bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2021–11–14
fifty papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit
  1. Fibroblast pyruvate carboxylase is required for collagen production in the tumour microenvironment.
  2. The Contextual Essentiality of Mitochondrial Genes in Cancer.
  3. The role of mitochondria in cellular senescence.
  4. MTHFD2 is a metabolic checkpoint controlling effector and regulatory T cell fate and function.
  5. Connecting copper and cancer: from transition metal signalling to metalloplasia.
  6. ATP-consuming futile cycles as energy dissipating mechanisms to counteract obesity.
  7. GRP75 mediates Endoplasmic Reticulum-Mitochondria coupling during palmitate-induced pancreatic β-cell apoptosis.
  8. Mitochondrial H+ Leak and Thermogenesis.
  9. Wild-type isocitrate dehydrogenase under the spotlight in glioblastoma.
  10. Acsbg1-dependent mitochondrial fitness is a metabolic checkpoint for tissue Treg cell homeostasis.
  11. Alternative Energy: Breaking Down the Diverse Metabolic Features of Lung Cancers.
  12. Regulation and functional role of the electron transport chain supercomplexes.
  13. Apoptotic stress-induced FGF signalling promotes non-cell autonomous resistance to cell death.
  14. TNF leads to mtDNA release and cGAS/STING-dependent interferon responses that support inflammatory arthritis.
  15. Upcycling the TCA cycle-rewiring tumour-associated fibroblasts.
  16. Mitochondrial Targeting Probes, Drug Conjugates, and Gene Therapeutics.
  17. Raptor is critical for increasing the mitochondrial proteome and skeletal muscle force during hypertrophy.
  18. Unfolding the role of autophagy in the cancer metabolism.
  19. Aspartate Metabolism Facilitates IL-1β Production in Inflammatory Macrophages.
  20. Olaparib Is a Mitochondrial Complex I Inhibitor That Kills Temozolomide-Resistant Human Glioblastoma Cells.
  21. Unlocking the Role of Exercise on CD4+ T Cell Plasticity.
  22. Dynamic regulation of mitochondrial pyruvate metabolism is necessary for orthotopic pancreatic tumor growth.
  23. The Neglected Liaison: Targeting Cancer Cell Metabolic Reprogramming Modifies the Composition of Non-Malignant Populations of the Tumor Microenvironment.
  24. Mitochondrial respiration restricts Listeria monocytogenes infection by slowing down host cell receptor recycling.
  25. A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing.
  26. Morpholinos meet mitochondria: Targeting organellar gene expression.
  27. 1-deoxysphingolipids bind to COUP-TF to modulate lymphatic and cardiac cell development.
  28. The hepatic compensatory response to elevated systemic sulfide promotes diabetes.
  29. Diverse alterations associated with resistance to KRAS(G12C) inhibition.
  30. Hepatocyte-specific perturbation of NAD+ biosynthetic pathways in mice induces reversible nonalcoholic steatohepatitis-like phenotypes.
  31. Regulation of NAD+ metabolism in aging and disease.
  32. Constraint-based modeling of yeast mitochondria reveals the dynamics of protein import and iron-sulfur cluster biogenesis.
  33. Comparison of metabolic states using genome-scale metabolic models.
  34. The FASTK family proteins fine-tune mitochondrial RNA processing.
  35. Nicotinamide effects on the metabolism of human fibroblasts and keratinocytes assessed by quantitative, label-free fluorescence imaging.
  36. The RNA helicase Ddx21 controls Vegfc-driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 function.
  37. Extrachromosomal DNA: An Emerging Hallmark in Human Cancer.
  38. Pyrophosphate and Irreversibility in Evolution, or why PPi Is Not an Energy Currency and why Nature Chose Triphosphates.
  39. 100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care - Preliminary Report.
  40. Co-Polarized [1-13C]Pyruvate and [1,3-13C2]Acetoacetate Provide a Simultaneous View of Cytosolic and Mitochondrial Redox in a Single Experiment.
  41. Cell size is a determinant of stem cell potential during aging.
  42. Dietary palmitic acid promotes a prometastatic memory via Schwann cells.
  43. MMAB promotes negative feedback control of cholesterol homeostasis.
  44. Acetyl-CoA derived from hepatic mitochondrial fatty acid β-oxidation aggravates inflammation by enhancing p65 acetylation.
  45. Evolutionary metabolic landscape from preneoplasia to invasive lung adenocarcinoma.
  46. Deciphering intratumoral heterogeneity using integrated clonal tracking and single-cell transcriptome analyses.
  47. Rab32 uses its effector reticulon 3L to trigger autophagic degradation of mitochondria-associated membrane (MAM) proteins.
  48. Linking Depression to Epigenetics: Role of the Circadian Clock.
  49. Computed structures of core eukaryotic protein complexes.
  50. Mitochondrial Extracellular Vesicles - Origins and Roles.
  1. Nat Metab. 2021 Nov 11.
    Fibroblast pyruvate carboxylase is required for collagen production in the tumour microenvironment.
    Simon Schwörer, Natalya N Pavlova, Francesco V Cimino, Bryan King, Xin Cai, Gina M Sizemore, Craig B Thompson.
      The aberrant production of collagen by fibroblasts is a hallmark of many solid tumours and can influence cancer progression. How the mesenchymal cells in the tumour microenvironment maintain their production of extracellular matrix proteins as the vascular delivery of glutamine and glucose becomes compromised remains unclear. Here we show that pyruvate carboxylase (PC)-mediated anaplerosis in tumour-associated fibroblasts contributes to tumour fibrosis and growth. Using cultured mesenchymal and cancer cells, as well as mouse allograft models, we provide evidence that extracellular lactate can be utilized by fibroblasts to maintain tricarboxylic acid (TCA) cycle anaplerosis and non-essential amino acid biosynthesis through PC activity. Furthermore, we show that fibroblast PC is required for collagen production in the tumour microenvironment. These results establish TCA cycle anaplerosis as a determinant of extracellular matrix collagen production, and identify PC as a potential target to inhibit tumour desmoplasia.
    DOI:  https://doi.org/10.1038/s42255-021-00480-x
  2. Front Cell Dev Biol. 2021 ;9 695351
    The Contextual Essentiality of Mitochondrial Genes in Cancer.
    Luke W Thomas, Margaret Ashcroft.
      Mitochondria are key organelles in eukaryotic evolution that perform crucial roles as metabolic and cellular signaling hubs. Mitochondrial function and dysfunction are associated with a range of diseases, including cancer. Mitochondria support cancer cell proliferation through biosynthetic reactions and their role in signaling, and can also promote tumorigenesis via processes such as the production of reactive oxygen species (ROS). The advent of (nuclear) genome-wide CRISPR-Cas9 deletion screens has provided gene-level resolution of the requirement of nuclear-encoded mitochondrial genes (NEMGs) for cancer cell viability (essentiality). More recently, it has become apparent that the essentiality of NEMGs is highly dependent on the cancer cell context. In particular, key tumor microenvironmental factors such as hypoxia, and changes in nutrient (e.g., glucose) availability, significantly influence the essentiality of NEMGs. In this mini-review we will discuss recent advances in our understanding of the contribution of NEMGs to cancer from CRISPR-Cas9 deletion screens, and discuss emerging concepts surrounding the context-dependent nature of mitochondrial gene essentiality.
    Keywords:  essentiality; metabolism; mitochondria; signaling; viability
    DOI:  https://doi.org/10.3389/fcell.2021.695351
  3. FASEB J. 2021 Dec;35(12): e21991
    The role of mitochondria in cellular senescence.
    Shohini K Ghosh-Choudhary, Jie Liu, Toren Finkel.
      Mitochondria are intimately connected to cell fate and function. Here, we review how these intracellular organelles participate in the induction and maintenance of the senescent state. In particular, we discuss how alterations in mitochondrial metabolism, quality control and dynamics are all involved in various aspects of cellular senescence. Together, these observations suggest that mitochondria are active participants and are mechanistically linked to the unique biology of senescence. We further describe how these insights can be potentially exploited for therapeutic benefit.
    Keywords:  aging; metabolism; mitophagy; reactive oxygen species; senolytic
    DOI:  https://doi.org/10.1096/fj.202101462R
  4. Immunity. 2021 Nov 03. pii: S1074-7613(21)00448-9. [Epub ahead of print]
    MTHFD2 is a metabolic checkpoint controlling effector and regulatory T cell fate and function.
