bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2022‒06‒12
sixty-two papers selected by
Christian Frezza,

  1. Metabolic evidence for distinct pyruvate pools inside plant mitochondria.
  2. GDAP1 loss of function inhibits the mitochondrial pyruvate dehydrogenase complex by altering the actin cytoskeleton.
  3. The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer.
  4. Cyclocreatine suppresses creatine metabolism and impairs prostate cancer progression.
  5. Limited nutrient availability in the tumor microenvironment renders pancreatic tumors sensitive to allosteric IDH1 inhibitors.
  6. Fungal Patterns Induce Cytokine Expression through Fluxes of Metabolic Intermediates That Support Glycolysis and Oxidative Phosphorylation.
  7. Lysosome lipid signalling from the periphery to neurons regulates longevity.
  8. Celastrol alleviates high-fat diet-induced obesity via enhanced muscle glucose utilization and mitochondrial oxidative metabolism-mediated upregulation of pyruvate dehydrogenase complex.
  9. Succinate metabolism in the retinal pigment epithelium uncouples respiration from ATP synthesis.
  10. 13C-Labeled Diethyl Ketoglutarate Derivatives as Hyperpolarized Probes of 2-Ketoglutarate Dehydrogenase Activity.
  11. Metabolic Messengers: fibroblast growth factor 1.
  12. Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq.
  13. Mitochondrial respiration in B lymphocytes is essential for humoral immunity by controlling the flux of the TCA cycle.
  14. Structural basis for MTA1c-mediated DNA N6-adenine methylation.
  15. Mitochondrial Cytochrome c Oxidase Defects Alter Cellular Homeostasis of Transition Metals.
  16. A reference tissue atlas for the human kidney.
  17. Metabolic reprogramming: a bridge between aging and tumorigenesis.
  18. Glycerate from intestinal fructose metabolism induces islet cell damage and glucose intolerance.
  19. The Acyl-CoA-Binding Protein Acb1 regulates mitochondria, lipid droplets, and cell proliferation.
  20. The "mitochondrial stress responses": the "Dr. Jekyll and Mr. Hyde" of neuronal disorders.
  21. Mining the mitochondrial proteome.
  22. Major construction entails major demolition.
  23. The metabolic enzyme hexokinase 2 localizes to the nucleus in AML and normal haematopoietic stem and progenitor cells to maintain stemness.
  24. A yeast suppressor screen links Coa4 to the mitochondrial copper delivery pathway for cytochrome c oxidase.
  25. PBRM1 deficiency oncogenic addiction is associated with activated AKT-mTOR signalling and aerobic glycolysis in clear cell renal cell carcinoma cells.
  26. Animal Models of Dysregulated Cardiac Metabolism.
  27. Itaconate is a lysosomal inducer that promotes antibacterial innate immunity.
  28. Prime Real Estate: Metals, Cofactors and MICOS.
  29. The polyol pathway is an evolutionarily conserved system for sensing glucose uptake.
  30. Fbxo7 promotes Cdk6 activity to inhibit PFKP and glycolysis in T cells.
  31. Circadian Regulation of Digestive & Metabolic Tissues.
  32. Mitochondria ROS and mitophagy in acute kidney injury.
  33. A CRISPR screen identifies redox vulnerabilities for KEAP1/NRF2 mutant non-small cell lung cancer.
  34. Non-coding 7S RNA inhibits transcription via mitochondrial RNA polymerase dimerization.
  35. A naturally DNase-free CRISPR-Cas12c enzyme silences gene expression.
  36. Multi-dimensional Fluorescence Live-Cell Imaging for Glucosome Dynamics in Living Human Cells.
  37. Translational Control by 4E-BP1/2 Suppressor Proteins Regulates Mitochondrial Biosynthesis and Function during CD8+ T Cell Proliferation.
  38. Mechanism of mitoribosomal small subunit biogenesis and preinitiation.
  39. IL-6 and CCL18 mediate crosstalk between VHL-deficient kidney cells and macrophages during development of renal cell carcinoma.
  40. A Resource to Infer Molecular Paths Linking Cancer Mutations to Perturbation of Cell Metabolism.
  41. Evidence for a novel, effective approach to targeting carcinoma catabolism exploiting the first-in-class, anti-cancer mitochondrial drug, CPI-613.
  42. PEX11β and FIS1 cooperate in peroxisome division independent of Mitochondrial Fission Factor.
  43. Visualizing cytoplasmic ATP in C. elegans larvae using PercevalHR.
  44. Towards a molecular mechanism underlying mitochondrial protein import through the TOM and TIM23 complexes.
  45. Distinct roles for two Caenorhabditis elegans acid-sensing ion channels in an ultradian clock.
  46. Diet high in branched-chain amino acid promotes PDAC development by USP1-mediated BCAT2 stabilization.
  47. Efferocytosis requires periphagosomal Ca2+-signaling and TRPM7-mediated electrical activity.
  48. Integration of metabolomics with genomics: Metabolic gene prioritization using metabolomics data and genomic variant (CADD) scores.
  49. Metabolic and immune-sensitive contacts between lipid droplets and endoplasmic reticulum reconstituted in vitro.
  50. Twist1 downregulation of PGC-1α decreases fatty acid oxidation in tubular epithelial cells, leading to kidney fibrosis.
  51. ATGL-dependent white adipose tissue lipolysis controls hepatocyte PPARα activity.
  52. Leucine-tRNA-synthase-2-expressing B cells contribute to colorectal cancer immunoevasion.
  53. Trade-offs predicted by metabolic network structure give rise to evolutionary specialization and phenotypic diversification.
  54. Vitamin B12 coordinates ileal epithelial cell and microbiota functions to resist Salmonella infection in mice.
  55. A single-cell map of dynamic chromatin landscapes of immune cells in renal cell carcinoma.
  56. Inhibition of ATP-citrate lyase improves NASH, liver fibrosis, and dyslipidemia.
  57. Cancer-Induced Metabolic Rewiring of Tumor Endothelial Cells.
  58. JMJD3 intrinsically disordered region links the 3D-genome structure to TGFβ-dependent transcription activation.
  59. SMAD4 Controls Cancer Cell Metabolism by Regulating Methylmalonic Aciduria Cobalamin Deficiency (cbl) B Type.
  60. BRCA1 haploinsufficiency promotes chromosomal amplification under Fenton reaction-based carcinogenesis through ferroptosis-resistance.
  61. Metabolomic studies in the inborn error of metabolism alkaptonuria reveal new biotransformations in tyrosine metabolism.
  62. ATGL is a biosynthetic enzyme for fatty acid esters of hydroxy fatty acids.
  1. Nat Plants. 2022 Jun 09.
    Metabolic evidence for distinct pyruvate pools inside plant mitochondria.
    Xuyen H Le, Chun Pong Lee, Dario Monachello, A Harvey Millar.
      The majority of the pyruvate inside plant mitochondria is either transported into the matrix from the cytosol via the mitochondria pyruvate carrier (MPC) or synthesized in the matrix by alanine aminotransferase (AlaAT) or NAD-malic enzyme (NAD-ME). Pyruvate from these origins could mix into a single pool in the matrix and contribute indistinguishably to respiration via the pyruvate dehydrogenase complex (PDC), or these molecules could maintain a degree of independence in metabolic regulation. Here we demonstrate that feeding isolated mitochondria with uniformly labelled 13C-pyruvate and unlabelled malate enables the assessment of pyruvate contribution from different sources to intermediate production in the tricarboxylic acid cycle. Imported pyruvate was the preferred source for citrate production even when the synthesis of NAD-ME-derived pyruvate was optimized. Genetic or pharmacological elimination of MPC activity removed this preference and allowed an equivalent amount of citrate to be generated from the pyruvate produced by NAD-ME. Increasing the mitochondrial pyruvate pool size by exogenous addition affected only metabolites from pyruvate transported by MPC, whereas depleting the pyruvate pool size by transamination to alanine affected only metabolic products derived from NAD-ME. PDC was more membrane-associated than AlaAT and NAD-ME, suggesting that the physical organization of metabolic machinery may influence metabolic rates. Together, these data reveal that the respiratory substrate supply in plants involves distinct pyruvate pools inside the matrix that can be flexibly mixed on the basis of the rate of pyruvate transport from the cytosol. These pools are independently regulated and contribute differentially to organic acid export from plant mitochondria.
    DOI:  https://doi.org/10.1038/s41477-022-01165-3
  2. Commun Biol. 2022 Jun 03. 5(1): 541
    GDAP1 loss of function inhibits the mitochondrial pyruvate dehydrogenase complex by altering the actin cytoskeleton.
    Christina Wolf, Alireza Pouya, Sara Bitar, Annika Pfeiffer, Diones Bueno, Liliana Rojas-Charry, Sabine Arndt, David Gomez-Zepeda, Stefan Tenzer, Federica Dal Bello, Caterina Vianello, Sandra Ritz, Jonas Schwirz, Kristina Dobrindt, Michael Peitz, Eva-Maria Hanschmann, Pauline Mencke, Ibrahim Boussaad, Marion Silies, Oliver Brüstle, Marta Giacomello, Rejko Krüger, Axel Methner.
      Charcot-Marie-Tooth (CMT) disease 4A is an autosomal-recessive polyneuropathy caused by mutations of ganglioside-induced differentiation-associated protein 1 (GDAP1), a putative glutathione transferase, which affects mitochondrial shape and alters cellular Ca2+ homeostasis. Here, we identify the underlying mechanism. We found that patient-derived motoneurons and GDAP1 knockdown SH-SY5Y cells display two phenotypes: more tubular mitochondria and a metabolism characterized by glutamine dependence and fewer cytosolic lipid droplets. GDAP1 interacts with the actin-depolymerizing protein Cofilin-1 and beta-tubulin in a redox-dependent manner, suggesting a role for actin signaling. Consistently, GDAP1 loss causes less F-actin close to mitochondria, which restricts mitochondrial localization of the fission factor dynamin-related protein 1, instigating tubularity. GDAP1 silencing also disrupts mitochondria-ER contact sites. These changes result in lower mitochondrial Ca2+ levels and inhibition of the pyruvate dehydrogenase complex, explaining the metabolic changes upon GDAP1 loss of function. Together, our findings reconcile GDAP1-associated phenotypes and implicate disrupted actin signaling in CMT4A pathophysiology.
    DOI:  https://doi.org/10.1038/s42003-022-03487-6
  3. Nature. 2022 Jun 08.
    The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer.
    Saroor A Patel, Shoko Hirosue, Paulo Rodrigues, Erika Vojtasova, Emma K Richardson, Jianfeng Ge, Saiful E Syafruddin, Alyson Speed, Evangelia K Papachristou, David Baker, David Clarke, Stephenie Purvis, Ludovic Wesolowski, Anna Dyas, Leticia Castillon, Veronica Caraffini, Dóra Bihary, Cissy Yong, David J Harrison, Grant D Stewart, Mitchell J Machiela, Mark P Purdue, Stephen J Chanock, Anne Y Warren, Shamith A Samarajiwa, Jason S Carroll, Sakari Vanharanta.
      Large-scale human genetic data1-3 have shown that cancer mutations display strong tissue-selectivity, but how this selectivity arises remains unclear. Here, using experimental models, functional genomics and analyses of patient samples, we demonstrate that the lineage transcription factor paired box 8 (PAX8) is required for oncogenic signalling by two common genetic alterations that cause clear cell renal cell carcinoma (ccRCC) in humans: the germline variant rs7948643 at 11q13.3 and somatic inactivation of the von Hippel-Lindau tumour suppressor (VHL)4-6. VHL loss, which is observed in about 90% of ccRCCs, can lead to hypoxia-inducible factor 2α (HIF2A) stabilization6,7. We show that HIF2A is preferentially recruited to PAX8-bound transcriptional enhancers, including a pro-tumorigenic cyclin D1 (CCND1) enhancer that is controlled by PAX8 and HIF2A. The ccRCC-protective allele C at rs7948643 inhibits PAX8 binding at this enhancer and downstream activation of CCND1 expression. Co-option of a PAX8-dependent physiological programme that supports the proliferation of normal renal epithelial cells is also required for MYC expression from the ccRCC metastasis-associated amplicons at 8q21.3-q24.3 (ref. 8). These results demonstrate that transcriptional lineage factors are essential for oncogenic signalling and that they mediate tissue-specific cancer risk associated with somatic and inherited genetic variants.
    DOI:  https://doi.org/10.1038/s41586-022-04809-8
  4. Cancer Res. 2022 Jun 08. pii: canres.1301.2021-5-4 10:59:25.103. [Epub ahead of print]
    Cyclocreatine suppresses creatine metabolism and impairs prostate cancer progression.
    Rachana Patel, Catriona A Ford, Lisa Rodgers, Linda K Rushworth, Janis Fleming, Ernest Mui, Tong Zhang, David Watson, Victoria Lynch, Gillian Mackay, David Sumpton, Owen J Sansom, Johan Vande Voorde, Hing Y Leung.
      Prostate cancer is the second most common cause of cancer mortality in men worldwide. Applying a novel genetically engineered mouse model (GEMM) of aggressive prostate cancer driven by deficiency of the tumour suppressors PTEN and SPRY2 (Sprouty 2), we identified enhanced creatine metabolism as a central component of progressive disease. Creatine treatment was associated with enhanced cellular basal respiration in vitro and increased tumour cell proliferation in vivo. Stable isotope tracing revealed that intracellular levels of creatine in prostate cancer cells are predominantly dictated by exogenous availability rather than by de novo synthesis from arginine. Genetic silencing of creatine transporter SLC6A8 depleted intracellular creatine levels and reduced the colony-forming capacity of human prostate cancer cells. Accordingly, in vitro treatment of prostate cancer cells with cyclocreatine, a creatine analog, dramatically reduced intracellular levels of creatine and its derivatives phosphocreatine and creatinine and suppressed proliferation. Supplementation with cyclocreatine impaired cancer progression in the PTEN and SPRY-deficient prostate cancer GEMMs and in a xenograft liver metastasis model. Collectively, these results identify a metabolic vulnerability in prostate cancer and demonstrate a rational therapeutic strategy to exploit this vulnerability to impede tumour progression.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-1301
  5. Nat Cancer. 2022 Jun 09.
    Limited nutrient availability in the tumor microenvironment renders pancreatic tumors sensitive to allosteric IDH1 inhibitors.
