bims-camemi 2020-04-26 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2020–04–26
forty-four papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit

Developmental and Tumor Angiogenesis Requires the Mitochondria-Shaping Protein Opa1.
The gluconeogenic enzyme PCK1 phosphorylates INSIG1/2 for lipogenesis.
α-ketobutyrate links alterations in cystine metabolism to glucose oxidation in mtDNA mutant cells.
Mitochondrial pyruvate and fatty acid flux modulate MICU1-dependent control of MCU activity.
Methylmalonyl acidemia: from mitochondrial metabolism to defective mitophagy and disease.
Regional metabolic signatures in the Ndufs4(KO) mouse brain implicate defective glutamate/α-ketoglutarate metabolism in mitochondrial disease.
Fission and fusion machineries converge at ER contact sites to regulate mitochondrial morphology.
Myotonic Dystrophy type 1 cells display impaired metabolism and mitochondrial dysfunction that are reversed by metformin.
Noncanonical Cell Fate Regulation by Bcl-2 Proteins.
Triptolide suppresses IDH1-mutated malignancy via Nrf2-driven glutathione metabolism.
Mitofusins as mitochondrial anchors and tethers.
Metabolic flux analysis and fluxomics-driven determination of reaction free energy using multiple isotopes.
New horizons in mitochondrial contact site research.
Tollip coordinates Parkin-dependent trafficking of mitochondrial-derived vesicles.
Rational Design of Allosteric and Selective Inhibitors of the Molecular Chaperone TRAP1.
The Mitochondrial Protein VDAC1 at the Crossroads of Cancer Cell Metabolism: The Epigenetic Link.
HIGD2A is required for assembly of the COX3 module of human mitochondrial complex IV.
Dissecting the Roles of Mitochondrial Complex I Intermediate Assembly Complex Factors in the Biogenesis of Complex I.
Mitochondrial lipoylation integrates age-associated decline in brown fat thermogenesis.
20,000 picometers under the OMM: diving into the vastness of mitochondrial metabolite transport.
EMT Factors and Metabolic Pathways in Cancer.
A kinome-wide screen identifies a CDKL5-SOX9 regulatory axis in epithelial cell death and kidney injury.
HDAC inhibitors elicit metabolic reprogramming by targeting super-enhancers in glioblastoma models.
Outlining the Complex Pathway of Mammalian Fe-S Cluster Biogenesis.
Drp1 regulates mitochondrial dysfunction and dysregulated metabolism in ischemic injury via Clec16a-, BAX-, and GSH- pathways.
Nitrogen limitation reveals large reserves in metabolic and translational capacities of yeast.
Crosstalk of lncRNA and Cellular Metabolism and Their Regulatory Mechanism in Cancer.
Structural Insights into the Activation of mTORC1 on the Lysosomal Surface.
Deamidation Shunts RelA from Mediating Inflammation to Aerobic Glycolysis.
Lesch-Nyhan disease: I. Construction of expression vectors for hypoxanthine-guanine phosphoribosyltransferase (HGprt) enzyme and amyloid precursor protein (APP).
Epigenetics and Mitochondrial Stability in the Metabolic Memory Phenomenon Associated with Continued Progression of Diabetic Retinopathy.
Starvation and antimetabolic therapy promote cytokine release and recruitment of immune cells.
The gene for the lysosomal protein LAMP3 is a direct target of the transcription factor ATF4.
Defective arginine metabolism impairs mitochondrial homeostasis in Caenorhabditiselegans.
Endogenous metabolites promote stress resistance through induction of mitohormesis.
Molecular mechanism of mitochondrial respiratory chain assembly and its relation to mitochondrial diseases.
Loss of AKAP1 triggers Drp1 dephosphorylation-mediated mitochondrial fission and loss in retinal ganglion cells.
Altered Iron Metabolism and Impact in Cancer Biology, Metastasis, and Immunology.
A reactive metabolite as an immune suppressant.
Malate Circulation: Linking Chloroplast Metabolism to Mitochondrial ROS.
Methylglyoxal couples metabolic and translational control of Notch signalling in mammalian neural stem cells.
Non-Coding RNAs as Key Regulators of Glutaminolysis in Cancer.
Physiological Role of Glutamate Dehydrogenase in Cancer Cells.
Cell Competition Spurs Selection of Aggressive Cancer Cells.

Cell Metab. 2020 Apr 17. pii: S1550-4131(20)30189-3. [Epub ahead of print]

Developmental and Tumor Angiogenesis Requires the Mitochondria-Shaping Protein Opa1.

Stéphanie Herkenne, Olivier Ek, Margherita Zamberlan, Anna Pellattiero, Maya Chergova, Iñigo Chivite, Eliška Novotná, Giovanni Rigoni, Tiago Branco Fonseca, Dijana Samardzic, Andrielly Agnellini, Camilla Bean, Giulietta Di Benedetto, Natascia Tiso, Francesco Argenton, Antonella Viola, Maria Eugenia Soriano, Marta Giacomello, Elena Ziviani, Gabriele Sales, Marc Claret, Mariona Graupera, Luca Scorrano.

  While endothelial cell (EC) function is influenced by mitochondrial metabolism, the role of mitochondrial dynamics in angiogenesis, the formation of new blood vessels from existing vasculature, is unknown. Here we show that the inner mitochondrial membrane mitochondrial fusion protein optic atrophy 1 (OPA1) is required for angiogenesis. In response to angiogenic stimuli, OPA1 levels rapidly increase to limit nuclear factor kappa-light-chain-enhancer of activated B cell (NFκB) signaling, ultimately allowing angiogenic genes expression and angiogenesis. Endothelial Opa1 is indeed required in an NFκB-dependent pathway essential for developmental and tumor angiogenesis, impacting tumor growth and metastatization. A first-in-class small molecule-specific OPA1 inhibitor confirms that EC Opa1 can be pharmacologically targeted to curtail tumor growth. Our data identify Opa1 as a crucial component of physiological and tumor angiogenesis.

Keywords:  NFκB; Opa1; angiogenesis; cancer; fusion-fission; lymphangiogenesis; metastasis; mitochondria; mouse; tumor; zebrafish

DOI:  https://doi.org/10.1016/j.cmet.2020.04.007
Nature. 2020 Apr;580(7804): 530-535

The gluconeogenic enzyme PCK1 phosphorylates INSIG1/2 for lipogenesis.

Daqian Xu, Zheng Wang, Yan Xia, Fei Shao, Weiya Xia, Yongkun Wei, Xinjian Li, Xu Qian, Jong-Ho Lee, Linyong Du, Yanhua Zheng, Guishuai Lv, Jia-Shiun Leu, Hongyang Wang, Dongming Xing, Tingbo Liang, Mien-Chie Hung, Zhimin Lu.

Cancer cells increase lipogenesis for their proliferation and the activation of sterol regulatory element-binding proteins (SREBPs) has a central role in this process. SREBPs are inhibited by a complex composed of INSIG proteins, SREBP cleavage-activating protein (SCAP) and sterols in the endoplasmic reticulum. Regulation of the interaction between INSIG proteins and SCAP by sterol levels is critical for the dissociation of the SCAP-SREBP complex from the endoplasmic reticulum and the activation of SREBPs1,2. However, whether this protein interaction is regulated by a mechanism other than the abundance of sterol-and in particular, whether oncogenic signalling has a role-is unclear. Here we show that activated AKT in human hepatocellular carcinoma (HCC) cells phosphorylates cytosolic phosphoenolpyruvate carboxykinase 1 (PCK1), the rate-limiting enzyme in gluconeogenesis, at Ser90. Phosphorylated PCK1 translocates to the endoplasmic reticulum, where it uses GTP as a phosphate donor to phosphorylate INSIG1 at Ser207 and INSIG2 at Ser151. This phosphorylation reduces the binding of sterols to INSIG1 and INSIG2 and disrupts the interaction between INSIG proteins and SCAP, leading to the translocation of the SCAP-SREBP complex to the Golgi apparatus, the activation of SREBP proteins (SREBP1 or SREBP2) and the transcription of downstream lipogenesis-related genes, proliferation of tumour cells, and tumorigenesis in mice. In addition, phosphorylation of PCK1 at Ser90, INSIG1 at Ser207 and INSIG2 at Ser151 is not only positively correlated with the nuclear accumulation of SREBP1 in samples from patients with HCC, but also associated with poor HCC prognosis. Our findings highlight the importance of the protein kinase activity of PCK1 in the activation of SREBPs, lipogenesis and the development of HCC.

DOI: https://doi.org/10.1038/s41586-020-2183-2
Metab Eng. 2020 Apr 21. pii: S1096-7176(20)30065-3. [Epub ahead of print]

α-ketobutyrate links alterations in cystine metabolism to glucose oxidation in mtDNA mutant cells.

Nicholas P Lesner, Amrita Gokhale, Kalyani Kota, Ralph J DeBerardinis, Prashant Mishra.