    Ayaka Sugiura, Gabriela Andrejeva, Kelsey Voss, Darren R Heintzman, Xincheng Xu, Matthew Z Madden, Xiang Ye, Katherine L Beier, Nowrin U Chowdhury, Melissa M Wolf, Arissa C Young, Dalton L Greenwood, Allison E Sewell, Shailesh K Shahi, Samantha N Freedman, Alanna M Cameron, Patrik Foerch, Tim Bourne, Juan C Garcia-Canaveras, John Karijolich, Dawn C Newcomb, Ashutosh K Mangalam, Joshua D Rabinowitz, Jeffrey C Rathmell.
      Antigenic stimulation promotes T cell metabolic reprogramming to meet increased biosynthetic, bioenergetic, and signaling demands. We show that the one-carbon (1C) metabolism enzyme methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) regulates de novo purine synthesis and signaling in activated T cells to promote proliferation and inflammatory cytokine production. In pathogenic T helper-17 (Th17) cells, MTHFD2 prevented aberrant upregulation of the transcription factor FoxP3 along with inappropriate gain of suppressive capacity. MTHFD2 deficiency also promoted regulatory T (Treg) cell differentiation. Mechanistically, MTHFD2 inhibition led to depletion of purine pools, accumulation of purine biosynthetic intermediates, and decreased nutrient sensor mTORC1 signaling. MTHFD2 was also critical to regulate DNA and histone methylation in Th17 cells. Importantly, MTHFD2 deficiency reduced disease severity in multiple in vivo inflammatory disease models. MTHFD2 is thus a metabolic checkpoint to integrate purine metabolism with pathogenic effector cell signaling and is a potential therapeutic target within 1C metabolism pathways.
    Keywords:  CD4(+) T cells; CRISPR screen; MTHFD2; T cell differentiation; inflammation; mTORC1; metabolic checkpoint; methylation; one carbon metabolism; purine metabolism
    DOI:  https://doi.org/10.1016/j.immuni.2021.10.011
  5. Nat Rev Cancer. 2021 Nov 11.
    Connecting copper and cancer: from transition metal signalling to metalloplasia.
    Eva J Ge, Ashley I Bush, Angela Casini, Paul A Cobine, Justin R Cross, Gina M DeNicola, Q Ping Dou, Katherine J Franz, Vishal M Gohil, Sanjeev Gupta, Stephen G Kaler, Svetlana Lutsenko, Vivek Mittal, Michael J Petris, Roman Polishchuk, Martina Ralle, Michael L Schilsky, Nicholas K Tonks, Linda T Vahdat, Linda Van Aelst, Dan Xi, Peng Yuan, Donita C Brady, Christopher J Chang.
      Copper is an essential nutrient whose redox properties make it both beneficial and toxic to the cell. Recent progress in studying transition metal signalling has forged new links between researchers of different disciplines that can help translate basic research in the chemistry and biology of copper into clinical therapies and diagnostics to exploit copper-dependent disease vulnerabilities. This concept is particularly relevant in cancer, as tumour growth and metastasis have a heightened requirement for this metal nutrient. Indeed, the traditional view of copper as solely an active site metabolic cofactor has been challenged by emerging evidence that copper is also a dynamic signalling metal and metalloallosteric regulator, such as for copper-dependent phosphodiesterase 3B (PDE3B) in lipolysis, mitogen-activated protein kinase kinase 1 (MEK1) and MEK2 in cell growth and proliferation and the kinases ULK1 and ULK2 in autophagy. In this Perspective, we summarize our current understanding of the connection between copper and cancer and explore how challenges in the field could be addressed by using the framework of cuproplasia, which is defined as regulated copper-dependent cell proliferation and is a representative example of a broad range of metalloplasias. Cuproplasia is linked to a diverse array of cellular processes, including mitochondrial respiration, antioxidant defence, redox signalling, kinase signalling, autophagy and protein quality control. Identifying and characterizing new modes of copper-dependent signalling offers translational opportunities that leverage disease vulnerabilities to this metal nutrient.
    DOI:  https://doi.org/10.1038/s41568-021-00417-2
  6. Rev Endocr Metab Disord. 2021 Nov 06.
    ATP-consuming futile cycles as energy dissipating mechanisms to counteract obesity.
    Alexandra J Brownstein, Michaela Veliova, Rebeca Acin-Perez, Marc Liesa, Orian S Shirihai.
      Obesity results from an imbalance in energy homeostasis, whereby excessive energy intake exceeds caloric expenditure. Energy can be dissipated out of an organism by producing heat (thermogenesis), explaining the long-standing interest in exploiting thermogenic processes to counteract obesity. Mitochondrial uncoupling is a process that expends energy by oxidizing nutrients to produce heat, instead of ATP synthesis. Energy can also be dissipated through mechanisms that do not involve mitochondrial uncoupling. Such mechanisms include futile cycles described as metabolic reactions that consume ATP to produce a product from a substrate but then converting the product back into the original substrate, releasing the energy as heat. Energy dissipation driven by cellular ATP demand can be regulated by adjusting the speed and number of futile cycles. Energy consuming futile cycles that are reviewed here are lipolysis/fatty acid re-esterification cycle, creatine/phosphocreatine cycle, and the SERCA-mediated calcium import and export cycle. Their reliance on ATP emphasizes that mitochondrial oxidative function coupled to ATP synthesis, and not just uncoupling, can play a role in thermogenic energy dissipation. Here, we review ATP consuming futile cycles, the evidence for their function in humans, and their potential employment as a strategy to dissipate energy and counteract obesity.
    Keywords:  Brown adipose tissue; Energy expenditure; Futile cycle; Malate aspartate shuttle; Metabolism; Thermogenesis
    DOI:  https://doi.org/10.1007/s11154-021-09690-w
  7. J Biol Chem. 2021 Oct 28. pii: S0021-9258(21)01174-1. [Epub ahead of print] 101368
    GRP75 mediates Endoplasmic Reticulum-Mitochondria coupling during palmitate-induced pancreatic β-cell apoptosis.
    Shweta Tiwary, Arun Nandwani, Rukshar Khan, Malabika Datta.
      The endoplasmic reticulum (ER) and mitochondria are structurally connected with each other at specific sites termed mitochondria-associated membranes (MAM). These physical links are composed of several tethering proteins and are important during varied cellular processes, such as calcium homeostasis, lipid metabolism and transport, membrane biogenesis and organelle remodeling. However, the attributes of specific tethering proteins in these cellular functions remain debatable. Here, we present data to show that one such tether protein, GRP75, is essential in increasing ER-mitochondria contact during palmitate-induced apoptosis in pancreatic insulinoma cells. We demonstrate that palmitate increased GRP75 levels in mouse and rat pancreatic insulinoma cells as well as in mouse primary islet cells. This was associated with increased mitochondrial Ca2+ transfer, impaired mitochondrial membrane potential, increased ROS production, and enhanced physical coupling between the ER and mitochondria. Interestingly, GRP75 inhibition prevented these palmitate-induced cellular aberrations. Additionally, GRP75 overexpression alone was sufficient to impair mitochondrial membrane potential, increase mitochondrial Ca2+ levels and ROS generation, augment ER-mitochondria contact, and induce apoptosis in these cells. In vivo injection of palmitate induced hyperglycemia and hypertriglyceridemia, as well as impaired glucose and insulin tolerance in mice. These animals also exhibited elevated GRP75 levels accompanied by enhanced apoptosis within the pancreatic islets. Our findings suggest that GRP75 is critical in mediating palmitate-induced ER-mitochondrial interaction leading to apoptosis in pancreatic islet cells.
    Keywords:  ER-mitochondria contact; GRP75; calcium apoptosis; palmitate
    DOI:  https://doi.org/10.1016/j.jbc.2021.101368
  8. Annu Rev Physiol. 2021 Nov 10.
    Mitochondrial H+ Leak and Thermogenesis.
    Ambre M Bertholet, Yuriy Kirichok.
      Mitochondria of all tissues convert various metabolic substrates into two forms of energy: ATP and heat. Historically, the primary focus of research in mitochondrial bioenergetics was on the mechanisms of ATP production, while mitochondrial thermogenesis received significantly less attention. Nevertheless, mitochondrial heat production is crucial for the maintenance of body temperature, regulation of the pace of metabolism, and prevention of oxidative damage to mitochondria and the cell. In addition, mitochondrial thermogenesis has gained significance as a pharmacological target for treating metabolic disorders. Mitochondria produce heat as the result of H+ leak across their inner membrane. This review provides a critical assessment of the current field of mitochondrial H+ leak and thermogenesis, with a focus on the molecular mechanisms involved in the function and regulation of uncoupling protein 1 and the ADP/ATP carrier, the two proteins that mediate mitochondrial H+ leak. Expected final online publication date for the Annual Review of Physiology, Volume 84 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-physiol-021119-034405
  9. Oncogene. 2021 Nov 11.
    Wild-type isocitrate dehydrogenase under the spotlight in glioblastoma.