    Ali Vaziri-Gohar, Joel Cassel, Farheen S Mohammed, Mehrdad Zarei, Jonathan J Hue, Omid Hajihassani, Hallie J Graor, Yellamelli V V Srikanth, Saadia A Karim, Ata Abbas, Erin Prendergast, Vanessa Chen, Erryk S Katayama, Katerina Dukleska, Imran Khokhar, Anthony Andren, Li Zhang, Chunying Wu, Bernadette Erokwu, Chris A Flask, Mahsa Zarei, Rui Wang, Luke D Rothermel, Andrea M P Romani, Jessica Bowers, Robert Getts, Curtis Tatsuoka, Jennifer P Morton, Ilya Bederman, Henri Brunengraber, Costas A Lyssiotis, Joseph M Salvino, Jonathan R Brody, Jordan M Winter.
      Nutrient-deprived conditions in the tumor microenvironment (TME) restrain cancer cell viability due to increased free radicals and reduced energy production. In pancreatic cancer cells a cytosolic metabolic enzyme, wild-type isocitrate dehydrogenase 1 (wtIDH1), enables adaptation to these conditions. Under nutrient starvation, wtIDH1 oxidizes isocitrate to generate α-ketoglutarate (αKG) for anaplerosis and NADPH to support antioxidant defense. In this study, we show that allosteric inhibitors of mutant IDH1 (mIDH1) are potent wtIDH1 inhibitors under conditions present in the TME. We demonstrate that low magnesium levels facilitate allosteric inhibition of wtIDH1, which is lethal to cancer cells when nutrients are limited. Furthermore, the Food & Drug Administration (FDA)-approved mIDH1 inhibitor ivosidenib (AG-120) dramatically inhibited tumor growth in preclinical models of pancreatic cancer, highlighting this approach as a potential therapeutic strategy against wild-type IDH1 cancers.
    DOI:  https://doi.org/10.1038/s43018-022-00393-y
  6. J Immunol. 2022 Jun 10. pii: ji2100666. [Epub ahead of print]
    Fungal Patterns Induce Cytokine Expression through Fluxes of Metabolic Intermediates That Support Glycolysis and Oxidative Phosphorylation.
    Cristina Mancebo, José Javier Fernández, Carmen Herrero-Sánchez, Yolanda Alvarez, Sara Alonso, Tito A Sandoval, Juan R Cubillos-Ruiz, Olimpio Montero, Nieves Fernández, Mariano Sánchez Crespo.
      Cytokine expression is fine-tuned by metabolic intermediates, which makes research on immunometabolism suitable to yield drugs with a wider prospect of application than the biological therapies that block proinflammatory cytokines. Switch from oxidative phosphorylation (OXPHOS) to glycolysis has been considered a characteristic feature of activated immune cells. However, some stimuli might enhance both routes concomitantly. The connection between the tricarboxylic acid cycle and cytokine expression was scrutinized in human monocyte-derived dendritic cells stimulated with the fungal surrogate zymosan. Results showed that nucleocytosolic citrate and ATP-citrate lyase activity drove IL1B, IL10, and IL23A expression by yielding acetyl-CoA and oxaloacetate, with the latter one supporting glycolysis and OXPHOS by maintaining cytosolic NAD+ and mitochondrial NADH levels through mitochondrial shuttles. Succinate dehydrogenase showed a subunit-specific ability to modulate IL23A and IL10 expression. Succinate dehydrogenase A subunit activity supported cytokine expression through the control of the 2-oxoglutarate/succinate ratio, whereas C and D subunits underpinned cytokine expression by conveying electron flux from complex II to complex III of the electron transport chain. Fatty acids may also fuel the tricarboxylic acid cycle and influence cytokine expression. Overall, these results show that fungal patterns support cytokine expression through a strong boost of glycolysis and OXPHOS supported by the use of pyruvate, citrate, and succinate, along with the compartmentalized NAD(H) redox state maintained by mitochondrial shuttles.
    DOI:  https://doi.org/10.4049/jimmunol.2100666
  7. Nat Cell Biol. 2022 Jun 09.
    Lysosome lipid signalling from the periphery to neurons regulates longevity.
    Marzia Savini, Andrew Folick, Yi-Tang Lee, Feng Jin, André Cuevas, Matthew C Tillman, Jonathon D Duffy, Qian Zhao, Isaiah A Neve, Pei-Wen Hu, Yong Yu, Qinghao Zhang, Youqiong Ye, William B Mair, Jin Wang, Leng Han, Eric A Ortlund, Meng C Wang.
      Lysosomes are key cellular organelles that metabolize extra- and intracellular substrates. Alterations in lysosomal metabolism are implicated in ageing-associated metabolic and neurodegenerative diseases. However, how lysosomal metabolism actively coordinates the metabolic and nervous systems to regulate ageing remains unclear. Here we report a fat-to-neuron lipid signalling pathway induced by lysosomal metabolism and its longevity-promoting role in Caenorhabditis elegans. We discovered that induced lysosomal lipolysis in peripheral fat storage tissue upregulates the neuropeptide signalling pathway in the nervous system to promote longevity. This cell-non-autonomous regulation is mediated by a specific polyunsaturated fatty acid, dihomo-γ-linolenic acid, and LBP-3 lipid chaperone protein transported from the fat storage tissue to neurons. LBP-3 binds to dihomo-γ-linolenic acid, and acts through NHR-49 nuclear receptor and NLP-11 neuropeptide in neurons to extend lifespan. These results reveal lysosomes as a signalling hub to coordinate metabolism and ageing, and lysosomal signalling mediated inter-tissue communication in promoting longevity.
    DOI:  https://doi.org/10.1038/s41556-022-00926-8
  8. Toxicol Appl Pharmacol. 2022 Jun 06. pii: S0041-008X(22)00244-7. [Epub ahead of print] 116099
    Celastrol alleviates high-fat diet-induced obesity via enhanced muscle glucose utilization and mitochondrial oxidative metabolism-mediated upregulation of pyruvate dehydrogenase complex.
    Mohamad Hafizi Abu Bakar, Nor Shafiqah Nor Shahril, Mohamad Shamil Faris Mohamad Khalid, Sharifah Mohammad, Khairul Anuar Shariff, Thiruventhan Karunakaran, Rabeta Mohd Salleh, Mohamad NorishamMohamad Rosdi.
      Celastrol, a natural triterpene from the Tripterygium wilfordii has been demonstrated to possess attributive properties to attenuate various animal models of obesity-associated conditions. The present study aimed to elucidate the putative targets of celastrol on intracellular glucose utilization and mitochondrial oxidative metabolism in the isolated quadriceps skeletal muscle of high-fat diet (HFD)-induced obese male C57BL6/J mice. Here we showed that celastrol remarkably attenuated obesity and insulin resistance through improvement of systemic glucose tolerance and insulin sensitivity. Enhanced mRNA transcription factors of key rate-limiting glycolytic and TCA cycle enzymes were observed following celastrol administration. The metabolic profiling revealed profound changes induced by celastrol administration on several key metabolites of glycolysis and tricarboxylic acid (TCA) cycle including glucose-1-phosphate, pyruvate, citrate, α-ketoglutarate, succinate and fumarate. Celastrol effectively increased mitochondrial oxidative functions via increased pyruvate dehydrogenase complex (PDC) activity and downregulated pyruvate dehydrogenase kinase 4 (PDK4) expressions. Enhanced succinate dehydrogenase (SDH) activity was noticed following celastrol co-supplementation, leading to a steady establishment of the electrochemical gradient across mitochondrial membrane for ATP production and mitochondrial biogenesis. In conclusion, the current findings accentuate the therapeutic potential of celastrol against HFD-induced obese mice via enhanced glucose utilization and mitochondrial oxidative metabolism-mediated upregulation of PDC activity in the skeletal muscle.
    Keywords:  Celastrol; Glucose metabolism; Mitochondria; Obesity; Pyruvate dehydrogenase complex; Skeletal muscle
    DOI:  https://doi.org/10.1016/j.taap.2022.116099
  9. Cell Rep. 2022 Jun 07. pii: S2211-1247(22)00694-5. [Epub ahead of print]39(10): 110917
    Succinate metabolism in the retinal pigment epithelium uncouples respiration from ATP synthesis.
    Daniel T Hass, Celia M Bisbach, Brian M Robbings, Martin Sadilek, Ian R Sweet, James B Hurley.
      Fumarate can be a surrogate for O2 as a terminal electron acceptor in the electron transport chain. Reduction of fumarate produces succinate, which can be exported. It is debated whether intact tissues can import and oxidize succinate produced by other tissues. In a previous report, we showed that mitochondria in retinal pigment epithelium (RPE)-choroid preparations can use succinate to reduce O2 to H2O. However, cells in that preparation could have been disrupted during tissue isolation. We now use multiple strategies to quantify intactness of the isolated RPE-choroid tissue. We find that exogenous 13C4-succinate is oxidized by intact cells then exported as fumarate or malate. Unexpectedly, we also find that oxidation of succinate is different from oxidation of other substrates because it uncouples electron transport from ATP synthesis. Retinas produce and export succinate. Our findings imply that retina succinate may substantially increase O2 consumption by uncoupling adjacent RPE mitochondria.
    Keywords:  CP: metabolism; anion transport; cell metabolism; energy metabolism; mitochondrial respiratory chain; retinal metabolism; retinal pigment epithelium; succinate; uncoupling
    DOI:  https://doi.org/10.1016/j.celrep.2022.110917
  10. Anal Sens. 2021 Nov;1(4): 156-160
    13C-Labeled Diethyl Ketoglutarate Derivatives as Hyperpolarized Probes of 2-Ketoglutarate Dehydrogenase Activity.
    Jaspal Singh, Eul Hyun Suh, Gaurav Sharma, Jun Chen, Edward P Hackett, Xiaodong Wen, A Dean Sherry, Chalermchai Khemtong, Craig R Malloy, Jae Mo Park, Zoltan Kovacs.
      The TCA cycle is a central metabolic pathway for energy production and biosynthesis. A major control point of metabolic flux through the cycle is the decarboxylation of 2-ketoglutarate by the TCA cycle enzyme 2-ketoglutarate dehydrogenase (2-KGDH). In this project, we developed 13C labeled 2-ketoglutarate derivatives to monitor 2-KGDH activity in vivo. 13C NMR analysis of liver extracts revealed that uniformly 13C labeled 2-ketogutarate, in its cell permeable ester form, was rapidly taken up and hydrolyzed in liver and underwent extensive metabolism to produce labeled glutamate, succinate, lactate and other metabolites. Diethyl [1,2-13C2]-2-ketoglutarate was successfully polarized by dynamic nuclear polarization and within seconds after injection into rats, the probe produced hyperpolarized [13C]bicarbonate in the liver reflecting flux through the TCA cycle. These experiments demonstrate that this tracer offers the possibility of directly monitoring flux through 2-KGDH in vivo.
    Keywords:  NMR spectroscopy; TCA cycle; hyperpolarization; isotopic labeling; ketoglutarates
    DOI:  https://doi.org/10.1002/anse.202100021
  11. Nat Metab. 2022 Jun 09.
    Metabolic Messengers: fibroblast growth factor 1.
    Emanuel Gasser, Gencer Sancar, Michael Downes, Ronald M Evans.
      
    DOI:  https://doi.org/10.1038/s42255-022-00580-2
  12. Cell. 2022 Jun 02. pii: S0092-8674(22)00597-9. [Epub ahead of print]
    Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq.
    Joseph M Replogle, Reuben A Saunders, Angela N Pogson, Jeffrey A Hussmann, Alexander Lenail, Alina Guna, Lauren Mascibroda, Eric J Wagner, Karen Adelman, Gila Lithwick-Yanai, Nika Iremadze, Florian Oberstrass, Doron Lipson, Jessica L Bonnar, Marco Jost, Thomas M Norman, Jonathan S Weissman.
      A central goal of genetics is to define the relationships between genotypes and phenotypes. High-content phenotypic screens such as Perturb-seq (CRISPR-based screens with single-cell RNA-sequencing readouts) enable massively parallel functional genomic mapping but, to date, have been used at limited scales. Here, we perform genome-scale Perturb-seq targeting all expressed genes with CRISPR interference (CRISPRi) across >2.5 million human cells. We use transcriptional phenotypes to predict the function of poorly characterized genes, uncovering new regulators of ribosome biogenesis (including CCDC86, ZNF236, and SPATA5L1), transcription (C7orf26), and mitochondrial respiration (TMEM242). In addition to assigning gene function, single-cell transcriptional phenotypes allow for in-depth dissection of complex cellular phenomena-from RNA processing to differentiation. We leverage this ability to systematically identify genetic drivers and consequences of aneuploidy and to discover an unanticipated layer of stress-specific regulation of the mitochondrial genome. Our information-rich genotype-phenotype map reveals a multidimensional portrait of gene and cellular function.
    Keywords:  CRISPR; Integrator complex; Perturb-seq; cell biology; chromosomal instability; genetic screens; genotype-phenotype map; mitochondrial genome stress response; single-cell RNA sequencing
    DOI:  https://doi.org/10.1016/j.cell.2022.05.013
  13. Cell Rep. 2022 Jun 07. pii: S2211-1247(22)00689-1. [Epub ahead of print]39(10): 110912
    Mitochondrial respiration in B lymphocytes is essential for humoral immunity by controlling the flux of the TCA cycle.
    Sophia Urbanczyk, Olivier R Baris, Jörg Hofmann, R Verena Taudte, Naïg Guegen, Florian Golombek, Kathrin Castiglione, Xianyi Meng, Aline Bozec, Jana Thomas, Leonie Weckwerth, Dimitrios Mougiakakos, Sebastian R Schulz, Wolfgang Schuh, Ursula Schlötzer-Schrehardt, Tobit D Steinmetz, Susanne Brodesser, Rudolf J Wiesner, Dirk Mielenz.
