bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2020–03–15
39 papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit
  1. CLUH granules coordinate translation of mitochondrial proteins with mTORC1 signaling and mitophagy.
  2. SLC25A32 sustains cancer cell proliferation by regulating flavin adenine nucleotide (FAD) metabolism.
  3. mTOR complex 2 is an integrator of cancer metabolism and epigenetics.
  4. Glutaminase-1 (GLS1) inhibition limits metastatic progression in osteosarcoma.
  5. Sirt4 Modulates Oxidative Metabolism and Sensitivity to Rapamycin Through Species-Dependent Phenotypes in Drosophila mtDNA Haplotypes.
  6. Mitochondrial peptide BRAWNIN is essential for vertebrate respiratory complex III assembly.
  7. Autophagy-Dependent Ferroptosis: Machinery and Regulation.
  8. Mitochondrial division inhibitor (mdivi-1) decreases oxidative metabolism in cancer.
  9. Site-Dependent Cysteine Lipidation Potentiates the Activation of Proapoptotic BAX.
  10. Mitochondrial complex I derived ROS regulate stress adaptation in Drosophila melanogaster.
  11. The 60-kDa heat shock protein regulates energy rearrangement and protein synthesis to promote proliferation of multiple myeloma cells.
  12. A Genome-wide ER-phagy Screen Highlights Key Roles of Mitochondrial Metabolism and ER-Resident UFMylation.
  13. Cancer associated fibroblast FAK regulates malignant cell metabolism.
  14. Mechanisms of mitochondrial DNA escape and its relationship with different metabolic diseases.
  15. Pharmacological targets of metabolism in disease: Opportunities from macrophages.
  16. Spatiotemporal gating of SIRT1 functions by O-GlcNAcylation is essential for liver metabolic switching and prevents hyperglycemia.
  17. PINK1/Parkin Mediated Mitophagy, Ca2+ Signalling, and ER-Mitochondria Contacts in Parkinson's Disease.
  18. ATP- and voltage-dependent electro-metabolic signaling regulates blood flow in heart.
  19. Lipid peroxidation and ferroptosis: The role of GSH and GPx4.
  20. DJ-1 is indispensable for the S-nitrosylation of Parkin, which maintains function of mitochondria.
  21. Effective Synergy of Sorafenib and Nutrient Shortage in Inducing Melanoma Cell Death through Energy Stress.
  22. Amino acid levels determine metabolism and CYP450 function of hepatocytes and hepatoma cell lines.
  23. Strong selective effects of mitochondrial DNA on the nuclear genome.
  24. DBC1, p300, HDAC3, and Siah1 coordinately regulate ELL stability and function for expression of its target genes.
  25. Dihydroorotate dehydrogenase in oxidative phosphorylation and cancer.
  26. Tumor-Derived Retinoic Acid Regulates Intratumoral Monocyte Differentiation to Promote Immune Suppression.
  27. Mapping mitochondrial respiratory chain deficiencies by respirometry: Beyond the Mito Stress Test.
  28. Mild depolarization of the inner mitochondrial membrane is a crucial component of an anti-aging program.
  29. HNF1A recruits KDM6A to activate differentiated acinar cell programs that suppress pancreatic cancer.
  30. Therapeutic targeting of SDHB-mutated pheochromocytoma/paraganglioma with pharmacologic ascorbic acid.
  31. The tethering function of mitofusin2 controls osteoclast differentiation by modulating the Ca2+-NFATC1 axis.
  32. A plausible accelerating function of intermediate states in cancer metastasis.
  33. Hyperoxia induces glutamine-fuelled anaplerosis in retinal Müller cells.
  34. Glutamine supports the protection of tissue cells against the damage caused by cholesterol-dependent cytolysins from pathogenic bacteria.
  35. Lactic acidosis induces resistance to the pan-Akt inhibitor uprosertib in colon cancer cells.
  36. A dynamic anchor domain in SLC13 transporters controls metabolite transport.
  37. Glutaminases as a Novel Target for SDHB-Associated Pheochromocytomas/Paragangliomas.
  38. RUNX1 is a driver of renal cell carcinoma correlating with clinical outcome.
  39. Cancer immune control needs senescence induction by interferon-dependent cell cycle regulator pathways in tumours.
  1. EMBO J. 2020 Mar 09. e102731
    CLUH granules coordinate translation of mitochondrial proteins with mTORC1 signaling and mitophagy.
    David Pla-Martín, Désirée Schatton, Janica L Wiederstein, Marie-Charlotte Marx, Salim Khiati, Marcus Krüger, Elena I Rugarli.
      Mitochondria house anabolic and catabolic processes that must be balanced and adjusted to meet cellular demands. The RNA-binding protein CLUH (clustered mitochondria homolog) binds mRNAs of nuclear-encoded mitochondrial proteins and is highly expressed in the liver, where it regulates metabolic plasticity. Here, we show that in primary hepatocytes, CLUH coalesces in specific ribonucleoprotein particles that define the translational fate of target mRNAs, such as Pcx, Hadha, and Hmgcs2, to match nutrient availability. Moreover, CLUH granules play signaling roles, by recruiting mTOR kinase and the RNA-binding proteins G3BP1 and G3BP2. Upon starvation, CLUH regulates translation of Hmgcs2, involved in ketogenesis, inhibits mTORC1 activation and mitochondrial anabolic pathways, and promotes mitochondrial turnover, thus allowing efficient reprograming of metabolic function. In the absence of CLUH, a mitophagy block causes mitochondrial clustering that is rescued by rapamycin treatment or depletion of G3BP1 and G3BP2. Our data demonstrate that metabolic adaptation of liver mitochondria to nutrient availability depends on a compartmentalized CLUH-dependent post-transcriptional mechanism that controls both mTORC1 and G3BP signaling and ensures survival.
    Keywords:  CLUH; G3BP; RNA metabolism; mTORC1; mitochondria
    DOI:  https://doi.org/10.15252/embj.2019102731
  2. Oncotarget. 2020 Feb 25. 11(8): 801-812
    SLC25A32 sustains cancer cell proliferation by regulating flavin adenine nucleotide (FAD) metabolism.
    Valeria Santoro, Ilya Kovalenko, Kim Vriens, Stefan Christen, Andreas Bernthaler, Andrea Haegebarth, Sarah-Maria Fendt, Sven Christian.
      SLC25A32 is a member of the solute carrier 25 family of mitochondrial transporters. SLC25A32 transports tetrahydrofolate (THF) as well as FAD into mitochondria and regulates mitochondrial one-carbon metabolism and redox balance. While it is known that cancer cells require one-carbon and FAD-dependent mitochondrial metabolism to sustain cell proliferation, the role of SLC25A32 in cancer cell growth remains unexplored. Our results indicate that the SLC25A32 gene is highly amplified in different tumors and that amplification correlates with increased mRNA expression and reduced patients´ survival. siRNA-mediated knock-down and CRISPR-mediated knock-out of SLC25A32 in cancer cells of different origins, resulted in the identification of cell lines sensitive and resistant to SLC25A32 inhibition. Mechanistically, tracing of deuterated serine revealed that SLC25A32 knock-down does not affect the mitochondrial/cytosolic folate flux as measured by Liquid Chromatography coupled Mass Spectrometry (LC-MS). Instead, SLC25A32 inhibition results in a respiratory chain dysfunction at the FAD-dependent complex II enzyme, induction of Reactive Oxygen Species (ROS) and depletion of reduced glutathione (GSH), which impairs cancer cell proliferation. Moreover, buthionine sulfoximine (BSO) treatment further sensitizes cells to ROS-mediated inhibition of cell proliferation upon SLC25A32 knock-down. Treatment of cells with the FAD precursor riboflavin and with GSH rescues cancer cell proliferation upon SLC25A32 down-regulation. Our results indicate that the reduction of mitochondrial FAD concentrations by targeting SLC25A32 has potential clinical applications as a single agent or in combination with approved cancer drugs that lead to increased oxidative stress and reduced tumor growth.
    Keywords:  FAD; ROS; metabolism; mitochondria; transporter
    DOI:  https://doi.org/10.18632/oncotarget.27486
  3. Cancer Lett. 2020 Mar 04. pii: S0304-3835(20)30118-X. [Epub ahead of print]
    mTOR complex 2 is an integrator of cancer metabolism and epigenetics.
    Kenta Masui, Mio Harachi, Webster K Cavenee, Paul S Mischel, Noriyuki Shibata.
      Metabolic reprogramming is a central hallmark of cancer and is driven by abnormalites of oncogenes and tumor suppressors. This enables tumor cells to obtain the macromolecular precursors and energy needed for rapid tumor growth. Accelerated metabolism also translates into cancer cell aggression through epigenetic changes. The aberrant signaling cascades activated by oncogenes coordinate metabolic reprogramming with epigenetic shifts and subsequent global transcriptional changes through the dysregulation of rate-limiting metabolic enzymes as well as by facilitating the production of intermediary metabolites. As the landscape of cancer cell metabolism has been elucidated, it is now time for this knowledge to be translated into benefit for patients. Here we review the recently identified central regulatory role for mechanistic/mammalian target of rapamycin complex 2 (mTORC2), a downstream effector of many cancer-causing mutations, in reprogramming the metabolic and epigenetic landscape. This leads to tumor cell survival and cancer drug resistance.
