bims-camemi 2018-12-02 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2018‒12‒02
35 papers selected by
Christian Frezza,

Macrophage de novo NAD+ synthesis specifies immune function in aging and inflammation.
Dissection of metabolic reprogramming in polycystic kidney disease reveals coordinated rewiring of bioenergetic pathways.
Suppression of mTORC1 activity in senescent Ras-transformed cells neither restores autophagy nor abrogates apoptotic death caused by inhibition of MEK/ERK kinases.
Mitochondria are a Substrate of Cellular Memory.
Mitochondrial Iron in Human Health and Disease.
Therapeutic effects of melatonin on cerebral ischemia reperfusion injury: Role of Yap-OPA1 signaling pathway and mitochondrial fusion.
Probing Mitochondrial Permeability Transition Pore Activity in Nucleated Cells and Platelets by High-Throughput Screening Assays Suggests Involvement of Protein Phosphatase 2B in Mitochondrial Dynamics.
Mitochondrial quality control in the cardiac system: An integrative view.
Combination of Coenzyme Q10 Intake and Moderate Physical Activity Counteracts Mitochondrial Dysfunctions in a SAMP8 Mouse Model.
Cyclin B1/CDK1-regulated mitochondrial bioenergetics in cell cycle progression and tumor resistance.
Mitochondrial ATP production provides long-range control of endothelial inositol trisphosphate-evoked calcium signaling.
Multiphoton imaging reveals axial differences in metabolic autofluorescence signals along the kidney proximal tubule.
Translating the Game: Ribosomes as Active Players.
Metabolic regulation of infection and inflammation.
MFF-dependent mitochondrial fission regulates presynaptic release and axon branching by limiting axonal mitochondria size.
PD-linked CHCHD2 mutations impair CHCHD10 and MICOS complex leading to mitochondria dysfunction.
The Mitochondrial Apoptotic Effectors BAX/BAK Activate Caspase-3 and -7 to Trigger NLRP3 Inflammasome and Caspase-8 Driven IL-1β Activation.
Dynamic Phosphorylation of the C Terminus of Hsp70 Regulates the Mitochondrial Import of SOD2 and Redox Balance.
Inflammasome-Independent Role of NLRP3 Mediates Mitochondrial Regulation in Renal Injury.
Cellular Metabolism in Lung Health and Disease.
Tissue-specific kinase expression and activity regulates flux through the pyruvate dehydrogenase complex.
BAX/BAK-Induced Apoptosis Results in Caspase-8-Dependent IL-1β Maturation in Macrophages.
The ERK and JNK pathways in the regulation of metabolic reprogramming.
Mouse Idh3a mutations cause retinal degeneration and reduced mitochondrial function.
Exercise inhibits tumor growth and central carbon metabolism in patient-derived xenograft models of colorectal cancer.
Lactate: A Metabolic Driver in the Tumour Landscape.
IKKβ activates p53 to promote cancer cell adaptation to glutamine deprivation.
Branched Chain Amino Acids.
Measurement of Metabolite Changes in Senescent Cells by Mass Spectrometry.
A CD4+ T cell population expanded in lupus blood provides B cell help through interleukin-10 and succinate.
Dystrophinopathy associated dysfunction of Krebs cycle metabolism.
Metabolic control of PPAR activity by aldehyde dehydrogenase regulates invasive cell behavior and predicts survival in hepatocellular and renal clear cell carcinoma.
Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate.
A New Mechanism for High-Affinity Uptake of C4-Dicarboxylates in Bacteria Revealed by the Structure of Rhodopseudomonas palustris MatC (RPA3494), a Periplasmic Binding-Protein of the Tripartite Tricarboxylate Transporter (TTT) Family.
Effect of dimethyl fumarate on neuroinflammation and apoptosis in PTZ kindling model in rats.

Nat Immunol. 2018 Nov 26.

Macrophage de novo NAD+ synthesis specifies immune function in aging and inflammation.

Paras S Minhas, Ling Liu, Peter K Moon, Amit U Joshi, Christopher Dove, Siddhita Mhatre, Kevin Contrepois, Qian Wang, Brittany A Lee, Michael Coronado, Daniel Bernstein, Michael P Snyder, Marie Migaud, Ravindra Majeti, Daria Mochly-Rosen, Joshua D Rabinowitz, Katrin I Andreasson.

Recent advances highlight a pivotal role for cellular metabolism in programming immune responses. Here, we demonstrate that cell-autonomous generation of nicotinamide adenine dinucleotide (NAD+) via the kynurenine pathway (KP) regulates macrophage immune function in aging and inflammation. Isotope tracer studies revealed that macrophage NAD+ derives substantially from KP metabolism of tryptophan. Genetic or pharmacological blockade of de novo NAD+ synthesis depleted NAD+, suppressed mitochondrial NAD+-dependent signaling and respiration, and impaired phagocytosis and resolution of inflammation. Innate immune challenge triggered upstream KP activation but paradoxically suppressed cell-autonomous NAD+ synthesis by limiting the conversion of downstream quinolinate to NAD+, a profile recapitulated in aging macrophages. Increasing de novo NAD+ generation in immune-challenged or aged macrophages restored oxidative phosphorylation and homeostatic immune responses. Thus, KP-derived NAD+ operates as a metabolic switch to specify macrophage effector responses. Breakdown of de novo NAD+ synthesis may underlie declining NAD+ levels and rising innate immune dysfunction in aging and age-associated diseases.

DOI: https://doi.org/10.1038/s41590-018-0255-3
Commun Biol. 2018 ;1 194

Dissection of metabolic reprogramming in polycystic kidney disease reveals coordinated rewiring of bioenergetic pathways.

Christine Podrini, Isaline Rowe, Roberto Pagliarini, Ana S H Costa, Marco Chiaravalli, Ivano Di Meo, Hyunho Kim, Gianfranco Distefano, Valeria Tiranti, Feng Qian, Diego di Bernardo, Christian Frezza, Alessandra Boletta.

Autosomal Dominant Polycystic Kidney Disease (ADPKD) is a genetic disorder caused by loss-of-function mutations in PKD1 or PKD2. Increased glycolysis is a prominent feature of the disease, but how it impacts on other metabolic pathways is unknown. Here, we present an analysis of mouse Pkd1 mutant cells and kidneys to investigate the metabolic reprogramming of this pathology. We show that loss of Pkd1 leads to profound metabolic changes that affect glycolysis, mitochondrial metabolism, and fatty acid synthesis (FAS). We find that Pkd1-mutant cells preferentially use glutamine to fuel the TCA cycle and to sustain FAS. Interfering with either glutamine uptake or FAS retards cell growth and survival. We also find that glutamine is diverted to asparagine via asparagine synthetase (ASNS). Transcriptional profiling of PKD1-mutant human kidneys confirmed these alterations. We find that silencing of Asns is lethal in Pkd1-mutant cells when combined with glucose deprivation, suggesting therapeutic approaches for ADPKD.

DOI: https://doi.org/10.1038/s42003-018-0200-x
Aging (Albany NY). 2018 Nov 27.

Suppression of mTORC1 activity in senescent Ras-transformed cells neither restores autophagy nor abrogates apoptotic death caused by inhibition of MEK/ERK kinases.

Elena Y Kochetkova, Galina I Blinova, Olga A Bystrova, Marina G Martynova, Valeriy A Pospelov, Tatiana V Pospelova.