      To elucidate the function of oxidative phosphorylation (OxPhos) during B cell differentiation, we employ CD23Cre-driven expression of the dominant-negative K320E mutant of the mitochondrial helicase Twinkle (DNT). DNT-expression depletes mitochondrial DNA during B cell maturation, reduces the abundance of respiratory chain protein subunits encoded by mitochondrial DNA, and, consequently, respiratory chain super-complexes in activated B cells. Whereas B cell development in DNT mice is normal, B cell proliferation, germinal centers, class switch to IgG, plasma cell maturation, and T cell-dependent as well as T cell-independent humoral immunity are diminished. DNT expression dampens OxPhos but increases glycolysis in lipopolysaccharide and B cell receptor-activated cells. Lipopolysaccharide-activated DNT-B cells exhibit altered metabolites of glycolysis, the pentose phosphate pathway, and the tricarboxylic acid cycle and a lower amount of phosphatidic acid. Consequently, mTORC1 activity and BLIMP1 induction are curtailed, whereas HIF1α is stabilized. Hence, mitochondrial DNA controls the metabolism of activated B cells via OxPhos to foster humoral immunity.
    Keywords:  B lymphocyte; CP: Immunology; HIF1; TCA cycle; class switch recombination; germinal center; hypoxia inducible factor 1; mTOR; mammalian target of Rapamycin; mitochondrial DNA; mitochondrial respiration; oxidative phosphorylation; phosphatidic acid; plasma cell
    DOI:  https://doi.org/10.1016/j.celrep.2022.110912
  14. Nat Commun. 2022 Jun 07. 13(1): 3257
    Structural basis for MTA1c-mediated DNA N6-adenine methylation.
    Jiyun Chen, Rong Hu, Ying Chen, Xiaofeng Lin, Wenwen Xiang, Hong Chen, Canglin Yao, Liang Liu.
      DNA N6-adenine methylation (6 mA) has recently been found to play a crucial role in epigenetic regulation in eukaryotes. MTA1c, a newly discovered 6 mA methyltransferase complex in ciliates, is composed of MTA1, MTA9, p1 and p2 subunits and specifically methylates ApT dinucleotides, yet its mechanism of action remains unknown. Here, we report the structures of Tetrahymena thermophila MTA1 (TthMTA1), Paramecium tetraurelia MTA9 (PteMTA9)-TthMTA1 binary complex, as well as the structures of TthMTA1-p1-p2 and TthMTA1-p2 complexes in apo, S-adenosyl methionine-bound and S-adenosyl homocysteine-bound states. We show that MTA1 is the catalytically active subunit, p1 and p2 are involved in the formation of substrate DNA-binding channel, and MTA9 plays a structural role in the stabilization of substrate binding. We identify that MTA1 is a cofactor-dependent catalytically active subunit, which exhibits stable SAM-binding activity only after assembly with p2. Our structures and corresponding functional studies provide a more detailed mechanistic understanding of 6 mA methylation.
    DOI:  https://doi.org/10.1038/s41467-022-31060-6
  15. Front Cell Dev Biol. 2022 ;10 892069
    Mitochondrial Cytochrome c Oxidase Defects Alter Cellular Homeostasis of Transition Metals.
    Michele Brischigliaro, Denis Badocco, Rodolfo Costa, Carlo Viscomi, Massimo Zeviani, Paolo Pastore, Erika Fernández-Vizarra.
      The redox activity of cytochrome c oxidase (COX), the terminal oxidase of the mitochondrial respiratory chain (MRC), depends on the incorporation of iron and copper into its catalytic centers. Many mitochondrial proteins have specific roles for the synthesis and delivery of metal-containing cofactors during COX biogenesis. In addition, a large set of different factors possess other molecular functions as chaperones or translocators that are also necessary for the correct maturation of these complexes. Pathological variants in genes encoding structural MRC subunits and these different assembly factors produce respiratory chain deficiency and lead to mitochondrial disease. COX deficiency in Drosophila melanogaster, induced by downregulated expression of three different assembly factors and one structural subunit, resulted in decreased copper content in the mitochondria accompanied by different degrees of increase in the cytosol. The disturbances in metal homeostasis were not limited only to copper, as some changes in the levels of cytosolic and/or mitochondrial iron, manganase and, especially, zinc were observed in several of the COX-deficient groups. The altered copper and zinc handling in the COX defective models resulted in a transcriptional response decreasing the expression of copper transporters and increasing the expression of metallothioneins. We conclude that COX deficiency is generally responsible for an altered mitochondrial and cellular homeostasis of transition metals, with variations depending on the origin of COX assembly defect.
    Keywords:  copper; cytochrome c oxidase; iron; manganese; metal homeostasis; mitochondrial respiratory chain; zinc
    DOI:  https://doi.org/10.3389/fcell.2022.892069
  16. Sci Adv. 2022 Jun 10. 8(23): eabn4965
    A reference tissue atlas for the human kidney.
    Kidney Precision Medicine Project
      Kidney Precision Medicine Project (KPMP) is building a spatially specified human kidney tissue atlas in health and disease with single-cell resolution. Here, we describe the construction of an integrated reference map of cells, pathways, and genes using unaffected regions of nephrectomy tissues and undiseased human biopsies from 56 adult subjects. We use single-cell/nucleus transcriptomics, subsegmental laser microdissection transcriptomics and proteomics, near-single-cell proteomics, 3D and CODEX imaging, and spatial metabolomics to hierarchically identify genes, pathways, and cells. Integrated data from these different technologies coherently identify cell types/subtypes within different nephron segments and the interstitium. These profiles describe cell-level functional organization of the kidney following its physiological functions and link cell subtypes to genes, proteins, metabolites, and pathways. They further show that messenger RNA levels along the nephron are congruent with the subsegmental physiological activity. This reference atlas provides a framework for the classification of kidney disease when multiple molecular mechanisms underlie convergent clinical phenotypes.
    DOI:  https://doi.org/10.1126/sciadv.abn4965
  17. Mol Oncol. 2022 Jun 05.
    Metabolic reprogramming: a bridge between aging and tumorigenesis.
    Stanislav Drapela, Didem Ilter, Ana P Gomes.
      Aging is the most robust risk factor for cancer development, with more than 60% of cancers occurring in those aged 60 and above. However, how aging and tumorigenesis are intertwined is poorly understood and a matter of significant debate. Metabolic changes are hallmarks of both aging and tumorigenesis. The deleterious consequences of aging include dysfunctional cellular processes, the build up of metabolic by-products and waste molecules in circulation and within tissues, and stiffer connective tissues that impede blood flow and oxygenation. Collectively, these age-driven changes lead to metabolic reprogramming in different cell types of a given tissue that significantly affects their cellular functions. Here, we put forward the idea that metabolic changes that happen during aging help create a favorable environment for tumorigenesis. We review parallels in metabolic changes that happen during aging and how these changes function both as adaptive mechanisms that enable the development of malignant phenotypes in a cell-autonomous manner and as mechanisms that suppress immune surveillance, collectively creating the perfect environment for cancers to thrive. Hence, anti-aging therapeutic strategies that target the metabolic reprogramming that occurs as we age might provide new opportunities to prevent cancer initiation and/or improve responses to standard-of-care anti-cancer therapies.
    Keywords:  Aging; cellular energetics; immune response; metabolic reprogramming; tumorigenesis
    DOI:  https://doi.org/10.1002/1878-0261.13261
  18. Cell Metab. 2022 Jun 01. pii: S1550-4131(22)00189-9. [Epub ahead of print]
    Glycerate from intestinal fructose metabolism induces islet cell damage and glucose intolerance.
    Yanru Wu, Chi Wut Wong, Eric N Chiles, Allyson L Mellinger, Hosung Bae, Sunhee Jung, Ted Peterson, Jamie Wang, Marcos Negrete, Qiang Huang, Lihua Wang, Cholsoon Jang, David C Muddiman, Xiaoyang Su, Ian Williamson, Xiling Shen.
      Dietary fructose, especially in the context of a high-fat western diet, has been linked to type 2 diabetes. Although the effect of fructose on liver metabolism has been extensively studied, a significant portion of the fructose is first metabolized in the small intestine. Here, we report that dietary fat enhances intestinal fructose metabolism, which releases glycerate into the blood. Chronic high systemic glycerate levels induce glucose intolerance by slowly damaging pancreatic islet cells and reducing islet sizes. Our findings provide a link between dietary fructose and diabetes that is modulated by dietary fat.
    Keywords:  diabetes; dietary fat; fructose; glucose intolerance; glycerate; insulin; intestine; islet cell; metabolism; western diet
    DOI:  https://doi.org/10.1016/j.cmet.2022.05.007
  19. FEBS Lett. 2022 Jun 03.
    The Acyl-CoA-Binding Protein Acb1 regulates mitochondria, lipid droplets, and cell proliferation.
    Jiajia He, Ke Liu, Shengnan Zheng, Yifan Wu, Chenhui Zhao, Shuaijie Yan, Ling Liu, Ke Ruan, Xiaopeng Ma, Chuanhai Fu.
      Mitochondria are involved in many cellular activities, including energy metabolism and biosynthesis of nucleotides, fatty acids, and amino acids. Mitochondrial morphology is a key factor in dictating mitochondrial functions. Here, we report that the acyl-CoA binding protein Acb1 in the fission yeast Schizosaccharomyces pombe is required for the maintenance of tubular mitochondrial morphology and proper mitochondrial respiration. The absence of Acb1 causes severe mitochondrial fragmentation in a dynamin-related protein Dnm1-dependent manner and impairs mitochondrial respiration. Moreover, Acb1 regulates the remodeling of lipid droplets in nutrient-rich conditions. Importantly, Acb1 promotes cell survival when cells are cultured in nutrient-rich medium. Hence, our findings establish roles of acyl-CoA binding proteins in regulating mitochondria, lipid droplets, and cell viability.
    Keywords:  Acyl-CoA-Binding Protein; Cell proliferation; Lipid droplets; Mitochondria; Schizosaccharomyces pombe
    DOI:  https://doi.org/10.1002/1873-3468.14415
  20. Neural Regen Res. 2022 Dec;17(12): 2563-2575
    The "mitochondrial stress responses": the "Dr. Jekyll and Mr. Hyde" of neuronal disorders.
    Simone Patergnani, Giampaolo Morciano, Marianna Carinci, Sara Leo, Paolo Pinton, Alessandro Rimessi.
      Neuronal disorders are associated with a profound loss of mitochondrial functions caused by various stress conditions, such as oxidative and metabolic stress, protein folding or import defects, and mitochondrial DNA alteration. Cells engage in different coordinated responses to safeguard mitochondrial homeostasis. In this review, we will explore the contribution of mitochondrial stress responses that are activated by the organelle to perceive these dangerous conditions, keep them under control and rescue the physiological condition of nervous cells. In the sections to come, particular attention will be dedicated to analyzing how compensatory mitochondrial hyperfusion, mitophagy, mitochondrial unfolding protein response, and apoptosis impact human neuronal diseases. Finally, we will discuss the relevance of the new concept: the "mito-inflammation", a mitochondria-mediated inflammatory response that is recently found to cover a relevant role in the pathogenesis of diverse inflammatory-related diseases, including neuronal disorders.
    Keywords:  Alzheimer’s disease; Parkinson’s disease; UPR mt; apoptosis; mito-inflammation; mitochondrial dynamics; mitophagy; multiple sclerosis; neurodegeneration
    DOI:  https://doi.org/10.4103/1673-5374.339473
  21. Nat Rev Mol Cell Biol. 2022 Jun 08.
    Mining the mitochondrial proteome.
    Paulina Strzyz.
      
    DOI:  https://doi.org/10.1038/s41580-022-00503-9
  22. Dev Cell. 2022 Jun 06. pii: S1534-5807(22)00361-6. [Epub ahead of print]57(11): 1311-1313
    Major construction entails major demolition.
    Ekaterina Korotkevich, Takashi Hiiragi.
      Embryonic cells of the early mouse embryo become hypersensitive to apoptotic stimuli before gastrulation. In this issue of Developmental Cell, Pernaute et al. show that this switch in sensitivity is a result of a change in mitochondrial dynamics and mitophagy levels controlled by DRP1, a regulator of mitochondrial fission.
    DOI:  https://doi.org/10.1016/j.devcel.2022.05.008
  23. Nat Cell Biol. 2022 Jun 06.
    The metabolic enzyme hexokinase 2 localizes to the nucleus in AML and normal haematopoietic stem and progenitor cells to maintain stemness.
    Geethu Emily Thomas, Grace Egan, Laura García-Prat, Aaron Botham, Veronique Voisin, Parasvi S Patel, Fieke W Hoff, Jordan Chin, Boaz Nachmias, Kerstin B Kaufmann, Dilshad H Khan, Rose Hurren, Xiaoming Wang, Marcela Gronda, Neil MacLean, Cristiana O'Brien, Rashim P Singh, Courtney L Jones, Shane M Harding, Brian Raught, Andrea Arruda, Mark D Minden, Gary D Bader, Razq Hakem, Steve Kornblau, John E Dick, Aaron D Schimmer.
      Mitochondrial metabolites regulate leukaemic and normal stem cells by affecting epigenetic marks. How mitochondrial enzymes localize to the nucleus to control stem cell function is less understood. We discovered that the mitochondrial metabolic enzyme hexokinase 2 (HK2) localizes to the nucleus in leukaemic and normal haematopoietic stem cells. Overexpression of nuclear HK2 increases leukaemic stem cell properties and decreases differentiation, whereas selective nuclear HK2 knockdown promotes differentiation and decreases stem cell function. Nuclear HK2 localization is phosphorylation-dependent, requires active import and export, and regulates differentiation independently of its enzymatic activity. HK2 interacts with nuclear proteins regulating chromatin openness, increasing chromatin accessibilities at leukaemic stem cell-positive signature and DNA-repair sites. Nuclear HK2 overexpression decreases double-strand breaks and confers chemoresistance, which may contribute to the mechanism by which leukaemic stem cells resist DNA-damaging agents. Thus, we describe a non-canonical mechanism by which mitochondrial enzymes influence stem cell function independently of their metabolic function.