    Keywords:  histone acetylation; iron metabolism; mTOR complex; metabolic reprogramming; microenvironment
    DOI:  https://doi.org/10.1016/j.canlet.2020.03.001
  4. Cancer Metab. 2020 ;8 4
    Glutaminase-1 (GLS1) inhibition limits metastatic progression in osteosarcoma.
    L Ren, V Ruiz-Rodado, T Dowdy, S Huang, S H Issaq, J Beck, H Wang, C Tran Hoang, A Lita, M Larion, A K LeBlanc.
       Background: Osteosarcoma (OS) is a malignant bone tumor that often develops during the period of rapid growth associated with adolescence. Despite successful primary tumor control accompanied by adjuvant chemotherapy, death from pulmonary metastases occurs in approximately 30% of patients within 5 years. As overall survival in patients remains unchanged over the last 30 years, urgent needs for novel therapeutic strategies exist. Cancer metastasis is characterized by complex molecular events which result from alterations in gene and protein expression/function. Recent studies suggest that metabolic adaptations, or "metabolic reprogramming," may similarly contribute to cancer metastasis. The goal of this study was to specifically interrogate the metabolic vulnerabilities of highly metastatic OS cell lines in a series of in vitro and in vivo experiments, in order to identify a tractable metabolically targeted therapeutic strategy for patients.
    Methods: Nutrient deprivation and drug treatment experiments were performed in MG63.3, 143B, and K7M2 OS cell lines to identify the impact of glutaminase-1 (GLS1) inhibition and metformin treatment on cell proliferation. We functionally validated the impact of drug treatment with extracellular flux analysis, nuclear magnetic resonance (NMR) spectroscopy, and mass spectrometry. 13C-glucose and 13C-glutamine tracing was employed to identify specific contributions of these nutrients to the global metabolic profiles generated with GLS1 inhibition and metformin treatment in vivo.
    Results: Highly metastatic OS cell lines require glutamine for proliferation, and exposure to CB-839, in combination with metformin, induces both primary tumor growth inhibition and a distinct reduction in metastatic outgrowth in vivo. Further, combination-treated OS cells showed a reduction in cellular mitochondrial respiration, while NMR confirmed the pharmacodynamic effects of glutaminase inhibition in tumor tissues. We observed global decreases in glycolysis and tricarboxylic acid (TCA) cycle functionality, alongside an increase in fatty acid oxidation and pyrimidine catabolism.
    Conclusions: This data suggests combination-treated cells cannot compensate for metformin-induced electron transport chain inhibition by upregulating glutaminolysis to generate TCA cycle intermediates required for cell proliferation, translating into significant reductions in tumor growth and metastatic progression. This therapeutic approach could be considered for future clinical development for OS patients presenting with or at high risk of developing metastasis.
    Keywords:  Glutaminase; Metabolism; Metastasis; Metformin; Osteosarcoma
    DOI:  https://doi.org/10.1186/s40170-020-0209-8
  5. G3 (Bethesda). 2020 Mar 09. pii: g3.401174.2020. [Epub ahead of print]
    Sirt4 Modulates Oxidative Metabolism and Sensitivity to Rapamycin Through Species-Dependent Phenotypes in Drosophila mtDNA Haplotypes.
    Richard Sejour, Roger A Sanguino, Monika Mikolajczak, Walishah Ahmadi, Eugenia Villa-Cuesta.
      The endosymbiotic theory proposes that eukaryotes evolved from the symbiotic relationship between anaerobic (host) and aerobic prokaryotes. Through iterative genetic transfers, the mitochondrial and nuclear genomes coevolved, establishing the mitochondria as the hub of oxidative metabolism. To study this coevolution, we disrupt mitochondrial-nuclear epistatic interactions by using strains that have mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) from evolutionarily divergent species. We undertake a multifaceted approach generating introgressed Drosophila strains containing D. simulans mtDNA and D. melanogaster nDNA with Sirtuin 4 (Sirt4)-knockouts. Sirt4 is a nuclear-encoded enzyme that functions, exclusively within the mitochondria, as a master regulator of oxidative metabolism. We exposed flies to the drug rapamycin in order to eliminate TOR signaling, thereby compromising the cytoplasmic crosstalk between the mitochondria and nucleus. Our results indicate that D. simulans and D. melanogaster mtDNA haplotypes display opposite Sirt4-mediated phenotypes in the regulation of whole-fly oxygen consumption. Moreover, our data reflect that the deletion of Sirt4 rescued the metabolic response to rapamycin among the introgressed strains. We propose that Sirt4 is a suitable candidate for studying the properties of mitochondrial-nuclear epistasis in modulating mitochondrial metabolism.
    Keywords:  SIRT4; TOR pathway; coevolution mtDNA/nDNA
    DOI:  https://doi.org/10.1534/g3.120.401174
  6. Nat Commun. 2020 Mar 11. 11(1): 1312
    Mitochondrial peptide BRAWNIN is essential for vertebrate respiratory complex III assembly.
    Shan Zhang, Boris Reljić, Chao Liang, Baptiste Kerouanton, Joel Celio Francisco, Jih Hou Peh, Camille Mary, Narendra Suhas Jagannathan, Volodimir Olexiouk, Claire Tang, Gio Fidelito, Srikanth Nama, Ruey-Kuang Cheng, Caroline Lei Wee, Loo Chien Wang, Paula Duek Roggli, Prabha Sampath, Lydie Lane, Enrico Petretto, Radoslaw M Sobota, Suresh Jesuthasan, Lisa Tucker-Kellogg, Bruno Reversade, Gerben Menschaert, Lei Sun, David A Stroud, Lena Ho.
      The emergence of small open reading frame (sORF)-encoded peptides (SEPs) is rapidly expanding the known proteome at the lower end of the size distribution. Here, we show that the mitochondrial proteome, particularly the respiratory chain, is enriched for small proteins. Using a prediction and validation pipeline for SEPs, we report the discovery of 16 endogenous nuclear encoded, mitochondrial-localized SEPs (mito-SEPs). Through functional prediction, proteomics, metabolomics and metabolic flux modeling, we demonstrate that BRAWNIN, a 71 a.a. peptide encoded by C12orf73, is essential for respiratory chain complex III (CIII) assembly. In human cells, BRAWNIN is induced by the energy-sensing AMPK pathway, and its depletion impairs mitochondrial ATP production. In zebrafish, Brawnin deletion causes complete CIII loss, resulting in severe growth retardation, lactic acidosis and early death. Our findings demonstrate that BRAWNIN is essential for vertebrate oxidative phosphorylation. We propose that mito-SEPs are an untapped resource for essential regulators of oxidative metabolism.
    DOI:  https://doi.org/10.1038/s41467-020-14999-2
  7. Cell Chem Biol. 2020 Mar 03. pii: S2451-9456(20)30069-6. [Epub ahead of print]
    Autophagy-Dependent Ferroptosis: Machinery and Regulation.
    Jiao Liu, Feimei Kuang, Guido Kroemer, Daniel J Klionsky, Rui Kang, Daolin Tang.
      Macroautophagy (hereafter referred to as autophagy) is an evolutionarily conserved cellular process capable of degrading various biological molecules (e.g., protein, glycogen, lipids, DNA, and RNA) and organelles (e.g., mitochondria, endoplasmic reticulum [ER] ribosomes, lysosomes, and micronuclei) via the lysosomal pathway. Ferroptosis is a type of oxidative stress-dependent regulated cell death associated with iron accumulation and lipid peroxidation. The recently discovered role of autophagy, especially selective types of autophagy (e.g., ferritinophagy, lipophagy, clockophagy, and chaperone-mediated autophagy), in driving cells toward ferroptotic death motivated us to explore the functional interactions between metabolism, immunity, and cell death. Here, we describe types of selective autophagy and discuss the regulatory mechanisms and signaling pathways of autophagy-dependent ferroptosis. We also summarize chemical modulators that are currently available for triggering or blocking autophagy-dependent ferroptosis and that may be developed for therapeutic interventions in human diseases.
    Keywords:  autophagy; ferroptosis; network; regulated cell death; selective autophagy
    DOI:  https://doi.org/10.1016/j.chembiol.2020.02.005
  8. Br J Cancer. 2020 Mar 09.
    Mitochondrial division inhibitor (mdivi-1) decreases oxidative metabolism in cancer.
    Wenting Dai, Guan Wang, Jason Chwa, Myung Eun Oh, Tharindumala Abeywardana, Yanzhong Yang, Qiong A Wang, Lei Jiang.
       BACKGROUND: Previous studies suggested that mdivi-1 (mitochondrial division inhibitor), a putative inhibitor of dynamin-related protein (DRP1), decreased cancer cell proliferation through inducing mitochondrial fusion and altering oxygen consumption. However, the metabolic reprogramming underlying the DRP1 inhibition is still unclear in cancer cells.
    METHODS: To better understand the metabolic effect of DRP1 inhibition, [U-13C]glucose isotope tracing was employed to assess mdivi-1 effects in several cancer cell lines, DRP1-WT (wild-type) and DRP1-KO (knockout) H460 lung cancer cells and mouse embryonic fibroblasts (MEFs).
    RESULTS: Mitochondrial staining confirmed that mdivi-1 treatment and DRP1 deficiency induced mitochondrial fusion. Surprisingly, metabolic isotope tracing found that mdivi-1 decreased mitochondrial oxidative metabolism in the lung cancer cell lines H460, A549 and the colon cancer cell line HCT116. [U-13C]glucose tracing studies also showed that the TCA cycle intermediates had significantly lower enrichment in mdivi-1-treated cells. In comparison, DRP1-WT and DRP1-KO H460 cells had similar oxidative metabolism, which was decreased by mdivi-1 treatment. Furthermore, mdivi-1-mediated effects on oxidative metabolism were independent of mitochondrial fusion.