  Autophagy is conservative catabolic process that degrades organelles, in particular, mitochondria, and misfolded proteins within the lysosomes, thus maintaining cellular viability. Despite the close relationship between mitochondrial dysfunction and cellular senescence, it is unclear how mitochondria damage can induce autophagy in senescent cells. We show that MEK/ERK suppression induces mitochondria damage followed by apoptosis of senescent Ras-expressing cells. To understand the role of persistent mTORC1 signaling in breaking the cAMPK-induced autophagy caused by mitochondrial damage, we inhibited mTORС1 with low concentrations of pp242. mTORC1 suppression neither restores the AMPK-induced autophagy nor decreases the level of apoptosis upon MEK/ERK inhibition. We discovered the existence of an alternative autophagy-like way that partially increases the viability of senescent cells under suppressed mTORC1. The pp242-treated cells survive due to formation of the non-autophagous LC3-negative vacuoles, which contain the damaged mitochondria and lysosomes with the following excretion the content from the cell. MEK/ERK activity is required to implement this process in senescent cells. Senescent cells exhibit distinctive spatial distribution of organelles and proteins that provides uncoupling of final participants of autophagy. We show that this feature stops the process of cytoprotective autophagy in response to MEK/ERK suppression, thus allowing selective elimination of senescent Ras-expressing cells.

Keywords:  MEK/ERK; autophagy; kinase inhibitors; lysosomes; mTOR; mitochondria damage; senescence

DOI:  https://doi.org/10.18632/aging.101686
Free Radic Biol Med. 2018 Nov 22. pii: S0891-5849(18)31624-1. [Epub ahead of print]

Mitochondria are a Substrate of Cellular Memory.

Amin Cheikhi, Callen Wallace, Claudette St Croix, Charles Cohen, Wan-Yee Tang, Peter Wipf, Panayiotis V Benos, Fabrisia Ambrosio, Aaron Barchowsky.

  Cellular memory underlies cellular identity, and thus constitutes a unifying mechanism of genetic disposition, environmental influences, and cellular adaptation. Here, we demonstrate that enduring physicochemical changes of mitochondrial networks invoked by transient stress, a phenomenon we term 'mitoengrams', underlie the transgenerational persistence of epigenetically scripted cellular behavior. Using C2C12 myogenic stem-like cells, we show that stress memory elicited by transient, low-level arsenite exposure is stored within a self-renewing subpopulation of progeny cells in a mitochondrial-dependent fashion. Importantly, we demonstrate that erasure of mitoengrams by administration of mitochondria-targeted electron scavenger was sufficient to reset key epigenetic marks of cellular memory and redirect the identity of the mitoengram-harboring progeny cells to a non-stress-like state. Together, our findings indicate that mnemonic information emanating from mitochondria support the balance between the persistence and transience of cellular memory.

Keywords:  XJB-5–131; arsenic; cellular memory; epigenetics; mitochondria

DOI:  https://doi.org/10.1016/j.freeradbiomed.2018.11.028
Annu Rev Physiol. 2018 Nov 28.

Mitochondrial Iron in Human Health and Disease.

Diane M Ward, Suzanne M Cloonan.

Mitochondria are an iconic distinguishing feature of eukaryotic cells. Mitochondria encompass an active organellar network that fuses, divides, and directs a myriad of vital biological functions, including energy metabolism, cell death regulation, and innate immune signaling in different tissues. Another crucial and often underappreciated function of these dynamic organelles is their central role in the metabolism of the most abundant and biologically versatile transition metals in mammalian cells, iron. In recent years, cellular and animal models of mitochondrial iron dysfunction have provided vital information in identifying new proteins that have elucidated the pathways involved in mitochondrial homeostasis and iron metabolism. Specific signatures of mitochondrial iron dysregulation that are associated with disease pathogenesis and/or progression are becoming increasingly important. Understanding the molecular mechanisms regulating mitochondrial iron pathways will help better define the role of this important metal in mitochondrial function and in human health and disease. Expected final online publication date for the Annual Review of Physiology Volume 81 is February 10, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI: https://doi.org/10.1146/annurev-physiol-020518-114742
Biomed Pharmacother. 2018 Nov 23. pii: S0753-3322(18)36980-4. [Epub ahead of print]110 203-212

Therapeutic effects of melatonin on cerebral ischemia reperfusion injury: Role of Yap-OPA1 signaling pathway and mitochondrial fusion.

Na Wei, Yuehua Pu, Zhonghua Yang, Yuesong Pan, Liping Liu.

  The role of OPA1-related mitochondrial fusion in brain reperfusion stress has remained elusive. The aim of our study is to explore whether melatonin alleviates cerebral IR injury by modulating OPA1-related mitochondrial fusion. We found that melatonin reduced infarct area and suppressed neuron death during reperfusion stress. Biological studies have revealed that IR-inhibited mitochondrial fusion was largely reversed by melatonin via upregulated OPA1 expression. Knocking down OPA1 abrogated the protective effects of melatonin on mitochondrial energy metabolism and mitochondrial apoptosis. In addition, we also found that melatonin modified OPA1 expression via the Yap-Hippo pathway; blockade of the Yap-Hippo pathway induced neuron death and mitochondrial damage despite treatment with melatonin. Altogether, our data demonstrated that cerebral IR injury is closely associated with defective OPA1-related mitochondrial fusion. Melatonin supplementation enhances OPA1-related mitochondrial fusion by activating the Yap-Hippo pathway, ultimately reducing brain reperfusion stress.

Keywords:  Melatonin; Mitochondrial fusion; OPA1; Reperfusion stress; Yap-Hippo pathway

DOI:  https://doi.org/10.1016/j.biopha.2018.11.060
Assay Drug Dev Technol. 2018 Nov 27.

Probing Mitochondrial Permeability Transition Pore Activity in Nucleated Cells and Platelets by High-Throughput Screening Assays Suggests Involvement of Protein Phosphatase 2B in Mitochondrial Dynamics.

Mao Xiang Chen, Emma Ward, Matilde Caivano, Sandy Toh, Kirsten Searle, Sumitra Ramachandran, Yannick Lacroix, Mahmood Ahmed, A Richard Rutter.

  Mitochondrial permeability transition pore (mPTP) formation is well documented in isolated mitochondria. However, convincing detection of mPTP in whole cells remains elusive. In this study, we describe a high-throughput assay for Ca2+-activated mPTP opening in platelets using HyperCyt flow cytometry. In addition, we demonstrate that in several nucleated cells, using multiple approaches, the detection of cyclophilin D-dependent mPTP opening is highly challenging. Results with the mitochondrial-targeted Ca2+-sensing green fluorescent protein (mito-Case12) suggest the involvement of protein phosphatase 2B (PP2B; calcineurin) in regulating mitochondrial dynamics. Our results highlight the danger of relying on cyclosporine A alone as a pharmacological tool, and the need for comprehensive studies of mPTP in the cell.

Keywords:  Case12; PP2B; calcineurin; calcium; cyclosporine A; mitochondria permeability transition pore; platelet

DOI:  https://doi.org/10.1089/adt.2018.872
Biochim Biophys Acta Mol Basis Dis. 2018 Nov 22. pii: S0925-4439(18)30480-0. [Epub ahead of print]

Mitochondrial quality control in the cardiac system: An integrative view.

Virgilio J J Cadete, Goutham Vasam, Keir J Menzies, Yan Burelle.

  Recent studies have led to the discovery of multiple mitochondrial quality control (mQC) processes that operate at various scales, ranging from the degradation of proteins by mitochondrial proteases to the degradation of selected cargos or entire organelles in lysosomes. While the mechanisms governing these mQC processes are progressively being delineated, their role and importance remain unclear. Converging evidence however point to a complex system whereby multiple and partly overlapping processes are recruited to orchestrate a cell type specific mQC response that is adapted to the physiological state and level of stress encountered. Knowledge gained from basic model systems of mQC therefore need to be integrated within organ-specific (patho)physiological frameworks. Building on this notion, this article focuses on mQC in the heart, where developmental metabolic reprogramming, sustained contraction, and multiple pathophysiological conditions pose broadly different constraints. We provide an overview of current knowledge of mQC processes, and discuss their implication in cardiac mQC under normal and diseased conditions.

Keywords:  Cardiac physiology and pathophysiology; Mitochondria; Mitochondrial Quality control; Mitochondrial proteases; Mitochondrial-derived vesicles; Mitophagy

DOI:  https://doi.org/10.1016/j.bbadis.2018.11.018
Oxid Med Cell Longev. 2018 ;2018 8936251

Combination of Coenzyme Q10 Intake and Moderate Physical Activity Counteracts Mitochondrial Dysfunctions in a SAMP8 Mouse Model.