    DOI:  https://doi.org/10.1038/s41556-022-00925-9
  24. Genetics. 2022 Jun 06. pii: iyac090. [Epub ahead of print]
    A yeast suppressor screen links Coa4 to the mitochondrial copper delivery pathway for cytochrome c oxidase.
    Abhinav B Swaminathan, Shivatheja Soma, Alison C Vicary, Mohammad Zulkifli, Harman Kaur, Vishal M Gohil.
      Cytochrome c oxidase (CcO) is a multimeric copper-containing enzyme of the mitochondrial respiratory chain that powers cellular energy production. The two core subunits of CcO, Cox1 and Cox2, harbor the catalytic CuB and CuA sites, respectively. Biogenesis of each copper site occurs separately and requires multiple proteins that constitute the mitochondrial copper delivery pathway. Currently, the identity of all the members of the pathway is not known, though several evolutionarily conserved twin CX9C motif-containing proteins have been implicated in this process. Here, we performed a targeted yeast suppressor screen that placed Coa4, a twin CX9C motif-containing protein, in the copper delivery pathway to the Cox1 subunit. Specifically, we show that overexpression of Cox11, a copper metallochaperone required for the formation of CuB site, can restore Cox1 abundance, CcO assembly, and mitochondrial respiration in coa4Δ cells. This rescue is dependent on the copper-coordinating cysteines of Cox11. The abundance of Coa4 and Cox11 in mitochondria is reciprocally regulated, further linking Coa4 to the CuB site biogenesis. Additionally, we find that coa4Δ cells have reduced levels of copper and exogenous copper supplementation can partially ameliorate its respiratory-deficient phenotype, a finding that connects Coa4 to cellular copper homeostasis. Finally, we demonstrate that human COA4 can replace the function of yeast Coa4 indicating its evolutionarily conserved role. Our work provides genetic evidences for the role of Coa4 in the copper delivery pathway to the CuB site of CcO.
    Keywords:  Coa4; Cox1; Cox11; copper; cytochrome c oxidase; mitochondria
    DOI:  https://doi.org/10.1093/genetics/iyac090
  25. J Cell Mol Med. 2022 Jun 07.
    PBRM1 deficiency oncogenic addiction is associated with activated AKT-mTOR signalling and aerobic glycolysis in clear cell renal cell carcinoma cells.
    Yu Tang, Yan-Hong Jin, Hu-Li Li, Hui Xin, Jin-Dong Chen, Xue-Ying Li, You-Fu Pan.
      The PBRM1 (PB1) gene which encodes the specific subunit BAF180 of the PBAF SWI/SNF complex, is highly mutated (~ 40%) in clear cell renal cell carcinoma (ccRCC). However, its functions and impact on cell signalling are still not fully understood. Aerobic glycolysis, also known as the 'Warburg Effect', is a hallmark of cancer, whether PB1 is involved in this metabolic shift in clear cell renal cell carcinoma remains unclear. Here, with established stable knockdown PB1 cell lines, we performed functional assays to access the effects on 786-O and SN12C cells. Based on the RNA-seq data, we selected some genes encoding key glycolytic enzymes, including PFKP, ENO1, PKM and LDHA, and examined the expression levels. The AKT-mTOR signalling pathway activity and expression of HIF1α were also analysed. Our data demonstrate that PB1 deficiency promotes the proliferation, migration, Xenograft growth of 786-O and SN12C cells. Notably, knockdown of PB1 activates AKT-mTOR signalling and increases the expression of key glycolytic enzymes at both mRNA and protein levels. Furthermore, we provide evidence that deficient PB1 and hypoxic conditions exert a synergistic effect on HIF 1α expression and lactate production. Thus, our study provides novel insights into the roles of tumour suppressor PB1 and suggests that the AKT-mTOR signalling pathway, as well as glycolysis, is a potential drug target for ccRCC patients with deficient PB1.
    Keywords:   PBRM1(PB1) ; AKT-mTOR signalling; HIF1α; aerobic glycolysis; ccRCC
    DOI:  https://doi.org/10.1111/jcmm.17418
  26. Circ Res. 2022 Jun 10. 130(12): 1965-1993
    Animal Models of Dysregulated Cardiac Metabolism.
    Heiko Bugger, Nikole J Byrne, E Dale Abel.
      As a muscular pump that contracts incessantly throughout life, the heart must constantly generate cellular energy to support contractile function and fuel ionic pumps to maintain electrical homeostasis. Thus, mitochondrial metabolism of multiple metabolic substrates such as fatty acids, glucose, ketones, and lactate is essential to ensuring an uninterrupted supply of ATP. Multiple metabolic pathways converge to maintain myocardial energy homeostasis. The regulation of these cardiac metabolic pathways has been intensely studied for many decades. Rapid adaptation of these pathways is essential for mediating the myocardial adaptation to stress, and dysregulation of these pathways contributes to myocardial pathophysiology as occurs in heart failure and in metabolic disorders such as diabetes. The regulation of these pathways reflects the complex interactions of cell-specific regulatory pathways, neurohumoral signals, and changes in substrate availability in the circulation. Significant advances have been made in the ability to study metabolic regulation in the heart, and animal models have played a central role in contributing to this knowledge. This review will summarize metabolic pathways in the heart and describe their contribution to maintaining myocardial contractile function in health and disease. The review will summarize lessons learned from animal models with altered systemic metabolism and those in which specific metabolic regulatory pathways have been genetically altered within the heart. The relationship between intrinsic and extrinsic regulators of cardiac metabolism and the pathophysiology of heart failure and how these have been informed by animal models will be discussed.
    Keywords:  diabetes; glucose; heart failure; mitochondria; models, animal
    DOI:  https://doi.org/10.1161/CIRCRESAHA.122.320334
  27. Mol Cell. 2022 May 25. pii: S1097-2765(22)00443-9. [Epub ahead of print]
    Itaconate is a lysosomal inducer that promotes antibacterial innate immunity.
    Zhenxing Zhang, Chao Chen, Fan Yang, Yi-Xin Zeng, Pengkai Sun, Ping Liu, Xinjian Li.
      Lysosomes are the main organelles in macrophages for killing invading bacteria. However, the precise mechanism underlying lysosomal biogenesis upon bacterial infection remains enigmatic. We demonstrate here that LPS stimulation increases IRG1-dependent itaconate production, which promotes lysosomal biogenesis by activating the transcription factor, TFEB. Mechanistically, itaconate directly alkylates human TFEB at cysteine 212 (Cys270 in mice) to induce its nuclear localization by antagonizing mTOR-mediated phosphorylation and cytosolic retention. Functionally, abrogation of itaconate synthesis by IRG1/Irg1 knockout or expression of an alkylation-deficient TFEB mutant impairs the antibacterial ability of macrophages in vitro. Furthermore, knockin mice harboring an alkylation-deficient TFEB mutant display elevated susceptibility to Salmonella typhimurium infection, whereas in vivo treatment of OI, a cell-permeable itaconate derivative, limits inflammation. Our study identifies itaconate as an endogenous metabolite that functions as a lysosomal inducer in macrophages in response to bacterial infection, implying the potential therapeutic utility of itaconate in treating human bacterial infection.
    Keywords:  TFEB; alkylation; bacterial infection; innate immunity; itaconate; lysosomal biogenesis; macrophage
    DOI:  https://doi.org/10.1016/j.molcel.2022.05.009
  28. Front Cell Dev Biol. 2022 ;10 892325
    Prime Real Estate: Metals, Cofactors and MICOS.
    Amy E Medlock, J Catrice Hixon, Tawhid Bhuiyan, Paul A Cobine.
      Metals are key elements for the survival and normal development of humans but can also be toxic to cells when mishandled. In fact, even mild disruption of metal homeostasis causes a wide array of disorders. Many of the metals essential to normal physiology are required in mitochondria for enzymatic activities and for the formation of essential cofactors. Copper is required as a cofactor in the terminal electron transport chain complex cytochrome c oxidase, iron is required for the for the formation of iron-sulfur (Fe-S) clusters and heme, manganese is required for the prevention of oxidative stress production, and these are only a few examples of the critical roles that mitochondrial metals play. Even though the targets of these metals are known, we are still identifying transporters, investigating the roles of known transporters, and defining regulators of the transport process. Mitochondria are dynamic organelles whose content, structure and localization within the cell vary in different tissues and organisms. Our knowledge of the impact that alterations in mitochondrial physiology have on metal content and utilization in these organelles is very limited. The rates of fission and fusion, the ultrastructure of the organelle, and rates of mitophagy can all affect metal homeostasis and cofactor assembly. This review will focus of the emerging areas of overlap between metal homeostasis, cofactor assembly and the mitochondrial contact site and cristae organizing system (MICOS) that mediates multiple aspects of mitochondrial physiology. Importantly the MICOS complexes may allow for localization and organization of complexes not only involved in cristae formation and contact between the inner and outer mitochondrial membranes but also acts as hub for metal-related proteins to work in concert in cofactor assembly and homeostasis.
    Keywords:  MICOS complex; copper; heme; iron; metals
    DOI:  https://doi.org/10.3389/fcell.2022.892325
  29. PLoS Biol. 2022 Jun 10. 20(6): e3001678
    The polyol pathway is an evolutionarily conserved system for sensing glucose uptake.
    Hiroko Sano, Akira Nakamura, Mariko Yamane, Hitoshi Niwa, Takashi Nishimura, Kimi Araki, Kazumasa Takemoto, Kei-Ichiro Ishiguro, Hiroki Aoki, Yuzuru Kato, Masayasu Kojima.
      Cells must adjust the expression levels of metabolic enzymes in response to fluctuating nutrient supply. For glucose, such metabolic remodeling is highly dependent on a master transcription factor ChREBP/MondoA. However, it remains elusive how glucose fluctuations are sensed by ChREBP/MondoA despite the stability of major glycolytic pathways. Here, we show that in both flies and mice, ChREBP/MondoA activation in response to glucose ingestion involves an evolutionarily conserved glucose-metabolizing pathway: the polyol pathway. The polyol pathway converts glucose to fructose via sorbitol. It has been believed that this pathway is almost silent, and its activation in hyperglycemic conditions has deleterious effects on human health. We show that the polyol pathway regulates the glucose-responsive nuclear translocation of Mondo, a Drosophila homologue of ChREBP/MondoA, which directs gene expression for organismal growth and metabolism. Likewise, inhibition of the polyol pathway in mice impairs ChREBP's nuclear localization and reduces glucose tolerance. We propose that the polyol pathway is an evolutionarily conserved sensing system for glucose uptake that allows metabolic remodeling.
    DOI:  https://doi.org/10.1371/journal.pbio.3001678
  30. J Cell Biol. 2022 Jul 04. pii: e202203095. [Epub ahead of print]221(7):
    Fbxo7 promotes Cdk6 activity to inhibit PFKP and glycolysis in T cells.
    Rebecca Harris, Ming Yang, Christina Schmidt, Chloe Royet, Sarbjit Singh, Amarnath Natarajan, May Morris, Christian Frezza, Heike Laman.
      Fbxo7 is associated with cancer and Parkinson's disease. Although Fbxo7 recruits substrates for SCF-type ubiquitin ligases, it also promotes Cdk6 activation in a ligase-independent fashion. We discovered PFKP, the gatekeeper of glycolysis, in a screen for Fbxo7 substrates. PFKP is an essential Cdk6 substrate in some T-ALL cells. We investigated the molecular relationship between Fbxo7, Cdk6, and PFKP, and the effect of Fbxo7 on T cell metabolism, viability, and activation. Fbxo7 promotes Cdk6-independent ubiquitination and Cdk6-dependent phosphorylation of PFKP. Importantly, Fbxo7-deficient cells have reduced Cdk6 activity, and hematopoietic and lymphocytic cells show high expression and significant dependency on Fbxo7. CD4+ T cells with reduced Fbxo7 show increased glycolysis, despite lower cell viability and activation levels. Metabolomic studies of activated CD4+ T cells confirm increased glycolytic flux in Fbxo7-deficient cells, alongside altered nucleotide biosynthesis and arginine metabolism. We show Fbxo7 expression is glucose-responsive at the mRNA and protein level and propose Fbxo7 inhibits PFKP and glycolysis via its activation of Cdk6.
    DOI:  https://doi.org/10.1083/jcb.202203095
  31. Am J Physiol Cell Physiol. 2022 Jun 08.
    Circadian Regulation of Digestive & Metabolic Tissues.
    Zainab Taleb, Phillip Karpowicz.
      The circadian clock is a self-sustained molecular timekeeper that drives 24-hour (circadian) rhythms in animals. The clock governs important aspects of behavior and physiology including wake/sleep activity cycles that regulate the activity of metabolic and digestive systems. Light/dark cycles (photoperiod) and cycles in the time of feeding synchronize the circadian clock to the surrounding environment, providing an anticipatory benefit that promotes digestive health. The availability of animal models targeting the genetic components of the circadian clock has made it possible to investigate the circadian clock's role in cellular functions. Circadian clock genes have been shown to regulate the physiological function of hepatocytes, gastrointestinal cells, and adipocytes; disruption of the circadian clock leads to the exacerbation of liver diseases and liver cancer, inflammatory bowel disease and colorectal cancer, and obesity. Previous findings provide strong evidence that the circadian clock plays an integral role in digestive/metabolic disease pathogenesis, hence, the circadian clock is a necessary component in metabolic and digestive health and homeostasis. Circadian rhythms and circadian clock function provide an opportunity to improve the prevention and treatment of digestive and metabolic diseases by aligning digestive system tissue with the 24-hour day.
    Keywords:  adipose; circadian clock; circadian rhythm; digestion; metabolism
    DOI:  https://doi.org/10.1152/ajpcell.00166.2022
  32. Autophagy. 2022 Jun 09. 1-14
    Mitochondria ROS and mitophagy in acute kidney injury.