  Pathogenic mutations in the mitochondrial genome (mtDNA) impair organellar ATP production, requiring mutant cells to activate metabolic adaptations for survival. Understanding how metabolism adapts to clinically relevant mtDNA mutations may provide insight into cellular strategies for metabolic flexibility. In this study, we use 13C isotope tracing and metabolic flux analysis to investigate central carbon and amino acid metabolic reprogramming in isogenic cells containing mtDNA mutations. We identify alterations in glutamine and cystine transport which indirectly regulate mitochondrial metabolism and electron transport chain function. Metabolism of cystine can promote glucose oxidation through the transsulfuration pathway and the production of α-ketobutyrate. Intriguingly, activating or inhibiting α-ketobutyrate production is sufficient to modulate both glucose oxidation and mitochondrial respiration in mtDNA mutant cells. Thus, cystine-stimulated transsulfuration serves as an adaptive mechanism linking glucose oxidation and amino acid metabolism in the setting of mtDNA mutations.

Keywords:  Metabolic reprogramming; Transsulfuration; mtDNA mutations

DOI:  https://doi.org/10.1016/j.ymben.2020.03.010
Sci Signal. 2020 Apr 21. pii: eaaz6206. [Epub ahead of print]13(628):

Mitochondrial pyruvate and fatty acid flux modulate MICU1-dependent control of MCU activity.

Neeharika Nemani, Zhiwei Dong, Cassidy C Daw, Travis R Madaris, Karthik Ramachandran, Benjamin T Enslow, Cherubina S Rubannelsonkumar, Santhanam Shanmughapriya, Varshini Mallireddigari, Soumya Maity, Pragya SinghMalla, Kalimuthusamy Natarajanseenivasan, Robert Hooper, Christopher E Shannon, Warren G Tourtellotte, Brij B Singh, W Brian Reeves, Kumar Sharma, Luke Norton, Subramanya Srikantan, Jonathan Soboloff, Muniswamy Madesh.

The tricarboxylic acid (TCA) cycle converts the end products of glycolysis and fatty acid β-oxidation into the reducing equivalents NADH and FADH2 Although mitochondrial matrix uptake of Ca2+ enhances ATP production, it remains unclear whether deprivation of mitochondrial TCA substrates alters mitochondrial Ca2+ flux. We investigated the effect of TCA cycle substrates on MCU-mediated mitochondrial matrix uptake of Ca2+, mitochondrial bioenergetics, and autophagic flux. Inhibition of glycolysis, mitochondrial pyruvate transport, or mitochondrial fatty acid transport triggered expression of the MCU gatekeeper MICU1 but not the MCU core subunit. Knockdown of mitochondrial pyruvate carrier (MPC) isoforms or expression of the dominant negative mutant MPC1R97W resulted in increased MICU1 protein abundance and inhibition of MCU-mediated mitochondrial matrix uptake of Ca2+ We also found that genetic ablation of MPC1 in hepatocytes and mouse embryonic fibroblasts resulted in reduced resting matrix Ca2+, likely because of increased MICU1 expression, but resulted in changes in mitochondrial morphology. TCA cycle substrate-dependent MICU1 expression was mediated by the transcription factor early growth response 1 (EGR1). Blocking mitochondrial pyruvate or fatty acid flux was linked to increased autophagy marker abundance. These studies reveal a mechanism that controls the MCU-mediated Ca2+ flux machinery and that depends on TCA cycle substrate availability. This mechanism generates a metabolic homeostatic circuit that protects cells from bioenergetic crisis and mitochondrial Ca2+ overload during periods of nutrient stress.

DOI: https://doi.org/10.1126/scisignal.aaz6206
Autophagy. 2020 Apr 22. 1-3

Methylmalonyl acidemia: from mitochondrial metabolism to defective mitophagy and disease.

Alessandro Luciani, Olivier Devuyst.

  Methylmalonic acidemia (MMA) is an autosomal recessive inborn error of metabolism due to the deficiency of mitochondrial MMUT (methylmalonyl-CoA mutase) - an enzyme that mediates the cellular breakdown of certain amino acids and lipids. The loss of MMUT leads to the accumulation of toxic organic acids causing severe organ dysfunctions and life-threatening complications. The mechanisms linking MMUT deficiency, mitochondrial alterations and cell toxicity remain uncharacterized. Using cell and animal-based models, we recently unveiled that MMUT deficiency impedes the PINK1-induced translocation of PRKN/Parkin to MMA-damaged mitochondria, thereby halting their delivery and subsequent degradation by macroautophagy/autophagy-lysosome systems. In turn, this defective mitophagy process instigates the accumulation of dysfunctional mitochondria that spark epithelial distress and tissue damage. Correction of PINK1-directed mitophagy defects or mitochondrial dysfunctions rescues epithelial distress in MMA cells and alleviates disease-relevant phenotypes in mmut‒deficient zebrafish. Our findings suggest a link between primary MMUT deficiency and diseased mitochondria, mitophagy dysfunction and cell distress, offering potential therapeutic perspectives for MMA and other metabolic diseases.

Keywords:  Cell damage; inherited metabolic disorders; kidney tubule; metabolism; mitochondria; mitophagy; oxidative stress

DOI:  https://doi.org/10.1080/15548627.2020.1753927
Mol Genet Metab. 2020 Apr 03. pii: S1096-7192(20)30081-0. [Epub ahead of print]

Regional metabolic signatures in the Ndufs4(KO) mouse brain implicate defective glutamate/α-ketoglutarate metabolism in mitochondrial disease.

Simon C Johnson, Ernst-Bernhard Kayser, Rebecca Bornstein, Julia Stokes, Alessandro Bitto, Kyung Yeon Park, Amanda Pan, Grace Sun, Daniel Raftery, Matt Kaeberlein, Margaret M Sedensky, Philip G Morgan.

  Leigh Syndrome (LS) is a mitochondrial disorder defined by progressive focal neurodegenerative lesions in specific regions of the brain. Defects in NDUFS4, a subunit of complex I of the mitochondrial electron transport chain, cause LS in humans; the Ndufs4 knockout mouse (Ndufs4(KO)) closely resembles the human disease. Here, we probed brain region-specific molecular signatures in pre-symptomatic Ndufs4(KO) to identify factors which underlie focal neurodegeneration. Metabolomics revealed that free amino acid concentrations are broadly different by region, and glucose metabolites are increased in a manner dependent on both region and genotype. We then tested the impact of the mTOR inhibitor rapamycin, which dramatically attenuates LS in Ndufs4(KO), on region specific metabolism. Our data revealed that loss of Ndufs4 drives pathogenic changes to CNS glutamine/glutamate/α-ketoglutarate metabolism which are rescued by mTOR inhibition Finally, restriction of the Ndufs4 deletion to pre-synaptic glutamatergic neurons recapitulated the whole-body knockout. Together, our findings are consistent with mTOR inhibition alleviating disease by increasing availability of α-ketoglutarate, which is both an efficient mitochondrial complex I substrate in Ndufs4(KO) and an important metabolite related to neurotransmitter metabolism in glutamatergic neurons.

Keywords:  Genetics; Leigh syndrome; Metabolism; Mitochondria; Mouse; Rapamycin; Reactive oxygen species

DOI:  https://doi.org/10.1016/j.ymgme.2020.03.007
J Cell Biol. 2020 Apr 06. pii: e201911122. [Epub ahead of print]219(4):

Fission and fusion machineries converge at ER contact sites to regulate mitochondrial morphology.

Robert G Abrisch, Samantha C Gumbin, Brett Taylor Wisniewski, Laura L Lackner, Gia K Voeltz.

The steady-state morphology of the mitochondrial network is maintained by a balance of constitutive fission and fusion reactions. Disruption of this steady-state morphology results in either a fragmented or elongated network, both of which are associated with altered metabolic states and disease. How the processes of fission and fusion are balanced by the cell is unclear. Here we show that mitochondrial fission and fusion are spatially coordinated at ER membrane contact sites (MCSs). Multiple measures indicate that the mitochondrial fusion machinery, Mitofusins, accumulate at ER MCSs where fusion occurs. Furthermore, fission and fusion machineries colocalize to form hotspots for membrane dynamics at ER MCSs that can persist through sequential events. Because these hotspots can undergo fission and fusion, they have the potential to quickly respond to metabolic cues. Indeed, we discover that ER MCSs define the interface between polarized and depolarized segments of mitochondria and can rescue the membrane potential of damaged mitochondria by ER-associated fusion.

DOI: https://doi.org/10.1083/jcb.201911122
Aging (Albany NY). 2020 Apr 08. 12(7): 6260-6275

Myotonic Dystrophy type 1 cells display impaired metabolism and mitochondrial dysfunction that are reversed by metformin.

Mikel García-Puga, Ander Saenz-Antoñanzas, Roberto Fernández-Torrón, Adolfo Lopez de Munain, Ander Matheu.