    CONCLUSIONS: Our data suggest that, in cancer cells, mdivi-1, a putative inhibitor of DRP1, decreases oxidative metabolism to impair cell proliferation.
    DOI:  https://doi.org/10.1038/s41416-020-0778-x
  9. Cell Rep. 2020 Mar 10. pii: S2211-1247(20)30225-4. [Epub ahead of print]30(10): 3229-3239.e6
    Site-Dependent Cysteine Lipidation Potentiates the Activation of Proapoptotic BAX.
    Daniel T Cohen, Thomas E Wales, Matthew W McHenry, John R Engen, Loren D Walensky.
      BCL-2 family proteins converge at the mitochondrial outer membrane to regulate apoptosis and maintain the critical balance between cellular life and death. This physiologic process is essential to organism homeostasis and relies on protein-protein and protein-lipid interactions among BCL-2 family proteins in the mitochondrial lipid environment. Here, we find that trans-2-hexadecenal (t-2-hex), previously implicated in regulating BAX-mediated apoptosis, does so by direct covalent reaction with C126, which is located on the surface of BAX at the junction of its α5/α6 core hydrophobic hairpin. The application of nuclear magnetic resonance spectroscopy, hydrogen-deuterium exchange mass spectrometry, specialized t-2-hex-containing liposomes, and BAX mutational studies in mitochondria and cells reveals structure-function insights into the mechanism by which covalent lipidation at the mitochondria sensitizes direct BAX activation. The functional role of BAX lipidation as a control point of mitochondrial apoptosis could provide a therapeutic strategy for BAX modulation by chemical modification of C126.
    Keywords:  BAX; BCL-2 family; apoptosis; cysteine lipidation; lipid-derived electrophile; membrane permeabilization; mitochondria; post-translational modification; sphingolipid metabolism
    DOI:  https://doi.org/10.1016/j.celrep.2020.02.057
  10. Redox Biol. 2020 Feb 07. pii: S2213-2317(19)31460-0. [Epub ahead of print] 101450
    Mitochondrial complex I derived ROS regulate stress adaptation in Drosophila melanogaster.
    Filippo Scialò, Ashwin Sriram, Rhoda Stefanatos, Ruth V Spriggs, Samantha H Y Loh, L Miguel Martins, Alberto Sanz.
      Reactive Oxygen Species (ROS) are essential cellular messengers required for cellular homeostasis and regulate the lifespan of several animal species. The main site of ROS production is the mitochondrion, and within it, respiratory complex I (CI) is the main ROS generator. ROS produced by CI trigger several physiological responses that are essential for the survival of neurons, cardiomyocytes and macrophages. Here, we show that CI produces ROS when electrons flow in either the forward (Forward Electron Transport, FET) or reverse direction (Reverse Electron Transport, RET). We demonstrate that ROS production via RET (ROS-RET) is activated under thermal stress conditions and that interruption of ROS-RET production, through ectopic expression of the alternative oxidase AOX, attenuates the activation of pro-survival pathways in response to stress. Accordingly, we find that both suppressing ROS-RET signalling or decreasing levels of mitochondrial H2O2 by overexpressing mitochondrial catalase (mtCAT), reduces survival dramatically in flies under stress. Our results uncover a specific ROS signalling pathway where hydrogen peroxide (H2O2) generated by CI via RET is required to activate adaptive mechanisms, maximising survival under stress conditions.
    Keywords:  AOX; Alternative oxidase; Complex I; Heat stress; Reactive oxygen species; Reverse electron transport
    DOI:  https://doi.org/10.1016/j.redox.2020.101450
  11. Br J Haematol. 2020 Mar 10.
    The 60-kDa heat shock protein regulates energy rearrangement and protein synthesis to promote proliferation of multiple myeloma cells.
    Xiaoxiao Wu, Jianying Guo, Yuling Chen, Xiaohui Liu, Guangzhong Yang, Yin Wu, Ying Tian, Nian Liu, Lin Yang, Songren Wei, Haiteng Deng, Wenming Chen.
      To investigate the cellular mechanisms of multiple myeloma (MM), we used liquid chromatography-tandem mass spectrometry for proteomics analysis of CD138+ plasma cells from patients with MM and healthy controls. We found that the 60-kDa heat shock protein (HSP60, also known as HSPD1) was significantly upregulated in myeloma cells. HSP60 is an important chaperone protein that regulates the homeostasis of mitochondrial proteins and maintains mitochondrial function. Knockdown (KD) of HSP60 in myeloma cells resulted in inhibition of proliferation and reduced the quality of the mitochondria. Mitochondrial stress tests showed that HSP60 KD inhibited glycolysis and mitochondrial activity. Metabolomics showed a decrease in glycolysis and tricarboxylic acid cycle metabolites, and inhibited the formation of creatine and phosphocreatine by the reaction of S-adenosylmethionine (SAM) with amino acids mediated by demethyladenosine transferase 1, mitochondrial (TFB1M) and reduced energy storage substances. Moreover, HSP60 silencing influenced the synthesis of ribonucleotides and nicotinamide adenine dinucleotide phosphate (NADPH) by the pentose phosphate pathway to inhibit cell proliferation. HSP60 KD inhibited 5' adenosine monophosphate-activated protein kinase (AMPK), which inhibited the key enzyme 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3), effecting the metabolism of fatty acids by inhibiting malonyl-coenzyme A. Our data suggest that reduced HSP60 expression alters metabolic reprogramming in MM, inhibits tumour progression and reduces mitochondrial-dependent biosynthesis, suggesting that HSP60 is a potential therapeutic target for MM treatment.
    Keywords:  HSP60; adenosine monophosphate-activated protein kinase (AMPK); metabolomics; multiple myeloma; proteomics
    DOI:  https://doi.org/10.1111/bjh.16569
  12. Cell. 2020 Mar 03. pii: S0092-8674(20)30161-6. [Epub ahead of print]
    A Genome-wide ER-phagy Screen Highlights Key Roles of Mitochondrial Metabolism and ER-Resident UFMylation.
    Jin Rui Liang, Emily Lingeman, Thao Luong, Saba Ahmed, Matthias Muhar, Truc Nguyen, James A Olzmann, Jacob E Corn.
      Selective autophagy of organelles is critical for cellular differentiation, homeostasis, and organismal health. Autophagy of the ER (ER-phagy) is implicated in human neuropathy but is poorly understood beyond a few autophagosomal receptors and remodelers. By using an ER-phagy reporter and genome-wide CRISPRi screening, we identified 200 high-confidence human ER-phagy factors. Two pathways were unexpectedly required for ER-phagy. First, reduced mitochondrial metabolism represses ER-phagy, which is opposite of general autophagy and is independent of AMPK. Second, ER-localized UFMylation is required for ER-phagy to repress the unfolded protein response via IRE1α. The UFL1 ligase is brought to the ER surface by DDRGK1 to UFMylate RPN1 and RPL26 and preferentially targets ER sheets for degradation, analogous to PINK1-Parkin regulation during mitophagy. Our data provide insight into the cellular logic of ER-phagy, reveal parallels between organelle autophagies, and provide an entry point to the relatively unexplored process of degrading the ER network.
    Keywords:  CRISPR; ER-phagy; UFMylation; autophagy; endoplasmic reticulum; genome-wide screen; organelle turnover; oxidative phosphorylation; post-translational modification
    DOI:  https://doi.org/10.1016/j.cell.2020.02.017
  13. Nat Commun. 2020 Mar 10. 11(1): 1290
    Cancer associated fibroblast FAK regulates malignant cell metabolism.
    Fevzi Demircioglu, Jun Wang, Juliana Candido, Ana S H Costa, Pedro Casado, Beatriz de Luxan Delgado, Louise E Reynolds, Jesus Gomez-Escudero, Emma Newport, Vinothini Rajeeve, Ann-Marie Baker, Marina Roy-Luzarraga, Trevor A Graham, Julie Foster, Yu Wang, James J Campbell, Rajinder Singh, Penglie Zhang, Thomas J Schall, Frances R Balkwill, Jane Sosabowski, Pedro R Cutillas, Christian Frezza, Patricia Sancho, Kairbaan Hodivala-Dilke.
      Emerging evidence suggests that cancer cell metabolism can be regulated by cancer-associated fibroblasts (CAFs), but the mechanisms are poorly defined. Here we show that CAFs regulate malignant cell metabolism through pathways under the control of FAK. In breast and pancreatic cancer patients we find that low FAK expression, specifically in the stromal compartment, predicts reduced overall survival. In mice, depletion of FAK in a subpopulation of CAFs regulates paracrine signals that increase malignant cell glycolysis and tumour growth. Proteomic and phosphoproteomic analysis in our mouse model identifies metabolic alterations which are reflected at the transcriptomic level in patients with low stromal FAK. Mechanistically we demonstrate that FAK-depletion in CAFs increases chemokine production, which via CCR1/CCR2 on cancer cells, activate protein kinase A, leading to enhanced malignant cell glycolysis. Our data uncover mechanisms whereby stromal fibroblasts regulate cancer cell metabolism independent of genetic mutations in cancer cells.