C Andreani, C Bartolacci, M Guescini, M Battistelli, V Stocchi, F Orlando, M Provinciali, A Amici, C Marchini, L Tiano, P Orlando, S Silvestri.

Aging skeletal muscles are characterized by a progressive decline in muscle mass and muscular strength. Such muscular dysfunctions are usually associated with structural and functional alterations of skeletal muscle mitochondria. The senescence-accelerated mouse-prone 8 (SAMP8) model, characterized by premature aging and high degree of oxidative stress, was used to investigate whether a combined intervention with mild physical exercise and ubiquinol supplementation was able to improve mitochondrial function and preserve skeletal muscle health during aging. 5-month-old SAMP8 mice, in a presarcopenia phase, have been randomly divided into 4 groups (n = 10): untreated controls and mice treated for two months with either physical exercise (0.5 km/h, on a 5% inclination, for 30 min, 5/7 days per week), ubiquinol 10 (500 mg/kg/day), or a combination of exercise and ubiquinol. Two months of physical exercise significantly increased mitochondrial damage in the muscles of exercised mice when compared to controls. On the contrary, ubiquinol and physical exercise combination significantly improved the overall status of the skeletal muscle, preserving mitochondrial ultrastructure and limiting mitochondrial depolarization induced by physical exercise alone. Accordingly, combination treatment while promoting mitochondrial biogenesis lowered autophagy and caspase 3-dependent apoptosis. In conclusion, the present study shows that ubiquinol supplementation counteracts the deleterious effects of physical exercise-derived ROS improving mitochondrial functionality in an oxidative stress model, such as SAMP8 in the presarcopenia phase.

DOI: https://doi.org/10.1155/2018/8936251
Cancer Lett. 2018 Nov 24. pii: S0304-3835(18)30685-2. [Epub ahead of print]

Cyclin B1/CDK1-regulated mitochondrial bioenergetics in cell cycle progression and tumor resistance.

Bowen Xie, Shuangyan Wang, Nian Jiang, Jian Jian Li.

  A mammalian cell houses two genomes located separately in the nucleus and mitochondria. During evolution, communications and adaptations between these two genomes occur extensively to achieve and sustain homeostasis for cellular functions and regeneration. Mitochondria provide the major cellular energy and contribute to gene regulation in the nucleus, whereas more than 98% of mitochondrial proteins are encoded by the nuclear genome. Such two-way signaling traffic presents an orchestrated dynamic between energy metabolism and consumption in cells. Recent reports have elucidated the way how mitochondrial bioenergetics synchronizes with the energy consumption for cell cycle progression mediated by cyclin B1/CDK1 as the communicator. This review is to recapitulate cyclin B1/CDK1 mediated mitochondrial activities in cell cycle progression and stress response as well as its potential link to reprogram energy metabolism in tumor adaptive resistance. Cyclin B1/CDK1-mediated mitochondrial bioenergetics is applied as an example to show how mitochondria could timely sense the cellular fuel demand and then coordinate ATP output. Such nucleus-mitochondria oscillation may play key roles in the flexible bioenergetics required for tumor cell survival and compromising the efficacy of anti-cancer therapy. Further deciphering the cyclin B1/CDK1-controlled mitochondrial metabolism may invent effect targets to treat resistant cancers.

Keywords:  CDK; cell cycle; metabolism; mitochondria; tumor resistance

DOI:  https://doi.org/10.1016/j.canlet.2018.11.019
J Biol Chem. 2018 Nov 29. pii: jbc.RA118.005913. [Epub ahead of print]

Mitochondrial ATP production provides long-range control of endothelial inositol trisphosphate-evoked calcium signaling.

Calum Wilson, Matthew D Lee, Helen Heathcote, Xun Zhang, Charlotte Buckley, John M Girkin, Christopher D Saunter, John G McCarron.

  Endothelial cells are reported to be glycolytic and to minimally rely on mitochondria for ATP generation. Rather than providing energy, mitochondria in endothelial cells may act as signaling organelles that control cytosolic Ca2+ signaling or modify reactive oxygen species (ROS). To control Ca2+ signaling, these organelles are often observed close to influx and release sites and may be tethered near Ca2+ transporters. In this study, we used high-resolution, wide-field fluorescence imaging to investigate the regulation of Ca2+ signaling by mitochondria in large numbers of endothelial cells (~50 per field) in intact arteries from rats. We observed that mitochondria were mostly spherical or form short rod structures and were distributed widely throughout the cytoplasm. The density of these organelles did not increase near contact sites with smooth muscle cells. However, local inositol trisphosphate (IP3)-mediated Ca2+ signaling predominated near these contact sites and required polarized mitochondria. Of note, mitochondrial control of Ca2+ signals occurred even when mitochondria were far from Ca2+ release sites. Indeed, the endothelial mitochondria were mobile and moved throughout the cytoplasm. Mitochondrial control of Ca2+ signaling was mediated by ATP production, which, when reduced by mitochondrial depolarization or ATP synthase inhibition, eliminated local IP3-mediated Ca2+ release events. ROS buffering did not significantly alter local Ca2+ release events. These results highlight the importance of mitochondrial ATP production in providing long-range control of endothelial signaling via IP3-evoked local Ca2+ release in intact endothelium.

Keywords:  calcium imaging; cell signaling; endoplasmic reticulum (ER); endothelial cell; fluorescence imaging; inositol 1,4,5-trisphosphate (IP3); inositol trisphosphate; mesenteric artery; mitochondria; reactive oxygen species (ROS)

DOI:  https://doi.org/10.1074/jbc.RA118.005913
Am J Physiol Renal Physiol. 2018 Dec 01. 315(6): F1613-F1625

Multiphoton imaging reveals axial differences in metabolic autofluorescence signals along the kidney proximal tubule.

Milica Bugarski, Joana Raquel Martins, Dominik Haenni, Andrew M Hall.

  Kidney proximal tubules (PTs) are densely packed with mitochondria, and defects in mitochondrial function are implicated in many kidney diseases. However, little is known about intrinsic mitochondrial function within PT cells. Here, using intravital multiphoton microscopy and live slices of mouse kidney cortex, we show that autofluorescence signals provide important functional readouts of redox state and substrate metabolism and that there are striking axial differences in signals along the PT. Mitochondrial NAD(P)H intensity was similar in both PT segment (S)1 and S2 and was sensitive to changes in respiratory chain (RC) redox state, whereas cytosolic NAD(P)H intensity was significantly higher in S2. Mitochondrial NAD(P)H increased in response to lactate and butyrate but decreased in response to glutamine and glutamate. Cytosolic NAD(P)H was sensitive to lactate and pyruvate and decreased dramatically in S2 in response to inhibition of glucose metabolism. Mitochondrial flavoprotein (FP) intensity was markedly higher in S2 than in S1 but was insensitive to changes in RC redox state. Mitochondrial FP signal increased in response to palmitate but decreased in response to glutamine and glutamate. Fluorescence lifetime decays were similar in both S1 and S2, suggesting that intensity differences are explained by differences in abundance of the same molecular species. Expression levels of known fluorescent mitochondrial FPs were higher in S2 than S1. In summary, substantial metabolic information can be obtained in kidney tissue using a label-free live imaging approach, and our findings suggest that metabolism is tailored to the specialized functions of S1 and S2 PT segments.

Keywords:  autofluorescence; kidney; mitochondria; multiphoton imaging; proximal tubule

DOI:  https://doi.org/10.1152/ajprenal.00165.2018
Front Genet. 2018 ;9 533

Translating the Game: Ribosomes as Active Players.

Piera Calamita, Guido Gatti, Annarita Miluzio, Alessandra Scagliola, Stefano Biffo.