  Myotonic dystrophy type 1 (DM1; MIM #160900) is an autosomal dominant disorder, clinically characterized by progressive muscular weakness and multisystem degeneration. The broad phenotypes observed in patients with DM1 resemble the appearance of a multisystem accelerated aging process. However, the molecular mechanisms underlying these phenotypes remain largely unknown. In this study, we characterized the impact of metabolism and mitochondria on fibroblasts and peripheral blood mononuclear cells (PBMCs) derived from patients with DM1 and healthy individuals. Our results revealed a decrease in oxidative phosphorylation system (OXPHOS) activity, oxygen consumption rate (OCR), ATP production, energy metabolism, and mitochondrial dynamics in DM1 fibroblasts, as well as increased accumulation of reactive oxygen species (ROS). PBMCs of DM1 patients also displayed reduced mitochondrial dynamics and energy metabolism. Moreover, treatment with metformin reversed the metabolic and mitochondrial defects as well as additional accelerated aging phenotypes, such as impaired proliferation, in DM1-derived fibroblasts. Our results identify impaired cell metabolism and mitochondrial dysfunction as important drivers of DM1 pathophysiology and, therefore, reveal the efficacy of metformin treatment in a pre-clinical setting.

Keywords:  aging; metabolism; metformin; mitochondria; myotonic dystrophy type 1; neuromuscular disease

DOI:  https://doi.org/10.18632/aging.103022
Trends Cell Biol. 2020 Apr 16. pii: S0962-8924(20)30070-2. [Epub ahead of print]

Noncanonical Cell Fate Regulation by Bcl-2 Proteins.

Stephen Jun Fei Chong, Saverio Marchi, Giulia Petroni, Guido Kroemer, Lorenzo Galluzzi, Shazib Pervaiz.

  Bcl-2 proteins are widely known as key controllers of mitochondrial outer membrane permeabilization, arguably the most important step of intrinsic apoptosis. Accumulating evidence indicate that most, if not all, members of the Bcl-2 protein family also mediate a number of apoptosis-unrelated functions. Intriguingly, many of these functions ultimately impinge on cell fate decisions via apoptosis-dependent or -independent mechanisms, delineating a complex network through which Bcl-2 family members regulate cell survival and death. Here, we critically discuss the mechanisms through which Bcl-2 proteins influence cell fate as they regulate autophagy, cellular senescence, inflammation, bioenergetic metabolism, Ca2+ fluxes, and redox homeostasis.

Keywords:  BCL-X(L); BH3 mimetics; MCL1; cancer; immunity; oxidative phosphorylation

DOI:  https://doi.org/10.1016/j.tcb.2020.03.004
Proc Natl Acad Sci U S A. 2020 Apr 20. pii: 201913633. [Epub ahead of print]

Triptolide suppresses IDH1-mutated malignancy via Nrf2-driven glutathione metabolism.

Di Yu, Yang Liu, Yiqiang Zhou, Victor Ruiz-Rodado, Mioara Larion, Guowang Xu, Chunzhang Yang.

  Isocitrate dehydrogenase (IDH) mutation is a common genetic abnormality in human malignancies characterized by remarkable metabolic reprogramming. Our present study demonstrated that IDH1-mutated cells showed elevated levels of reactive oxygen species and higher demands on Nrf2-guided glutathione de novo synthesis. Our findings showed that triptolide, a diterpenoid epoxide from Tripterygium wilfordii, served as a potent Nrf2 inhibitor, which exhibited selective cytotoxicity to patient-derived IDH1-mutated glioma cells in vitro and in vivo. Mechanistically, triptolide compromised the expression of GCLC, GCLM, and SLC7A11, which disrupted glutathione metabolism and established synthetic lethality with reactive oxygen species derived from IDH1 mutant neomorphic activity. Our findings highlight triptolide as a valuable therapeutic approach for IDH1-mutated malignancies by targeting the Nrf2-driven glutathione synthesis pathway.

Keywords:  IDH1 mutation; Nrf2; glutathione; reactive oxygen species; triptolide

DOI:  https://doi.org/10.1073/pnas.1913633117
J Mol Cell Cardiol. 2020 Apr 15. pii: S0022-2828(20)30099-7. [Epub ahead of print]

Mitofusins as mitochondrial anchors and tethers.

Gerald W Dorn.

  Mitochondria have their own genomes and their own agendas. Like their primitive bacterial ancestors, mitochondria interact with their environment and organelle colleagues at their physical interfaces, the outer mitochondrial membrane. Among outer membrane proteins, mitofusins (MFN) are increasingly recognized for their roles as arbiters of mitochondria-mitochondria and mitochondria-reticular interactions. This review examines the roles of MFN1 and MFN2 in the heart and other organs as proteins that tether mitochondria to each other or to other organelles, and as mitochondrial anchoring proteins for various macromolecular complexes. The consequences of MFN-mediated tethering and anchoring on mitochondrial fusion, motility, mitophagy, and mitochondria-ER calcium cross-talk are reviewed. Pathophysiological implications are explored from the perspective of mitofusin common functioning as tethering and anchoring proteins, rather than as mediators of individual processes. Finally, some informed speculation is provided for why mouse MFN knockout studies show severe multi-system phenotypes whereas rare human diseases linked to MFN mutations are limited in scope.

Keywords:  Metabolism; Mitochondrial dynamics; Mitochondrial fusion; Mitochondrial transport; Mitophagy

DOI:  https://doi.org/10.1016/j.yjmcc.2020.04.016
Curr Opin Biotechnol. 2020 Apr 15. pii: S0958-1669(20)30035-5. [Epub ahead of print]64 151-160

Metabolic flux analysis and fluxomics-driven determination of reaction free energy using multiple isotopes.

Jimmy Xu, Julia Martien, Cole Gilbertson, Junyu Ma, Daniel Amador-Noguez, Junyoung O Park.

Metabolite concentrations, fluxes, and free energies constitute the basis for understanding and controlling metabolism. Mass spectrometry and stable isotopes are integral tools in quantifying these metabolic features. For absolute metabolite concentration and flux measurement, 13C internal standards and tracers have been the gold standard. In contrast, no established methods exist for comprehensive thermodynamic quantitation under physiological environments. Recently, using high-resolution mass spectrometry and multi-isotope tracing, flux quantitation has been increasingly adopted in broader metabolism. The improved flux quantitation led to determination of Gibbs free energy of reaction (ΔG) in central carbon metabolism using a relationship between reaction reversibility and thermodynamic driving force. Here we highlight recent advances in multi-isotope tracing for metabolic flux and free energy analysis.

DOI: https://doi.org/10.1016/j.copbio.2020.02.018
Biol Chem. 2020 Apr 01. pii: /j/bchm.just-accepted/hsz-2020-0133/hsz-2020-0133.xml. [Epub ahead of print]

New horizons in mitochondrial contact site research.

Naama Zung, Maya Schuldiner.

  Contact sites, areas where two organelles are held in close proximity through the action of molecular tethers, enable non-vesicular communication between compartments. Mitochondria have been center stage in the contact site field since the discovery of the first contact between mitochondria and the endoplasmic reticulum (ER) over 60 years ago. However, only now, in the last decade, has there been a burst of discoveries regarding contact site biology in general and mitochondrial contacts specifically. The number and types of characterized contacts increased dramatically, new molecular mechanisms enabling contact formation were discovered, additional unexpected functions for contacts were shown, and their roles in cellular and organismal physiology were emphasized. Here, we focus on mitochondria as we highlight the most recent developments, future goals and unresolved questions in the field.

Keywords:  contact-site; disease; intra-cellular communication; mitochondria; organelles; tethers

DOI:  https://doi.org/10.1515/hsz-2020-0133
EMBO J. 2020 Apr 20. e102539

Tollip coordinates Parkin-dependent trafficking of mitochondrial-derived vesicles.

Thomas A Ryan, Elliott O Phillips, Charlotte L Collier, Alice Jb Robinson, Daniel Routledge, Rebecca E Wood, Emelia A Assar, David A Tumbarello.

  Multiple mitochondrial quality control pathways exist to maintain the health of mitochondria and ensure cell homeostasis. Here, we investigate the role of the endosomal adaptor Tollip during the mitochondrial stress response and identify its interaction and colocalisation with the Parkinson's disease-associated E3 ubiquitin ligase Parkin. The interaction between Tollip and Parkin is dependent on the ubiquitin-binding CUE domain of Tollip, but independent of Tom1 and mitophagy. Interestingly, this interaction is independent of Parkin mitochondrial recruitment and ligase activity but requires an intact ubiquitin-like (UBL) domain. Importantly, Tollip regulates Parkin-dependent endosomal trafficking of a discrete subset of mitochondrial-derived vesicles (MDVs) to facilitate delivery to lysosomes. Retromer function and an interaction with Tom1 allow Tollip to facilitate late endosome/lysosome trafficking in response to mitochondrial stress. We find that upregulation of TOM20-positive MDVs upon mitochondrial stress requires Tollip interaction with ubiquitin, endosomal membranes and Tom1 to ensure their trafficking to the lysosomes. Thus, we conclude that Tollip, via an association with Parkin, is an essential coordinator to sort damaged mitochondrial-derived cargo to the lysosomes.

Keywords:  Parkinson's disease; lysosome; membrane trafficking; mitochondria; vesicle transport

DOI:  https://doi.org/10.15252/embj.2019102539
Cell Rep. 2020 Apr 21. pii: S2211-1247(20)30431-9. [Epub ahead of print]31(3): 107531

Rational Design of Allosteric and Selective Inhibitors of the Molecular Chaperone TRAP1.