    DOI:  https://doi.org/10.1038/s41467-020-15104-3
  14. Biochim Biophys Acta Mol Basis Dis. 2020 Mar 10. pii: S0925-4439(20)30106-X. [Epub ahead of print] 165761
    Mechanisms of mitochondrial DNA escape and its relationship with different metabolic diseases.
    Perla Pérez-Treviño, Mónica Velásquez, Noemí García.
      It is well-known that mitochondrial DNA (mtDNA) can escape to intracellular or extracellular compartments under different stress conditions, yet understanding their escape mechanisms remains a challenge. Although Bax/Bak pores and VDAC oligomers are the strongest possibilities, other mechanisms may be involved. For example, mitochondria permeability transition, altered mitophagy, and mitochondrial dynamics are associated with intracellular mtDNA escape, while extracellular traps and extracellular vesicles can participate in extracellular mtDNA escape. The evidence suggests that mtDNA escape is a complex event with more than one mechanism involved. In addition, once the mtDNA is outside the mitochondria, the effects can be complex. Different danger signal sensors recognize the mtDNA as a damage-associated molecular pattern, triggering an innate immune inflammatory response that can be observed in multiple metabolic diseases characterized by chronic inflammation, including autoimmune diseases, diabetes, cancer, and cardiovascular disorders. For these reasons, we will review the most recent evidence regarding mtDNA escape mechanisms and their impact on different metabolic diseases.
    Keywords:  Cytosolic mtDNA; Extracellular mtDNA; Inflammation; Oxidative stress; Oxidized mtDNA
    DOI:  https://doi.org/10.1016/j.bbadis.2020.165761
  15. Pharmacol Ther. 2020 Mar 06. pii: S0163-7258(20)30049-8. [Epub ahead of print] 107521
    Pharmacological targets of metabolism in disease: Opportunities from macrophages.
    Alessandra Castegna, Rosanna Gissi, Alessio Menga, Monica Montopoli, Maria Favia, Antonella Viola, Marcella Canton.
      From advances in the knowledge of the immune system, it is emerging that the specialized functions displayed by macrophages during the course of an immune response are supported by specific and dynamically-connected metabolic programs. The study of immunometabolism is demonstrating that metabolic adaptations play a critical role in modulating inflammation and, conversely, inflammation deeply influences the acquisition of specific metabolic settings. This strict connection has been proven to be crucial for the execution of defined immune functional programs and it is now under investigation with respect to several human disorders, such as diabetes, sepsis, cancer, and autoimmunity. The abnormal remodelling of the metabolic pathways in macrophages is now emerging as both marker of disease and potential target of therapeutic intervention. By focusing on key pathological conditions, namely obesity and diabetes, rheumatoid arthritis, atherosclerosis and cancer, we will review the metabolic targets suitable for therapeutic intervention in macrophages. In addition, we will discuss the major obstacles and challenges related to the development of therapeutic strategies for a pharmacological targeting of macrophage's metabolism.
    Keywords:  Autoimmunity; Cancer; Immunometabolism; Macrophage; Metabolic immunotherapy; Mitochondria; Therapy
    DOI:  https://doi.org/10.1016/j.pharmthera.2020.107521
  16. Proc Natl Acad Sci U S A. 2020 Mar 09. pii: 201909943. [Epub ahead of print]
    Spatiotemporal gating of SIRT1 functions by O-GlcNAcylation is essential for liver metabolic switching and prevents hyperglycemia.
    Tandrika Chattopadhyay, Babukrishna Maniyadath, Hema P Bagul, Arindam Chakraborty, Namrata Shukla, Srikanth Budnar, Abinaya Rajendran, Arushi Shukla, Siddhesh S Kamat, Ullas Kolthur-Seetharam.
      Inefficient physiological transitions are known to cause metabolic disorders. Therefore, investigating mechanisms that constitute molecular switches in a central metabolic organ like the liver becomes crucial. Specifically, upstream mechanisms that control temporal engagement of transcription factors, which are essential to mediate physiological fed-fast-refed transitions are less understood. SIRT1, a NAD+-dependent deacetylase, is pivotal in regulating hepatic gene expression and has emerged as a key therapeutic target. Despite this, if/how nutrient inputs regulate SIRT1 interactions, stability, and therefore downstream functions are still unknown. Here, we establish nutrient-dependent O-GlcNAcylation of SIRT1, within its N-terminal domain, as a crucial determinant of hepatic functions. Our findings demonstrate that during a fasted-to-refed transition, glycosylation of SIRT1 modulates its interactions with various transcription factors and a nodal cytosolic kinase involved in insulin signaling. Moreover, sustained glycosylation in the fed state causes nuclear exclusion and cytosolic ubiquitin-mediated degradation of SIRT1. This mechanism exerts spatiotemporal control over SIRT1 functions by constituting a previously unknown molecular relay. Of note, loss of SIRT1 glycosylation discomposed these interactions resulting in aberrant gene expression, mitochondrial dysfunctions, and enhanced hepatic gluconeogenesis. Expression of nonglycosylatable SIRT1 in the liver abrogated metabolic flexibility, resulting in systemic insulin resistance, hyperglycemia, and hepatic inflammation, highlighting the physiological costs associated with its overactivation. Conversely, our study also reveals that hyperglycosylation of SIRT1 is associated with aging and high-fat-induced obesity. Thus, we establish that nutrient-dependent glycosylation of SIRT1 is essential to gate its functions and maintain physiological fitness.
    Keywords:  PGC1α; fed–fast cycle; gluconeogenesis; insulin signaling; ubiquitinylation
    DOI:  https://doi.org/10.1073/pnas.1909943117
  17. Int J Mol Sci. 2020 Mar 05. pii: E1772. [Epub ahead of print]21(5):
    PINK1/Parkin Mediated Mitophagy, Ca2+ Signalling, and ER-Mitochondria Contacts in Parkinson's Disease.
    Lucia Barazzuol, Flavia Giamogante, Marisa Brini, Tito Calì.
      Endoplasmic reticulum (ER)-mitochondria contact sites are critical structures for cellular function. They are implicated in a plethora of cellular processes, including Ca2+ signalling and mitophagy, the selective degradation of damaged mitochondria. Phosphatase and tensin homolog (PTEN)-induced kinase (PINK) and Parkin proteins, whose mutations are associated with familial forms of Parkinson's disease, are two of the best characterized mitophagy players. They accumulate at ER-mitochondria contact sites and modulate organelles crosstalk. Alterations in ER-mitochondria tethering are a common hallmark of many neurodegenerative diseases including Parkinson's disease. Here, we summarize the current knowledge on the involvement of PINK1 and Parkin at the ER-mitochondria contact sites and their role in the modulation of Ca2+ signalling and mitophagy.
    Keywords:  Ca2+; ER–mitochondria tethering; PINK1; Parkin; mitophagy
    DOI:  https://doi.org/10.3390/ijms21051772
  18. Proc Natl Acad Sci U S A. 2020 Mar 13. pii: 201922095. [Epub ahead of print]
    ATP- and voltage-dependent electro-metabolic signaling regulates blood flow in heart.
    Guiling Zhao, Humberto C Joca, Mark T Nelson, W Jonathan Lederer.
      Local control of blood flow in the heart is important yet poorly understood. Here we show that ATP-sensitive K+ channels (KATP), hugely abundant in cardiac ventricular myocytes, sense the local myocyte metabolic state and communicate a negative feedback signal-correction upstream electrically. This electro-metabolic voltage signal is transmitted instantaneously to cellular elements in the neighboring microvascular network through gap junctions, where it regulates contractile pericytes and smooth muscle cells and thus blood flow. As myocyte ATP is consumed in excess of production, [ATP]i decreases to increase the openings of KATP channels, which biases the electrically active myocytes in the hyperpolarization (negative) direction. This change leads to relative hyperpolarization of the electrically connected cells that include capillary endothelial cells, pericytes, and vascular smooth muscle cells. Such hyperpolarization decreases pericyte and vascular smooth muscle [Ca2+]i levels, thereby relaxing the contractile cells to increase local blood flow and delivery of nutrients to the local cardiac myocytes and to augment ATP production by their mitochondria. Our findings demonstrate the pivotal roles of local cardiac myocyte metabolism and KATP channels and the minor role of inward rectifier K+ (Kir2.1) channels in regulating blood flow in the heart. These findings establish a conceptually new framework for understanding the hugely reliable and incredibly robust local electro-metabolic microvascular regulation of blood flow in heart.
    Keywords:  ATP-sensitive potassium channel; capillary; electro-metabolic signaling; heart; pericyte
    DOI:  https://doi.org/10.1073/pnas.1922095117
  19. Free Radic Biol Med. 2020 Mar 09. pii: S0891-5849(19)32437-2. [Epub ahead of print]
    Lipid peroxidation and ferroptosis: The role of GSH and GPx4.
    Fulvio Ursini, Matilde Maiorino.