  Ribosomes have been long considered as executors of the translational program. The fact that ribosomes can control the translation of specific mRNAs or entire cellular programs is often neglected. Ribosomopathies, inherited diseases with mutations in ribosomal factors, show tissue specific defects and cancer predisposition. Studies of ribosomopathies have paved the way to the concept that ribosomes may control translation of specific mRNAs. Studies in Drosophila and mice support the existence of heterogeneous ribosomes that differentially translate mRNAs to coordinate cellular programs. Recent studies have now shown that ribosomal activity is not only a critical regulator of growth but also of metabolism. For instance, glycolysis and mitochondrial function have been found to be affected by ribosomal availability. Also, ATP levels drop in models of ribosomopathies. We discuss findings highlighting the relevance of ribosome heterogeneity in physiological and pathological conditions, as well as the possibility that in rate-limiting situations, ribosomes may favor some translational programs. We discuss the effects of ribosome heterogeneity on cellular metabolism, tumorigenesis and aging. We speculate a scenario in which ribosomes are not only executors of a metabolic program but act as modulators.

Keywords:  RACK1; Shwachman-diamond syndrome; eIF6; metabolism; ribosomal proteins; ribosome heterogeneity; ribosomopathies

DOI:  https://doi.org/10.3389/fgene.2018.00533
Cytokine. 2018 Nov 21. pii: S1043-4666(18)30427-7. [Epub ahead of print]

Metabolic regulation of infection and inflammation.

Prashant Chauhan, Bhaskar Saha.

  Immunometabolic framework provides a way to understand the immune regulation via cell intrinsic metabolic fluxes and metabolites during infections, tumors, and inflammatory disorders. During these diseases, the immune cells are activated requiring more energy and moderating their metabolic functions. The two categories of metabolic alterations are therefore causally associated with energy derivation and cellular functions. Pathogens, tumors and inflammation target energy metabolism, primarily glucose uptake, glucose catabolism, gluconeogenesis for continuing lipid metabolism through mainstream pathways such as glycolysis, tricarboxylic acid cycle, mitochondrial respiration and pentose phosphate pathway. Many biosynthetic pathways such as those of cholesterol, ceramide, sphingolipids, and fatty acids are altered explaining the metabolic interface in molecular pathogenesis in various infectious and non-infectious inflammatory diseases. The emerging immune-metabolic framework also identifies the key regulatory elements such as metabolites, signalling intermediates and transcription factors. These regulatory elements play key roles in deciding the fate of an infection, tumor or autoimmune diseases. The original research articles and the review articles in this Special issue of Cytokine on "Infection, Inflammation and Immunometabolomes" highlight these aspects of metabolic reprogramming and the role of some 'metabolomic regulators' in controlling the outcome of infectious and non-infectious diseases. In this Editorial, we introduce the readers to these articles discussing the elements in immune-metabolic framework.

Keywords:  Infection; Inflammation; Macrophage; Metabolism; T-cell

DOI:  https://doi.org/10.1016/j.cyto.2018.11.016
Nat Commun. 2018 Nov 27. 9(1): 5008

MFF-dependent mitochondrial fission regulates presynaptic release and axon branching by limiting axonal mitochondria size.

Tommy L Lewis, Seok-Kyu Kwon, Annie Lee, Reuben Shaw, Franck Polleux.

Neurons display extreme degrees of polarization, including compartment-specific organelle morphology. In cortical, long-range projecting, pyramidal neurons (PNs), dendritic mitochondria are long and tubular whereas axonal mitochondria display uniformly short length. Here we explored the functional significance of maintaining small mitochondria for axonal development in vitro and in vivo. We report that the Drp1 'receptor' Mitochondrial fission factor (MFF) is required for determining the size of mitochondria entering the axon and then for maintenance of their size along the distal portions of the axon without affecting their trafficking properties, presynaptic capture, membrane potential or ability to generate ATP. Strikingly, this increase in presynaptic mitochondrial size upon MFF downregulation augments their capacity for Ca2+ ([Ca2+]m) uptake during neurotransmission, leading to reduced presynaptic [Ca2+]c accumulation, decreased presynaptic release and terminal axon branching. Our results uncover a novel mechanism controlling neurotransmitter release and axon branching through fission-dependent regulation of presynaptic mitochondrial size.

DOI: https://doi.org/10.1038/s41467-018-07416-2
Hum Mol Genet. 2018 Nov 29.

PD-linked CHCHD2 mutations impair CHCHD10 and MICOS complex leading to mitochondria dysfunction.

Wei Zhou, Dongrui Ma, Alfred Xuyang Sun, Hoang-Dai Tran, Dong-Liang Ma, Brijesh K Singh, Jin Zhou, Jinyan Zhang, Danlei Wang, Yi Zhao, Paul M Yen, Eyleen Goh, Eng-King Tan.

CHCHD2 mutations were linked with autosomal dominant Parkinson's disease (PD) and recently, Alzheimer's disease/ Frontotemporal dementia. In current study, we generated isogenic human stem cell (hESC) lines harboring PD-associated CHCHD2 mutation R145Q or Q126X via CRISPR-Cas9 method, aiming to unravel pathophysiologic mechanism and seek potential intervention strategy against CHCHD2 mutant-caused defects. By engaging super resolution microscopy, we identified a physical proximity and similar distribution pattern of CHCHD2 along mitochondria with MICOS (mitochondrial inner membrane organizing system), a large protein complex maintaining mitochondria cristae. Isogenic hESCs and differentiated neural progenitor cells (NPCs) harboring CHCHD2 R145Q or Q126X mutation, showed impaired mitochondria function, reduced CHCHD2 and MICOS components, and exhibited nearly hollow mitochondria with reduced cristae. Furthermore, PD-linked CHCHD2 mutations lost their interaction with CHCHD10, while transient knockdown of either CHCHD2 or CHCHD10 reduced MICOS and mitochondria cristae. Importantly, a specific mitochondria-targeted peptide Elamipretide (MTP-131), now tested in phase 3 clinical trials for mitochondrial diseases was found to enhance CHCHD2 with MICOS and mitochondria oxidative phosphorylation enzymes in isogenic NPCs harboring heterozygous R145Q, suggesting that Elamipretide is able to attenuate CHCHD2 R145Q-induced mitochondria dysfunction. Taken together, our results suggested CHCHD2-CHCHD10 complex may be a novel therapeutic target for PD and related neurodegenerative disorders and Elamipretide may benefit CHCHD2 mutation-linked PD.

DOI: https://doi.org/10.1093/hmg/ddy413
Cell Rep. 2018 Nov 27. pii: S2211-1247(18)31725-X. [Epub ahead of print]25(9): 2339-2353.e4

The Mitochondrial Apoptotic Effectors BAX/BAK Activate Caspase-3 and -7 to Trigger NLRP3 Inflammasome and Caspase-8 Driven IL-1β Activation.

James E Vince, Dominic De Nardo, Wenqing Gao, Angelina J Vince, Cathrine Hall, Kate McArthur, Daniel Simpson, Swarna Vijayaraj, Lisa M Lindqvist, Philippe Bouillet, Mark A Rizzacasa, Si Ming Man, John Silke, Seth L Masters, Guillaume Lessene, David C S Huang, Daniel H D Gray, Benjamin T Kile, Feng Shao, Kate E Lawlor.

  Intrinsic apoptosis resulting from BAX/BAK-mediated mitochondrial membrane damage is regarded as immunologically silent. We show here that in macrophages, BAX/BAK activation results in inhibitor of apoptosis (IAP) protein degradation to promote caspase-8-mediated activation of IL-1β. Furthermore, BAX/BAK signaling induces a parallel pathway to NLRP3 inflammasome-mediated caspase-1-dependent IL-1β maturation that requires potassium efflux. Remarkably, following BAX/BAK activation, the apoptotic executioner caspases, caspase-3 and -7, act upstream of both caspase-8 and NLRP3-induced IL-1β maturation and secretion. Conversely, the pyroptotic cell death effectors gasdermin D and gasdermin E are not essential for BAX/BAK-induced IL-1β release. These findings highlight that innate immune cells undergoing BAX/BAK-mediated apoptosis have the capacity to generate pro-inflammatory signals and provide an explanation as to why IL-1β activation is often associated with cellular stress, such as during chemotherapy.