    Gabriel Alzial, Ophelie Renoult, François Paris, Catherine Gratas, Anne Clavreul, Claire Pecqueur.
      Brain tumors actively reprogram their cellular metabolism to survive and proliferate, thus offering potential therapeutic opportunities. Over the past decade, extensive research has been done on mutant IDH enzymes as markers of good prognosis in glioblastoma, a highly aggressive brain tumor in adults with dismal prognosis. Yet, 95% of glioblastoma are IDH wild-type. Here, we review current knowledge about IDH wild-type enzymes and their putative role in mechanisms driving tumor progression. After a brief overview on tumor metabolic adaptation, we present the diverse metabolic function of IDH enzymes and their roles in glioblastoma initiation, progression and response to treatments. Finally, we will discuss wild-type IDH targeting in primary glioblastoma.
    DOI:  https://doi.org/10.1038/s41388-021-02056-1
  10. Cell Rep. 2021 Nov 09. pii: S2211-1247(21)01394-2. [Epub ahead of print]37(6): 109921
    Acsbg1-dependent mitochondrial fitness is a metabolic checkpoint for tissue Treg cell homeostasis.
    Toshio Kanno, Takahiro Nakajima, Yusuke Kawashima, Satoru Yokoyama, Hikari K Asou, Shigemi Sasamoto, Koji Hayashizaki, Yuki Kinjo, Osamu Ohara, Toshinori Nakayama, Yusuke Endo.
      Regulatory T (Treg) cells are critical for immunological tolerance and immune homeostasis. Treg cells strongly rely on mitochondrial metabolism and show a lower level of glycolysis. However, little is known about the role of lipid metabolism in the regulation of Treg cell homeostasis. Some members of the ACSL family of acyl-coenzyme A (CoA) synthases are expressed in T cells, but their function remains unclear. A combination of RNA-sequencing and proteome analyses shows that Acsbg1, a member of ACSL, is selectively expressed in Treg cells. We show that the genetic deletion of Acsbg1 not only causes mitochondrial dysfunction, but it also dampens other metabolic pathways. The extrinsic supplementation of Acsbg1-deficient Treg cells with oleoyl-CoA restores the phenotype of the Treg metabolic signature. Furthermore, this pathway in ST2+ effector Treg cells enhances immunosuppressive capacity in airway inflammation. Thus, Acsbg1 serves as a metabolic checkpoint governing Treg cell homeostasis and the resolution of lung inflammation.
    Keywords:  Acsbg1; IL-33; IL-5; Treg cells; airway inflammation; fatty acid metabolism; mitochondrial fitness; pathogenic Th2 cells
    DOI:  https://doi.org/10.1016/j.celrep.2021.109921
  11. Front Oncol. 2021 ;11 757323
    Alternative Energy: Breaking Down the Diverse Metabolic Features of Lung Cancers.
    Kasey R Cargill, William L Hasken, Carl M Gay, Lauren A Byers.
      Metabolic reprogramming is a hallmark of cancer initiation, progression, and relapse. From the initial observation that cancer cells preferentially ferment glucose to lactate, termed the Warburg effect, to emerging evidence indicating that metabolic heterogeneity and mitochondrial metabolism are also important for tumor growth, the complex mechanisms driving cancer metabolism remain vastly unknown. These unique shifts in metabolism must be further investigated in order to identify unique therapeutic targets for individuals afflicted by this aggressive disease. Although novel therapies have been developed to target metabolic vulnerabilities in a variety of cancer models, only limited efficacy has been achieved. In particular, lung cancer metabolism has remained relatively understudied and underutilized for the advancement of therapeutic strategies, however recent evidence suggests that lung cancers have unique metabolic preferences of their own. This review aims to provide an overview of essential metabolic mechanisms and potential therapeutic agents in order to increase evidence of targeted metabolic inhibition for the treatment of lung cancer, where novel therapeutics are desperately needed.
    Keywords:  glycolysis (Warburg effect); lung cancer; metabolic inhibitors; metabolism; oxidative phosphorylation
    DOI:  https://doi.org/10.3389/fonc.2021.757323
  12. Biochem Soc Trans. 2021 Nov 08. pii: BST20210460. [Epub ahead of print]
    Regulation and functional role of the electron transport chain supercomplexes.
    Sara Cogliati, Jose Luis Cabrera-Alarcón, Jose Antonio Enriquez.
      Mitochondria are one of the most exhaustively investigated organelles in the cell and most attention has been paid to the components of the mitochondrial electron transport chain (ETC) in the last 100 years. The ETC collects electrons from NADH or FADH2 and transfers them through a series of electron carriers within multiprotein respiratory complexes (complex I to IV) to oxygen, therefore generating an electrochemical gradient that can be used by the F1-F0-ATP synthase (also named complex V) in the mitochondrial inner membrane to synthesize ATP. The organization and function of the ETC is a continuous source of surprises. One of the latest is the discovery that the respiratory complexes can assemble to form a variety of larger structures called super-complexes (SCs). This opened an unexpected level of complexity in this well-known and fundamental biological process. This review will focus on the current evidence for the formation of different SCs and will explore how they modulate the ETC organization according to the metabolic state. Since the field is rapidly growing, we also comment on the experimental techniques used to describe these SC and hope that this overview may inspire new technologies that will help to advance the field.
    Keywords:  N-respirasome; OXPHOS; Q-respirsome; electon transport chain; supercomplexes
    DOI:  https://doi.org/10.1042/BST20210460
  13. Nat Commun. 2021 Nov 12. 12(1): 6572
    Apoptotic stress-induced FGF signalling promotes non-cell autonomous resistance to cell death.
    Florian J Bock, Egor Sedov, Elle Koren, Anna L Koessinger, Catherine Cloix, Désirée Zerbst, Dimitris Athineos, Jayanthi Anand, Kirsteen J Campbell, Karen Blyth, Yaron Fuchs, Stephen W G Tait.
      Damaged or superfluous cells are typically eliminated by apoptosis. Although apoptosis is a cell-autonomous process, apoptotic cells communicate with their environment in different ways. Here we describe a mechanism whereby cells under apoptotic stress can promote survival of neighbouring cells. We find that upon apoptotic stress, cells release the growth factor FGF2, leading to MEK-ERK-dependent transcriptional upregulation of pro-survival BCL-2 proteins in a non-cell autonomous manner. This transient upregulation of pro-survival BCL-2 proteins protects neighbouring cells from apoptosis. Accordingly, we find in certain cancer types a correlation between FGF-signalling, BCL-2 expression and worse prognosis. In vivo, upregulation of MCL-1 occurs in an FGF-dependent manner during skin repair, which regulates healing dynamics. Importantly, either co-treatment with FGF-receptor inhibitors or removal of apoptotic stress restores apoptotic sensitivity to cytotoxic therapy and delays wound healing. These data reveal a pathway by which cells under apoptotic stress can increase resistance to cell death in surrounding cells. Beyond mediating cytotoxic drug resistance, this process also provides a potential link between tissue damage and repair.
    DOI:  https://doi.org/10.1038/s41467-021-26613-0
  14. Cell Rep. 2021 Nov 09. pii: S2211-1247(21)01456-X. [Epub ahead of print]37(6): 109977
    TNF leads to mtDNA release and cGAS/STING-dependent interferon responses that support inflammatory arthritis.
    Joschka Willemsen, Marie-Therese Neuhoff, Thomas Hoyler, Emma Noir, Clemence Tessier, Sophie Sarret, Tara N Thorsen, Amanda Littlewood-Evans, Juan Zhang, Maroof Hasan, James S Rush, Danilo Guerini, Richard M Siegel.
      Tumor necrosis factor (TNF) is a key driver of several inflammatory diseases, such as rheumatoid arthritis, inflammatory bowel disease, and psoriasis, in which affected tissues show an interferon-stimulated gene signature. Here, we demonstrate that TNF triggers a type-I interferon response that is dependent on the cyclic guanosine monophosphate-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway. We show that TNF inhibits PINK1-mediated mitophagy and leads to altered mitochondrial function and to an increase in cytosolic mtDNA levels. Using cGAS-chromatin immunoprecipitation (ChIP), we demonstrate that cytosolic mtDNA binds to cGAS after TNF treatment. Furthermore, TNF induces a cGAS-STING-dependent transcriptional response that mimics that of macrophages from rheumatoid arthritis patients. Finally, in an inflammatory arthritis mouse model, cGAS deficiency blocked interferon responses and reduced inflammatory cell infiltration and joint swelling. These findings elucidate a molecular mechanism linking TNF to type-I interferon signaling and suggest a potential benefit for therapeutic targeting of cGAS/STING in TNF-driven diseases.