      Ferroptosis (FPT) is a form of cell death due to missed control of membrane lipid peroxidation (LPO). According to the axiomatic definition of non-accidental cell death, LPO takes place in a scenario of altered homeostasis. FPT, differently from apoptosis, occurs in the absence of any known specific genetically encoded death pathway or specific agonist, and thus must be rated as a regulated, although not "programmed", death pathway. It follows that LPO is under a homeostatic metabolic control and is only permitted when indispensable constraints are satisfied and the antiperoxidant machinery collapses. The activity of the selenoperoxidase Glutathione Peroxidase 4 (GPx4) is the cornerstone of the antiperoxidant defence. Converging evidence on both mechanism of LPO and GPx4 enzymology indicates that LPO is initiated by alkoxyl radicals produced by ferrous iron from the hydroperoxide derivatives of lipids (LOOH), traces of which are the unavoidable drawback of aerobic metabolism. FPT takes place when a threshold has been exceeded. This occurs when the major conditions are satisfied: i) oxygen metabolism leading to the continuous formation of traces of LOOH from phospholipid-containing polyunsaturated fatty acids; ii) missed enzymatic reduction of LOOH; iii) availability of ferrous iron from the labile iron pool. Although the effectors impacting on homeostasis and leading to FPT in physiological conditions are not known, from the available knowledge on LPO and GPx4 enzymology we propose that it is aerobic life itself that, while supporting bioenergetics, is also a critical requisite of FPT. Yet, when the homeostatic control of the steady state between LOOH formation and reduction is lost, LPO is activated and FPT is executed.
    Keywords:  GPx4; GSH; Lipid hydroperoxide; Lipid peroxidation; Oxygen toxicity; Selenium; cell death; ferroptosis
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2020.02.027
  20. Sci Rep. 2020 Mar 09. 10(1): 4377
    DJ-1 is indispensable for the S-nitrosylation of Parkin, which maintains function of mitochondria.
    Kentaro Ozawa, Hiroki Tsumoto, Yuri Miura, Junji Yamaguchi, Sanae M M Iguchi-Ariga, Tetsushi Sakuma, Takashi Yamamoto, Yasuo Uchiyama.
      The DJ-1 gene, a causative gene for familial Parkinson's disease (PD), has been reported to have various functions, including transcriptional regulation, antioxidant response, and chaperone and protease functions; however, the molecular mechanism associated with the pathogenesis of PD remains elusive. To further explore the molecular function of DJ-1 in the pathogenesis of PD, we compared protein expression profiles in brain tissues from wild-type and DJ-1-deficient mice. Two-dimensional difference gel electrophoresis analysis and subsequent analysis using data mining methods revealed alterations in the expression of molecules associated with energy production. We demonstrated that DJ-1 deletion inhibited S-nitrosylation of endogenous Parkin as well as overexpressed Parkin in neuroblastoma cells and mouse brain tissues. Thus, we used genome editing to generate neuroblastoma cells with DJ-1 deletion or S-nitrosylated cysteine mutation in Parkin and demonstrated that these cells exhibited similar phenotypes characterized by enhancement of cell death under mitochondrial depolarization and dysfunction of mitochondria. Our data indicate that DJ-1 is required for the S-nitrosylation of Parkin, which positively affects mitochondrial function, and suggest that the denitrosylation of Parkin via DJ-1 inactivation might contribute to PD pathogenesis and act as a therapeutic target.
    DOI:  https://doi.org/10.1038/s41598-020-61287-6
  21. Cells. 2020 Mar 06. pii: E640. [Epub ahead of print]9(3):
    Effective Synergy of Sorafenib and Nutrient Shortage in Inducing Melanoma Cell Death through Energy Stress.
    Fernanda Antunes, Gustavo J S Pereira, Renata F Saito, Marcus V Buri, Mara Gagliardi, Claudia Bincoletto, Roger Chammas, Gian Maria Fimia, Mauro Piacentini, Marco Corazzari, Soraya Soubhi Smaili.
      Skin melanoma is one of the most aggressive and difficult-to-treat human malignancies, characterized by poor survival rates, thus requiring urgent novel therapeutic approaches. Although metabolic reprogramming has represented so far, a cancer hallmark, accumulating data indicate a high plasticity of cancer cells in modulating cellular metabolism to adapt to a heterogeneous and continuously changing microenvironment, suggesting a novel therapeutic approach for dietary manipulation in cancer therapy. To this aim, we exposed melanoma cells to combined nutrient-restriction/sorafenib. Results indicate that cell death was efficiently induced, with apoptosis representing the prominent feature. In contrast, autophagy was blocked in the final stage by this treatment, similarly to chloroquine, which also enhanced melanoma cell sensitization to combined treatment. Energy stress was evidenced by associated treatment with mitochondrial dysfunction and glycolysis impairment, suggesting metabolic stress determining melanoma cell death. A reduction of tumor growth after cycles of intermittent fasting together with sorafenib treatment was also observed in vivo, reinforcing that the nutrient shortage can potentiate anti-melanoma therapy. Our findings showed that the restriction of nutrients by intermittent fasting potentiates the effects of sorafenib due to the modulation of cellular metabolism, suggesting that it is possible to harness the energy of cancer cells for the treatment of melanoma.
    Keywords:  apoptosis; autophagy; energy stress; melanoma; sorafenib
    DOI:  https://doi.org/10.3390/cells9030640
  22. Nat Commun. 2020 Mar 13. 11(1): 1393
    Amino acid levels determine metabolism and CYP450 function of hepatocytes and hepatoma cell lines.
    Ruben Boon, Manoj Kumar, Tine Tricot, Ilaria Elia, Laura Ordovas, Frank Jacobs, Jennifer One, Jonathan De Smedt, Guy Eelen, Matthew Bird, Philip Roelandt, Ginevra Doglioni, Kim Vriens, Matteo Rossi, Marta Aguirre Vazquez, Thomas Vanwelden, François Chesnais, Adil El Taghdouini, Mustapha Najimi, Etienne Sokal, David Cassiman, Jan Snoeys, Mario Monshouwer, Wei-Shou Hu, Christian Lange, Peter Carmeliet, Sarah-Maria Fendt, Catherine M Verfaillie.
      Predicting drug-induced liver injury in a preclinical setting remains challenging, as cultured primary human hepatocytes (PHHs), pluripotent stem cell-derived hepatocyte-like cells (HLCs), and hepatoma cells exhibit poor drug biotransformation capacity. We here demonstrate that hepatic functionality depends more on cellular metabolism and extracellular nutrients than on developmental regulators. Specifically, we demonstrate that increasing extracellular amino acids beyond the nutritional need of HLCs and HepG2 cells induces glucose independence, mitochondrial function, and the acquisition of a transcriptional profile that is closer to PHHs. Moreover, we show that these high levels of amino acids are sufficient to drive HLC and HepG2 drug biotransformation and liver-toxin sensitivity to levels similar to those in PHHs. In conclusion, we provide data indicating that extracellular nutrient levels represent a major determinant of cellular maturity and can be utilized to guide stem cell differentiation to the hepatic lineage.
    DOI:  https://doi.org/10.1038/s41467-020-15058-6
  23. Proc Natl Acad Sci U S A. 2020 Mar 10. pii: 201910141. [Epub ahead of print]
    Strong selective effects of mitochondrial DNA on the nuclear genome.
    Timothy M Healy, Ronald S Burton.
      Oxidative phosphorylation, the primary source of cellular energy in eukaryotes, requires gene products encoded in both the nuclear and mitochondrial genomes. As a result, functional integration between the genomes is essential for efficient adenosine triphosphate (ATP) generation. Although within populations this integration is presumably maintained by coevolution, the importance of mitonuclear coevolution in key biological processes such as speciation and mitochondrial disease has been questioned. In this study, we crossed populations of the intertidal copepod Tigriopus californicus to disrupt putatively coevolved mitonuclear genotypes in reciprocal F2 hybrids. We utilized interindividual variation in developmental rate among these hybrids as a proxy for fitness to assess the strength of selection imposed on the nuclear genome by alternate mitochondrial genotypes. Developmental rate varied among hybrid individuals, and in vitro ATP synthesis rates of mitochondria isolated from high-fitness hybrids were approximately two-fold greater than those of mitochondria isolated from low-fitness individuals. We then used Pool-seq to compare nuclear allele frequencies for high- or low-fitness hybrids. Significant biases for maternal alleles were detected on 5 (of 12) chromosomes in high-fitness individuals of both reciprocal crosses, whereas maternal biases were largely absent in low-fitness individuals. Therefore, the most fit hybrids were those with nuclear alleles that matched their mitochondrial genotype on these chromosomes, suggesting that mitonuclear effects underlie individual-level variation in developmental rate and that intergenomic compatibility is critical for high fitness. We conclude that mitonuclear interactions can have profound impacts on both physiological performance and the evolutionary trajectory of the nuclear genome.
    Keywords:  coevolution; copepod; incompatibilities; intergenomic; mitonuclear
    DOI:  https://doi.org/10.1073/pnas.1910141117
  24. Proc Natl Acad Sci U S A. 2020 Mar 09. pii: 201912375. [Epub ahead of print]
    DBC1, p300, HDAC3, and Siah1 coordinately regulate ELL stability and function for expression of its target genes.
    Subham Basu, Mahesh Barad, Dipika Yadav, Arijit Nandy, Bidisha Mukherjee, Jit Sarkar, Partha Chakrabarti, Satinath Mukhopadhyay, Debabrata Biswas.