Keywords:  BAK; BAX; BCL-XL; Gasdermin; IAPs; MCL-1; NLRP3; caspase-1; caspase-8; mitochondria

DOI:  https://doi.org/10.1016/j.celrep.2018.10.103
Cell Rep. 2018 Nov 27. pii: S2211-1247(18)31761-3. [Epub ahead of print]25(9): 2605-2616.e7

Dynamic Phosphorylation of the C Terminus of Hsp70 Regulates the Mitochondrial Import of SOD2 and Redox Balance.

Sara Zemanovic, Maxim V Ivanov, Lena V Ivanova, Amogh Bhatnagar, Teresa Michalkiewicz, Ru-Jeng Teng, Suresh Kumar, Rajendra Rathore, Kirkwood A Pritchard, Girija G Konduri, Adeleye J Afolayan.

  The import of superoxide dismutase-2 (SOD2) into mitochondria is vital for the survival of eukaryotic cells. SOD2 is encoded within the nuclear genome and translocated into mitochondria for activation after translation in the cytosol. The molecular chaperone Hsp70 modulates SOD2 activity by promoting import of SOD2 into mitochondria. In turn, the activity of Hsp70 is controlled by co-chaperones, particularly CHIP, which directs Hsp70-bound proteins for degradation in the proteasomes. We investigated the mechanisms controlling the activity of SOD2 to signal activation and maintain mitochondrial redox balance. We demonstrate that Akt1 binds to and phosphorylates the C terminus of Hsp70 on Serine631, which inhibits CHIP-mediated SOD2 degradation thereby stabilizing and promoting SOD2 import. Conversely, increased mitochondrial-H2O2 formation disrupts Akt1-mediated phosphorylation of Hsp70, and non-phosphorylatable Hsp70 mutants decrease SOD2 import, resulting in mitochondrial oxidative stress. Our findings identify Hsp70 phosphorylation as a physiological mechanism essential for regulation of mitochondrial redox balance.

Keywords:  Akt; C-terminal domain; CHIP; PP2C; STUB1; heat shock protein 70; hydrogen peroxide; mitochondria; phosphorylation; superoxide anion; superoxide dismutase-2

DOI:  https://doi.org/10.1016/j.celrep.2018.11.015
Front Immunol. 2018 ;9 2563

Inflammasome-Independent Role of NLRP3 Mediates Mitochondrial Regulation in Renal Injury.

Su-Mi Kim, Yang Gyun Kim, Dong-Jin Kim, Seon Hwa Park, Kyung-Hwan Jeong, Yu Ho Lee, Sung Jig Lim, Sang-Ho Lee, Ju-Young Moon.

  The NOD-like receptor family, pyrin domain containing-3 (NLRP3) inflammasome has been implicated in renal inflammation and fibrosis. However, the biological function of inflammasome-independent NLRP3 in non-immune cells is still unclear. We evaluated the role of inflammasome-independent NLRP3 in renal tubular cells and assessed the value of NLRP3 as a therapeutic target for acute kidney injury (AKI). Various renal tubular cell lines and primary cultured tubular cells from NLRP3 knockout (KO) mice were used for in vitro studies. We also tested the role of tubular NLRP3 in AKI with a unilateral ureter obstruction model (UUO). Hypoxia induced significant increase of NLRP3 independent of ASC, caspase-1, and IL-1β. NLRP3 in renal tubular cells relocalized from the cytosol to the mitochondria during hypoxia and bound to mitochondrial antiviral signal protein (MAVS). The deletion of NLRP3 or MAVS in renal tubular cells attenuated mitochondrial reactive oxygen species (ROS) production and depolarization of the mitochondrial membrane potentials under hypoxia. In response to UUO, NLRP3 KO mice showed less fibrosis, apoptosis, and ROS injury than wild type (WT) mice. Compared with WT kidney, mitophagy was up-regulated in NLRP3 KO kidney relative to the baseline and it was protective against AKI. Our results indicate that inflammasome-independent NLRP3 in renal tubular cells plays important role in mitochondrial ROS production and injury by binding to MAVS after hypoxic injury. This mitochondrial regulation in the absence of NLRP3 increases autophagy and attenuates apoptosis after UUO. We suggest that inflammasome-independent NLRP3 could be a therapeutic target of AKI to prevent the progression of chronic kidney disease.

Keywords:  NLRP3; acute kidney injury (AKI); apoptosis; mitochondrial ROS; mitophagy

DOI:  https://doi.org/10.3389/fimmu.2018.02563
Annu Rev Physiol. 2018 Nov 28.

Cellular Metabolism in Lung Health and Disease.

Gang Liu, Ross Summer.

The lung is often overlooked as a metabolically active organ, yet biochemical studies have long demonstrated that glucose utilization surpasses that of many other organs, including the heart, kidney, and brain. For most cells in the lung, energy consumption is relegated to performing common cellular tasks, like mRNA transcription and protein translation. However, certain lung cell populations engage in more specialized types of energy-consuming behaviors, such as the beating of cilia or the production of surfactant. While many extrapulmonary diseases are now linked to abnormalities in cellular metabolism, the pulmonary community has only recently embraced the concept of metabolic dysfunction as a driver of respiratory pathology. Herein, we provide an overview of the major metabolic pathways in the lung and discuss how cells sense and adapt to low-energy states. Moreover, we review some of the emerging evidence that links alterations in cellular metabolism to the pathobiology of several common respiratory diseases. Expected final online publication date for the Annual Review of Physiology Volume 81 is February 10, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI: https://doi.org/10.1146/annurev-physiol-020518-114640
J Biol Chem. 2018 Nov 27. pii: jbc.RA118.006433. [Epub ahead of print]

Tissue-specific kinase expression and activity regulates flux through the pyruvate dehydrogenase complex.

Alla Klyuyeva, Alina Tuganova, Natalia Y Kedishvili, Kirill M Popov.

  The pyruvate dehydrogenase complex (PDC) is a multienzyme assembly that converts pyruvate to acetyl-CoA. As pyruvate and acetyl-CoA play central roles in cellular metabolism, understanding PDC regulation is pivotal to understanding the larger metabolic network. The activity of mammalian PDC is regulated through reversible phosphorylation governed by at least four isozymes of pyruvate dehydrogenase kinase (PDK). Deciphering which kinase regulates PDC in organisms at specific times or places has been challenging. In this study, we analyzed mouse strains carrying targeted mutations of individual isozymes to explore their role in regulating PDC activity. Analysis of protein content of PDK isozymes in major metabolic tissues revealed that PDK1 and PDK2 were ubiquitously expressed, while PDK3 and PDK4 displayed a rather limited tissue distribution. Measurement of kinase activity showed that PDK1 is the principal isozyme regulating hepatic PDC. PDK2 was largely responsible for inactivation of PDC in tissues of muscle origin and BAT. PDK3 was the principal kinase regulating pyruvate dehydrogenase activity in kidney and brain. In well-fed state, the tissue levels of PDK4 protein were fairly low. In most tissues tested, PDK4 ablation had little effect on the overall rates of inactivation of PDC in kinase reaction. Taken together, these data strongly suggest that the activity of PDC is regulated by different isozymes in different tissues. Furthermore, it appears that the overall flux through PDC in a given tissue largely reflects the properties of PDK isozyme that is principally responsible for the regulation of PDC activity in that tissue.

Keywords:  carbohydrate metabolism; mitochondria; oxidative decarboxylation of pyruvate; protein kinase; protein phosphorylation; pyruvate dehydrogenase complex (PDC); pyruvate dehydrogenase kinase (PDC kinase)

DOI:  https://doi.org/10.1074/jbc.RA118.006433
Cell Rep. 2018 Nov 27. pii: S2211-1247(18)31691-7. [Epub ahead of print]25(9): 2354-2368.e5

BAX/BAK-Induced Apoptosis Results in Caspase-8-Dependent IL-1β Maturation in Macrophages.