    Lianjiu Su, Jiahao Zhang, Hernando Gomez, John A Kellum, Zhiyong Peng.
      Mitophagy is an essential mitochondrial quality control mechanism that eliminates damaged mitochondria and the production of reactive oxygen species (ROS). The relationship between mitochondria oxidative stress, ROS production and mitophagy are intimately interwoven, and these processes are all involved in various pathological conditions of acute kidney injury (AKI). The elimination of damaged mitochondria through mitophagy in mammals is a complicated process which involves several pathways. Furthermore, the interplay between mitophagy and different types of cell death, such as apoptosis, pyroptosis and ferroptosis in kidney injury is unclear. Here we will review recent advances in our understanding of the relationship between ROS and mitophagy, the different mitophagy pathways, the relationship between mitophagy and cell death, and the relevance of these processes in the pathogenesis of AKI.Abbreviations: AKI: acute kidney injury; AMBRA1: autophagy and beclin 1 regulator 1; ATP: adenosine triphosphate; BAK1: BCL2 antagonist/killer 1; BAX: BCL2 associated X, apoptosis regulator; BCL2: BCL2 apoptosis regulator; BECN1: beclin 1; BH3: BCL2 homology domain 3; BNIP3: BCL2 interacting protein 3; BNIP3L/NIX: BCL2 interacting protein 3 like; CASP1: caspase 1; CAT: catalase; CCCP: carbonyl cyanide m-chlorophenylhydrazone; CI-AKI: contrast-induced acute kidney injury; CISD1: CDGSH iron sulfur domain 1; CL: cardiolipin; CNP: 2',3'-cyclic nucleotide 3'-phosphodiesterase; DNM1L/DRP1: dynamin 1 like; E3: enzyme 3; ETC: electron transport chain; FA: folic acid; FUNDC1: FUN14 domain containing 1; G3P: glycerol-3-phosphate; G6PD: glucose-6-phosphate dehydrogenase; GPX: glutathione peroxidase; GSH: glutathione; GSK3B: glycogen synthase kinase 3 beta; GSR: glutathione-disulfide reductase; HIF1A: hypoxia inducible factor 1 subunit alpha; HUWE1: HECT, UBA and WWE domain containing 1; IL1B: interleukin 1 beta; IMM: inner mitochondrial membrane; IPC: ischemic preconditioning; IRI: ischemia-reperfusion injury; LIR: LC3-interacting region; LPS: lipopolysaccharide; MA: malate-aspartate; MPT: mitochondrial permeability transition; MUL1: mitochondrial E3 ubiquitin protein ligase 1; mtROS: mitochondrial ROS; NLR: NOD-like receptor; NLRP3: NLR family pyrin domain containing 3; NOX: NADPH oxidase; OGD-R: oxygen-glucose deprivation-reperfusion; OMM: outer mitochondrial membrane; OPA1: OPA1 mitochondrial dynamin like GTPase; OXPHOS: oxidative phosphorylation; PARL: presenilin associated rhomboid like; PINK1: PTEN induced kinase 1; PLSCR3: phospholipid scramblase 3; PMP: peptidase, mitochondrial processing; PRDX: peroxiredoxin; PRKN: parkin RBR E3 ubiquitin protein ligase; RPTC: rat proximal tubular cells; ROS: reactive oxygen species; SLC7A11/xCT: solute carrier family 7 member 11; SOD: superoxide dismutase; SOR: superoxide reductase; SQSTM1/p62: sequestosome 1; TCA: tricarboxylic acid; TIMM: translocase of inner mitochondrial membrane; TOMM: translocase of outer mitochondrial membrane; TXN: thioredoxin; VDAC: voltage dependent anion channel; VCP: valosin containing protein.
    Keywords:  Acute kidney injury; cell death; mitochondria; mitophagy; reactive oxygen species
    DOI:  https://doi.org/10.1080/15548627.2022.2084862
  33. Redox Biol. 2022 Jun 02. pii: S2213-2317(22)00130-6. [Epub ahead of print]54 102358
    A CRISPR screen identifies redox vulnerabilities for KEAP1/NRF2 mutant non-small cell lung cancer.
    Chang Jiang, Nathan P Ward, Nicolas Prieto-Farigua, Yun Pyo Kang, Anish Thalakola, Mingxiang Teng, Gina M DeNicola.
      The redox regulator NRF2 is hyperactivated in a large percentage of non-small cell lung cancer (NSCLC) cases, which is associated with chemotherapy and radiation resistance. To identify redox vulnerabilities for KEAP1/NRF2 mutant NSCLC, we conducted a CRISPR-Cas9-based negative selection screen for antioxidant enzyme genes whose loss sensitized cells to sub-lethal concentrations of the superoxide (O2•-) -generating drug β-Lapachone. While our screen identified expected hits in the pentose phosphate pathway, the thioredoxin-dependent antioxidant system, and glutathione reductase, we also identified the mitochondrial superoxide dismutase 2 (SOD2) as one of the top hits. Surprisingly, β-Lapachone did not generate mitochondrial O2•- but rather SOD2 loss enhanced the efficacy of β-Lapachone due to loss of iron-sulfur protein function, loss of mitochondrial ATP maintenance and deficient NADPH production. Importantly, inhibition of mitochondrial electron transport activity sensitized cells to β-Lapachone, demonstrating that these effects may be translated to increase ROS sensitivity therapeutically.
    Keywords:  KEAP1; NADPH; NFE2L2; NSCLC; ROS; SOD2; β-Lapachone
    DOI:  https://doi.org/10.1016/j.redox.2022.102358
  34. Cell. 2022 May 30. pii: S0092-8674(22)00590-6. [Epub ahead of print]
    Non-coding 7S RNA inhibits transcription via mitochondrial RNA polymerase dimerization.
    Xuefeng Zhu, Xie Xie, Hrishikesh Das, Benedict G Tan, Yonghong Shi, Ali Al-Behadili, Bradley Peter, Elisa Motori, Sebastian Valenzuela, Viktor Posse, Claes M Gustafsson, B Martin Hällberg, Maria Falkenberg.
      The mitochondrial genome encodes 13 components of the oxidative phosphorylation system, and altered mitochondrial transcription drives various human pathologies. A polyadenylated, non-coding RNA molecule known as 7S RNA is transcribed from a region immediately downstream of the light strand promoter in mammalian cells, and its levels change rapidly in response to physiological conditions. Here, we report that 7S RNA has a regulatory function, as it controls levels of mitochondrial transcription both in vitro and in cultured human cells. Using cryo-EM, we show that POLRMT dimerization is induced by interactions with 7S RNA. The resulting POLRMT dimer interface sequesters domains necessary for promoter recognition and unwinding, thereby preventing transcription initiation. We propose that the non-coding 7S RNA molecule is a component of a negative feedback loop that regulates mitochondrial transcription in mammalian cells.
    Keywords:  7S RNA; POLRMT; SUV3; cryo-EM; dimer; mitochondria; mtDNA; mtEXO; non-coding RNA; transcription
    DOI:  https://doi.org/10.1016/j.cell.2022.05.006
  35. Mol Cell. 2022 Jun 02. pii: S1097-2765(22)00383-5. [Epub ahead of print]82(11): 2148-2160.e4
    A naturally DNase-free CRISPR-Cas12c enzyme silences gene expression.
    Carolyn J Huang, Benjamin A Adler, Jennifer A Doudna.
      Used widely for genome editing, CRISPR-Cas enzymes provide RNA-guided immunity to microbes by targeting foreign nucleic acids for cleavage. We show here that the native activity of CRISPR-Cas12c protects bacteria from phage infection by binding to DNA targets without cleaving them, revealing that antiviral interference can be accomplished without chemical attack on the invader or general metabolic disruption in the host. Biochemical experiments demonstrate that Cas12c is a site-specific ribonuclease capable of generating mature CRISPR RNAs (crRNAs) from precursor transcripts. Furthermore, we find that crRNA maturation is essential for Cas12c-mediated DNA targeting. These crRNAs direct double-stranded DNA binding by Cas12c using a mechanism that precludes DNA cutting. Nevertheless, Cas12c represses transcription and can defend bacteria against lytic bacteriophage infection when targeting an essential phage gene. Together, these results show that Cas12c employs targeted DNA binding to provide antiviral immunity in bacteria, providing a native DNase-free pathway for transient antiviral immunity.
    Keywords:  CRISPR; CRISPR interference; CRISPRi; Cas12c; bacterial immunity; genome editing; pre-crRNA; sgRNA
    DOI:  https://doi.org/10.1016/j.molcel.2022.04.020
  36. Methods Mol Biol. 2022 ;2487 15-26
    Multi-dimensional Fluorescence Live-Cell Imaging for Glucosome Dynamics in Living Human Cells.
    Songon An, Prakash Parajuli, Erin L Kennedy, Minjoung Kyoung.
      Fluorescence live-cell imaging that has contributed to our understanding of cell biology is now at the frontline of studying quantitative biochemistry in a cell. Particularly, technological advancements of fluorescence live-cell imaging and associated strategies in recent years have allowed us to discover various subcellular macromolecular assemblies in living human cells. Here we describe how real-time dynamics of a multienzyme metabolic assembly, the "glucosome," that is responsible for regulating glucose flux at subcellular levels, has been investigated in both 2- and 3-dimensional space of single human cells. We envision that such multi-dimensional fluorescence live-cell imaging will continue to revolutionize our understanding of how intracellular metabolic pathways and their network are functionally orchestrated at single-cell levels.
    Keywords:  Cancer Metabolism; Fluorescence Microscopy; Glucose Metabolism; Glucosome; Glycolysis; Lattice Light-sheet Microscopy; Live-cell Imaging; Macromolecular Assembly; Metabolic Complex; Metabolic Condensate
    DOI:  https://doi.org/10.1007/978-1-0716-2269-8_2
  37. J Immunol. 2022 Jun 06. pii: ji2101090. [Epub ahead of print]
    Translational Control by 4E-BP1/2 Suppressor Proteins Regulates Mitochondrial Biosynthesis and Function during CD8+ T Cell Proliferation.
    Ioannis D Dimitriou, David Meiri, Yulia Jitkova, Alisha R Elford, Marianne Koritzinsky, Aaron D Schimmer, Pamela S Ohashi, Nahum Sonenberg, Robert Rottapel.
      CD8+ T cell proliferation and differentiation into effector and memory states are high-energy processes associated with changes in cellular metabolism. CD28-mediated costimulation of T cells activates the PI3K/AKT/mammalian target of rapamycin signaling pathway and induces eukaryotic translation initiation factor 4E-dependent translation through the derepression by 4E-BP1 and 4E-BP2. In this study, we demonstrate that 4E-BP1/2 proteins are required for optimum proliferation of mouse CD8+ T cells and the development of an antiviral effector function. We show that translation of genes encoding mitochondrial biogenesis is impaired in T cells derived from 4E-BP1/2-deficient mice. Our findings demonstrate an unanticipated role for 4E-BPs in regulating a metabolic program that is required for cell growth and biosynthesis during the early stages of CD8+ T cell expansion.
    DOI:  https://doi.org/10.4049/jimmunol.2101090
  38. Nature. 2022 Jun 08.
    Mechanism of mitoribosomal small subunit biogenesis and preinitiation.
    Yuzuru Itoh, Anas Khawaja, Ivan Laptev, Miriam Cipullo, Ilian Atanassov, Petr Sergiev, Joanna Rorbach, Alexey Amunts.
      Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) intermediates in complex with auxiliary factors, revealing a sequential assembly mechanism. The methyltransferase TFB1M binds to partially unfolded rRNA h45 that is promoted by RBFA, while the mRNA channel is blocked. This enables binding of METTL15 that promotes further rRNA maturation and a large conformational change of RBFA. The new conformation allows initiation factor mtIF3 to already occupy the subunit interface during the assembly. Finally, the mitochondria-specific ribosomal protein mS37 (ref. 1) outcompetes RBFA to complete the assembly with the SSU-mS37-mtIF3 complex2 that proceeds towards mtIF2 binding and translation initiation. Our results explain how the action of step-specific factors modulate the dynamic assembly of the SSU, and adaptation of a unique protein, mS37, links the assembly to initiation to establish the catalytic human mitoribosome.
    DOI:  https://doi.org/10.1038/s41586-022-04795-x
  39. Cancer Res. 2022 Jun 06. pii: canres.3749.2021-11-3 04:32:07.783. [Epub ahead of print]
    IL-6 and CCL18 mediate crosstalk between VHL-deficient kidney cells and macrophages during development of renal cell carcinoma.
    Thi-Ngoc Nguyen, Hieu-Huy Nguyen-Tran, Chen-Yun Chen, Tien Hsu.
      Loss of the von Hippel-Lindau (VHL) tumor suppressor gene function accounts for 70-80% of all clear-cell renal cell carcinoma (ccRCC) cases, the most prevalent form of RCC. Accumulating evidence has indicated that ccRCC arises from sites of chronic inflammation, yet how ccRCC tumor cells interact with immune components of the microenvironment has not been fully elucidated. In this study, we employed unbiased proteomic and genomic analyses on components of the tumor microenvironment under different conditions, identifying the molecular and cellular mechanisms that underlie the crosstalk between VHL-deficient kidney tubule cells and macrophages. In vitro and in a Vhlh conditional knockout mouse model, VHL-deficient non-cancerous kidney epithelial cells, representing the early stage of ccRCC initiation, secreted IL-6 that induced macrophage infiltration and polarization toward the pro-tumorigenic M2 phenotype. Activated human macrophages secreted CCL18 and TGF-β1 to stimulate epithelial-to-mesenchymal transition (EMT) of the kidney tubule cells. Treatment with IL-6-neutralizing antibody rescued inflammatory, proliferative, and EMT phenotypes of kidney epithelial cells in Vhlh conditional knockout mice. Furthermore, in a human ccRCC xenograft model, exogenous human primary or cultured macrophages significantly promoted primary tumor growth and metastasis in a CCL18-dependent manner. These findings identify specific factors involved in reciprocal crosstalk between tumor cells and immune components in the microenvironment, thus providing an avenue for early intervention in ccRCC.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-3749
  40. Front Mol Biosci. 2022 ;9 893256
    A Resource to Infer Molecular Paths Linking Cancer Mutations to Perturbation of Cell Metabolism.
