme J Gowans, Joseph B Bridgers, Jibo Zhang, Raghuvar Dronamraju, Anthony Burnetti, Devin A King, Aline V Thiengmany, Stephen A Shinsky, Natarajan V Bhanu, Benjamin A Garcia, Nicolas E Buchler, Brian D Strahl, Ashby J Morrison.
      Metabolic signaling to chromatin often underlies how adaptive transcriptional responses are controlled. While intermediary metabolites serve as co-factors for histone-modifying enzymes during metabolic flux, how these modifications contribute to transcriptional responses is poorly understood. Here, we utilize the highly synchronized yeast metabolic cycle (YMC) and find that fatty acid β-oxidation genes are periodically expressed coincident with the β-oxidation byproduct histone crotonylation. Specifically, we found that H3K9 crotonylation peaks when H3K9 acetylation declines and energy resources become limited. During this metabolic state, pro-growth gene expression is dampened; however, mutation of the Taf14 YEATS domain, a H3K9 crotonylation reader, results in de-repression of these genes. Conversely, exogenous addition of crotonic acid results in increased histone crotonylation, constitutive repression of pro-growth genes, and disrupted YMC oscillations. Together, our findings expose an unexpected link between metabolic flux and transcription and demonstrate that histone crotonylation and Taf14 participate in the repression of energy-demanding gene expression.
    DOI:  https://doi.org/10.1016/j.molcel.2019.09.029
  48. Semin Cell Dev Biol. 2019 Oct 24. pii: S1084-9521(19)30265-4. [Epub ahead of print]
    Mitochondrial metabolic alterations in cancer cells and related therapeutic targets.
    Chiara Riganti, Massimo Donadelli.
      
    DOI:  https://doi.org/10.1016/j.semcdb.2019.10.005
  49. Nutr Metab Cardiovasc Dis. 2019 Aug 31. pii: S0939-4753(19)30332-1. [Epub ahead of print]
    Circulating glutamate level as a potential biomarker for abdominal obesity and metabolic risk.
    Ina Maltais-Payette, Benedicte Allam-Ndoul, Louis Pérusse, Marie-Claude Vohl, André Tchernof.
       BACKGROUND AND AIM: Circulating level of glutamate, a by-product of the catabolism of branched-chain amino acids, has been positively correlated with visceral adipose tissue accumulation and waist circumference (WC). The aim of the present study was to assess the potential of using glutamate level to identify individuals with abdominal obesity and a high cardiometabolic risk.
    METHODS AND RESULTS: The study sample included 99 men and 99 women. Fasting serum glutamate was measured using the Biocrates p180 kit. Anthropometric and metabolic variables were used to identify individuals with abdominal obesity (WC ≥ 95 cm in both sexes), the hypertriglyceridemic waist (HTW) phenotype and the metabolic syndrome (MetS). Mean (±SD) age was 34.1 ± 10.1 years, mean BMI was 29.0 ± 6.2 kg/m2 and mean WC was 92.7 ± 16.5 cm. Glutamate was strongly correlated with WC (r = 0.66 for men; r = 0.76 for women, both p < 0.0001) and multiple markers of metabolic dysfunction, particularly fasting triglyceride level (r = 0.59 for men; r = 0.57 for women, both p < 0.0001), HDL-cholesterol level (r = -0.45, p < 0.0001 in both sexes) and the HOMA-IR index (r = 0.65 for men; r = 0.60 for women, both p < 0.0001). Logistic regressions showed that glutamate had an excellent accuracy to identify individuals with abdominal obesity (ROC_AUC: 0.90 for both sexes), a good accuracy to identify those with the HTW phenotype (ROC_AUC: 0.82 for men; 0.85 for women) and fair-to-good accuracy for the MetS (ROC_AUC: 0.78 for men; 0.89 for women).
    CONCLUSION: Glutamate level may represent an interesting potential biomarker of abdominal obesity and metabolic risk.
    Keywords:  Branched-chain amino acid; Glutamate; Hypertriglyceridemic waist; Men; Metabolic syndrome; Metabolomics; Women
    DOI:  https://doi.org/10.1016/j.numecd.2019.08.015
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