Dhruv Chauhan, Eva Bartok, Moritz M Gaidt, Florian J Bock, Jennifer Herrmann, Jens M Seeger, Petr Broz, Roland Beckmann, Hamid Kashkar, Stephen W G Tait, Rolf Müller, Veit Hornung.

  IL-1β is a cytokine of pivotal importance to the orchestration of inflammatory responses. Synthesized as an inactive pro-cytokine, IL-1β requires proteolytic maturation to gain biological activity. Here, we identify intrinsic apoptosis as a non-canonical trigger of IL-1β maturation. Guided by the discovery of the immunomodulatory activity of vioprolides, cyclic peptides isolated from myxobacteria, we observe IL-1β maturation independent of canonical inflammasome pathways, yet dependent on intrinsic apoptosis. Mechanistically, vioprolides inhibit MCL-1 and BCL2, which in turn triggers BAX/BAK-dependent mitochondrial outer membrane permeabilization (MOMP). Induction of MOMP results in the release of pro-apoptotic factors initiating intrinsic apoptosis, as well as the depletion of IAPs (inhibitors of apoptosis proteins). IAP depletion, in turn, operates upstream of ripoptosome complex formation, subsequently resulting in caspase-8-dependent IL-1β maturation. These results establish the ripoptosome/caspase-8 complex as a pro-inflammatory checkpoint that senses the perturbation of mitochondrial integrity.

Keywords:  BAX/BAK; BCL2; IAP depletion; IL-1β; MCL-1; NLRP3; caspase-8; intrinsic apoptosis; ripoptosome

DOI:  https://doi.org/10.1016/j.celrep.2018.10.087
Oncogene. 2018 Nov 28.

The ERK and JNK pathways in the regulation of metabolic reprogramming.

Salvatore Papa, Pui Man Choy, Concetta Bubici.

Most tumor cells reprogram their glucose metabolism as a result of mutations in oncogenes and tumor suppressors, leading to the constitutive activation of signaling pathways involved in cell growth. This metabolic reprogramming, known as aerobic glycolysis or the Warburg effect, allows tumor cells to sustain their fast proliferation and evade apoptosis. Interfering with oncogenic signaling pathways that regulate the Warburg effect in cancer cells has therefore become an attractive anticancer strategy. However, evidence for the occurrence of the Warburg effect in physiological processes has also been documented. As such, close consideration of which signaling pathways are beneficial targets and the effect of their inhibition on physiological processes are essential. The MAPK/ERK and MAPK/JNK pathways, crucial for normal cellular responses to extracellular stimuli, have recently emerged as key regulators of the Warburg effect during tumorigenesis and normal cellular functions. In this review, we summarize our current understanding of the roles of the ERK and JNK pathways in controlling the Warburg effect in cancer and discuss their implication in controlling this metabolic reprogramming in physiological processes and opportunities for targeting their downstream effectors for therapeutic purposes.

DOI: https://doi.org/10.1038/s41388-018-0582-8
Dis Model Mech. 2018 Nov 26. pii: dmm.036426. [Epub ahead of print]

Mouse Idh3a mutations cause retinal degeneration and reduced mitochondrial function.

Amy S Findlay, Roderick N Carter, Becky Starbuck, Lisa McKie, Klára Nováková, Peter S Budd, Margaret A Keighren, Joseph A Marsh, Sally H Cross, Michelle M Simon, Paul K Potter, Nicholas M Morton, Ian J Jackson.

  Isocitrate dehydrogenase (IDH) is an enzyme required for the production of α-ketoglutarate from isocitrate. IDH3 generates the NADH used in the mitochondria for ATP production, and is a tetramer made up of two α, a β and a γ subunit. Loss of function and missense mutations in both IDH3A andIDH3B have previously been implicated in families exhibiting retinal degeneration. Using mouse models we have investigated the role of IDH3 in retinal disease and mitochondrial function.We identified mice with late-onset retinal degeneration in a screen of ageing mice carrying an ENU-induced mutation, E229K, in Idh3a Mice homozygous for this mutation exhibit signs of retinal stress, indicated by GFAP staining, as early as 3 months, but no other tissues appear to be affected. We produced a knockout of Idh3a and found that homozygous mice do not survive past early embryogenesis. Idh3a-/E229K compound heterozygous mutants exhibit a more severe retinal degeneration when compared to Idh3aE229K/E229K Analysis of mitochondrial function in mutant cell lines highlighted a reduction in mitochondrial maximal respiration and reserve capacity levels in both Idh3a E229K/E229K and Idh3a -/E229K cells. Loss-of function Idh3b mutants do not exhibit the same retinal degeneration phenotype, with no signs of retinal stress or reduction in mitochondrial respiration.It has been previously reported that the retina operates with a limited mitochondrial reserve capacity and we suggest that this, in combination with the reduced reserve capacity in mutants, explains the degenerative phenotype observed in Idh3a mutant mice.

Keywords:  Krebs cycle; Mouse model; Retinitis pigmentosa

DOI:  https://doi.org/10.1242/dmm.036426
Cancer Metab. 2018 ;6 14

Exercise inhibits tumor growth and central carbon metabolism in patient-derived xenograft models of colorectal cancer.

Min Lu, Sydney M Sanderson, Amelia Zessin, Kathleen A Ashcraft, Lee W Jones, Mark W Dewhirst, Jason W Locasale, David S Hsu.

  Background: While self-reported exercise is associated with a reduction in the risk of recurrence in colorectal cancer, the molecular mechanisms underpinning this relationship are unknown. Furthermore, the effect of exercise on intratumoral metabolic processes has not been investigated in detail in human cancers. In our current study, we generated six colorectal patient patient-derived xenografts (CRC PDXs) models and treated each PDX to voluntary wheel running (exercise) for 6-8 weeks or no exposure to the wheel (control). A comprehensive metabolomics analysis was then performed on the PDXs to identify exercise induced changes in the tumor that were associated with slower growth.Results: Tumor growth inhibition was observed in the voluntary wheel running group compared to the control group in three of the six models. A metabolomics analysis first revealed that central carbon metabolism was affected in each model irrespective of treatment. Interestingly, comparison of responsive and resistant models showed that levels of metabolites in nucleotide metabolism, known to be coupled to mitochondrial metabolism, were predictive of response. Furthermore, phosphocreatine levels which are linked to mitochondrial energy demands were associated with inhibition of tumor growth.
Conclusion: Altogether, this study provides evidence that changes to tumor cell mitochondrial metabolism may underlie in part the benefits of exercise.

Keywords:  Central carbon metabolism; Colorectal cancer; Exercise; Mitochondrial metabolism; Patient-derived xenograft

DOI:  https://doi.org/10.1186/s40170-018-0190-7
Trends Biochem Sci. 2018 Nov 22. pii: S0968-0004(18)30227-5. [Epub ahead of print]

Lactate: A Metabolic Driver in the Tumour Landscape.

Luigi Ippolito, Andrea Morandi, Elisa Giannoni, Paola Chiarugi.

  The presence of lactate in human tumours has been long neglected, confined to the role of a waste product derived from glycolysis and as a biomarker of malignancy. More recently, lactate has been rediscovered as signalling molecule that plays important roles in the regulation of the metabolic pathways, the immune response, and cell-to-cell communication within the tumour microenvironment. This review examines recent discoveries about the functional role of lactate in shaping the behaviour and the phenotype of tumour and tumour-associated cells, and describes potential clinical approaches to target lactate transport and metabolism in tumours.

Keywords:  mitochondria; tumour metabolism; tumour microenvironment; tumour–stroma interplay

DOI:  https://doi.org/10.1016/j.tibs.2018.10.011
Oncogenesis. 2018 Nov 26. 7(11): 93

IKKβ activates p53 to promote cancer cell adaptation to glutamine deprivation.