    Marta Iannuccelli, Prisca Lo Surdo, Luana Licata, Luisa Castagnoli, Gianni Cesareni, Livia Perfetto.
      Some inherited or somatically-acquired gene variants are observed significantly more frequently in the genome of cancer cells. Although many of these cannot be confidently classified as driver mutations, they may contribute to shaping a cell environment that favours cancer onset and development. Understanding how these gene variants causally affect cancer phenotypes may help developing strategies for reverting the disease phenotype. Here we focus on variants of genes whose products have the potential to modulate metabolism to support uncontrolled cell growth. Over recent months our team of expert curators has undertaken an effort to annotate in the database SIGNOR 1) metabolic pathways that are deregulated in cancer and 2) interactions connecting oncogenes and tumour suppressors to metabolic enzymes. In addition, we refined a recently developed graph analysis tool that permits users to infer causal paths leading from any human gene to modulation of metabolic pathways. The tool grounds on a human signed and directed network that connects ∼8400 biological entities such as proteins and protein complexes via causal relationships. The network, which is based on more than 30,000 published causal links, can be downloaded from the SIGNOR website. In addition, as SIGNOR stores information on drugs or other chemicals targeting the activity of many of the genes in the network, the identification of likely functional paths offers a rational framework for exploring new therapeutic strategies that revert the disease phenotype.
    Keywords:  SIGNOR; cancer; causal interaction; metabolic pathway; network; rate limiting enzyme
    DOI:  https://doi.org/10.3389/fmolb.2022.893256
  41. PLoS One. 2022 ;17(6): e0269620
    Evidence for a novel, effective approach to targeting carcinoma catabolism exploiting the first-in-class, anti-cancer mitochondrial drug, CPI-613.
    Moises O Guardado Rivas, Shawn D Stuart, Daniel Thach, Michael Dahan, Robert Shorr, Zuzana Zachar, Paul M Bingham.
      Clinical targeting of the altered metabolism of tumor cells has long been considered an attractive hypothetical approach. However, this strategy has yet to perform well clinically. Metabolic redundancy is among the limitations on effectiveness of many approaches, engendering intrinsic single-agent resistance or efficient evolution of such resistance. We describe new studies of the multi-target, tumor-preferential inhibition of the mitochondrial tricarboxylic acid (TCA) cycle by the first-in-class drug CPI-613® (devimistat). By suppressing the TCA hub, indispensable to many metabolic pathways, CPI-613 substantially reduces the effective redundancy of tumor catabolism. This TCA cycle suppression also engenders an apparently homeostatic accelerated, inefficient consumption of nutrient stores in carcinoma cells, eroding some sources of drug resistance. Nonetheless, sufficiently abundant, cell line-specific lipid stores in carcinoma cells are among remaining sources of CPI-613 resistance in vitro and during the in vivo pharmacological drug pulse. Specifically, the fatty acid beta-oxidation step delivers electrons directly to the mitochondrial electron transport system (ETC), by-passing the TCA cycle CPI-613 target and producing drug resistance. Strikingly, tested carcinoma cell lines configure much of this fatty acid flow to initially traverse the peroxisome enroute to additional mitochondrial beta-oxidation. This feature facilitates targeting as clinically practical agents disrupting this flow are available. Two such agents significantly sensitize an otherwise fully CPI-613-resistant carcinoma xenograft in vivo. These and related results are strong empirical support for a potentially general class of strategies for enhanced clinical targeting of carcinoma catabolism.
    DOI:  https://doi.org/10.1371/journal.pone.0269620
  42. J Cell Sci. 2022 Jun 09. pii: jcs.259924. [Epub ahead of print]
    PEX11β and FIS1 cooperate in peroxisome division independent of Mitochondrial Fission Factor.
    Tina A Schrader, Ruth E Carmichael, Markus Islinger, Joseph L Costello, Christian Hacker, Nina A Bonekamp, Jochen H Weishaupt, Peter M Andersen, Michael Schrader.
      Peroxisome membrane dynamics and division are essential to adapt the peroxisomal compartment to cellular needs. The peroxisomal membrane protein PEX11β, and the tail-anchored adaptor proteins FIS1 (mitochondrial fission protein 1) and MFF (mitochondrial fission factor), which recruit the fission GTPase DRP1 (dynamin-related protein 1) to both peroxisomes and mitochondria, are key factors of peroxisomal division. The current model suggests MFF is essential for peroxisome division, whereas the role of FIS1 is unclear. Here, we reveal that PEX11β can promote peroxisome division in the absence of MFF in a DRP1- and FIS1-dependent manner. We also demonstrate that MFF permits peroxisome division independent of PEX11β and restores peroxisome morphology in PEX11β-deficient patient cells. Moreover, targeting of PEX11β to mitochondria induces mitochondrial division indicating the potential for PEX11β to modulate mitochondrial dynamics. Our findings suggest the existence of an alternative, MFF-independent pathway in peroxisome division and report a function for FIS1 in peroxisome division.
    Keywords:  FIS1; MFF; Mitochondria; Organelle division; PEX11; Peroxisomes
    DOI:  https://doi.org/10.1242/jcs.259924
  43. STAR Protoc. 2022 Jun 17. 3(2): 101429
    Visualizing cytoplasmic ATP in C. elegans larvae using PercevalHR.
    Aastha Garde, David R Sherwood.
      Measuring ATP levels within the cytosol of living cells in animals is important to understand how cellular activities are energetically supported, but is challenging because of tissue complexity and ATP sensor limitations. In this protocol, we describe how to quantify ATP levels using PercevalHR in C. elegans larvae during anchor cell invasion. PercevalHR is a fluorescent biosensor that reports the cytoplasmic ATP:ADP ratio. The protocol can be adapted to analyze the ATP:ADP ratios within other cell types in C. elegans. For complete details on the use and execution of this protocol, please refer to Garde et al. (2022).
    Keywords:  Cancer; Cell Biology; Developmental biology; Metabolism; Microscopy; Model Organisms; Molecular/Chemical Probes
    DOI:  https://doi.org/10.1016/j.xpro.2022.101429
  44. Elife. 2022 Jun 08. pii: e75426. [Epub ahead of print]11
    Towards a molecular mechanism underlying mitochondrial protein import through the TOM and TIM23 complexes.
    Holly C Ford, William J Allen, Gonçalo C Pereira, Xia Liu, Mark Simon Dillingham, Ian Collinson.
      Nearly all mitochondrial proteins need to be targeted for import from the cytosol. For the majority, the first port of call is the translocase of the outer membrane (TOM complex), followed by a procession of alternative molecular machines, conducting transport to their final destination. The pre-sequence translocase of the inner-membrane (TIM23-complex) imports proteins with cleavable pre-sequences. Progress in understanding these transport mechanisms has been hampered by the poor sensitivity and time-resolution of import assays. However, with the development of an assay based on split NanoLuc luciferase, we can now explore this process in greater detail. Here, we apply this new methodology to understand how ∆ψ and ATP hydrolysis, the two main driving forces for import into the matrix, contribute to the transport of pre-sequence-containing precursors (PCPs) with varying properties. Notably, we found that two major rate-limiting steps define PCP import time: passage of PCP across the outer membrane and initiation of inner membrane transport by the pre-sequence - the rates of which are influenced by PCP properties such as size and net charge. The apparent distinction between transport through the two membranes (passage through TOM is substantially complete before PCP-TIM engagement) is in contrast with the current view that import occurs through TOM and TIM in a single continuous step. Our results also indicate that PCPs spend very little time in the TIM23 channel - presumably rapid success or failure of import is critical for maintaining mitochondrial fitness.
    Keywords:  S. cerevisiae; biochemistry; chemical biology
    DOI:  https://doi.org/10.7554/eLife.75426
  45. Elife. 2022 Jun 06. pii: e75837. [Epub ahead of print]11
    Distinct roles for two Caenorhabditis elegans acid-sensing ion channels in an ultradian clock.
    Eva Kaulich, Trae Carroll, Brian Ackley, Yi-Quan Tang, Iris Hardege, Keith Nehrke, William R Schafer, Denise S Walker.
      Biological clocks are fundamental to an organism's health, controlling periodicity of behaviour and metabolism. Here, we identify two acid-sensing ion channels, with very different proton sensing properties, and describe their role in an ultradian clock, the defecation motor program (DMP) of the nematode Caenorhabditis elegans. An ACD-5-containing channel, on the apical membrane of the intestinal epithelium, is essential for maintenance of luminal acidity, and thus the rhythmic oscillations in lumen pH. In contrast, the second channel, composed of FLR-1, ACD-3 and/or DEL-5, located on the basolateral membrane, controls the intracellular Ca2+ wave and forms a core component of the master oscillator that controls timing and rhythmicity of the DMP. flr-1 and acd-3/del-5 mutants show severe developmental and metabolic defects. We thus directly link the proton-sensing properties of these channels to their physiological roles in pH regulation and Ca2+ signalling, the generation of an ultradian oscillator, and its metabolic consequences.
    Keywords:  C. elegans; cell biology
    DOI:  https://doi.org/10.7554/eLife.75837
  46. Natl Sci Rev. 2022 May;9(5): nwab212
    Diet high in branched-chain amino acid promotes PDAC development by USP1-mediated BCAT2 stabilization.
    Jin-Tao Li, Kai-Yue Li, Ying Su, Yuan Shen, Ming-Zhu Lei, Fan Zhang, Miao Yin, Zheng-Jun Chen, Wen-Yu Wen, Wei-Guo Hu, Dan Su, Jia Qu, Qun-Ying Lei.
      BCAT2-mediated branched-chain amino acid (BCAA) catabolism is critical for pancreatic ductal adenocarcinoma (PDAC) development, especially at an early stage. However, whether a high-BCAA diet promotes PDAC development in vivo, and the underlying mechanism of BCAT2 upregulation, remain undefined. Here, we find that a high-BCAA diet promotes pancreatic intraepithelial neoplasia (PanIN) progression in LSL-KrasG12D/+ ; Pdx1-Cre (KC) mice. Moreover, we screened with an available deubiquitylase library which contains 31 members of USP family and identified that USP1 deubiquitylates BCAT2 at the K229 site. Furthermore, BCAA increases USP1 protein at the translational level via the GCN2-eIF2α pathway both in vitro and in vivo. More importantly, USP1 inhibition recedes cell proliferation and clone formation in PDAC cells and attenuates pancreas tumor growth in an orthotopic transplanted mice model. Consistently, a positive correlation between USP1 and BCAT2 is found in KC; LSL-KrasG12D/+ ; p53flox/+ ; Pdx1-Cre mice and clinical samples. Thus, a therapeutic targeting USP1-BCAT2-BCAA metabolic axis could be considered as a rational strategy for treatment of PDAC and precisive dietary intervention of BCAA has potentially translational significance.
    Keywords:  BCAT2; PDAC; PanIN; USP1; deubiquitylation
    DOI:  https://doi.org/10.1093/nsr/nwab212
  47. Nat Commun. 2022 Jun 09. 13(1): 3230
    Efferocytosis requires periphagosomal Ca2+-signaling and TRPM7-mediated electrical activity.
    Michael S Schappe, Marta E Stremska, Gregory W Busey, Taylor K Downs, Philip V Seegren, Suresh K Mendu, Zachary Flegal, Catherine A Doyle, Eric J Stipes, Bimal N Desai.
      Efficient clearance of apoptotic cells by phagocytosis, also known as efferocytosis, is fundamental to developmental biology, organ physiology, and immunology. Macrophages use multiple mechanisms to detect and engulf apoptotic cells, but the signaling pathways that regulate the digestion of the apoptotic cell cargo, such as the dynamic Ca2+ signals, are poorly understood. Using an siRNA screen, we identify TRPM7 as a Ca2+-conducting ion channel essential for phagosome maturation during efferocytosis. Trpm7-targeted macrophages fail to fully acidify or digest their phagosomal cargo in the absence of TRPM7. Through perforated patch electrophysiology, we demonstrate that TRPM7 mediates a pH-activated cationic current necessary to sustain phagosomal acidification. Using mice expressing a genetically-encoded Ca2+ sensor, we observe that phagosome maturation requires peri-phagosomal Ca2+-signals dependent on TRPM7. Overall, we reveal TRPM7 as a central regulator of phagosome maturation during macrophage efferocytosis.
    DOI:  https://doi.org/10.1038/s41467-022-30959-4
  48. Mol Genet Metab. 2022 May 25. pii: S1096-7192(22)00321-3. [Epub ahead of print]
    Integration of metabolomics with genomics: Metabolic gene prioritization using metabolomics data and genomic variant (CADD) scores.
    Michiel Bongaerts, Ramon Bonte, Serwet Demirdas, Hidde H Huidekoper, Janneke Langendonk, Martina Wilke, Walter de Valk, Henk J Blom, Marcel J T Reinders, George J G Ruijter.
      The integration of metabolomics data with sequencing data is a key step towards improving the diagnostic process for finding the disease-causing genetic variant(s) in patients suspected of having an inborn error of metabolism (IEM). The measured metabolite levels could provide additional phenotypical evidence to elucidate the degree of pathogenicity for variants found in genes associated with metabolic processes. We present a computational approach, called Reafect, that calculates for each reaction in a metabolic pathway a score indicating whether that reaction is deficient or not. When calculating this score, Reafect takes multiple factors into account: the magnitude and sign of alterations in the metabolite levels, the reaction distances between metabolites and reactions in the pathway, and the biochemical directionality of the reactions. We applied Reafect to untargeted metabolomics data of 72 patient samples with a known IEM and found that in 81% of the cases the correct deficient enzyme was ranked within the top 5% of all considered enzyme deficiencies. Next, we integrated Reafect with Combined Annotation Dependent Depletion (CADD) scores (a measure for gene variant deleteriousness) and ranked the metabolic genes of 27 IEM patients. We observed that this integrated approach significantly improved the prioritization of the genes containing the disease-causing variant when compared with the two approaches individually. For 15/27 IEM patients the correct affected gene was ranked within the top 0.25% of the set of potentially affected genes. Together, our findings suggest that metabolomics data improves the identification of affected genes in patients suffering from IEM.