Carlos Sanchez-Martin, Elisabetta Moroni, Mariarosaria Ferraro, Claudio Laquatra, Giuseppe Cannino, Ionica Masgras, Alessandro Negro, Paolo Quadrelli, Andrea Rasola, Giorgio Colombo.

  TRAP1 is the mitochondrial paralog of the heat shock protein 90 (HSP90) chaperone family. Its activity as an energy metabolism regulator has important implications in cancer, neurodegeneration, and ischemia. Selective inhibitors of TRAP1 could inform on its mechanisms of action and set the stage for targeted drug development, but their identification was hampered by the similarity among active sites in HSP90 homologs. We use a dynamics-based approach to identify a TRAP1 allosteric pocket distal to its active site that can host drug-like molecules, and we select small molecules with optimal stereochemical features to target the pocket. These leads inhibit TRAP1, but not HSP90, ATPase activity and revert TRAP1-dependent downregulation of succinate dehydrogenase activity in cancer cells and in zebrafish larvae. TRAP1 inhibitors are not toxic per se, but they abolish tumorigenic growth of neoplastic cells. Our results indicate that exploiting conformational dynamics can expand the chemical space of chaperone antagonists to TRAP1-specific inhibitors with wide therapeutic opportunities.

Keywords:  HSP90; TRAP1; allosteric ligands; anticancer compound; cancer cells; chaperone inhibitors; mitochondria; mitochondrial biology; molecular dynamics; neurofibroma; zebrafish

DOI:  https://doi.org/10.1016/j.celrep.2020.107531
Cancers (Basel). 2020 Apr 22. pii: E1031. [Epub ahead of print]12(4):

The Mitochondrial Protein VDAC1 at the Crossroads of Cancer Cell Metabolism: The Epigenetic Link.

Zohar Amsalem, Tasleem Arif, Anna Shteinfer-Kuzmine, Vered Chalifa-Caspi, Varda Shoshan-Barmatz.

  Carcinogenesis is a complicated process that involves the deregulation of epigenetics, resulting in cellular transformational events, such as proliferation, differentiation, and metastasis. Most chromatin-modifying enzymes utilize metabolites as co-factors or substrates and thus are directly dependent on such metabolites as acetyl-coenzyme A, S-adenosylmethionine, and NAD+. Here, we show that using specific siRNA to deplete a tumor of VDAC1 not only led to reprograming of the cancer cell metabolism but also altered several epigenetic-related enzymes and factors. VDAC1, in the outer mitochondrial membrane, controls metabolic cross-talk between the mitochondria and the rest of the cell, thus regulating the metabolic and energetic functions of mitochondria, and has been implicated in apoptotic-relevant events. We previously demonstrated that silencing VDAC1 expression in glioblastoma (GBM) U-87MG cell-derived tumors, resulted in reprogramed metabolism leading to inhibited tumor growth, angiogenesis, epithelial-mesenchymal transition and invasiveness, and elimination of cancer stem cells, while promoting the differentiation of residual tumor cells into neuronal-like cells. These VDAC1 depletion-mediated effects involved alterations in transcription factors regulating signaling pathways associated with cancer hallmarks. As the epigenome is sensitive to cellular metabolism, this study was designed to assess whether depleting VDAC1 affects the metabolism-epigenetics axis. Using DNA microarrays, q-PCR, and specific antibodies, we analyzed the effects of si-VDAC1 treatment of U-87MG-derived tumors on histone modifications and epigenetic-related enzyme expression levels, as well as the methylation and acetylation state, to uncover any alterations in epigenetic properties. Our results demonstrate that metabolic rewiring of GBM via VDAC1 depletion affects epigenetic modifications, and strongly support the presence of an interplay between metabolism and epigenetics.

Keywords:  VDAC1; cancer; histones epigenetics; metabolism; mitochondria

DOI:  https://doi.org/10.3390/cancers12041031
Mol Cell Proteomics. 2020 Apr 21. pii: mcp.RA120.002076. [Epub ahead of print]

HIGD2A is required for assembly of the COX3 module of human mitochondrial complex IV.

Daniella H Hock, Boris Reljic, Ching-Seng Ang, Linden Muellner-Wong, Hayley S Mountford, Alison G Compton, Michael T Ryan, David R Thorburn, David A Stroud.

  Assembly factors play a critical role in the biogenesis of mitochondrial respiratory chain complexes I-IV where they assist in the membrane insertion of subunits, attachment of co-factors, and stabilization of assembly intermediates. The major fraction of complexes I, III and IV are present together in large molecular structures known as respiratory chain supercomplexes. A number of assembly factors have been proposed as required for supercomplex assembly, including the hypoxia inducible gene 1 domain family member HIGD2A. Using gene-edited human cell lines and extensive steady state, translation and affinity enrichment proteomics techniques we show that loss of HIGD2A leads to defects in the de novo biogenesis of mtDNA-encoded COX3, subsequent accumulation of complex IV intermediates and turnover of COX3 partner proteins. Deletion of HIGD2A also leads to defective complex IV activity. The impact of HIGD2A loss on complex IV was not altered by growth under hypoxic conditions, consistent with its role being in basal complex IV assembly. While in the absence of HIGD2A we show that mitochondria do contain an altered supercomplex assembly, we demonstrate it to harbor a crippled complex IV lacking COX3. Our results redefine HIGD2A as a classical assembly factor required for building the COX3 module of complex IV.

Keywords:  Cytochrome c oxidase; Energy metabolism; Knockouts*; Mitochondria function or biology; Mitochondrial disease; OXPHOS; Translation*; mitochondria; mtDNA translation; respirasome

DOI:  https://doi.org/10.1074/mcp.RA120.002076
Cell Rep. 2020 Apr 21. pii: S2211-1247(20)30441-1. [Epub ahead of print]31(3): 107541

Dissecting the Roles of Mitochondrial Complex I Intermediate Assembly Complex Factors in the Biogenesis of Complex I.

Luke E Formosa, Linden Muellner-Wong, Boris Reljic, Alice J Sharpe, Thomas D Jackson, Traude H Beilharz, Diana Stojanovski, Michael Lazarou, David A Stroud, Michael T Ryan.

  Mitochondrial complex I harbors 7 mitochondrial and 38 nuclear-encoded subunits. Its biogenesis requires the assembly and integration of distinct intermediate modules, mediated by numerous assembly factors. The mitochondrial complex I intermediate assembly (MCIA) complex, containing assembly factors NDUFAF1, ECSIT, ACAD9, and TMEM126B, is required for building the intermediate ND2-module. The role of the MCIA complex and the involvement of other proteins in the biogenesis of this module is unclear. Cell knockout studies reveal that while each MCIA component is critical for complex I assembly, a hierarchy of stability exists centered on ACAD9. We also identify TMEM186 and COA1 as bona fide components of the MCIA complex with loss of either resulting in MCIA complex defects and reduced complex I assembly. TMEM186 enriches with newly translated ND3, and COA1 enriches with ND2. Our findings provide new functional insights into the essential nature of the MCIA complex in complex I assembly.

Keywords:  MCIA complex; NADH-ubiquinone dehydrogenase; assembly factors; complex I; mitochondria; oxidative phosphorylation

DOI:  https://doi.org/10.1016/j.celrep.2020.107541
Nat Metab. 2019 Sep;1(9): 886-898

Mitochondrial lipoylation integrates age-associated decline in brown fat thermogenesis.

Kazuki Tajima, Kenji Ikeda, Hsin-Yi Chang, Chih-Hsiang Chang, Takeshi Yoneshiro, Yasuo Oguri, Heejin Jun, Jun Wu, Yasushi Ishihama, Shingo Kajimura.

  Thermogenesis in brown adipose tissue (BAT) declines with age; however, what regulates this process remains poorly understood. Here, we identify mitochondria lipoylation as a previously unappreciated molecular hallmark of aged BAT in mice. Using mitochondrial proteomics, we show that mitochondrial lipoylation is disproportionally reduced in aged BAT through a post-transcriptional decrease in the iron-sulfur (Fe-S) cluster formation pathway. A defect in the Fe-S cluster formation by the fat-specific deletion of Bola3 significantly reduces mitochondrial lipoylation and fuel oxidation in BAT, leading to glucose intolerance and obesity. In turn, enhanced mitochondrial lipoylation by α-lipoic acid supplementation effectively restores BAT function in old mice, thereby preventing age-associated obesity and glucose intolerance. The effect of α-lipoic acids requires mitochondrial lipoylation via the Bola3 pathway and does not depend on the anti-oxidant activity of α-lipoic acid. These results open up the possibility to alleviate the age-associated decline in energy expenditure by enhancing the mitochondrial lipoylation pathway.

Keywords:  Brown adipose tissue; Glucose metabolism; Mitochondria; Thermogenesis

DOI:  https://doi.org/10.1038/s42255-019-0106-z
EMBO Rep. 2020 Apr 23. e50071

20,000 picometers under the OMM: diving into the vastness of mitochondrial metabolite transport.

Corey N Cunningham, Jared Rutter.