Mari B Ishak Gabra, Ying Yang, Xazmin H Lowman, Michael A Reid, Thai Q Tran, Mei Kong.

One of the hallmarks of cancer is the ability to reprogram cellular metabolism to increase the uptake of necessary nutrients such as glucose and glutamine. Driven by oncogenes, cancer cells have increased glutamine uptake to support their highly proliferative nature. However, as cancer cells continue to replicate and grow, they lose access to vascular tissues and deplete local supply of nutrients and oxygen. We previously showed that many tumor cells situate in a low glutamine microenvironment in vivo, yet the mechanisms of how they are able to adapt to this metabolic stress are still not fully understood. Here, we report that IκB-kinase β (IKKβ) is needed to promote survival and its activation is accompanied by phosphorylation of the metabolic sensor, p53, in response to glutamine deprivation. Knockdown of IKKβ decreases the level of wild-type and mutant p53 phosphorylation and its transcriptional activity, indicating a novel relationship between IKKβ and p53 in mediating cancer cell survival in response to glutamine withdrawal. Phosphopeptide mass spectrometry analysis further reveals that IKKβ phosphorylates p53 on Ser392 to facilitate its activation upon glutamine deprivation, independent of the NF-κB pathway. The results of this study offer an insight into the metabolic reprogramming in cancer cells that is dependent on a previously unidentified IKKβ-p53 signaling axis in response to glutamine depletion. More importantly, this study highlights a new therapeutic strategy for cancer treatment and advances our understanding of adaptive mechanisms that could lead to resistance to current glutamine targeting therapies.

DOI: https://doi.org/10.1038/s41389-018-0104-0
Annu Rev Physiol. 2018 Nov 28.

Branched Chain Amino Acids.

Michael Neinast, Danielle Murashige, Zoltan Arany.

Branched chain amino acids (BCAAs) are building blocks for all life forms. We review here the fundamentals of BCAA metabolism in mammalian physiology. Decades of studies have elicited a deep understanding of biochemical reactions involved in BCAA catabolism. In addition, BCAAs and various catabolic products act as signaling molecules, activating programs ranging from protein synthesis to insulin secretion. How these processes are integrated at an organismal level is less clear. Inborn errors of metabolism highlight the importance of organismal regulation of BCAA physiology. More recently, subtle alterations of BCAA metabolism have been suggested to contribute to numerous prevalent diseases, including diabetes, cancer, and heart failure. Understanding the mechanisms underlying altered BCAA metabolism and how they contribute to disease pathophysiology will keep researchers busy for the foreseeable future. Expected final online publication date for the Annual Review of Physiology Volume 81 is February 10, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI: https://doi.org/10.1146/annurev-physiol-020518-114455
Methods Mol Biol. 2019 ;1896 139-147

Measurement of Metabolite Changes in Senescent Cells by Mass Spectrometry.

Christopher D Wiley, Sonnet Davis, Arvind Ramanathan.

  Senescent cells display altered metabolic signatures that can either be causal for aspects the senescent phenotype, or act as biomarkers for senescence. Steady state levels of multiple metabolites change with senescence, and can be detected using analytical methods. Here, we describe a liquid chromatography-mass spectrometry (LC-MS) method for detecting altered metabolites from cultured senescent cells.

Keywords:  Mass spectrometry; Metabolites; Metabolomics; Senescence

DOI:  https://doi.org/10.1007/978-1-4939-8931-7_13
Nat Med. 2018 Nov 26.

A CD4+ T cell population expanded in lupus blood provides B cell help through interleukin-10 and succinate.

Simone Caielli, Diogo Troggian Veiga, Preetha Balasubramanian, Shruti Athale, Bojana Domic, Elise Murat, Romain Banchereau, Zhaohui Xu, Manjari Chandra, Cheng-Han Chung, Lynnette Walters, Jeanine Baisch, Tracey Wright, Marilynn Punaro, Lorien Nassi, Katie Stewart, Julie Fuller, Duygu Ucar, Hideki Ueno, Joseph Zhou, Jacques Banchereau, Virginia Pascual.

Understanding the mechanisms underlying autoantibody development will accelerate therapeutic target identification in autoimmune diseases such as systemic lupus erythematosus (SLE)1. Follicular helper T cells (TFH cells) have long been implicated in SLE pathogenesis. Yet a fraction of autoantibodies in individuals with SLE are unmutated, supporting that autoreactive B cells also differentiate outside germinal centers2. Here, we describe a CXCR5-CXCR3+ programmed death 1 (PD1)hiCD4+ helper T cell population distinct from TFH cells and expanded in both SLE blood and the tubulointerstitial areas of individuals with proliferative lupus nephritis. These cells produce interleukin-10 (IL-10) and accumulate mitochondrial reactive oxygen species as the result of reverse electron transport fueled by succinate. Furthermore, they provide B cell help, independently of IL-21, through IL-10 and succinate. Similar cells are generated in vitro upon priming naive CD4+ T cells with plasmacytoid dendritic cells activated with oxidized mitochondrial DNA, a distinct class of interferogenic toll-like receptor 9 ligand3. Targeting this pathway might blunt the initiation and/or perpetuation of extrafollicular humoral responses in SLE.

DOI: https://doi.org/10.1038/s41591-018-0254-9
Hum Mol Genet. 2018 Nov 21.

Dystrophinopathy associated dysfunction of Krebs cycle metabolism.

Angus Lindsay, Christopher M Chamberlain, Bruce A Witthuhn, Dawn A Lowe, James M Ervasti.

Duchenne muscular dystrophy is a deadly muscle wasting disorder caused by loss of dystrophin protein. Studies suggest metabolic alterations are important to disease pathogenesis. Because muscle accounts for ~40% of body mass, we hypothesized that dystrophy-mediated metabolic changes would be measurable in biofluids and that a metabolomic analysis of urine would provide insight into the metabolic status of dystrophic muscle. Using the mdx mouse model, we performed a large-scale metabolomic screen at 1 and 3 months. While 10% of metabolites were altered at age 1 month, 40% were changed at 3 months. Principal component analysis distinguished wild-type from mdx animals, with the greatest separation at 3 months. A critical distinguishing pathway was Krebs cycle metabolite depletion in mdx urine. Five of 7 detected Krebs cycle metabolites were depleted in mdx urine, with succinate being the most robustly affected metabolite. Using selected reaction monitoring mass spectrometry, we demonstrated that muscle-specific dystrophin expression corrects mdx succinate depletion. When subjected to downhill treadmill running, wild-type and mdx mice expressing recombinant dystrophin in skeletal muscle displayed significant increases in urinary succinate levels. However, mdx succinate levels were unchanged, suggesting urinary succinate depletion may reflect an inability to upregulate the Krebs cycle following exercise. Finally, we show that supplementing the Krebs cycle in an ex vivo fatigue/recovery assay significantly impacts mdx muscle performance, but has no effect on wild-type muscle. Our results suggest that global metabolic impairment is associated with mdx disease progression and that Krebs cycle deficiencies are a downstream consequence of dystrophin loss.

DOI: https://doi.org/10.1093/hmg/ddy404
BMC Cancer. 2018 Nov 28. 18(1): 1180

Metabolic control of PPAR activity by aldehyde dehydrogenase regulates invasive cell behavior and predicts survival in hepatocellular and renal clear cell carcinoma.

Diana Andrejeva, Jan-Michael Kugler, Hung Thanh Nguyen, Anders Malmendal, Mette Lind Holm, Birgitte Groenkaer Toft, Anand C Loya, Stephen M Cohen.