    Keywords:  CADD scores; Data integration; ES; Inborn errors of metabolism; Metabolic pathways; Untargeted metabolomics
    DOI:  https://doi.org/10.1016/j.ymgme.2022.05.002
  49. Proc Natl Acad Sci U S A. 2022 Jun 14. 119(24): e2200513119
    Metabolic and immune-sensitive contacts between lipid droplets and endoplasmic reticulum reconstituted in vitro.
    Sukrut Kamerkar, Jagjeet Singh, Subham Tripathy, Hemangi Bhonsle, Mukesh Kumar, Roop Mallik.
      Coordinated cell function requires a variety of subcellular organelles to exchange proteins and lipids across physical contacts that are also referred to as membrane contact sites. Such organelle-to-organelle contacts also evoke interest because they can appear in response to metabolic changes, immune activation, and possibly other stimuli. The microscopic size and complex, crowded geometry of these contacts, however, makes them difficult to visualize, manipulate, and understand inside cells. To address this shortcoming, we deposited endoplasmic reticulum (ER)-enriched microsomes purified from rat liver or from cultured cells on a coverslip in the form of a proteinaceous planar membrane. We visualized real-time lipid and protein exchange across contacts that form between this ER-mimicking membrane and lipid droplets (LDs) purified from the liver of rat. The high-throughput imaging possible in this geometry reveals that in vitro LD-ER contacts increase dramatically when the metabolic state is changed by feeding the animal and also when the immune system is activated. Contact formation in both cases requires Rab18 GTPase and phosphatidic acid, thus revealing common molecular targets operative in two very different biological pathways. An optical trap is used to demonstrate physical tethering of individual LDs to the ER-mimicking membrane and to estimate the strength of this tether. These methodologies can potentially be adapted to understand and target abnormal contact formation between different cellular organelles in the context of neurological and metabolic disorders or pathogen infection.
    Keywords:  Rab18; lipid droplets; membrane contact sites; optical trap; supported lipid bilayer
    DOI:  https://doi.org/10.1073/pnas.2200513119
  50. Theranostics. 2022 ;12(8): 3758-3775
    Twist1 downregulation of PGC-1α decreases fatty acid oxidation in tubular epithelial cells, leading to kidney fibrosis.
    Limin Liu, Xiaoxuan Ning, Lei Wei, Ying Zhou, Lijuan Zhao, Feng Ma, Ming Bai, Xiaoxia Yang, Di Wang, Shiren Sun.
      Rationale: A deficiency of fatty acid oxidation (FAO) is the metabolic hallmark in proximal tubular cells (PTCs) in renal fibrosis owing to utilization of fatty acids by PTCs as the main energy source. Lipid accumulation may promote lipotoxicity-induced pathological injury in renal tissue. However, the molecular mechanism underlying lipotoxicity and renal tubulointerstitial fibrosis (TIF) remains unclear. Twist1 has been identified to play an essential role in fatty acid metabolism. We hypothesized that Twist1 may regulate FAO in PTCs and consequently facilitate lipotoxicity-induced TIF. Methods: We used hypoxia-induced Twist1 overexpression to incite defective mitochondrial FAO in PTCs, and used renal ischemia-reperfusion or unilateral ureteral obstruction to induce renal injury in mice. We used knockout cells, mice of Twist1, and Harmine to determine the role of Twist1 in FAO and TIF. Results: Overexpression of Twist1 downregulates the transcription of PGC-1α and further inhibits the expression of FAO-associated genes, such as PPARα, CPT1 and ACOX1. Consequently, reduced FAO and increased intracellular lipid droplet accumulation in a human PTC line (HK-2), leads to mitochondrial dysfunction, and production of increased profibrogenic factors. Twist1 knockout mice with renal injury had increased expression of PGC-1α, which restored FAO and obstructed progression of TIF. Strikingly, pharmacological inhibition of Twist1 by using Harmine reduced lipid accumulation and restored FAO in vitro and in vivo. Conclusion: Our findings suggest that Twist1-mediated inhibition of FAO in PTCs results in TIF and suggest that Twist1-targeted inhibition could provide a potential strategy for the treatment of renal fibrosis.
    Keywords:  Renal tubulointerstitial fibrosis; Twist1; fatty acid metabolism; hypoxia; pharmacological inhibition strategy
    DOI:  https://doi.org/10.7150/thno.71722
  51. Cell Rep. 2022 Jun 07. pii: S2211-1247(22)00687-8. [Epub ahead of print]39(10): 110910
    ATGL-dependent white adipose tissue lipolysis controls hepatocyte PPARα activity.
    Anne Fougerat, Gabriele Schoiswohl, Arnaud Polizzi, Marion Régnier, Carina Wagner, Sarra Smati, Tiffany Fougeray, Yannick Lippi, Frederic Lasserre, Ilyès Raho, Valentine Melin, Blandine Tramunt, Raphaël Métivier, Caroline Sommer, Fadila Benhamed, Chantal Alkhoury, Franziska Greulich, Céline Jouffe, Anthony Emile, Michael Schupp, Pierre Gourdy, Patricia Dubot, Thierry Levade, Delphine Meynard, Sandrine Ellero-Simatos, Laurence Gamet-Payrastre, Ganna Panasyuk, Henriette Uhlenhaut, Ez-Zoubir Amri, Céline Cruciani-Guglielmacci, Catherine Postic, Walter Wahli, Nicolas Loiseau, Alexandra Montagner, Dominique Langin, Achim Lass, Hervé Guillou.
      In hepatocytes, peroxisome proliferator-activated receptor α (PPARα) orchestrates a genomic and metabolic response required for homeostasis during fasting. This includes the biosynthesis of ketone bodies and of fibroblast growth factor 21 (FGF21). Here we show that in the absence of adipose triglyceride lipase (ATGL) in adipocytes, ketone body and FGF21 production is impaired upon fasting. Liver gene expression analysis highlights a set of fasting-induced genes sensitive to both ATGL deletion in adipocytes and PPARα deletion in hepatocytes. Adipose tissue lipolysis induced by activation of the β3-adrenergic receptor also triggers such PPARα-dependent responses not only in the liver but also in brown adipose tissue (BAT). Intact PPARα activity in hepatocytes is required for the cross-talk between adipose tissues and the liver during fat mobilization.
    Keywords:  ATGL; CP: Metabolism; FGF21; PPARα; fasting; ketogenesis; lipolysis
    DOI:  https://doi.org/10.1016/j.celrep.2022.110910
  52. Immunity. 2022 May 27. pii: S1074-7613(22)00188-1. [Epub ahead of print]
    Leucine-tRNA-synthase-2-expressing B cells contribute to colorectal cancer immunoevasion.
    Zhiqiang Wang, Zhou Lu, Shengli Lin, Jie Xia, Ziwen Zhong, Zhangjuan Xie, Yun Xing, Jingbo Qie, Mengxia Jiao, Yifan Li, Haoyu Wen, Pengyuan Zhao, Dan Zhang, Pinghong Zhou, Jiawen Qian, Feifei Luo, Luman Wang, Hongxiu Yu, Jie Liu, Jie Gu, Ronghua Liu, Yiwei Chu.
      Immunoregulatory B cells impede antitumor immunity through unknown features and mechanisms. We report the existence of leucine-tRNA-synthase-2 (LARS2)-expressing B cell (LARS B) subset with a transforming growth factor-β1 (TGF-β1)-dominant regulatory feature in both mouse and human progressive colorectal cancer (CRC). Of note, LARS B cells exhibited a leucine nutrient preference and displayed active mitochondrial aminoacyl-tRNA biosynthesis. They were located outside the tertiary lymphoid structure and correlated with colorectal hyperplasia and shortened survival in CRC patients. A leucine diet induced LARS B cell generation, whereas LARS B cell deletion by Lars2 gene ablation or leucine blockage repressed CRC immunoevasion. Mechanistically, LARS2 programmed mitochondrial nicotinamide adenine dinucleotide (NAD+) regeneration and oxidative metabolism, thus determining the regulatory feature of LARS B cells in which the NAD-dependent protein deacetylase sirtuin-1 (SIRT1) was involved. We propose a leucine-dieting scheme to inhibit LARS B cells, which is safe and useful for CRC therapy.
    Keywords:  NAD(+); TGF-β1; colorectal cancer; leucine; regulatory B cells
    DOI:  https://doi.org/10.1016/j.immuni.2022.04.017
  53. Mol Biol Evol. 2022 Jun 09. pii: msac124. [Epub ahead of print]
    Trade-offs predicted by metabolic network structure give rise to evolutionary specialization and phenotypic diversification.
    David M Ekkers, Sergio Tusso, Stefany Moreno-Gamez, Marina C Rillo, Oscar P Kuipers, G Sander van Doorn.
      Mitigating trade-offs between different resource-utilization functions is key to an organism's ecological and evolutionary success. These trade-offs often reflect metabolic constraints with a complex molecular underpinning; therefore, their consequences for evolutionary processes have remained elusive. Here, we investigate how metabolic architecture induces resource utilization constraints and how these constraints, in turn, elicit evolutionary specialization and diversification. Guided by the metabolic network structure of the bacterium Lactococcus cremoris, we selected two carbon sources (fructose and galactose) with predicted co-utilization constraints. By evolving L. cremoris on either fructose, galactose or a mix of both sugars, we imposed selection favoring divergent metabolic specializations or co-utilization of both resources, respectively. Phenotypic characterization revealed the evolution of either fructose or galactose specialists in the single-sugar treatments. In the mixed sugar regime, we observed adaptive diversification: both specialists coexisted, and no generalist evolved. Divergence from the ancestral phenotype occurred at key pathway junctions in the central carbon metabolism. Fructose specialists evolved mutations in the fbp and pfk genes that appear to balance anabolic and catabolic carbon fluxes. Galactose specialists evolved increased expression of pgmA (the primary metabolic bottleneck of galactose metabolism) and silencing of ptnABCD (the main glucose transporter) and ldh (regulator/enzyme of downstream carbon metabolism). Overall, our study shows how metabolic network architecture and historical contingency serve to predict targets of selection and inform the functional interpretation of evolved mutations. The elucidation of the relationship between molecular constraints and phenotypic trade-offs contributes to an integrative understanding of evolutionary specialization and diversification.
    Keywords:   Lactococcus cremoris ; adaptive diversification; central carbon metabolism; experimental evolution; metabolic network analysis; metabolic trade-offs
    DOI:  https://doi.org/10.1093/molbev/msac124
  54. J Exp Med. 2022 Jul 04. pii: e20220057. [Epub ahead of print]219(7):
    Vitamin B12 coordinates ileal epithelial cell and microbiota functions to resist Salmonella infection in mice.
    Yong Ge, Mojgan Zadeh, Mansour Mohamadzadeh.
      Deprivation of vitamin B12 (VB12) is linked to various diseases, but the underlying mechanisms in disease progression are poorly understood. Using multiomic approaches, we elucidated the responses of ileal epithelial cells (iECs) and gut microbiome to VB12 dietary restriction. Here, VB12 deficiency impaired the transcriptional and metabolic programming of iECs and reduced epithelial mitochondrial respiration and carnitine shuttling during intestinal Salmonella Typhimurium (STm) infection. Fecal microbial and untargeted metabolomic profiling identified marked changes related to VB12 deficiency, including reductions of metabolites potentially activating mitochondrial β-oxidation in iECs and short-chain fatty acids (SCFAs). Depletion of SCFA-producing microbes by streptomycin treatment decreased the VB12-dependent STm protection. Moreover, compromised mitochondrial function of iECs correlated with declined cell capability to utilize oxygen, leading to uncontrolled oxygen-dependent STm expansion in VB12-deficient mice. Our findings uncovered previously unrecognized mechanisms through which VB12 coordinates ileal epithelial mitochondrial homeostasis and gut microbiota to regulate epithelial oxygenation, resulting in the control of aerobic STm infection.
    DOI:  https://doi.org/10.1084/jem.20220057
  55. Nat Cancer. 2022 Jun 06.
    A single-cell map of dynamic chromatin landscapes of immune cells in renal cell carcinoma.
    Nikos Kourtis, Qingqing Wang, Bei Wang, Erin Oswald, Christina Adler, Samvitha Cherravuru, Evangelia Malahias, Lance Zhang, Jacquelynn Golubov, Qiaozhi Wei, Samantha Lemus, Min Ni, Yueming Ding, Yi Wei, Gurinder S Atwal, Gavin Thurston, Lynn E Macdonald, Andrew J Murphy, Ankur Dhanik, Matthew A Sleeman, Scott S Tykodi, Dimitris Skokos.
      A complete chart of the chromatin regulatory elements of immune cells in patients with cancer and their dynamic behavior is necessary to understand the developmental fates and guide therapeutic strategies. Here, we map the single-cell chromatin landscape of immune cells from blood, normal tumor-adjacent kidney tissue and malignant tissue from patients with early-stage clear cell renal cell carcinoma (ccRCC). We catalog the T cell states dictated by tissue-specific and developmental-stage-specific chromatin accessibility patterns, infer key chromatin regulators and observe rewiring of regulatory networks in the progression to dysfunction in CD8+ T cells. Unexpectedly, among the transcription factors orchestrating the path to dysfunction, NF-κB is associated with a pro-apoptotic program in late stages of dysfunction in tumor-infiltrating CD8+ T cells. Importantly, this epigenomic profiling stratified ccRCC patients based on a NF-κB-driven pro-apoptotic signature. This study provides a rich resource for understanding the functional states and regulatory dynamics of immune cells in ccRCC.
    DOI:  https://doi.org/10.1038/s43018-022-00391-0
  56. Cell Metab. 2022 Jun 07. pii: S1550-4131(22)00186-3. [Epub ahead of print]34(6): 919-936.e8
    Inhibition of ATP-citrate lyase improves NASH, liver fibrosis, and dyslipidemia.