    Keywords:  ISG; STING; TNF; arthritis; autoimmune; cGAS; interferon; mitophagy; mtDNA
    DOI:  https://doi.org/10.1016/j.celrep.2021.109977
  15. Nat Metab. 2021 Nov 11.
    Upcycling the TCA cycle-rewiring tumour-associated fibroblasts.
    Zachary A Bacigalupa, W Kimryn Rathmell.
      
    DOI:  https://doi.org/10.1038/s42255-021-00473-w
  16. Methods Mol Biol. 2022 ;2383 429-446
    Mitochondrial Targeting Probes, Drug Conjugates, and Gene Therapeutics.
    Carmine Pasquale Cerrato, Tove Kivijärvi, Ülo Langel.
      Mitochondria represent an important drug target for many phatology, including neurodegeneration, metabolic disease, heart failure, ischemia-reperfusion injury, and cancer. Mitochondrial dysfunctions are caused by mutation in mitochondrial DNA or in nuclear genes encoding mitochondrial proteins. Cell-penetrating peptides (CPPs) have been employed to overcome biological barriers, target this organelle, and therapeuticaly restore mitochondrial functions. Here, we describe recent methods used to deliver oligonucleotides targeting mitochondrial protein by using mitochondrial penetrating peptides. In particular, we highlight recent advances of formulated peptides/oligonucleotides nanocomplexes as a proof-of-principle for pharmaceutical form of peptide-based therapeutics.
    Keywords:  Intracellular delivery; Mitochondria; Nanocarriers; Nanoparticles; mitFects
    DOI:  https://doi.org/10.1007/978-1-0716-1752-6_27
  17. FASEB J. 2021 Dec;35(12): e22031
    Raptor is critical for increasing the mitochondrial proteome and skeletal muscle force during hypertrophy.
    Martina Baraldo, Leonardo Nogara, Georgia Ana Dumitras, Achille Homère Tchampda Dondjang, Alessia Geremia, Marco Scalabrin, Clara Türk, Frederik Telkamp, Lorena Zentilin, Mauro Giacca, Marcus Krüger, Bert Blaauw.
      Loss of skeletal muscle mass and force is of critical importance in numerous pathologies, like age-related sarcopenia or cancer. It has been shown that the Akt-mTORC1 pathway is critical for stimulating adult muscle mass and function, however, it is unknown if mTORC1 is the only mediator downstream of Akt and which intracellular processes are required for functional muscle growth. Here, we show that loss of Raptor reduces muscle hypertrophy after Akt activation and completely prevents increases in muscle force. Interestingly, the residual hypertrophy after Raptor deletion can be completely prevented by administration of the mTORC1 inhibitor rapamycin. Using a quantitative proteomics approach we find that loss of Raptor affects the increases in mitochondrial proteins, while rapamycin mainly affects ribosomal proteins. Taken together, these results suggest that mTORC1 is the key mediator of Akt-dependent muscle growth and its regulation of the mitochondrial proteome is critical for increasing muscle force.
    Keywords:  Raptor; hypertrophy; mTOR; mitochondria; rapamycin; skeletal muscle
    DOI:  https://doi.org/10.1096/fj.202101054RR
  18. Biochem Biophys Rep. 2021 Dec;28 101158
    Unfolding the role of autophagy in the cancer metabolism.
    Anchala Pandey, Pooja Yadav, Sanjeev Shukla.
      Autophagy is considered an indispensable process that scavenges toxins, recycles complex macromolecules, and sustains the essential cellular functions. In addition to its housekeeping role, autophagy plays a substantial role in many pathophysiological processes such as cancer. Certainly, it adapts cancer cells to thrive in the stress conditions such as hypoxia and starvation. Cancer cells indeed have also evolved by exploiting the autophagy process to fulfill energy requirements through the production of metabolic fuel sources and fundamentally altered metabolic pathways. Occasionally autophagy as a foe impedes tumorigenesis and promotes cell death. The complex role of autophagy in cancer makes it a potent therapeutic target and has been actively tested in clinical trials. Moreover, the versatility of autophagy has opened new avenues of effective combinatorial therapeutic strategies. Thereby, it is imperative to comprehend the specificity of autophagy in cancer-metabolism. This review summarizes the recent research and conceptual framework on the regulation of autophagy by various metabolic pathways, enzymes, and their cross-talk in the cancer milieu, including the implementation of altered metabolism and autophagy in clinically approved and experimental therapeutics.
    Keywords:  Autophagy; Cancer; Hypoxia; Metabolism; Starvation; Therapeutics
    DOI:  https://doi.org/10.1016/j.bbrep.2021.101158
  19. Front Immunol. 2021 ;12 753092
    Aspartate Metabolism Facilitates IL-1β Production in Inflammatory Macrophages.
    Hao Wang, Xueyue Zheng, Bingnan Liu, Yaoyao Xia, Zhongquan Xin, Baichuan Deng, Liuqin He, Jinping Deng, Wenkai Ren.
      Increasing evidence support that cellular amino acid metabolism shapes the fate of immune cells; however, whether aspartate metabolism dictates macrophage function is still enigmatic. Here, we found that the metabolites in aspartate metabolism are depleted in lipopolysaccharide (LPS) plus interferon gamma (IFN-γ)-stimulated macrophages. Aspartate promotes interleukin-1β (IL-1β) secretion in M1 macrophages. Mechanistically, aspartate boosts the activation of hypoxia-inducible factor-1α (HIF-1α) and inflammasome and increases the levels of metabolites in aspartate metabolism, such as asparagine. Interestingly, asparagine also accelerates the activation of cellular signaling pathways and promotes the production of inflammatory cytokines from macrophages. Moreover, aspartate supplementation augments the macrophage-mediated inflammatory responses in mice and piglets. These results uncover a previously uncharacterized role for aspartate metabolism in directing M1 macrophage polarization.
    Keywords:  HIF-1α; asparagine; aspartate; inflammasome; macrophage
    DOI:  https://doi.org/10.3389/fimmu.2021.753092
  20. Int J Mol Sci. 2021 Nov 03. pii: 11938. [Epub ahead of print]22(21):
    Olaparib Is a Mitochondrial Complex I Inhibitor That Kills Temozolomide-Resistant Human Glioblastoma Cells.
    Luca X Zampieri, Martina Sboarina, Andrea Cacace, Debora Grasso, Léopold Thabault, Loïc Hamelin, Thibaut Vazeille, Elodie Dumon, Rodrigue Rossignol, Raphaël Frédérick, Etienne Sonveaux, Florence Lefranc, Pierre Sonveaux.
      Glioblastoma represents the highest grade of brain tumors. Despite maximal resection surgery associated with radiotherapy and concomitant followed by adjuvant chemotherapy with temozolomide (TMZ), patients have a very poor prognosis due to the rapid recurrence and the acquisition of resistance to TMZ. Here, initially considering that TMZ is a prodrug whose activation is pH-dependent, we explored the contribution of glioblastoma cell metabolism to TMZ resistance. Using isogenic TMZ-sensitive and TMZ-resistant human glioblastoma cells, we report that the expression of O6-methylguanine DNA methyltransferase (MGMT), which is known to repair TMZ-induced DNA methylation, does not primarily account for TMZ resistance. Rather, fitter mitochondria in TMZ-resistant glioblastoma cells are a direct cause of chemoresistance that can be targeted by inhibiting oxidative phosphorylation and/or autophagy/mitophagy. Unexpectedly, we found that PARP inhibitor olaparib, but not talazoparib, is also a mitochondrial Complex I inhibitor. Hence, we propose that the anticancer activities of olaparib in glioblastoma and other cancer types combine DNA repair inhibition and impairment of cancer cell respiration.
    Keywords:  PARP inhibitors; cancer metabolism; chemoresistance; glioblastoma; metformin; mitochondria; temozolomide (TMZ)
    DOI:  https://doi.org/10.3390/ijms222111938
  21. Front Immunol. 2021 ;12 729366
    Unlocking the Role of Exercise on CD4+ T Cell Plasticity.
    Chloé D Goldsmith, Thomasina Donovan, Nicole Vlahovich, David B Pyne.
      A hallmark of T cell ageing is a loss of effector plasticity. Exercise delays T cell ageing, yet the mechanisms driving the effects of exercise on T cell biology are not well elucidated. T cell plasticity is closely linked with metabolism, and consequently sensitive to metabolic changes induced by exercise. Mitochondrial function is essential for providing the intermediate metabolites necessary to generate and modify epigenetic marks in the nucleus, thus metabolic activity and epigenetic mechanisms are intertwined. In this perspective we propose a role for exercise in CD4+ T cell plasticity, exploring links between exercise, metabolism and epigenetic reprogramming.