BACKGROUND: Changes in cellular metabolism are now recognized as potential drivers of cancer development, rather than as secondary consequences of disease. Here, we explore the mechanism by which metabolic changes dependent on aldehyde dehydrogenase impact cancer development.METHODS: ALDH7A1 was identified as a potential cancer gene using a Drosophila in vivo metastasis model. The role of the human ortholog was examined using RNA interference in cell-based assays of cell migration and invasion. 1H-NMR metabolite profiling was used to identify metabolic changes in ALDH7A1-depleted cells. Publically available cancer gene expression data was interrogated to identify a gene-expression signature associated with depletion of ALDH7A1. Computational pathway and gene set enrichment analysis was used to identify signaling pathways and cellular processes that were correlated with reduced ALDH7A1 expression in cancer. A variety of statistical tests used to evaluate these analyses are described in detail in the methods section. Immunohistochemistry was used to assess ALDH7A1 expression in tissue samples from cancer patients.
RESULTS: Depletion of ALDH7A1 increased cellular migration and invasiveness in vitro. Depletion of ALDH7A1 led to reduced levels of metabolites identified as ligands for Peroxisome proliferator-activated receptor (PPARα). Analysis of publically available cancer gene expression data revealed that ALDH7A1 mRNA levels were reduced in many human cancers, and that this correlated with poor survival in kidney and liver cancer patients. Using pathway and gene set enrichment analysis, we establish a correlation between low ALDH7A1 levels, reduced PPAR signaling and reduced patient survival. Metabolic profiling showed that endogenous PPARα ligands were reduced in ALDH7A1-depleted cells. ALDH7A1-depletion led to reduced PPAR transcriptional activity. Treatment with a PPARα agonist restored normal cellular behavior. Low ALDH7A1 protein levels correlated with poor clinical outcome in hepatocellular and renal clear cell carcinoma patients.
CONCLUSIONS: We provide evidence that low ALDH7A1 expression is a useful prognostic marker of poor clinical outcome for hepatocellular and renal clear cell carcinomas and hypothesize that patients with low ALDH7A1 might benefit from therapeutic approaches addressing PPARα activity.

DOI: https://doi.org/10.1186/s12885-018-5061-7
Nat Commun. 2018 Nov 29. 9(1): 5071

Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate.

Sebastian Knorr, Malte Sinn, Dmitry Galetskiy, Rhys M Williams, Changhao Wang, Nicolai Müller, Olga Mayans, David Schleheck, Jörg S Hartig.

Lysine degradation has remained elusive in many organisms including Escherichia coli. Here we report catabolism of lysine to succinate in E. coli involving glutarate and L-2-hydroxyglutarate as intermediates. We show that CsiD acts as an α-ketoglutarate-dependent dioxygenase catalysing hydroxylation of glutarate to L-2-hydroxyglutarate. CsiD is found widespread in bacteria. We present crystal structures of CsiD in complex with glutarate, succinate, and the inhibitor N-oxalyl-glycine, demonstrating strong discrimination between the structurally related ligands. We show that L-2-hydroxyglutarate is converted to α-ketoglutarate by LhgO acting as a membrane-bound, ubiquinone-linked dehydrogenase. Lysine enters the pathway via 5-aminovalerate by the promiscuous enzymes GabT and GabD. We demonstrate that repression of the pathway by CsiR is relieved upon glutarate binding. In conclusion, lysine degradation provides an important link in central metabolism. Our results imply the gut microbiome as a potential source of glutarate and L-2-hydroxyglutarate associated with human diseases such as cancer and organic acidurias.

DOI: https://doi.org/10.1038/s41467-018-07563-6
J Mol Biol. 2018 Nov 21. pii: S0022-2836(18)30977-X. [Epub ahead of print]

A New Mechanism for High-Affinity Uptake of C4-Dicarboxylates in Bacteria Revealed by the Structure of Rhodopseudomonas palustris MatC (RPA3494), a Periplasmic Binding-Protein of the Tripartite Tricarboxylate Transporter (TTT) Family.

Leonardo T Rosa, Samuel R Dix, John B Rafferty, David J Kelly.

  C4-dicarboxylates play a central role in cellular physiology as key metabolic intermediates. Under aerobic conditions, they participate in the citric-acid cycle, while in anaerobic bacteria, they are important in energy-conserving fermentation and respiration processes. Ten different families of secondary transporters have been described to participate in C4-dicarboxylate movement across biological membranes but only one of these utilizes an extracytoplasmic solute binding protein to achieve high-affinity uptake. Here, we identify the MatBAC system from the photosynthetic bacterium Rhodopseudomonas palustris as the first member of the Tripartite Tricarboxylate Transport (TTT) family to be involved in C4-dicarboxylate transport. Tryptophan fluorescence spectroscopy showed that MatC, the periplasmic binding protein from this system, binds to L- and D-malate with Kd values of 27 and 21 nM respectively, the highest reported affinity to date for these C4-dicarboxylates, and to succinate (Kd 110 nM) and fumarate (Kd 400 nM). The 2.1 Å crystal structure of MatC with bound malate shows a high level of substrate coordination, with participation of two water molecules that bridge hydrogen bonds between the ligand proximal carboxylic group and the main chain of two conserved loops in the protein structure. The substrate coordination in MatC correlates with the binding data, and explains the protein's selectivity for different substrates and respective binding affinities. Our results reveal a new function in C4-dicarboxylate transport by members of the poorly characterized TTT family, which are widely distributed in bacterial genomes but for which details of structure-function relationships and transport mechanisms have been lacking.

Keywords:  Malate; Periplasm; Secondary transporter; Substrate binding-protein; Tryptophan fluorescence

DOI:  https://doi.org/10.1016/j.jmb.2018.11.016
Brain Res Bull. 2018 Nov 22. pii: S0361-9230(18)30669-5. [Epub ahead of print]

Effect of dimethyl fumarate on neuroinflammation and apoptosis in PTZ kindling model in rats.

Neha Singh, Lekha Saha, Puja Kumari, Jagjit Singh, Alka Bhatia, Dibyajyoti Banerjee, Amitava Chakrabarti.

  OBJECTIVE: Role of apoptosis and neuroinflammation have been well established in the pathogenesis of epilepsy. It has been reported that the activation of nuclear factor-erythroid 2-related factor-2 (Nrf2) contributes to the attenuation of inflammation by inhibiting nuclear factor-kB (NF-kB) pathway. Therefore, the present study was designed to evaluate anti-inflammatory, anti-apoptotic and anti-oxidative role of dimethyl fumarate (DMF), an activator of Nrf2, in chemical kindling model in rats.METHODS: Chemical kindling model was established in Wistar rats by intraperitoneal (i.p.) administration of pentylenetetrazole (PTZ). Animals were treated with DMF (60 mg/kg) to activate the Nrf2 antioxidant response element (ARE) pathway. The animals were assessed for seizure score, neuronal damage and inflammatory cytokines levels (IL-1β, IL-6 and TNF-α) in hippocampus. The mRNA levels of various genes (Nrf2, HO-1, NQO1, Bcl2, Bax, Caspase 3, NF-kB, IL-6, IL-1β and TNF-α) were quantified by real-time PCR. The expression of anti-oxidative (Nrf2), apoptotic (Bax, Bcl2) and inflammatory (NF-kB) proteins were analysed by western blot. Immunohistochemistry (Bax) and electron microscopy were done to assess apoptosis.
RESULT: The results showed reduction in the seizure score, percentage of kindled rats and neurological damage score in DMF treated rats. The levels of pro-inflammatory cytokines were also decreased by DMF treatment. DMF downregulated the expression of inflammatory (NF-kB) and apoptotic (Bax, Caspase-3) genes and protein. DMF treatment increased the gene expression of Nrf2, HO-1, NQO1, Bcl-2 and protein expression of Nrf2 and Bcl2.
CONCLUSION: DMF demonstrated anti-apoptotic, anti-inflammatory and anti-oxidative effect in hippocampus, which might be regulated by increased level of antioxidant response elements.

Keywords:  NF-kB; Nrf2; PTZ chemical kindling model; apoptosis; dimethyl fumarate

DOI:  https://doi.org/10.1016/j.brainresbull.2018.11.013