      Among all of the Super Elongation Complex (SEC) components, ELL1 (also known as ELL) is the only bona fide elongation factor that directly stimulates transcription elongation by RNA polymerase II. However, the mechanism(s) of functional regulation of ELL1 (referred to as ELL hereafter), through its stabilization, is completely unknown. Here, we report a function of human DBC1 in regulating ELL stability involving HDAC3, p300, and Siah1. Mechanistically, we show that p300-mediated site-specific acetylation increases, whereas HDAC3-mediated deacetylation decreases, ELL stability through polyubiquitylation by the E3 ubiquitin ligase Siah1. DBC1 competes with HDAC3 for the same binding sites on ELL and thus increases its acetylation and stability. Knockdown of DBC1 reduces ELL levels and expression of a significant number of genes, including those involved in glucose metabolism. Consistently, Type 2 diabetes patient-derived peripheral blood mononuclear cells show reduced expression of DBC1 and ELL and associated key target genes required for glucose homeostasis. Thus, we describe a pathway of regulating stability and functions of key elongation factor ELL for expression of diverse sets of genes, including ones that are linked to Type 2 diabetes pathogenesis.
    Keywords:  DBC1; ELL; acetylation; transcription; ubiquitylation
    DOI:  https://doi.org/10.1073/pnas.1912375117
  25. Biochim Biophys Acta Mol Basis Dis. 2020 Mar 06. pii: S0925-4439(20)30104-6. [Epub ahead of print] 165759
    Dihydroorotate dehydrogenase in oxidative phosphorylation and cancer.
    Stepana Boukalova, Sona Hubackova, Mirko Milosevic, Zuzana Ezrova, Jiri Neuzil, Jakub Rohlena.
      Dihydroorotate dehydrogenase (DHODH) is an enzyme of the de novo pyrimidine synthesis pathway that provides nucleotides for RNA/DNA synthesis essential for proliferation. In mammalian cells, DHODH is localized in mitochondria, linked to the respiratory chain via the coenzyme Q pool. Here we discuss the role of DHODH in the oxidative phosphorylation system and in the initiation and progression of cancer. We summarize recent findings on DHODH biology, the progress made in the development of new, specific inhibitors of DHODH intended for cancer therapy, and the mechanistic insights into the consequences of DHODH inhibition.
    Keywords:  Bioenergetics; Cancer; De novo pyrimidine synthesis; Dehydroorotate dehydrogenase; Oxidative phosphorylation
    DOI:  https://doi.org/10.1016/j.bbadis.2020.165759
  26. Cell. 2020 Mar 09. pii: S0092-8674(20)30219-1. [Epub ahead of print]
    Tumor-Derived Retinoic Acid Regulates Intratumoral Monocyte Differentiation to Promote Immune Suppression.
    Samir Devalaraja, Tsun Ki Jerrick To, Ian W Folkert, Ramakrishnan Natesan, Md Zahidul Alam, Minghong Li, Yuma Tada, Konstantin Budagyan, Mai T Dang, Li Zhai, Graham P Lobel, Gabrielle E Ciotti, T S Karin Eisinger-Mathason, Irfan A Asangani, Kristy Weber, M Celeste Simon, Malay Haldar.
      The immunosuppressive tumor microenvironment (TME) is a major barrier to immunotherapy. Within solid tumors, why monocytes preferentially differentiate into immunosuppressive tumor-associated macrophages (TAMs) rather than immunostimulatory dendritic cells (DCs) remains unclear. Using multiple murine sarcoma models, we find that the TME induces tumor cells to produce retinoic acid (RA), which polarizes intratumoral monocyte differentiation toward TAMs and away from DCs via suppression of DC-promoting transcription factor Irf4. Genetic inhibition of RA production in tumor cells or pharmacologic inhibition of RA signaling within TME increases stimulatory monocyte-derived cells, enhances T cell-dependent anti-tumor immunity, and synergizes with immune checkpoint blockade. Furthermore, an RA-responsive gene signature in human monocytes correlates with an immunosuppressive TME in multiple human tumors. RA has been considered as an anti-cancer agent, whereas our work demonstrates its tumorigenic capability via myeloid-mediated immune suppression and provides proof of concept for targeting this pathway for tumor immunotherapy.
    Keywords:  dendritic cell; immune checkpoint blockade; immune evasion; macrophage; monocyte; retinoic acid; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.cell.2020.02.042
  27. Exp Neurol. 2020 Mar 09. pii: S0014-4886(20)30113-8. [Epub ahead of print] 113282
    Mapping mitochondrial respiratory chain deficiencies by respirometry: Beyond the Mito Stress Test.
    Sausan M Jaber, Nagendra Yadava, Brian M Polster.
      Cell-based respirometers such as the Seahorse Extracellular Flux Analyzer are valuable tools to assess the functionality of mitochondria within adherent neurons, as well as other cell types. The Mito Stress Test is the most frequently employed protocol of drug additions to evaluate mitochondrial bioenergetic function. Sequential exposure of cells to an ATP synthase inhibitor such as oligomycin and an uncoupler such as FCCP cause changes in oxygen consumption rate that allow estimation of the cellular efficiency and capacity for mitochondrial ATP synthesis. While a useful first step in assessing whether an experimental treatment or genetic manipulation affects mitochondrial energetics, the Mito Stress Test does not identify specific sites of altered respiratory chain function. This article discusses limitations of the Mito Stress Test, proposes a refined protocol for comparing cell populations that requires independent drug titrations at multiple cell densities, and describes a stepwise series of respirometry-based assays that "map" locations of electron transport deficiency. These include strategies to test for cytochrome c release, to probe the functionality of specific electron transport chain complexes within intact or permeabilized cells, and to measure NADH oxidation by the linked activity of Complexes I, III, and IV. To illustrate utility, we show that although UK5099 and ABT-737 each decrease the spare respiratory capacity of cortical neurons, the stepwise assays reveal different underlying mechanisms consistent with their established drug targets: deficient Complex I substrate supply induced by the mitochondrial pyruvate carrier inhibitor UK5099 and cytochrome c release induced by the anti-apoptotic BCL-2 family protein inhibitor ABT-737.
    Keywords:  ABT-737; BCL-2; BH3; Bioenergetics; Cytochrome c; Oxygen; Pyruvate; Respiration; Seahorse; UK5099
    DOI:  https://doi.org/10.1016/j.expneurol.2020.113282
  28. Proc Natl Acad Sci U S A. 2020 Mar 09. pii: 201916414. [Epub ahead of print]
    Mild depolarization of the inner mitochondrial membrane is a crucial component of an anti-aging program.
    Mikhail Y Vyssokikh, Susanne Holtze, Olga A Averina, Konstantin G Lyamzaev, Alisa A Panteleeva, Maria V Marey, Roman A Zinovkin, Fedor F Severin, Maxim V Skulachev, Nicolas Fasel, Thomas B Hildebrandt, Vladimir P Skulachev.
      The mitochondria of various tissues from mice, naked mole rats (NMRs), and bats possess two mechanistically similar systems to prevent the generation of mitochondrial reactive oxygen species (mROS): hexokinases I and II and creatine kinase bound to mitochondrial membranes. Both systems operate in a manner such that one of the kinase substrates (mitochondrial ATP) is electrophoretically transported by the ATP/ADP antiporter to the catalytic site of bound hexokinase or bound creatine kinase without ATP dilution in the cytosol. One of the kinase reaction products, ADP, is transported back to the mitochondrial matrix via the antiporter, again through an electrophoretic process without cytosol dilution. The system in question continuously supports H+-ATP synthase with ADP until glucose or creatine is available. Under these conditions, the membrane potential, ∆ψ, is maintained at a lower than maximal level (i.e., mild depolarization of mitochondria). This ∆ψ decrease is sufficient to completely inhibit mROS generation. In 2.5-y-old mice, mild depolarization disappears in the skeletal muscles, diaphragm, heart, spleen, and brain and partially in the lung and kidney. This age-dependent decrease in the levels of bound kinases is not observed in NMRs and bats for many years. As a result, ROS-mediated protein damage, which is substantial during the aging of short-lived mice, is stabilized at low levels during the aging of long-lived NMRs and bats. It is suggested that this mitochondrial mild depolarization is a crucial component of the mitochondrial anti-aging system.
    Keywords:  aging; antioxidant; mild depolarization; mitochondria; naked mole rat
    DOI:  https://doi.org/10.1073/pnas.1916414117
  29. EMBO J. 2020 Mar 10. e102808
    HNF1A recruits KDM6A to activate differentiated acinar cell programs that suppress pancreatic cancer.
    Mark Kalisz, Edgar Bernardo, Anthony Beucher, Miguel Angel Maestro, Natalia Del Pozo, Irene Millán, Lena Haeberle, Martin Schlensog, Sami Alexander Safi, Wolfram Trudo Knoefel, Vanessa Grau, Matías de Vas, Karl B Shpargel, Eva Vaquero, Terry Magnuson, Sagrario Ortega, Irene Esposito, Francisco X Real, Jorge Ferrer.
      Defects in transcriptional regulators of pancreatic exocrine differentiation have been implicated in pancreatic tumorigenesis, but the molecular mechanisms are poorly understood. The locus encoding the transcription factor HNF1A harbors susceptibility variants for pancreatic ductal adenocarcinoma (PDAC), while KDM6A, encoding Lysine-specific demethylase 6A, carries somatic mutations in PDAC. Here, we show that pancreas-specific Hnf1a null mutant transcriptomes phenocopy those of Kdm6a mutations, and both defects synergize with KrasG12D to cause PDAC with sarcomatoid features. We combine genetic, epigenomic, and biochemical studies to show that HNF1A recruits KDM6A to genomic binding sites in pancreatic acinar cells. This remodels the acinar enhancer landscape, activates differentiated acinar cell programs, and indirectly suppresses oncogenic and epithelial-mesenchymal transition genes. We also identify a subset of non-classical PDAC samples that exhibit the HNF1A/KDM6A-deficient molecular phenotype. These findings provide direct genetic evidence that HNF1A deficiency promotes PDAC. They also connect the tumor-suppressive role of KDM6A deficiency with a cell-specific molecular mechanism that underlies PDAC subtype definition.