  The metabolic compartmentalization enabled by mitochondria is key feature of many cellular processes such as energy conversion to ATP production, redox balance, and the biosynthesis of heme, urea, nucleotides, lipids, and others. For a majority of these functions, metabolites need to be transported across the impermeable inner mitochondrial membrane by dedicated carrier proteins. Here, we examine the substrates, structural features, and human health implications of four mitochondrial metabolite carrier families: the SLC25A family, the mitochondrial ABCB transporters, the mitochondrial pyruvate carrier (MPC), and the sideroflexin proteins.

Keywords:  metabolism; metabolite carriers; mitochondria; transporters

DOI:  https://doi.org/10.15252/embr.202050071
Front Oncol. 2020 ;10 499

EMT Factors and Metabolic Pathways in Cancer.

Ilias Georgakopoulos-Soares, Dionysios V Chartoumpekis, Venetsana Kyriazopoulou, Apostolos Zaravinos.

  The epithelial-mesenchymal transition (EMT) represents a biological program during which epithelial cells lose their cell identity and acquire a mesenchymal phenotype. EMT is normally observed during organismal development, wound healing and tissue fibrosis. However, this process can be hijacked by cancer cells and is often associated with resistance to apoptosis, acquisition of tissue invasiveness, cancer stem cell characteristics, and cancer treatment resistance. It is becoming evident that EMT is a complex, multifactorial spectrum, often involving episodic, transient or partial events. Multiple factors have been causally implicated in EMT including transcription factors (e.g., SNAIL, TWIST, ZEB), epigenetic modifications, microRNAs (e.g., miR-200 family) and more recently, long non-coding RNAs. However, the relevance of metabolic pathways in EMT is only recently being recognized. Importantly, alterations in key metabolic pathways affect cancer development and progression. In this review, we report the roles of key EMT factors and describe their interactions and interconnectedness. We introduce metabolic pathways that are involved in EMT, including glycolysis, the TCA cycle, lipid and amino acid metabolism, and characterize the relationship between EMT factors and cancer metabolism. Finally, we present therapeutic opportunities involving EMT, with particular focus on cancer metabolic pathways.

Keywords:  EMT; cancer metabolism; metabolic pathways; non-coding RNAs; transcription factors

DOI:  https://doi.org/10.3389/fonc.2020.00499
Nat Commun. 2020 Apr 21. 11(1): 1924

A kinome-wide screen identifies a CDKL5-SOX9 regulatory axis in epithelial cell death and kidney injury.

Ji Young Kim, Yuntao Bai, Laura A Jayne, Ralph D Hector, Avinash K Persaud, Su Sien Ong, Shreshtha Rojesh, Radhika Raj, Mei Ji He Ho Feng, Sangwoon Chung, Rachel E Cianciolo, John W Christman, Moray J Campbell, David S Gardner, Sharyn D Baker, Alex Sparreboom, Rajgopal Govindarajan, Harpreet Singh, Taosheng Chen, Ming Poi, Katalin Susztak, Stuart R Cobb, Navjot Singh Pabla.

Renal tubular epithelial cells (RTECs) perform the essential function of maintaining the constancy of body fluid composition and volume. Toxic, inflammatory, or hypoxic-insults to RTECs can cause systemic fluid imbalance, electrolyte abnormalities and metabolic waste accumulation- manifesting as acute kidney injury (AKI), a common disorder associated with adverse long-term sequelae and high mortality. Here we report the results of a kinome-wide RNAi screen for cellular pathways involved in AKI-associated RTEC-dysfunction and cell death. Our screen and validation studies reveal an essential role of Cdkl5-kinase in RTEC cell death. In mouse models, genetic or pharmacological Cdkl5 inhibition mitigates nephrotoxic and ischemia-associated AKI. We propose that Cdkl5 is a stress-responsive kinase that promotes renal injury in part through phosphorylation-dependent suppression of pro-survival transcription regulator Sox9. These findings reveal a surprising non-neuronal function of Cdkl5, identify a pathogenic Cdkl5-Sox9 axis in epithelial cell-death, and support CDKL5 antagonism as a therapeutic approach for AKI.

DOI: https://doi.org/10.1038/s41467-020-15638-6
J Clin Invest. 2020 Apr 21. pii: 129049. [Epub ahead of print]

HDAC inhibitors elicit metabolic reprogramming by targeting super-enhancers in glioblastoma models.

Trang Nguyen, Yiru Zhang, Enyuan Shang, Chang Shu, Consuelo Torrini, Junfei Zhao, Elena Bianchetti, Angeliki Mela, Nelson Humala, Aayushi Mahajan, Arif O Harmanci, Zhengdeng Lei, Mark Maienschein-Cline, Catarina Maria Quinzii, Mike-Andrew Westhoff, Georg Karpel-Massler, Jeffrey N Bruce, Peter Canoll, Markus D Siegelin.

  The Warburg effect is a tumor related phenomenon that may be targeted therapeutically. Here, we showed that glioblastoma cultures and patient tumors harbored super-enhancers in several genes related to the Warburg effect. By conducting a transcriptome analysis followed by chromatin immunoprecipitation (CHIP) sequencing coupled with a comprehensive metabolite analysis in GBM models, we unraveled that FDA-approved global (panobinostat, vorinostat) and selective (romidepsin) histone-deacetylase (HDAC) inhibitors elicited metabolic reprogramming in concert with disruption of several Warburg-effect related super-enhancers. Extracellular flux and carbon tracing analyses revealed that HDAC inhibitors blunted glycolysis in a c-Myc dependent manner accompanied by lower ATP levels. This resulted in engagement of oxidative phosphorylation (OXPHOS) driven by elevated fatty acid oxidation (FAO), rendering GBM cells dependent on these pathways. Mechanistically, interference with HDAC1/2 elicited a suppression of c-Myc protein levels and a concomitant increase of two transcriptional drivers of oxidative metabolism, PGC1A and PPARD, suggesting an inverse relationship. Rescue and CHIP experiments indicated that c-Myc bound to the promoter regions of PGC1A and PPARD to counteract their up-regulation driven by HDAC1/2 inhibition. Finally, we demonstrated that the combination treatment of HDAC and FAO inhibitors extended animal survival in patient-derived xenograft (PDX) model systems in vivo more potently than single treatments in the absence of toxicity.

Keywords:  Intermediary metabolism; Oncology

DOI:  https://doi.org/10.1172/JCI129049
Trends Biochem Sci. 2020 May;pii: S0968-0004(20)30034-7. [Epub ahead of print]45(5): 411-426

Outlining the Complex Pathway of Mammalian Fe-S Cluster Biogenesis.

Nunziata Maio, Tracey A Rouault.

  Iron-sulfur (Fe-S) clusters (ISCs) are ubiquitous cofactors essential to numerous fundamental cellular processes. Assembly of ISCs and their insertion into apoproteins involves the function of complex cellular machineries that operate in parallel in the mitochondrial and cytosolic/nuclear compartments of mammalian cells. The spectrum of diseases caused by inherited defects in genes that encode the Fe-S assembly proteins has recently expanded to include multiple rare human diseases, which manifest distinctive combinations and severities of global and tissue-specific impairments. In this review, we provide an overview of our understanding of ISC biogenesis in mammalian cells, discuss recent work that has shed light on the molecular interactions that govern ISC assembly, and focus on human diseases caused by failures of the biogenesis pathway.

Keywords:  CIAO1; FAM96B; HSC20; HSPA9; MMS19; frataxin; mitochondrial iron overload; multiple mitochondrial dysfunctions syndromes; secondary carriers

DOI:  https://doi.org/10.1016/j.tibs.2020.02.001
Cell Death Dis. 2020 Apr 20. 11(4): 251

Drp1 regulates mitochondrial dysfunction and dysregulated metabolism in ischemic injury via Clec16a-, BAX-, and GSH- pathways.

Chenyang Duan, Lei Kuang, Xinming Xiang, Jie Zhang, Yu Zhu, Yue Wu, Qingguang Yan, Liangming Liu, Tao Li.

The adaptation of mitochondrial homeostasis to ischemic injury is not fully understood. Here, we studied the role of dynamin-related protein 1 (Drp1) in this process. We found that mitochondrial morphology was altered in the early stage of ischemic injury while mitochondrial dysfunction occurred in the late stage of ischemia. Drp1 appeared to inhibit mitophagy by upregulating mito-Clec16a, which suppressed mito-Parkin recruitment and subsequently impaired the formation of autophagosomes in vascular tissues after ischemic injury. Moreover, ischemia-induced Drp1 activation enhanced apoptosis through inducing mitochondrial translocation of BAX and thereby increasing release of Cytochrome C to activate caspase-3/-9 signalling. Furthermore, Drp1 mediated metabolic disorders and inhibited the levels of mitochondrial glutathione to impair free radical scavenging, leading to further increases in ROS and the exacerbation of mitochondrial dysfunction after ischemic injury. Together, our data suggest a critical role for Drp1 in ischemic injury.

DOI: https://doi.org/10.1038/s41419-020-2461-9
Nat Commun. 2020 Apr 20. 11(1): 1881

Nitrogen limitation reveals large reserves in metabolic and translational capacities of yeast.

Rosemary Yu, Kate Campbell, Rui Pereira, Johan Björkeroth, Qi Qi, Egor Vorontsov, Carina Sihlbom, Jens Nielsen.