    Marisa R Morrow, Battsetseg Batchuluun, Jianhan Wu, Elham Ahmadi, Julie M Leroux, Pedrum Mohammadi-Shemirani, Eric M Desjardins, Zhichao Wang, Evangelia E Tsakiridis, Declan C T Lavoie, Amir Reihani, Brennan K Smith, Jacek M Kwiecien, James S V Lally, Tracy L Nero, Michael W Parker, Kjetil Ask, John W Scott, Lei Jiang, Guillaume Paré, Stephen L Pinkosky, Gregory R Steinberg.
      Elevated liver de novo lipogenesis contributes to non-alcoholic steatohepatitis (NASH) and can be inhibited by targeting acetyl-CoA carboxylase (ACC). However, hypertriglyceridemia limits the use of pharmacological ACC inhibitors as a monotherapy. ATP-citrate lyase (ACLY) generates acetyl-CoA and oxaloacetate from citrate, but whether inhibition is effective for treating NASH is unknown. Here, we characterize a new mouse model that replicates many of the pathological and molecular drivers of NASH and find that genetically inhibiting ACLY in hepatocytes reduces liver malonyl-CoA, oxaloacetate, steatosis, and ballooning as well as blood glucose, triglycerides, and cholesterol. Pharmacological inhibition of ACLY mirrors genetic inhibition but has additional positive effects on hepatic stellate cells, liver inflammation, and fibrosis. Mendelian randomization of human variants that mimic reductions in ACLY also associate with lower circulating triglycerides and biomarkers of NASH. These data indicate that inhibiting liver ACLY may be an effective approach for treatment of NASH and dyslipidemia.
    Keywords:  NASH; cardiovascular disease; diabetes; fatty acid oxidation; gluconeogenesis; hypertriglyceridemia; insulin resistance; lipogenesis; non-alcoholic steatohepatitis; steatosis
    DOI:  https://doi.org/10.1016/j.cmet.2022.05.004
  57. Cancers (Basel). 2022 May 31. pii: 2735. [Epub ahead of print]14(11):
    Cancer-Induced Metabolic Rewiring of Tumor Endothelial Cells.
    Jacopo Lidonnici, Massimo M Santoro, Roxana E Oberkersch.
      Cancer is a leading cause of death worldwide. If left untreated, tumors tend to grow and spread uncontrolled until the patient dies. To support this growth, cancer cells need large amounts of nutrients and growth factors that are supplied and distributed to the tumor tissue by the vascular system. The aberrant tumor vasculature shows deep morphological, molecular, and metabolic differences compared to the blood vessels belonging to the non-malignant tissues (also referred as normal). A better understanding of the metabolic mechanisms driving the differences between normal and tumor vasculature will allow the designing of new drugs with a higher specificity of action and fewer side effects to target tumors and improve a patient's life expectancy. In this review, we aim to summarize the main features of tumor endothelial cells (TECs) and shed light on the critical metabolic pathways that characterize these cells. A better understanding of such mechanisms will help to design innovative therapeutic strategies in healthy and diseased angiogenesis.
    Keywords:  endothelial metabolism in cancer; tumor endothelial cells; tumor vasculature
    DOI:  https://doi.org/10.3390/cancers14112735
  58. Nat Commun. 2022 Jun 07. 13(1): 3263
    JMJD3 intrinsically disordered region links the 3D-genome structure to TGFβ-dependent transcription activation.
    Marta Vicioso-Mantis, Raquel Fueyo, Claudia Navarro, Sara Cruz-Molina, Wilfred F J van Ijcken, Elena Rebollo, Álvaro Rada-Iglesias, Marian A Martínez-Balbás.
      Enhancers are key regulatory elements that govern gene expression programs in response to developmental signals. However, how multiple enhancers arrange in the 3D-space to control the activation of a specific promoter remains unclear. To address this question, we exploited our previously characterized TGFβ-response model, the neural stem cells, focusing on a ~374 kb locus where enhancers abound. Our 4C-seq experiments reveal that the TGFβ pathway drives the assembly of an enhancer-cluster and precise gene activation. We discover that the TGFβ pathway coactivator JMJD3 is essential to maintain these structures. Using live-cell imaging techniques, we demonstrate that an intrinsically disordered region contained in JMJD3 is involved in the formation of phase-separated biomolecular condensates, which are found in the enhancer-cluster. Overall, in this work we uncover novel functions for the coactivator JMJD3, and we shed light on the relationships between the 3D-conformation of the chromatin and the TGFβ-driven response during mammalian neurogenesis.
    DOI:  https://doi.org/10.1038/s41467-022-30614-y
  59. Mol Cells. 2022 Jun 30. 45(6): 413-424
    SMAD4 Controls Cancer Cell Metabolism by Regulating Methylmalonic Aciduria Cobalamin Deficiency (cbl) B Type.
    Kyoung Song, Hun Seok Lee, Lina Jia, Chaithanya Chelakkot, Nirmal Rajasekaran, Young Kee Shin.
      Suppressor of mothers against decapentaplegic homolog (SMAD) 4 is a pluripotent signaling mediator that regulates myriad cellular functions, including cell growth, cell division, angiogenesis, apoptosis, cell invasion, and metastasis, through transforming growth factor β (TGF-β)-dependent and -independent pathways. SMAD4 is a critical modulator in signal transduction and functions primarily as a transcription factor or cofactor. Apart from being a DNA-binding factor, the additional SMAD4 mechanisms in tumor suppression remain elusive. We previously identified methyl malonyl aciduria cobalamin deficiency B type (MMAB) as a critical SMAD4 binding protein using a proto array analysis. This study confirmed the interaction between SMAD4 and MMAB using bimolecular fluorescence complementation (BiFC) assay, proximity ligation assay (PLA), and conventional immunoprecipitation. We found that transient SMAD4 overexpression down-regulates MMAB expression via a proteasome-dependent pathway. SMAD4-MMAB interaction was independent of TGF-β signaling. Finally, we determined the effect of MMAB downregulation on cancer cells. siRNA-mediated knockdown of MMAB affected cancer cell metabolism in HeLa cells by decreasing ATP production and glucose consumption as well as inducing apoptosis. These findings suggest that SMAD4 controls cancer cell metabolism by regulating MMAB.
    Keywords:  methyl malonyl aciduria cobalamin deficiency B type; mitochondrial energy production; proteasomal pathway; suppressor of mothers against decapentaplegic homolog 4
    DOI:  https://doi.org/10.14348/molcells.2022.0067
  60. Redox Biol. 2022 May 28. pii: S2213-2317(22)00128-8. [Epub ahead of print]54 102356
    BRCA1 haploinsufficiency promotes chromosomal amplification under Fenton reaction-based carcinogenesis through ferroptosis-resistance.
    Yingyi Kong, Shinya Akatsuka, Yashiro Motooka, Hao Zheng, Zhen Cheng, Yukihiro Shiraki, Tomoji Mashimo, Tatsuhiko Imaoka, Shinya Toyokuni.
      Germline-mutation in BRCA1 tumor suppressor gene is an established risk for carcinogenesis not only in females but also in males. Deficiency in the repair of DNA double-strand breaks is hypothesized as a responsible mechanism for carcinogenesis. However, supporting data is insufficient both in the mutation spectra of cancers in the patients with BRCA1 germline-mutation and in murine knockout/knock-in models of Brca1 haploinsufficiency. Furthermore, information on the driving force toward carcinogenesis in BRCA1 mutation carriers is lacking. Here we applied Fenton reaction-based renal carcinogenesis to a rat heterozygously knockout model of BRCA1 haploinsufficiency (mutant [MUT] model; L63X/+). Rat MUT model revealed significant promotion of renal cell carcinoma (RCC) induced by ferric nitrilotriacetate (Fe-NTA). Array-based comparative genome hybridization of the RCCs identified significant increase in chromosomal amplification, syntenic to those in breast cancers of BRCA1 mutation carriers, including c-Myc, in comparison to those in the wild-type. Subacute-phase analysis of the kidney after repeated Fe-NTA treatment in the MUT model revealed dysregulated iron metabolism with mitochondrial malfunction assessed by expression microarray and electron microscopy, leading to renal tubular proliferation with iron overload. In conclusion, we for the first time demonstrate that biallelic wild-type BRCA1 provides more robust protection for mitochondrial metabolism under iron-catalyzed oxidative stress, preventing the emergence of neoplastic cells with chromosomal amplification. Our results suggest that oxidative stress via excess iron is a major driving force for carcinogenesis in BRCA1 haploinsufficiency, which can be a target for cancer prevention and therapeutics.
    Keywords:  BRCA1; Chromosomal amplification; Iron; Mitochondria; Renal cell carcinoma
    DOI:  https://doi.org/10.1016/j.redox.2022.102356
  61. Genes Dis. 2022 Jul;9(4): 1129-1142
    Metabolomic studies in the inborn error of metabolism alkaptonuria reveal new biotransformations in tyrosine metabolism.
    Brendan P Norman, Andrew S Davison, Juliette H Hughes, Hazel Sutherland, Peter Jm Wilson, Neil G Berry, Andrew T Hughes, Anna M Milan, Jonathan C Jarvis, Norman B Roberts, Lakshminarayan R Ranganath, George Bou-Gharios, James A Gallagher.
      Alkaptonuria (AKU) is an inherited disorder of tyrosine metabolism caused by lack of active enzyme homogentisate 1,2-dioxygenase (HGD). The primary consequence of HGD deficiency is increased circulating homogentisic acid (HGA), the main agent in the pathology of AKU disease. Here we report the first metabolomic analysis of AKU homozygous Hgd knockout (Hgd -/-) mice to model the wider metabolic effects of Hgd deletion and the implication for AKU in humans. Untargeted metabolic profiling was performed on urine from Hgd -/- AKU (n = 15) and Hgd +/- non-AKU control (n = 14) mice by liquid chromatography high-resolution time-of-flight mass spectrometry (Experiment 1). The metabolites showing alteration in Hgd -/- were further investigated in AKU mice (n = 18) and patients from the UK National AKU Centre (n = 25) at baseline and after treatment with the HGA-lowering agent nitisinone (Experiment 2). A metabolic flux experiment was carried out after administration of 13C-labelled HGA to Hgd -/-(n = 4) and Hgd +/-(n = 4) mice (Experiment 3) to confirm direct association with HGA. Hgd -/- mice showed the expected increase in HGA, together with unexpected alterations in tyrosine, purine and TCA-cycle pathways. Metabolites with the greatest abundance increases in Hgd -/- were HGA and previously unreported sulfate and glucuronide HGA conjugates, these were decreased in mice and patients on nitisinone and shown to be products from HGA by the 13C-labelled HGA tracer. Our findings reveal that increased HGA in AKU undergoes further metabolism by mainly phase II biotransformations. The data advance our understanding of overall tyrosine metabolism, demonstrating how specific metabolic conditions can elucidate hitherto undiscovered pathways in biochemistry and metabolism.
    Keywords:  AKU, alkaptonuria; AMRT, accurate mass/retention time; Alkaptonuria; Biotransformation; CV, coefficient of variation; FC, fold change; FDR, false-discovery rate; HGA, homogentisic acid; HGD, homogentisate 1,2-dioxygenase; HPPD, hydroxyphenylpyruvic acid dioxygenase; LC-QTOF-MS, liquid chromatography quadrupole time-of-flight mass spectrometry; MS/MS, tandem mass spectrometry; MSC, Molecular Structure Correlator; Metabolism; Metabolomics; Mice; PCA, principal component analysis; QC, quality control; RT, retention time
    DOI:  https://doi.org/10.1016/j.gendis.2021.02.007
  62. Nature. 2022 Jun 08.
    ATGL is a biosynthetic enzyme for fatty acid esters of hydroxy fatty acids.
    Rucha Patel, Anna Santoro, Peter Hofer, Dan Tan, Monika Oberer, Andrew T Nelson, Srihari Konduri, Dionicio Siegel, Rudolf Zechner, Alan Saghatelian, Barbara B Kahn.
      Branched fatty acid (FA) esters of hydroxy FAs (HFAs; FAHFAs) are recently discovered lipids that are conserved from yeast to mammals1,2. A subfamily, palmitic acid esters of hydroxy stearic acids (PAHSAs), are anti-inflammatory and anti-diabetic1,3. Humans and mice with insulin resistance have lower PAHSA levels in subcutaneous adipose tissue and serum1. PAHSA administration improves glucose tolerance and insulin sensitivity and reduces inflammation in obesity, diabetes and immune-mediated diseases1,4-7. The enzyme(s) responsible for FAHFA biosynthesis in vivo remains unknown. Here we identified adipose triglyceride lipase (ATGL, also known as patatin-like phospholipase domain containing 2 (PNPLA2)) as a candidate biosynthetic enzyme for FAHFAs using chemical biology and proteomics. We discovered that recombinant ATGL uses a transacylation reaction that esterifies an HFA with a FA from triglyceride (TG) or diglyceride to produce FAHFAs. Overexpression of wild-type, but not catalytically dead, ATGL increases FAHFA biosynthesis. Chemical inhibition of ATGL or genetic deletion of Atgl inhibits FAHFA biosynthesis and reduces the levels of FAHFA and FAHFA-TG. Levels of endogenous and nascent FAHFAs and FAHFA-TGs are 80-90 per cent lower in adipose tissue of mice in which Atgl is knocked out specifically in the adipose tissue. Increasing TG levels by upregulating diacylglycerol acyltransferase (DGAT) activity promotes FAHFA biosynthesis, and decreasing DGAT activity inhibits it, reinforcing TGs as FAHFA precursors. ATGL biosynthetic transacylase activity is present in human adipose tissue underscoring its potential clinical relevance. In summary, we discovered the first, to our knowledge, biosynthetic enzyme that catalyses the formation of the FAHFA ester bond in mammals. Whereas ATGL lipase activity is well known, our data establish a paradigm shift demonstrating that ATGL transacylase activity is biologically important.
    DOI:  https://doi.org/10.1038/s41586-022-04787-x
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