    Keywords:  DNA methylation; chromatin remodeling; epigenetics; histone modification; immune; metabolism; mitochondria
    DOI:  https://doi.org/10.3389/fimmu.2021.729366
  22. Cancer Metab. 2021 Nov 08. 9(1): 39
    Dynamic regulation of mitochondrial pyruvate metabolism is necessary for orthotopic pancreatic tumor growth.
    Nancy P Echeverri Ruiz, Vijay Mohan, Jinghai Wu, Sabina Scott, McKenzie Kreamer, Martin Benej, Tereza Golias, Ioanna Papandreou, Nicholas C Denko.
       BACKGROUND: Pyruvate dehydrogenase complex (PDC) plays a central role in carbohydrate metabolism, linking cytoplasmic glycolysis to the mitochondrial tricarboxylic acid (TCA) cycle. PDC is a conserved E1-E2-E3 dehydrogenase with a PDHA1 and PDHB heterotetramer functioning as the E1 subunit. PDHA1 contains three serine residues that can be reversibly phosphorylated by a dedicated family of four inhibitory pyruvate dehydrogenase kinases (PDHK1-4) and two reactivating phosphatases (PDP1, 2). Hypoxia induces the expression of PDHK1 and PDHK3 and hyperphosphorylates PDHA1. The role of PDC in metabolic reprogramming and tumor progression appears to be for the integration of oncogenic and environmental signals which supports tumor growth.
    METHODS: To isolate the function of the serine-dependent regulation of PDC, we engineered MiaPaca2 cells to express PDHA1 protein with either intact serines at positions 232, 293, and 300 or all the combinations of non-phosphorylatable alanine substitution mutations. These lines were compared in vitro for biochemical response to hypoxia by western blot, metabolic activity by biochemical assay and Seahorse XF flux analysis, and growth in media with reduced exogenous metabolites. The lines were also tested for growth in vivo after orthotopic injection into the pancreata of immune-deficient mice.
    RESULTS: In this family of cells with non-phosphorylatable PDHA1, we found reduced hypoxic phosphorylation of PDHA1, decreased PDH enzymatic activity in normoxia and hypoxia, decreased mitochondrial function by Seahorse flux assay, reduced in vitro growth of cells in media depleted of lipids, and reduced growth of tumors after orthotopic transplantation of cells into the pancreata of immune-deficient mice.
    CONCLUSIONS: We found that any substitution of alanine for serine at regulatory sites generated a hypomorphic PDC. However, the reduced PDC activity was insensitive to further reduction in hypoxia. These cells had a very modest reduction of growth in vitro, but failed to grow as tumors indicating that dynamic PDC adaptation to microenvironmental conditions is necessary to support pancreatic cancer growth in vivo.
    Keywords:  Glucose metabolism; Hypoxia; Mitochondria; Orthotopic pancreatic tumors; Pyruvate dehydrogenase
    DOI:  https://doi.org/10.1186/s40170-021-00275-4
  23. Cancers (Basel). 2021 Oct 29. pii: 5447. [Epub ahead of print]13(21):
    The Neglected Liaison: Targeting Cancer Cell Metabolic Reprogramming Modifies the Composition of Non-Malignant Populations of the Tumor Microenvironment.
    Maria Iorio, Nikkitha Umesh Ganesh, Monica De Luise, Anna Maria Porcelli, Giuseppe Gasparre, Ivana Kurelac.
      Metabolic reprogramming is a well-known hallmark of cancer, whereby the development of drugs that target cancer cell metabolism is gaining momentum. However, when establishing preclinical studies and clinical trials, it is often neglected that a tumor mass is a complex system in which cancer cells coexist and interact with several types of microenvironment populations, including endothelial cells, fibroblasts and immune cells. We are just starting to understand how such populations are affected by the metabolic changes occurring in a transformed cell and little is known about the impact of metabolism-targeting drugs on the non-malignant tumor components. Here we provide a general overview of the links between cancer cell metabolism and tumor microenvironment (TME), particularly focusing on the emerging literature reporting TME-specific effects of metabolic therapies.
    Keywords:  cancer metabolism; cancer-associated fibroblasts; metabolic reprogramming; tumor microenvironment; tumor-associated macrophages
    DOI:  https://doi.org/10.3390/cancers13215447
  24. Cell Rep. 2021 Nov 09. pii: S2211-1247(21)01468-6. [Epub ahead of print]37(6): 109989
    Mitochondrial respiration restricts Listeria monocytogenes infection by slowing down host cell receptor recycling.
    Anna Spier, Michael G Connor, Thomas Steiner, Filipe Carvalho, Pascale Cossart, Wolfgang Eisenreich, Timothy Wai, Fabrizia Stavru.
      Mutations in mitochondrial genes impairing energy production cause mitochondrial diseases (MDs), and clinical studies have shown that MD patients are prone to bacterial infections. However, the relationship between mitochondrial (dys)function and infection remains largely unexplored, especially in epithelial cells, the first barrier to many pathogens. Here, we generate an epithelial cell model for one of the most common mitochondrial diseases, Leigh syndrome, by deleting surfeit locus protein 1 (SURF1), an assembly factor for respiratory chain complex IV. We use this genetic model and a complementary, nutrient-based approach to modulate mitochondrial respiration rates and show that impaired mitochondrial respiration favors entry of the human pathogen Listeria monocytogenes, a well-established bacterial infection model. Reversely, enhanced mitochondrial energy metabolism decreases infection efficiency. We further demonstrate that endocytic recycling is reduced in mitochondrial respiration-dependent cells, dampening L. monocytogenes infection by slowing the recycling of its host cell receptor c-Met, highlighting a previously undescribed role of mitochondrial respiration during infection.
    Keywords:  (13)C isotopologue profiling; Listeria monocytogenes; Rab11; endocytic recycling; infection; metabolism; mitochondria; mitochondrial disease; respiration
    DOI:  https://doi.org/10.1016/j.celrep.2021.109989
  25. Nat Commun. 2021 Nov 11. 12(1): 6512
    A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing.
    Sanju Sinha, Karina Barbosa, Kuoyuan Cheng, Mark D M Leiserson, Prashant Jain, Anagha Deshpande, David M Wilson, Bríd M Ryan, Ji Luo, Ze'ev A Ronai, Joo Sang Lee, Aniruddha J Deshpande, Eytan Ruppin.
      Recent studies have reported that genome editing by CRISPR-Cas9 induces a DNA damage response mediated by p53 in primary cells hampering their growth. This could lead to a selection of cells with pre-existing p53 mutations. In this study, employing an integrated computational and experimental framework, we systematically investigated the possibility of selection of additional cancer driver mutations during CRISPR-Cas9 gene editing. We first confirm the previous findings of the selection for pre-existing p53 mutations by CRISPR-Cas9. We next demonstrate that similar to p53, wildtype KRAS may also hamper the growth of Cas9-edited cells, potentially conferring a selective advantage to pre-existing KRAS-mutant cells. These selective effects are widespread, extending across cell-types and methods of CRISPR-Cas9 delivery and the strength of selection depends on the sgRNA sequence and the gene being edited. The selection for pre-existing p53 or KRAS mutations may confound CRISPR-Cas9 screens in cancer cells and more importantly, calls for monitoring patients undergoing CRISPR-Cas9-based editing for clinical therapeutics for pre-existing p53 and KRAS mutations.
    DOI:  https://doi.org/10.1038/s41467-021-26788-6
  26. Cell. 2021 Nov 11. pii: S0092-8674(21)01235-6. [Epub ahead of print]184(23): 5693-5695
    Morpholinos meet mitochondria: Targeting organellar gene expression.
    Heike Rampelt, Nikolaus Pfanner.
      The mitochondrial genome encodes proteins central to mitochondrial function; however, transcript-specific mechanistic studies of mitochondrial gene products have been difficult because of challenges in their experimental manipulation. Cruz-Zaragoza et al. provide a solution to this challenge, introducing an elegant system for efficient translational silencing of transcripts in human mitochondria.
    DOI:  https://doi.org/10.1016/j.cell.2021.10.019
  27. Dev Cell. 2021 Nov 05. pii: S1534-5807(21)00849-2. [Epub ahead of print]
    1-deoxysphingolipids bind to COUP-TF to modulate lymphatic and cardiac cell development.