Cells maintain reserves in their metabolic and translational capacities as a strategy to quickly respond to changing environments. Here we quantify these reserves by stepwise reducing nitrogen availability in yeast steady-state chemostat cultures, imposing severe restrictions on total cellular protein and transcript content. Combining multi-omics analysis with metabolic modeling, we find that seven metabolic superpathways maintain >50% metabolic capacity in reserve, with glucose metabolism maintaining >80% reserve capacity. Cells maintain >50% reserve in translational capacity for 2490 out of 3361 expressed genes (74%), with a disproportionately large reserve dedicated to translating metabolic proteins. Finally, ribosome reserves contain up to 30% sub-stoichiometric ribosomal proteins, with activation of reserve translational capacity associated with selective upregulation of 17 ribosomal proteins. Together, our dataset provides a quantitative link between yeast physiology and cellular economics, which could be leveraged in future cell engineering through targeted proteome streamlining.

DOI: https://doi.org/10.1038/s41467-020-15749-0
Int J Mol Sci. 2020 Apr 22. pii: E2947. [Epub ahead of print]21(8):

Crosstalk of lncRNA and Cellular Metabolism and Their Regulatory Mechanism in Cancer.

Yang-Hsiang Lin.

  The imbalanced regulation of metabolic homeostasis and energy production is highly associated with inflammation, tumor growth, metastasis and cancer progression. Both glycolysis and oxidative phosphorylation maintain metabolic homeostasis and energy production in cells. Long noncoding RNAs (lncRNAs) are a class of non-protein-coding transcripts longer than 200 nucleotides. Furthermore, lncRNAs can function as either tumor suppressors or oncogenes in cancer. Dysregulated lncRNAs reportedly regulate cancer hallmarks such as tumor growth, metabolism and metastasis. Accordingly, uncovering the interaction between lncRNAs and cellular metabolism has become a necessity when attempting to identify effective therapeutic and preventive strategies in cancer progression. This review summarizes important knowledge of the actions of known lncRNAs-mediated cancer metabolism.

Keywords:  cancer; glycolysis; lncRNA; mitochondria; therapeutic target

DOI:  https://doi.org/10.3390/ijms21082947
Trends Biochem Sci. 2020 May;pii: S0968-0004(20)30050-5. [Epub ahead of print]45(5): 367-369

Structural Insights into the Activation of mTORC1 on the Lysosomal Surface.

Jin H Park, Gina Lee, John Blenis.

Using cryo-electron microscopy and molecular characterization, David Sabatini and colleagues provide crucial new insights that validate and expand their model of how amino acids are sensed and signal at the lysosome to activate mechanistic target of rapamycin complex 1 (mTORC1) and cell growth-regulating processes. This work also reveals new therapeutic opportunities for mTORC1-driven diseases.

DOI: https://doi.org/10.1016/j.tibs.2020.02.004
Cell Metab. 2020 Apr 17. pii: S1550-4131(20)30188-1. [Epub ahead of print]

Deamidation Shunts RelA from Mediating Inflammation to Aerobic Glycolysis.

Jun Zhao, Mao Tian, Shu Zhang, Alireza Delfarah, Ruoyun Gao, Youliang Rao, Ali Can Savas, Anjie Lu, Larissa Bubb, Xiao Lei, Rosa Moshirian, Wenjie Zhu, Cheng Peng, Taijiao Jiang, Lin Chen, Nicholas A Graham, Pinghui Feng.

  Cell proliferation and inflammation are two metabolically demanding biological processes. How these competing processes are selectively executed in the same cell remains unknown. Here, we report that the enzyme carbamoyl-phosphate synthetase, aspartyl transcarbamoylase, and dihydroorotase (CAD) deamidates the RelA subunit of NF-κB in cancer cells to promote aerobic glycolysis and fuel cell proliferation in tumorigenesis. This post-translational modification switches RelA function from mediating the expression of NF-κB-responsive genes to that of glycolytic enzymes, thus shunting the cell's inflammatory response to aerobic glycolysis. Further, we profiled diverse human cancer cell lines and found that high CAD expression and a subset of RELA mutations correlated with RelA deamidation. And by use of inhibitors of key glycolytic enzymes, we validated the pivotal role of RelA deamidation in tumorigenesis of cancer cell lines. This work illuminates a mechanism by which protein deamidation selectively specifies gene expression and consequent biological processes.

Keywords:  NF-κB, deamidation, CAD, glycolysis, nucleotide synthesis, cancer stratification, gene expression, cell proliferation, metabolic reprogramming, inflammatory response

DOI:  https://doi.org/10.1016/j.cmet.2020.04.006
Nucleosides Nucleotides Nucleic Acids. 2020 Apr 20. 1-18

Lesch-Nyhan disease: I. Construction of expression vectors for hypoxanthine-guanine phosphoribosyltransferase (HGprt) enzyme and amyloid precursor protein (APP).

Khue Vu Nguyen, Robert K Naviaux, William L Nyhan.

  Lesch-Nyhan disease (LND) is a rare X-linked inherited neurogenetic disorder of purine metabolism in which the enzyme, hypoxanthine-guanine phosphoribosyltransferase (HGprt) is defective. Despite having been characterized over 50 years ago, it remains unclear precisely how deficits in HGprt enzyme activity can lead to the neurological syndrome, especially the self-injury of LND. Several studies have proposed different hypotheses regarding the etiology of this disease, and several treatments have been tried in patients. However, up to now, there is no satisfactory explanation of the disease and for many LND patients, efficacious treatment for persistent self-injurious behavior remains unreachable. A role for epistasis between mutated hypoxanthine phosphoribosyltransferase 1 (HPRT1) and amyloid precursor protein (APP) genes has been recently suggested. This finding may provide new directions not only for investigating the role of APP in neuropathology associated with HGprt-deficiency in LND but also for the research in neurodevelopmental and neurodegenerative disorders in which the APP gene is involved in the pathogenesis of diseases and may pave the way for new strategies applicable to rational antisense drugs design. It is therefore necessary to study the HGprt enzyme and APP using expression vectors for exploring their impacts on LND as well as other human diseases, especially the ones related to APP such as Alzheimer's disease in which the physiologic function and the structure of the entire APP remain largely unclear until now. For such a purpose, we report here the construction of expression vectors as the first step (Part I) of our investigation.

Keywords:  APP gene; HEK 293 cells; HGprt enzyme; HPRT1 gene; Lesch-Nyhan disease; antisense drugs; epigenetics; epistasis; expression vectors; mutation

DOI:  https://doi.org/10.1080/15257770.2020.1714653
Sci Rep. 2020 Apr 20. 10(1): 6655

Epigenetics and Mitochondrial Stability in the Metabolic Memory Phenomenon Associated with Continued Progression of Diabetic Retinopathy.

Renu A Kowluru, Ghulam Mohammad.

Retinopathy continues to progress even when diabetic patients try to control their blood sugar, but the molecular mechanism of this 'metabolic memory' phenomenon remains elusive. Retinal mitochondria remain damaged and vicious cycle of free radicals continues to self-propagate. DNA methylation suppresses gene expression, and diabetes activates DNA methylation machinery. Our aim was to investigate the role of DNA methylation in continued compromised mitochondrial dynamics and genomic stability in diabetic retinopathy. Using retinal endothelial cells, incubated in 20 mM glucose for four days, followed by 5 mM glucose for four days, and retinal microvessels from streptozotocin-induced diabetic rats in poor glycemia for four months, followed by normal glycemia for four additional months, DNA methylation of mitochondrial fusion and mismatch repair proteins, Mfn2 and Mlh1 respectively, was determined. Retinopathy was detected in trypsin-digested microvasculature. Re-institution of good glycemia had no beneficial effect on hypermethylation of Mfn2 and Mlh1 and retinal function (electroretinogram), and the retinopathy continued to progress. However, intervention of good glycemia directly with DNA methylation inhibitors (Azacytidine or Dnmt1-siRNA), prevented Mfn2 and Mlh1 hypermethylation, and ameliorated retinal dysfunction and diabetic retinopathy. Thus, direct regulation of DNA methylation can prevent/reverse diabetic retinopathy by maintaining mitochondrial dynamics and DNA stability, and prevent retinal functional damage.

DOI: https://doi.org/10.1038/s41598-020-63527-1
Proc Natl Acad Sci U S A. 2020 Apr 20. pii: 201913707. [Epub ahead of print]

Starvation and antimetabolic therapy promote cytokine release and recruitment of immune cells.

Franziska Püschel, Francesca Favaro, Jaime Redondo-Pedraza, Estefanía Lucendo, Raffaella Iurlaro, Sandrine Marchetti, Blanca Majem, Eric Eldering, Ernest Nadal, Jean-Ehrland Ricci, Eric Chevet, Cristina Muñoz-Pinedo.