    Keywords:  HNF1A; KDM6A; non-classical PDAC; pancreas; pancreas differentiation
    DOI:  https://doi.org/10.15252/embj.2019102808
  30. Clin Cancer Res. 2020 Mar 09. pii: clincanres.2335.2019. [Epub ahead of print]
    Therapeutic targeting of SDHB-mutated pheochromocytoma/paraganglioma with pharmacologic ascorbic acid.
    Yang Liu, Ying Pang, Boqun Zhu, Ondrej Uher, Veronika Caisova, Thanh-Truc Huynh, David Taieb, Katerina Hadrava Vanova, Hans Kumar Ghayee, Jiri Neuzil, Mark Levine, Chunzhang Yang, Karel Pacak.
       PURPOSE: Pheochromocytomas and paragangliomas (PCPGs) are usually benign neuroendocrine tumors. However, PCPGs with mutations in the succinate dehydrogenase B subunit (SDHB) have a poor prognosis and frequently develop metastatic lesions. SDHB-mutated PCPGs exhibit dysregulation in oxygen metabolic pathways, including pseudohypoxia and formation of reactive oxygen species (ROS), suggesting that targeting redox balance pathway could be a potential therapeutic approach.
    EXPERIMENTAL DESIGN: We studied the genetic alterations of Cluster I PCPGs compared to Cluster II PCPGs, which usually present as benign tumors. By targeting the signature molecular pathway, we investigated the therapeutic effect of ascorbic acid on PCPGs using in vitro and in vivo models.
    RESULTS: By investigating PCPG cells with low SDHB levels, we show that pseudohypoxia resulted in elevated expression of iron transport proteins, including transferrin (TF), transferrin receptor 2 (TFR2) and the divalent metal transporter 1 (SLC11A2; DMT1), leading to iron accumulation. This iron overload contributed to elevated oxidative stress. Ascorbic acid at pharmacologic concentrations disrupted redox homeostasis, inducing DNA oxidative damage and cell apoptosis in PCPG cells with low SDHB levels. In addition, a preclinical animal model with PCPG allografts, we demonstrated that pharmacologic ascorbic acid suppressed SDHB-low metastatic lesions and prolonged overall survival.
    CONCLUSIONS: The data here demonstrate that targeting redox homeostasis as a cancer vulnerability with pharmacologic ascorbic acid is a promising therapeutic strategy for SDHB-mutated PCPGs.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-19-2335
  31. J Biol Chem. 2020 Mar 12. pii: jbc.RA119.012023. [Epub ahead of print]
    The tethering function of mitofusin2 controls osteoclast differentiation by modulating the Ca2+-NFATC1 axis.
    Anna Ballard, Rong Zeng, Allahdad Zarei, Christine Shao, Linda Cox, Hui Yan, Antonietta Franco, Gerald W Dorn, Roberta Faccio, Deborah J Veis.
      Dynamic regulation of the mitochondrial network by mitofusins (MFNs) modulates energy production, cell survival, and many intracellular signaling events including calcium handling. However, the relative importance of specific mitochondrial functions and their dependence on MFNs vary greatly among cell types. Osteoclasts have many mitochondria, and increased mitochondrial biogenesis and oxidative phosphorylation enhance bone resorption, but little is known about the mitochondrial network or MFNs in osteoclasts. Because expression of each MFN isoform increases with osteoclastogenesis, we conditionally deleted both MFN1 and -2 (dcKO) in murine osteoclast precursors, finding that this increased bone mass in young female mice, and abolished osteoclast precursor differentiation into mature osteoclasts, in vitro.  Defective osteoclastogenesis was reversed by overexpression of MFN2 but not MFN1; therefore we generated mice lacking only MFN2 in osteoclasts. MFN2-deficient female mice had increased bone mass at 1 year and resistance to RANKL-induced osteolysis at 8 weeks. To explore whether MFN-mediated tethering or mitophagy is important for osteoclastogenesis, we overexpressed MFN2 variants defective in either function in MFN1/2 dcKO precursors and found that although mitophagy was dispensable for differentiation, tethering was required. Since the master osteoclastogenic transcriptional regulator nuclear factor of activated T cells 1 (NFATC1) is calcium-regulated, we assessed calcium release from the endoplasmic reticulum (ER) and store-operated calcium entry and found that the latter was blunted in dcKO cells. Restored osteoclast differentiation by expression of intact MFN2 or the mitophagy-defective variant was associated with normalization of store-operated calcium entry and Nfatc1 levels, indicating that MFN2 controls mitochondria-ER tethering in osteoclasts.
    Keywords:  animal model; bone; calcium; mitochondria; mitochondrial dynamics; mus musculus; osteoclast; osteoclastogenesis
    DOI:  https://doi.org/10.1074/jbc.RA119.012023
  32. PLoS Comput Biol. 2020 Mar 10. 16(3): e1007682
    A plausible accelerating function of intermediate states in cancer metastasis.
    Hanah Goetz, Juan R Melendez-Alvarez, Luonan Chen, Xiao-Jun Tian.
      Epithelial-to-mesenchymal transition (EMT) is a fundamental cellular process and plays an essential role in development, tissue regeneration, and cancer metastasis. Interestingly, EMT is not a binary process but instead proceeds with multiple partial intermediate states. However, the functions of these intermediate states are not fully understood. Here, we focus on a general question about how the number of partial EMT states affects cell transformation. First, by fitting a hidden Markov model of EMT with experimental data, we propose a statistical mechanism for EMT in which many unobservable microstates may exist within one of the observable macrostates. Furthermore, we find that increasing the number of intermediate states can accelerate the EMT process and that adding parallel paths or transition layers may accelerate the process even further. Last, a stabilized intermediate state traps cells in one partial EMT state. This work advances our understanding of the dynamics and functions of EMT plasticity during cancer metastasis.
    DOI:  https://doi.org/10.1371/journal.pcbi.1007682
  33. Nat Commun. 2020 Mar 09. 11(1): 1277
    Hyperoxia induces glutamine-fuelled anaplerosis in retinal Müller cells.
    Charandeep Singh, Vincent Tran, Leah McCollum, Youstina Bolok, Kristin Allan, Alex Yuan, George Hoppe, Henri Brunengraber, Jonathan E Sears.
      Although supplemental oxygen is required to promote survival of severely premature infants, hyperoxia is simultaneously harmful to premature developing tissues such as in the retina. Here we report the effect of hyperoxia on central carbon metabolism in primary mouse Müller glial cells and a human Müller glia cell line (M10-M1 cells). We found decreased flux from glycolysis entering the tricarboxylic acid cycle in Müller cells accompanied by increased glutamine consumption in response to hyperoxia. In hyperoxia, anaplerotic catabolism of glutamine by Müller cells increased ammonium release two-fold. Hyperoxia induces glutamine-fueled anaplerosis that reverses basal Müller cell metabolism from production to consumption of glutamine.
    DOI:  https://doi.org/10.1038/s41467-020-15066-6
  34. PLoS One. 2020 ;15(3): e0219275
    Glutamine supports the protection of tissue cells against the damage caused by cholesterol-dependent cytolysins from pathogenic bacteria.
    Matthew L Turner, Sian E Owens, I Martin Sheldon.
      Pathogenic bacteria often damage tissues by secreting toxins that form pores in cell membranes, and the most common pore-forming toxins are cholesterol-dependent cytolysins. During bacterial infections, glutamine becomes a conditionally essential amino acid, and glutamine is an important nutrient for immune cells. However, the role of glutamine in protecting tissue cells against pore-forming toxins is unclear. Here we tested the hypothesis that glutamine supports the protection of tissue cells against the damage caused by cholesterol-dependent cytolysins. Stromal and epithelial cells were sensitive to damage by the cholesterol-dependent cytolysins, pyolysin and streptolysin O, as determined by leakage of potassium and lactate dehydrogenase from cells, and reduced cell viability. However, glutamine deprivation increased the leakage of lactate dehydrogenase and reduced the viability of cells challenged with cholesterol-dependent cytolysins. Without glutamine, stromal cells challenged with pyolysin leaked lactate dehydrogenase (control vs. pyolysin, 2.6 ± 0.6 vs. 34.4 ± 4.5 AU, n = 12), which was more than three-fold the leakage from cells supplied with 2 mM glutamine (control vs. pyolysin, 2.2 ± 0.3 vs. 9.4 ± 1.0 AU). Glutamine cytoprotection did not depend on glutaminolysis, replenishing the Krebs cycle via succinate, changes in cellular cholesterol, or regulators of cell metabolism (AMPK and mTOR). In conclusion, although the mechanism remains elusive, we found that glutamine supports the protection of tissue cells against the damage caused by cholesterol-dependent cytolysins from pathogenic bacteria.
    DOI:  https://doi.org/10.1371/journal.pone.0219275
  35. Br J Cancer. 2020 Mar 10.
    Lactic acidosis induces resistance to the pan-Akt inhibitor uprosertib in colon cancer cells.
    Emily M E Barnes, Yitao Xu, Adrian Benito, Lili Herendi, Alexandros P Siskos, Eric O Aboagye, Anke Nijhuis, Hector C Keun.