    Ting Wang, Zheng Wang, Lauriane de Fabritus, Jinglian Tao, Essa M Saied, Ho-Joon Lee, Bulat R Ramazanov, Benjamin Jackson, Daniel Burkhardt, Mikhail Parker, Anne S Gleinich, Zhirui Wang, Dong Eun Seo, Ting Zhou, Shihao Xu, Irina Alecu, Parastoo Azadi, Christoph Arenz, Thorsten Hornemann, Smita Krishnaswamy, Serge A van de Pavert, Susan M Kaech, Natalia B Ivanova, Fabio R Santori.
      Identification of physiological modulators of nuclear hormone receptor (NHR) activity is paramount for understanding the link between metabolism and transcriptional networks that orchestrate development and cellular physiology. Using libraries of metabolic enzymes alongside their substrates and products, we identify 1-deoxysphingosines as modulators of the activity of NR2F1 and 2 (COUP-TFs), which are orphan NHRs that are critical for development of the nervous system, heart, veins, and lymphatic vessels. We show that these non-canonical alanine-based sphingolipids bind to the NR2F1/2 ligand-binding domains (LBDs) and modulate their transcriptional activity in cell-based assays at physiological concentrations. Furthermore, inhibition of sphingolipid biosynthesis phenocopies NR2F1/2 deficiency in endothelium and cardiomyocytes, and increases in 1-deoxysphingosine levels activate NR2F1/2-dependent differentiation programs. Our findings suggest that 1-deoxysphingosines are physiological regulators of NR2F1/2-mediated transcription.
    Keywords:  1-deoxysphingosine; COUP-TF; NR2F1; NR2F2; NR2F6; SPTLC2; cardiomyocyte; lymphatic; metabolism; sphingolipid
    DOI:  https://doi.org/10.1016/j.devcel.2021.10.018
  28. Cell Rep. 2021 Nov 09. pii: S2211-1247(21)01435-2. [Epub ahead of print]37(6): 109958
    The hepatic compensatory response to elevated systemic sulfide promotes diabetes.
    Roderick N Carter, Matthew T G Gibbins, Martin E Barrios-Llerena, Stephen E Wilkie, Peter L Freddolino, Marouane Libiad, Victor Vitvitsky, Barry Emerson, Thierry Le Bihan, Madara Brice, Huizhong Su, Scott G Denham, Natalie Z M Homer, Clare Mc Fadden, Anne Tailleux, Nourdine Faresse, Thierry Sulpice, Francois Briand, Tom Gillingwater, Kyo Han Ahn, Subhankar Singha, Claire McMaster, Richard C Hartley, Bart Staels, Gillian A Gray, Andrew J Finch, Colin Selman, Ruma Banerjee, Nicholas M Morton.
      Impaired hepatic glucose and lipid metabolism are hallmarks of type 2 diabetes. Increased sulfide production or sulfide donor compounds may beneficially regulate hepatic metabolism. Disposal of sulfide through the sulfide oxidation pathway (SOP) is critical for maintaining sulfide within a safe physiological range. We show that mice lacking the liver- enriched mitochondrial SOP enzyme thiosulfate sulfurtransferase (Tst-/- mice) exhibit high circulating sulfide, increased gluconeogenesis, hypertriglyceridemia, and fatty liver. Unexpectedly, hepatic sulfide levels are normal in Tst-/- mice because of exaggerated induction of sulfide disposal, with associated suppression of global protein persulfidation and nuclear respiratory factor 2 target protein levels. Hepatic proteomic and persulfidomic profiles converge on gluconeogenesis and lipid metabolism, revealing a selective deficit in medium-chain fatty acid oxidation in Tst-/- mice. We reveal a critical role of TST in hepatic metabolism that has implications for sulfide donor strategies in the context of metabolic disease.
    Keywords:  TST; fatty liver; gluconeogenesis; insulin sensitivity; persulfidation; sulfide; sulfide donor; sulfide oxidation pathway; thiosulfate sulfur transferase; type 2 diabetes
    DOI:  https://doi.org/10.1016/j.celrep.2021.109958
  29. Nature. 2021 Nov 10.
    Diverse alterations associated with resistance to KRAS(G12C) inhibition.
    Yulei Zhao, Yonina R Murciano-Goroff, Jenny Y Xue, Agnes Ang, Jessica Lucas, Trang T Mai, Arnaud F Da Cruz Paula, Anne Y Saiki, Deanna Mohn, Pragathi Achanta, Ann E Sisk, Kanika S Arora, Rohan S Roy, Dongsung Kim, Chuanchuan Li, Lee P Lim, Mark Li, Amber Bahr, Brian R Loomis, Elisa de Stanchina, Jorge S Reis-Filho, Britta Weigelt, Michael Berger, Gregory Riely, Kathryn C Arbour, J Russell Lipford, Bob T Li, Piro Lito.
      Inactive state-selective KRAS(G12C) inhibitors1-8 demonstrate a 30-40% response rate and result in approximately 6-month median progression-free survival in patients with lung cancer9. The genetic basis for resistance to these first-in-class mutant GTPase inhibitors remains under investigation. Here we evaluated matched pre-treatment and post-treatment specimens from 43 patients treated with the KRAS(G12C) inhibitor sotorasib. Multiple treatment-emergent alterations were observed across 27 patients, including alterations in KRAS, NRAS, BRAF, EGFR, FGFR2, MYC and other genes. In preclinical patient-derived xenograft and cell line models, resistance to KRAS(G12C) inhibition was associated with low allele frequency hotspot mutations in KRAS(G12V or G13D), NRAS(Q61K or G13R), MRAS(Q71R) and/or BRAF(G596R), mirroring observations in patients. Single-cell sequencing in an isogenic lineage identified secondary RAS and/or BRAF mutations in the same cells as KRAS(G12C), where they bypassed inhibition without affecting target inactivation. Genetic or pharmacological targeting of ERK signalling intermediates enhanced the antiproliferative effect of G12C inhibitor treatment in models with acquired RAS or BRAF mutations. Our study thus suggests a heterogenous pattern of resistance with multiple subclonal events emerging during G12C inhibitor treatment. A subset of patients in our cohort acquired oncogenic KRAS, NRAS or BRAF mutations, and resistance in this setting may be delayed by co-targeting of ERK signalling intermediates. These findings merit broader evaluation in prospective clinical trials.
    DOI:  https://doi.org/10.1038/s41586-021-04065-2
  30. J Biol Chem. 2021 Nov 08. pii: S0021-9258(21)01194-7. [Epub ahead of print] 101388
    Hepatocyte-specific perturbation of NAD+ biosynthetic pathways in mice induces reversible nonalcoholic steatohepatitis-like phenotypes.
    Morten Dall, Anna S Hassing, Lili Niu, Thomas S Nielsen, Lars R Ingerslev, Karolina Sulek, Samuel A J Trammell, Matthew P Gillum, Romain Barrès, Steen Larsen, Steen S Poulsen, Matthias Mann, Cathrine Ørskov, Jonas T Treebak.
      Nicotinamide phosphoribosyltransferase (NAMPT) converts nicotinamide to nicotinamide adenine dinucleotide (NAD+). As low hepatic NAD+ levels have been linked to the development of nonalcoholic fatty liver disease (NAFLD), we hypothetized that ablation of hepatic Nampt would affect susceptibility to liver injury in response to diet-induced metabolic stress. Following 3 weeks on a low-methionine, choline-free 60% high-fat diet (MCD), hepatocyte-specific Nampt knockout mice (HNKO) accumulated less triglyceride than wild-type littermates, but had increased histological scores for liver inflammation, necrosis, and fibrosis. Surprisingly, liver injury was also observed in HNKO mice on the purified control diet (PD). This HNKO phenotype was also associated with decreased abundance of mitochondrial proteins, especially proteins involved in oxidoreductase activity. High-resolution respirometry revealed lower respiratory capacity in PD-fed HNKO liver. In addition, fibrotic area in HNKO liver sections negatively correlated with hepatic NAD+, and liver injury was prevented by supplementation with NAD+ precursors nicotinamide riboside (NR) and nicotinic acid. Mass spectrometry (MS)-based proteomic analysis revealed that NR supplementation rescued hepatic levels of oxidoreductase- and OXPHOS proteins. Finally, single nucleus RNAseq showed that transcriptional changes in the HNKO liver mainly occurred in hepatocytes, and changes in the hepatocyte transcriptome were associated with liver necrosis. In conclusion, HNKO livers have reduced respiratory capacity, decreased abundance of mitochondrial proteins, and are susceptible to fibrosis due to low NAD+ levels. Our data suggest a critical threshold level of hepatic NAD+ that determines the predisposition to liver injury and supports that NAD+ precursor supplementation can prevent liver injury and NAFLD progression.