  Cellular starvation is typically a consequence of tissue injury that disrupts the local blood supply but can also occur where cell populations outgrow the local vasculature, as observed in solid tumors. Cells react to nutrient deprivation by adapting their metabolism, or, if starvation is prolonged, it can result in cell death. Cell starvation also triggers adaptive responses, like angiogenesis, that promote tissue reorganization and repair, but other adaptive responses and their mediators are still poorly characterized. To explore this issue, we analyzed secretomes from glucose-deprived cells, which revealed up-regulation of multiple cytokines and chemokines, including IL-6 and IL-8, in response to starvation stress. Starvation-induced cytokines were cell type-dependent, and they were also released from primary epithelial cells. Most cytokines were up-regulated in a manner dependent on NF-κB and the transcription factor of the integrated stress response ATF4, which bound directly to the IL-8 promoter. Furthermore, glutamine deprivation, as well as the antimetabolic drugs 2-deoxyglucose and metformin, also promoted the release of IL-6 and IL-8. Finally, some of the factors released from starved cells induced chemotaxis of B cells, macrophages, and neutrophils, suggesting that nutrient deprivation in the tumor environment can serve as an initiator of tumor inflammation.

Keywords:  cancer immunity; cancer metabolism; cytokines; glucose

DOI:  https://doi.org/10.1073/pnas.1913707117
J Biol Chem. 2020 Apr 20. pii: jbc.RA119.011864. [Epub ahead of print]

The gene for the lysosomal protein LAMP3 is a direct target of the transcription factor ATF4.

Thomas D Burton, Anthony O Fedele, Jianling Xie, Lauren Sandeman, Christopher G Proud.

  Autophagy and lysosomal activities play a key role in the cell by initiating and carrying out the degradation of misfolded proteins. Transcription factor EB (TFEB) functions as a master controller of lysosomal biogenesis and function during lysosomal stress, controlling most, but, importantly, not all lysosomal genes. Here, we sought to better understand the regulation of lysosomal genes whose expression does not appear to be controlled by TFEB. Sixteen of these genes were screened for transactivation in response to diverse cellular insults. mRNA levels for lysosomal-associated membrane protein 3 (LAMP3), a gene that is highly up-regulated in many forms of cancer, including breast and cervical cancers, were significantly increased during the integrated stress response (ISR), which occurs in eukaryotic cells in response to accumulation of unfolded and misfolded proteins. Of note, results from siRNA-mediated knockdown of activating transcription factor 4 (ATF4) and overexpression of exogenous ATF4 cDNA, indicated that ATF4 up-regulates LAMP3 mRNA levels. Finally, ChIP assays verified an ATF4-binding site in the LAMP3 gene promoter, and a dual luciferase assay confirmedthat this ATF4-binding site is indeed required for transcriptional up-regulation of LAMP3 These results reveal that ATF4 directly regulates LAMP3, representing the first identification of a gene for a lysosomal component whose expression is directly controlled by ATF4. This finding may provide a key link between stresses such as accumulation of unfolded proteins and modulation of autophagy, which removes them.

Keywords:  activating transcription factor 4 (ATF4); autophagy; cell stress; eukaryotic initiation factor 2 (eIF2); lysosomal-associated membrane protein 3 (LAMP3); lysosome; mammalian target of rapamycin complex 1 (mTORC1); protein misfolding; transcription factor EB (TFEB); unfolded protein response (UPR)

DOI:  https://doi.org/10.1074/jbc.RA119.011864
J Genet Genomics. 2020 Mar 18. pii: S1673-8527(20)30049-7. [Epub ahead of print]

Defective arginine metabolism impairs mitochondrial homeostasis in Caenorhabditiselegans.

Ruofeng Tang, Xin Wang, Junxiang Zhou, Fengxia Zhang, Shan Zhao, Qiwen Gan, Liyuan Zhao, Fengyang Wang, Qian Zhang, Jie Zhang, Guodong Wang, Chonglin Yang.

  Arginine catabolism involves enzyme-dependent reactions in both mitochondria and the cytosol, defects in which may lead to hyperargininemia, a devastating developmental disorder. It is largely unknown if defective arginine catabolism has any effects on mitochondria. Here we report that normal arginine catabolism is essential for mitochondrial homeostasis in Caenorhabditiselegans. Mutations of the arginase gene argn-1 lead to abnormal mitochondrial enlargement and reduced adenosine triphosphate (ATP) production in C. elegans hypodermal cells. ARGN-1 localizes to mitochondria and its loss causes arginine accumulation, which disrupts mitochondrial dynamics. Heterologous expression of human ARG1 or ARG2 rescued the mitochondrial defects of argn-1 mutants. Importantly, genetic inactivation of the mitochondrial basic amino acid transporter SLC-25A29 or the mitochondrial glutamate transporter SLC-25A18.1 fully suppressed the mitochondrial defects caused by argn-1 mutations. These findings suggest that mitochondrial damage probably contributes to the pathogenesis of hyperargininemia and provide clues for developing therapeutic treatments for hyperargininemia.

Keywords:  Arginase; Arginine; C. elegans; Hyperargininemia; Mitochondrial homeostasis

DOI:  https://doi.org/10.1016/j.jgg.2020.02.007
EMBO Rep. 2020 Apr 23. e50340

Endogenous metabolites promote stress resistance through induction of mitohormesis.

Fabian Fischer, Michael Ristow.

Interventions and small molecules, which promote formation of reactive oxygen species (ROS), have repeatedly been shown to increase stress resistance and lifespan of different model organisms. These phenotypes occur only in response to low concentrations of ROS, while higher concentrations exert opposing effects. This non-linear or hormetic dose-response relationship has been termed mitohormesis, since ROS are mainly generated within the mitochondrial compartment. A report by Matsumura et al in this issue of EMBO Reports now demonstrates that an endogenously formed metabolite, namely N-acetyl-L-tyrosine (NAT), is instrumental in promoting cellular and organismal resilience by inducing mitohormetic mechanisms, likely in an evolutionarily conserved manner [1].

DOI: https://doi.org/10.15252/embr.202050340
Mitochondrion. 2020 Apr 15. pii: S1567-7249(19)30348-4. [Epub ahead of print]

Molecular mechanism of mitochondrial respiratory chain assembly and its relation to mitochondrial diseases.

Soumyajit Mukherjee, Alok Ghosh.

  The mitochondrial respiratory chain (MRC) is comprised of ∼92 nuclear and mitochondrial DNA-encoded protein subunits that are organized into five different multi-subunit respiratory complexes. These complexes produce 90% of the ATP required for cell sustenance. Specific sets of subunits are assembled in a modular or non-modular fashion to construct the MRC complexes. The complete assembly process is gradually chaperoned by a myriad of assembly factors that must coordinate with several other prosthetic groups to reach maturity, makingthe entire processextensively complicated. Further, the individual respiratory complexes can be integrated intovarious giant super-complexes whose functional roles have yet to be explored. Mutations in the MRC subunits and in the related assembly factors often give rise to defects in the proper assembly of the respiratory chain, which then manifests as a group of disorders called mitochondrial diseases, the most common inborn errors of metabolism. This review summarizes the current understanding of the biogenesis of individual MRC complexes and super-complexes, and explores how mutations in the different subunits and assembly factors contribute to mitochondrial disease pathology.

Keywords:  Assembly factors; Mitochondrial diseases; Mitochondrial respiratory chain; Mutations; Super-complexes

DOI:  https://doi.org/10.1016/j.mito.2020.04.002
Cell Death Dis. 2020 Apr 20. 11(4): 254

Loss of AKAP1 triggers Drp1 dephosphorylation-mediated mitochondrial fission and loss in retinal ganglion cells.

Genea Edwards, Guy A Perkins, Keun-Young Kim, YeEun Kong, Yonghoon Lee, Soo-Ho Choi, Yujia Liu, Dorota Skowronska-Krawczyk, Robert N Weinreb, Linda Zangwill, Stefan Strack, Won-Kyu Ju.

Impairment of mitochondrial structure and function is strongly linked to glaucoma pathogenesis. Despite the widely appreciated disease relevance of mitochondrial dysfunction and loss, the molecular mechanisms underlying mitochondrial fragmentation and metabolic stress in glaucoma are poorly understood. We demonstrate here that glaucomatous retinal ganglion cells (RGCs) show loss of A-kinase anchoring protein 1 (AKAP1), activation of calcineurin (CaN) and reduction of dynamin-related protein 1 (Drp1) phosphorylation at serine 637 (Ser637). These findings suggest that AKAP1-mediated phosphorylation of Drp1 at Ser637 has a critical role in RGC survival in glaucomatous neurodegeneration. Male mice lacking AKAP1 show increases in CaN and total Drp1 levels, as well as a decrease in Drp1 phosphorylation at Ser637 in the retina. Ultrastructural analysis of mitochondria shows that loss of AKAP1 triggers mitochondrial fragmentation and loss, as well as mitophagosome formation in RGCs. Loss of AKAP1 deregulates oxidative phosphorylation (OXPHOS) complexes (Cxs) by increasing CxII and decreasing CxIII-V, leading to metabolic and oxidative stress. Also, loss of AKAP1 decreases Akt phosphorylation at Serine 473 (Ser473) and threonine 308 (Thr308) and activates the Bim/Bax signaling pathway in the retina. These results suggest that loss of AKAP1 has a critical role in RGC dysfunction by decreasing Drp1 phosphorylation at Ser637, deregulating OXPHOS, decreasing Akt phosphorylation at Ser473 and Thr308, and activating the Bim/Bax pathway in glaucomatous neurodegeneration. Thus, we propose that overexpression of AKAP1 or modulation of Drp1 phosphorylation at Ser637 are potential therapeutic strategies for neuroprotective intervention in glaucoma and other mitochondria-related optic neuropathies.