       BACKGROUND: Akt signalling regulates glycolysis and drives the Warburg effect in cancer, thus decreased glucose utilisation is a pharmacodynamic marker of Akt inhibition. However, cancer cells can utilise alternative nutrients to glucose for energy such as lactate, which is often elevated in tumours together with increased acidity. We therefore hypothesised that lactic acidosis may confer resistance to Akt inhibition.
    METHODS: The effect of the pan-Akt inhibitor uprosertib (GSK2141795), on HCT116 and LS174T colon cancer cells was evaluated in the presence and absence of lactic acid in vitro. Expression of downstream Akt signalling proteins was determined using a phosphokinase array and immunoblotting. Metabolism was assessed using 1H nuclear magnetic resonance spectroscopy, stable isotope labelling and gas chromatography-mass spectrometry.
    RESULTS: Lactic acid-induced resistance to uprosertib was characterised by increased cell survival and reduced apoptosis. Uprosertib treatment reduced Akt signalling and glucose uptake irrespective of lactic acid supplementation. However, incorporation of lactate carbon and enhanced respiration was maintained in the presence of uprosertib and lactic acid. Inhibiting lactate transport or oxidative phosphorylation was sufficient to potentiate apoptosis in the presence of uprosertib.
    CONCLUSIONS: Lactic acidosis confers resistance to uprosertib, which can be reversed by inhibiting lactate transport or oxidative metabolism.
    DOI:  https://doi.org/10.1038/s41416-020-0777-y
  36. J Biol Chem. 2020 Mar 09. pii: jbc.RA119.010911. [Epub ahead of print]
    A dynamic anchor domain in SLC13 transporters controls metabolite transport.
    Ahlam Khamaysi, Sara Aharon, Hadar Eini-Rider, Ehud Ohana.
      Metabolite transport across cellular membranes is required for bioenergetic processes and metabolic signaling. The solute carrier family 13 (SLC13) transporters mediate transport of the metabolites succinate and citrate and hence are of paramount physiological importance. Nevertheless, the mechanisms of SLC13 transport and regulation are poorly understood. Here, a dynamic structural SLC13 model suggested that an interfacial helix, H4c, which is common to all SLC13s, stabilizes the stationary scaffold domain by anchoring it to the membrane, thereby facilitating movement of the SLC13 catalytic domain. Moreover, we found that intracellular determinants interact with the H4c anchor domain to modulate transport. This dual function is achieved by basic residues that alternately face either the membrane phospholipids or the intracellular milieu. This mechanism was supported by several experimental findings obtained using biochemical methods, electrophysiological measurements in Xenopus oocytes, and fluorescent microscopy of mammalian cells. First, a positively charged and highly conserved H4c residue, R108, was indispensable and crucial for metabolite transport. Furthermore, neutralization of other H4c basic residues inhibited SLC13 transport function, thus mimicking the inhibitory effect of the SLC13 inhibitor, SLC26A6. Our findings suggest that the positive charge distribution across H4c domain controls SLC13 transporter function and is utilized by SLC13-interacting proteins in the regulation of metabolite transport.
    Keywords:  NaCT; SLC13; SLC26; bioenergetics; cell metabolism; citrate; computer modeling; membrane transport; tricarboxylic acid cycle (TCA cycle) (Krebs cycle)
    DOI:  https://doi.org/10.1074/jbc.RA119.010911
  37. Cancers (Basel). 2020 Mar 05. pii: E599. [Epub ahead of print]12(3):
    Glutaminases as a Novel Target for SDHB-Associated Pheochromocytomas/Paragangliomas.
    Balazs Sarkadi, Katalin Meszaros, Ildiko Krencz, Letizia Canu, Lilla Krokker, Sara Zakarias, Gabor Barna, Anna Sebestyen, Judit Papay, Zoltan Hujber, Henriett Butz, Otto Darvasi, Peter Igaz, Judit Doczi, Michaela Luconi, Christos Chinopoulos, Attila Patocs.
      Pheochromocytoma/paragangliomas (Pheo/PGL) are rare endocrine cancers with strong genetic background. Mutations in the SDHB subunit of succinate dehydrogenase (SDH) predispose patients to malignant disease with limited therapeutic options and poor prognosis. Using a host of cellular and molecular biology techniques in 2D and 3D cell culture formats we show that SDH inhibition had cell line specific biological and biochemical consequences. Based on our studies performed on PC12 (rat chromaffin cell line), Hela (human cervix epithelial cell line), and H295R (human adrenocortical cell line) cells, we demonstrated that chromaffin cells were not affected negatively by the inhibition of SDH either by siRNA directed against SDHB or treatment with SDH inhibitors (itaconate and atpenin A5). Cell viability and intracellular metabolite measurements pointed to the cell line specific consequences of SDH impairment and to the importance of glutamate metabolism in chromaffin cells. A significant increase in glutaminase-1 (GLS-1) expression after SDH impairment was observed in PC12 cells. GLS-1 inhibitor BPTES was capable of significantly decreasing proliferation of SDH impaired PC12 cells. Glutaminase-1 and SDHB expressions were tested in 35 Pheo/PGL tumor tissues. Expression of GLS1 was higher in the SDHB low expressed group compared to SDHB high expressed tumors. Our data suggest that the SDH-associated malignant potential of Pheo/PGL is strongly dependent on GLS-1 expression and glutaminases may be novel targets for therapy.
    Keywords:  GLS-1; SDH; SDHB; paraganglioma; pheochromocytoma; succinate
    DOI:  https://doi.org/10.3390/cancers12030599
  38. Cancer Res. 2020 Mar 10. pii: canres.3870.2019. [Epub ahead of print]
    RUNX1 is a driver of renal cell carcinoma correlating with clinical outcome.
    Nicholas Rooney, Susan M Mason, Laura McDonald, J Henry M Däbritz, Kirsteen J Campbell, Ann Hedley, Steven Howard, Dimitris Athineos, Colin Nixon, William Clark, Joshua D G Leach, Owen J Sansom, Joanne Edwards, Ewan R Cameron, Karen Blyth.
      The recurring association of specific genetic lesions with particular types of cancer is a fascinating, and largely unexplained area of cancer biology. This is particularly true of clear cell renal cell carcinoma (ccRCC) where although key mutations such as loss of VHL is an almost ubiquitous finding, there remains a conspicuous lack of targetable genetic drivers. In this study, we have identified a previously unknown pro-tumorigenic role for the RUNX genes in this disease setting. Analysis of patient tumor biopsies together with loss of function studies in preclinical models established the importance of RUNX1 and RUNX2 in ccRCC. Patients with high RUNX1 (and RUNX2) expression exhibited significantly poorer clinical survival compared to patients with low expression. This was functionally relevant as deletion of RUNX1 in ccRCC cell lines reduced tumor cell growth and viability in vitro and in vivo. Transcriptional profiling of RUNX1-CRISPR-deleted cells revealed a gene signature dominated by extracellular matrix remodelling, notably affecting STMN3, SERPINH1, and EPHRIN signaling. Finally, RUNX1 deletion in a genetic mouse model of kidney cancer improved overall survival and reduced tumor cell proliferation. In summary, these data attest to the validity of targeting a RUNX1-transcriptional program in ccRCC.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-19-3870
  39. Nat Commun. 2020 Mar 12. 11(1): 1335
    Cancer immune control needs senescence induction by interferon-dependent cell cycle regulator pathways in tumours.
    Ellen Brenner, Barbara F Schörg, Fatima Ahmetlić, Thomas Wieder, Franz Joachim Hilke, Nadine Simon, Christopher Schroeder, German Demidov, Tanja Riedel, Birgit Fehrenbacher, Martin Schaller, Andrea Forschner, Thomas Eigentler, Heike Niessner, Tobias Sinnberg, Katharina S Böhm, Nadine Hömberg, Heidi Braumüller, Daniel Dauch, Stefan Zwirner, Lars Zender, Dominik Sonanini, Albert Geishauser, Jürgen Bauer, Martin Eichner, Katja J Jarick, Andreas Beilhack, Saskia Biskup, Dennis Döcker, Dirk Schadendorf, Leticia Quintanilla-Martinez, Bernd J Pichler, Manfred Kneilling, Ralph Mocikat, Martin Röcken.
      Immune checkpoint blockade (ICB)-based or natural cancer immune responses largely eliminate tumours. Yet, they require additional mechanisms to arrest those cancer cells that are not rejected. Cytokine-induced senescence (CIS) can stably arrest cancer cells, suggesting that interferon-dependent induction of senescence-inducing cell cycle regulators is needed to control those cancer cells that escape from killing. Here we report in two different cancers sensitive to T cell-mediated rejection, that deletion of the senescence-inducing cell cycle regulators p16Ink4a/p19Arf (Cdkn2a) or p21Cip1 (Cdkn1a) in the tumour cells abrogates both the natural and the ICB-induced cancer immune control. Also in humans, melanoma metastases that progressed rapidly during ICB have losses of senescence-inducing genes and amplifications of senescence inhibitors. Metastatic cells also resist CIS. Such genetic and functional alterations are infrequent in metastatic melanomas regressing during ICB. Thus, activation of tumour-intrinsic, senescence-inducing cell cycle regulators is required to stably arrest cancer cells that escape from eradication.
    DOI:  https://doi.org/10.1038/s41467-020-14987-6
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