    Keywords:  NAD(+) biosynthesis; NAMPT; fibrosis; hepatocyte; mitochondria; nicotinamide adenine dinucleotide (NAD)
    DOI:  https://doi.org/10.1016/j.jbc.2021.101388
  31. Metabolism. 2021 Oct 28. pii: S0026-0495(21)00223-7. [Epub ahead of print]126 154923
    Regulation of NAD+ metabolism in aging and disease.
    Xiaogang Chu, Raghavan Pillai Raju.
      More than a century after discovering NAD+, information is still evolving on the role of this molecule in health and diseases. The biological functions of NAD+ and NAD+ precursors encompass pathways in cellular energetics, inflammation, metabolism, and cell survival. Several metabolic and neurological diseases exhibit reduced tissue NAD+ levels. Significantly reduced levels of NAD+ are also associated with aging, and enhancing NAD+ levels improved healthspan and lifespan in animal models. Recent studies suggest a causal link between senescence, age-associated reduction in tissue NAD+ and enzymatic degradation of NAD+. Furthermore, the discovery of transporters and receptors involved in NAD+ precursor (nicotinic acid, or niacin, nicotinamide, and nicotinamide riboside) metabolism allowed for a better understanding of their role in cellular homeostasis including signaling functions that are independent of their functions in redox reactions. We also review studies that demonstrate that the functional effect of niacin is partially due to the activation of its cell surface receptor, GPR109a. Based on the recent progress in understanding the mechanism and function of NAD+ and NAD+ precursors in cell metabolism, new strategies are evolving to exploit these molecules' pharmacological potential in the maintenance of metabolic balance.
    Keywords:  NAD; Niacin; Niacin receptor; Nicotinamide adenine mononucleotide; Nicotinamide riboside
    DOI:  https://doi.org/10.1016/j.metabol.2021.154923
  32. iScience. 2021 Nov 19. 24(11): 103294
    Constraint-based modeling of yeast mitochondria reveals the dynamics of protein import and iron-sulfur cluster biogenesis.
    Carl Malina, Francesca Di Bartolomeo, Eduard J Kerkhoven, Jens Nielsen.
      Mitochondria are a hallmark of eukaryal cells and play an important role in cellular metabolism. There is a vast amount of knowledge available on mitochondrial metabolism and essential mitochondrial functions, such as protein import and iron-sulfur cluster biosynthesis, including multiple studies on the mitochondrial proteome. Therefore, there is a need for in silico approaches to facilitate the analysis of these data. Here, we present a detailed model of mitochondrial metabolism Saccharomyces cerevisiae, including protein import, iron-sulfur cluster biosynthesis, and a description of the coupling between charge translocation processes and ATP synthesis. Model analysis implied a dual dependence of absolute levels of proteins in protein import, iron-sulfur cluster biogenesis and cluster abundance on growth rate and respiratory activity. The model is instrumental in studying dynamics and perturbations in these processes and given the high conservation of mitochondrial metabolism in humans, it can provide insight into their role in human disease.
    Keywords:  Cell biology; Cellular physiology; In silico biology; Integrative aspects of cell biology; Systems biology
    DOI:  https://doi.org/10.1016/j.isci.2021.103294
  33. PLoS Comput Biol. 2021 Nov 08. 17(11): e1009522
    Comparison of metabolic states using genome-scale metabolic models.
    Chaitra Sarathy, Marian Breuer, Martina Kutmon, Michiel E Adriaens, Chris T Evelo, Ilja C W Arts.
      Genome-scale metabolic models (GEMs) are comprehensive knowledge bases of cellular metabolism and serve as mathematical tools for studying biological phenotypes and metabolic states or conditions in various organisms and cell types. Given the sheer size and complexity of human metabolism, selecting parameters for existing analysis methods such as metabolic objective functions and model constraints is not straightforward in human GEMs. In particular, comparing several conditions in large GEMs to identify condition- or disease-specific metabolic features is challenging. In this study, we showcase a scalable, model-driven approach for an in-depth investigation and comparison of metabolic states in large GEMs which enables identifying the underlying functional differences. Using a combination of flux space sampling and network analysis, our approach enables extraction and visualisation of metabolically distinct network modules. Importantly, it does not rely on known or assumed objective functions. We apply this novel approach to extract the biochemical differences in adipocytes arising due to unlimited vs blocked uptake of branched-chain amino acids (BCAAs, considered as biomarkers in obesity) using a human adipocyte GEM (iAdipocytes1809). The biological significance of our approach is corroborated by literature reports confirming our identified metabolic processes (TCA cycle and Fatty acid metabolism) to be functionally related to BCAA metabolism. Additionally, our analysis predicts a specific altered uptake and secretion profile indicating a compensation for the unavailability of BCAAs. Taken together, our approach facilitates determining functional differences between any metabolic conditions of interest by offering a versatile platform for analysing and comparing flux spaces of large metabolic networks.
    DOI:  https://doi.org/10.1371/journal.pcbi.1009522
  34. PLoS Genet. 2021 Nov 08. 17(11): e1009873
    The FASTK family proteins fine-tune mitochondrial RNA processing.
    Akira Ohkubo, Lindsey Van Haute, Danielle L Rudler, Maike Stentenbach, Florian A Steiner, Oliver Rackham, Michal Minczuk, Aleksandra Filipovska, Jean-Claude Martinou.
      Transcription of the human mitochondrial genome and correct processing of the two long polycistronic transcripts are crucial for oxidative phosphorylation. According to the tRNA punctuation model, nucleolytic processing of these large precursor transcripts occurs mainly through the excision of the tRNAs that flank most rRNAs and mRNAs. However, some mRNAs are not punctuated by tRNAs, and it remains largely unknown how these non-canonical junctions are resolved. The FASTK family proteins are emerging as key players in non-canonical RNA processing. Here, we have generated human cell lines carrying single or combined knockouts of several FASTK family members to investigate their roles in non-canonical RNA processing. The most striking phenotypes were obtained with loss of FASTKD4 and FASTKD5 and with their combined double knockout. Comprehensive mitochondrial transcriptome analyses of these cell lines revealed a defect in processing at several canonical and non-canonical RNA junctions, accompanied by an increase in specific antisense transcripts. Loss of FASTKD5 led to the most severe phenotype with marked defects in mitochondrial translation of key components of the electron transport chain complexes and in oxidative phosphorylation. We reveal that the FASTK protein family members are crucial regulators of non-canonical junction and non-coding mitochondrial RNA processing.
    DOI:  https://doi.org/10.1371/journal.pgen.1009873
  35. Biomed Opt Express. 2021 Oct 01. 12(10): 6375-6390
    Nicotinamide effects on the metabolism of human fibroblasts and keratinocytes assessed by quantitative, label-free fluorescence imaging.
    Zhiyi Liu, Chung-Yi Chiang, John Nip, Lin Feng, Yang Zhang, Sheila Rocha, Irene Georgakoudi.
      Alterations in metabolism are central to the aging process. Therefore, understanding the subcellular functional and structural changes associated with metabolic aging is critical. Current established methods for exploring cell metabolism either require the use of exogenous agents or are destructive to the tissue or cells. Two-photon excited fluorescence (TPEF) imaging has emerged as a method for monitoring subtle metabolic changes non-invasively. In this study, we use TPEF imaging to acquire high-resolution fluorescence images from two coenzymes, NAD(P)H (reduced form of nicotinamide adenine dinucleotide) and FAD (flavin adenine dinucleotide), within human fibroblasts and keratinocytes in response to B3 (a nicotinamide precursor) supplementation and/or UV irradiation, without addition of exogenous labels. In addition, multi-parametric analysis methods are used to extract functional information of cellular metabolism, including cellular redox state, NAD(P)H fluorescence lifetime, and mitochondrial organization. Our results demonstrate that such optical metabolic assessments can serve as sensitive, label-free, non-destructive reporters of known effects of B3 to maintain and in some cases even enhance the respiratory function of mitochondria, while lowering oxidative damage. Thus, TPEF imaging, supported by highly-quantitative analysis, can serve as a tool to understand aging-dependent metabolic changes as well as the effect of actives on human epidermal and dermal cells.
    DOI:  https://doi.org/10.1364/BOE.432561
  36. Nat Cell Biol. 2021 Nov;23(11): 1136-1147
    The RNA helicase Ddx21 controls Vegfc-driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 function.
    Katarzyna Koltowska, Kazuhide S Okuda, Marleen Gloger, Maria Rondon-Galeano, Elizabeth Mason, Jiachen Xuan, Stefanie Dudczig, Huijun Chen, Hannah Arnold, Renae Skoczylas, Neil I Bower, Scott Paterson, Anne Karine Lagendijk, Gregory J Baillie, Ignaty Leshchiner, Cas Simons, Kelly A Smith, Wolfram Goessling, Joan K Heath, Richard B Pearson, Elaine Sanij, Stefan Schulte-Merker, Benjamin M Hogan.