DOI: https://doi.org/10.1038/s41419-020-2456-6
Front Oncol. 2020 ;10 476

Altered Iron Metabolism and Impact in Cancer Biology, Metastasis, and Immunology.

Rikki A M Brown, Kirsty L Richardson, Tasnuva D Kabir, Debbie Trinder, Ruth Ganss, Peter J Leedman.

  Iron is an essential nutrient that plays a complex role in cancer biology. Iron metabolism must be tightly controlled within cells. Whilst fundamental to many cellular processes and required for cell survival, excess labile iron is toxic to cells. Increased iron metabolism is associated with malignant transformation, cancer progression, drug resistance and immune evasion. Depleting intracellular iron stores, either with the use of iron chelating agents or mimicking endogenous regulation mechanisms, such as microRNAs, present attractive therapeutic opportunities, some of which are currently under clinical investigation. Alternatively, iron overload can result in a form of regulated cell death, ferroptosis, which can be activated in cancer cells presenting an alternative anti-cancer strategy. This review focuses on alterations in iron metabolism that enable cancer cells to meet metabolic demands required during different stages of tumorigenesis in relation to metastasis and immune response. The strength of current evidence is considered, gaps in knowledge are highlighted and controversies relating to the role of iron and therapeutic targeting potential are discussed. The key question we address within this review is whether iron modulation represents a useful approach for treating metastatic disease and whether it could be employed in combination with existing targeted drugs and immune-based therapies to enhance their efficacy.

Keywords:  cancer biology; drug resistance; ferroptosis; iron chelator; iron metabolism; metastasis; microRNAs; tumor microenvironment

DOI:  https://doi.org/10.3389/fonc.2020.00476
Nat Immunol. 2020 May;21(5): 497-498

A reactive metabolite as an immune suppressant.

Vijyendra Ramesh, Jason W Locasale.

DOI: https://doi.org/10.1038/s41590-020-0664-y
Trends Plant Sci. 2020 May;pii: S1360-1385(20)30027-3. [Epub ahead of print]25(5): 446-454

Malate Circulation: Linking Chloroplast Metabolism to Mitochondrial ROS.

Yannan Zhao, Hong Yu, Jian-Min Zhou, Steven M Smith, Jiayang Li.

  In photosynthetic cells, chloroplasts and mitochondria are the sites of the core redox reactions underpinning energy metabolism. Such reactions generate reactive oxygen species (ROS) when oxygen is partially reduced. ROS signaling leads to responses by cells which enable them to adjust to changes in redox status. Recent studies in Arabidopsis thaliana reveal that chloroplast NADH can be used to generate malate which is exported to the mitochondrion where its oxidation regenerates NADH. Oxidation of this NADH produces mitochondrial ROS (mROS) which can activate signaling systems to modulate energy metabolism, and in certain cases can lead to programmed cell death (PCD). We propose the term 'malate circulation' to describe such redistribution of reducing equivalents to mediate energy homeostasis in the cell.

Keywords:  chloroplast-to-mitochondrion communication; malate circulation; malate valve; programmed cell death; reactive oxygen species; reducing power

DOI:  https://doi.org/10.1016/j.tplants.2020.01.010
Nat Commun. 2020 Apr 24. 11(1): 2018

Methylglyoxal couples metabolic and translational control of Notch signalling in mammalian neural stem cells.

Deivid Carvalho Rodrigues, Emily M Harvey, Rejitha Suraj, Sarah L Erickson, Lamees Mohammad, Mengli Ren, Hongrui Liu, Guiqiong He, David R Kaplan, James Ellis, Guang Yang.

Gene regulation and metabolism are two fundamental processes that coordinate the self-renewal and differentiation of neural precursor cells (NPCs) in the developing mammalian brain. However, little is known about how metabolic signals instruct gene expression to control NPC homeostasis. Here, we show that methylglyoxal, a glycolytic intermediate metabolite, modulates Notch signalling to regulate NPC fate decision. We find that increased methylglyoxal suppresses the translation of Notch1 receptor mRNA in mouse and human NPCs, which is mediated by binding of the glycolytic enzyme GAPDH to an AU-rich region within Notch1 3'UTR. Interestingly, methylglyoxal inhibits the enzymatic activity of GAPDH and engages it as an RNA-binding protein to suppress Notch1 translation. Reducing GAPDH levels or restoring Notch signalling rescues methylglyoxal-induced NPC depletion and premature differentiation in the developing mouse cortex. Taken together, our data indicates that methylglyoxal couples the metabolic and translational control of Notch signalling to control NPC homeostasis.

DOI: https://doi.org/10.1038/s41467-020-15941-2
Int J Mol Sci. 2020 Apr 20. pii: E2872. [Epub ahead of print]21(8):

Non-Coding RNAs as Key Regulators of Glutaminolysis in Cancer.

Yunuen Ortiz-Pedraza, J Omar Muñoz-Bello, Leslie Olmedo-Nieva, Adriana Contreras-Paredes, Imelda Martínez-Ramírez, Elizabeth Langley, Marcela Lizano.

  Cancer cells exhibit exacerbated metabolic activity to maintain their accelerated proliferation and microenvironmental adaptation in order to survive under nutrient-deficient conditions. Tumors display an increase in glycolysis, glutaminolysis and fatty acid biosynthesis, which provide their energy source. Glutamine is critical for fundamental cellular processes, where intermediate metabolites produced through glutaminolysis are necessary for the maintenance of mitochondrial metabolism. These include antioxidants to remove reactive oxygen species, and the generation of the nonessential amino acids, purines, pyrimidines and fatty acids required for cellular replication and the activation of cell signaling. Some cancer cells are highly dependent on glutamine consumption since its catabolism provides an anaplerotic pathway to feed the Krebs cycle. Intermediate members of the glutaminolysis pathway have been found to be deregulated in several types of cancers and have been proposed as therapeutic targets and prognostic biomarkers. This review summarizes the main players in the glutaminolysis pathway, how they have been found to be deregulated in cancer and their implications for cancer maintenance. Furthermore, non-coding RNAs are now recognized as new participants in the regulation of glutaminolysis; therefore, their involvement in glutamine metabolism in cancer is discussed in detail.

Keywords:  cancer; glutaminolysis; lncRNAs; miRNAs

DOI:  https://doi.org/10.3390/ijms21082872
Front Oncol. 2020 ;10 429

Physiological Role of Glutamate Dehydrogenase in Cancer Cells.

Rafael Moreno-Sánchez, Álvaro Marín-Hernández, Juan C Gallardo-Pérez, Silvia C Pacheco-Velázquez, Diana X Robledo-Cadena, Joaquín Alberto Padilla-Flores, Emma Saavedra, Sara Rodríguez-Enríquez.

  NH4+ increased growth rates and final densities of several human metastatic cancer cells. To assess whether glutamate dehydrogenase (GDH) in cancer cells may catalyze the reverse reaction of NH4+ fixation, its covalent regulation and kinetic parameters were determined under near-physiological conditions. Increased total protein and phosphorylation were attained in NH4+ -supplemented metastatic cells, but total cell GDH activity was unchanged. Higher V max values for the GDH reverse reaction vs. forward reaction in both isolated hepatoma (HepM) and liver mitochondria [rat liver mitochondria (RLM)] favored an NH4+ -fixing role. GDH sigmoidal kinetics with NH4+ , ADP, and leucine fitted to Hill equation showed n H values of 2 to 3. However, the K 0.5 values for NH4+ were over 20 mM, questioning the physiological relevance of the GDH reverse reaction, because intracellular NH4+ in tumors is 1 to 5 mM. In contrast, data fitting to the Monod-Wyman-Changeux (MWC) model revealed lower K m values for NH4+ , of 6 to 12 mM. In silico analysis made with MWC equation, and using physiological concentrations of substrates and modulators, predicted GDH N-fixing activity in cancer cells. Therefore, together with its thermodynamic feasibility, GDH may reach rates for its reverse, NH4+ -fixing reaction that are compatible with an anabolic role for supporting growth of cancer cells.

Keywords:  GDH kinetics; ammonium; cooperativity; metastatic cancer cells; monod–wyman–changeux model

DOI:  https://doi.org/10.3389/fonc.2020.00429
Trends Cancer. 2020 Apr 20. pii: S2405-8033(20)30117-5. [Epub ahead of print]

Cell Competition Spurs Selection of Aggressive Cancer Cells.

Taylor Parker, Esha Madan, Kartik Gupta, Eduardo Moreno, Rajan Gogna.

  Within heterogeneous tumors, cancer cells are constantly interacting. Cell competition (CC) is a fitness-based selection mechanism that results in increased proliferation of discrete populations at the expense of their less fit neighbors. CC-based selection of fit cells may also drive selection of the most aggressive cancer cells.

Keywords:  Col17A; Flower; Hippo; JAK/STAT; Myc; Tead; cell competition; p53; tumor heterogeneity

DOI:  https://doi.org/10.1016/j.trecan.2020.03.008