      The development of a functional vasculature requires the coordinated control of cell fate, lineage differentiation and network growth. Cellular proliferation is spatiotemporally regulated in developing vessels, but how this is orchestrated in different lineages is unknown. Here, using a zebrafish genetic screen for lymphatic-deficient mutants, we uncover a mutant for the RNA helicase Ddx21. Ddx21 cell-autonomously regulates lymphatic vessel development. An established regulator of ribosomal RNA synthesis and ribosome biogenesis, Ddx21 is enriched in sprouting venous endothelial cells in response to Vegfc-Flt4 signalling. Ddx21 function is essential for Vegfc-Flt4-driven endothelial cell proliferation. In the absence of Ddx21, endothelial cells show reduced ribosome biogenesis, p53 and p21 upregulation and cell cycle arrest that blocks lymphangiogenesis. Thus, Ddx21 coordinates the lymphatic endothelial cell response to Vegfc-Flt4 signalling by balancing ribosome biogenesis and p53 function. This mechanism may be targetable in diseases of excessive lymphangiogenesis such as cancer metastasis or lymphatic malformation.
    DOI:  https://doi.org/10.1038/s41556-021-00784-w
  37. Annu Rev Pathol. 2021 Nov 09.
    Extrachromosomal DNA: An Emerging Hallmark in Human Cancer.
    Sihan Wu, Vineet Bafna, Howard Y Chang, Paul S Mischel.
      Human genes are arranged on 23 pairs of chromosomes, but in cancer, tumor-promoting genes and regulatory elements can free themselves from chromosomes and relocate to circular, extrachromosomal pieces of DNA (ecDNA). ecDNA, because of its nonchromosomal inheritance, drives high-copy-number oncogene amplification and enables tumors to evolve their genomes rapidly. Furthermore, the circular ecDNA architecture fundamentally alters gene regulation and transcription, and the higher-order organization of ecDNA contributes to tumor pathogenesis. Consequently, patients whose cancers harbor ecDNA have significantly shorter survival. Although ecDNA was first observed more than 50 years ago, its critical importance has only recently come to light. In this review, we discuss the current state of understanding of how ecDNAs form and function as well as how they contribute to drug resistance and accelerated cancer evolution. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-pathmechdis-051821-114223
  38. Front Microbiol. 2021 ;12 759359
    Pyrophosphate and Irreversibility in Evolution, or why PPi Is Not an Energy Currency and why Nature Chose Triphosphates.
    Jessica L E Wimmer, Karl Kleinermanns, William F Martin.
      The possible evolutionary significance of pyrophosphate (PPi) has been discussed since the early 1960s. Lipmann suggested that PPi could have been an ancient currency or a possible environmental source of metabolic energy at origins, while Kornberg proposed that PPi vectorializes metabolism because ubiquitous pyrophosphatases render PPi forming reactions kinetically irreversible. To test those ideas, we investigated the reactions that consume phosphoanhydride bonds among the 402 reactions of the universal biosynthetic core that generates amino acids, nucleotides, and cofactors from H2, CO2, and NH3. We find that 36% of the core's phosphoanhydride hydrolyzing reactions generate PPi, while no reactions use PPi as an energy currency. The polymerization reactions that generate ~80% of cell mass - protein, RNA, and DNA synthesis - all generate PPi, while none use PPi as an energy source. In typical prokaryotic cells, aminoacyl tRNA synthetases (AARS) underlie ~80% of PPi production. We show that the irreversibility of the AARS reaction is a kinetic, not a thermodynamic effect. The data indicate that PPi is not an ancient energy currency and probably never was. Instead, PPi hydrolysis is an ancient mechanism that imparts irreversibility, as Kornberg suggested, functioning like a ratchet's pawl to vectorialize the life process toward growth. The two anhydride bonds in nucleoside triphosphates offer ATP-cleaving enzymes an option to impart either thermodynamic control (Pi formation) or kinetic control (PPi formation) upon reactions. This dual capacity explains why nature chose the triphosphate moiety of ATP as biochemistry's universal energy currency.
    Keywords:  bioenergetics; chemical evolution; early evolution; energetics; kinetics; metabolism; origin of life; thermodynamics
    DOI:  https://doi.org/10.3389/fmicb.2021.759359
  39. N Engl J Med. 2021 Nov 11. 385(20): 1868-1880
    100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care - Preliminary Report.
    100,000 Genomes Project Pilot Investigators
       BACKGROUND: The U.K. 100,000 Genomes Project is in the process of investigating the role of genome sequencing in patients with undiagnosed rare diseases after usual care and the alignment of this research with health care implementation in the U.K. National Health Service. Other parts of this project focus on patients with cancer and infection.
    METHODS: We conducted a pilot study involving 4660 participants from 2183 families, among whom 161 disorders covering a broad spectrum of rare diseases were present. We collected data on clinical features with the use of Human Phenotype Ontology terms, undertook genome sequencing, applied automated variant prioritization on the basis of applied virtual gene panels and phenotypes, and identified novel pathogenic variants through research analysis.
    RESULTS: Diagnostic yields varied among family structures and were highest in family trios (both parents and a proband) and families with larger pedigrees. Diagnostic yields were much higher for disorders likely to have a monogenic cause (35%) than for disorders likely to have a complex cause (11%). Diagnostic yields for intellectual disability, hearing disorders, and vision disorders ranged from 40 to 55%. We made genetic diagnoses in 25% of the probands. A total of 14% of the diagnoses were made by means of the combination of research and automated approaches, which was critical for cases in which we found etiologic noncoding, structural, and mitochondrial genome variants and coding variants poorly covered by exome sequencing. Cohortwide burden testing across 57,000 genomes enabled the discovery of three new disease genes and 19 new associations. Of the genetic diagnoses that we made, 25% had immediate ramifications for clinical decision making for the patients or their relatives.
    CONCLUSIONS: Our pilot study of genome sequencing in a national health care system showed an increase in diagnostic yield across a range of rare diseases. (Funded by the National Institute for Health Research and others.).
    DOI:  https://doi.org/10.1056/NEJMoa2035790
  40. ACS Sens. 2021 Nov 11.
    Co-Polarized [1-13C]Pyruvate and [1,3-13C2]Acetoacetate Provide a Simultaneous View of Cytosolic and Mitochondrial Redox in a Single Experiment.
    Gaurav Sharma, Xiaodong Wen, Nesmine R Maptue, Thomas Hever, Craig R Malloy, A Dean Sherry, Chalermchai Khemtong.
      Cellular redox is intricately linked to energy production and normal cell function. Although the redox states of mitochondria and cytosol are connected by shuttle mechanisms, the redox state of mitochondria may differ from redox in the cytosol in response to stress. However, detecting these differences in functioning tissues is difficult. Here, we employed 13C magnetic resonance spectroscopy (MRS) and co-polarized [1-13C]pyruvate and [1,3-13C2]acetoacetate ([1,3-13C2]AcAc) to monitor production of hyperpolarized (HP) lactate and β-hydroxybutyrate as indicators of cytosolic and mitochondrial redox, respectively. Isolated rat hearts were examined under normoxic conditions, during low-flow ischemia, and after pretreatment with either aminooxyacetate (AOA) or rotenone. All interventions were associated with an increase in [Pi]/[ATP] measured by 31P NMR. In well-oxygenated untreated hearts, rapid conversion of HP [1-13C]pyruvate to [1-13C]lactate and [1,3-13C2]AcAc to [1,3-13C2]β-hydroxybutyrate ([1,3-13C2]β-HB) was readily detected. A significant increase in HP [1,3-13C2]β-HB but not [1-13C]lactate was observed in rotenone-treated and ischemic hearts, consistent with an increase in mitochondrial NADH but not cytosolic NADH. AOA treatments did not alter the productions of HP [1-13C]lactate or [1,3-13C2]β-HB. This study demonstrates that biomarkers of mitochondrial and cytosolic redox may be detected simultaneously in functioning tissues using co-polarized [1-13C]pyruvate and [1,3-13C2]AcAc and 13C MRS and that changes in mitochondrial redox may precede changes in cytosolic redox.
    Keywords:  acetoacetate; cardiac ischemia; hyperpolarized 13C MR; pyruvate; redox metabolism
    DOI:  https://doi.org/10.1021/acssensors.1c01225
  41. Sci Adv. 2021 Nov 12. 7(46): eabk0271
    Cell size is a determinant of stem cell potential during aging.
    Jette Lengefeld, Chia-Wei Cheng, Pema Maretich, Marguerite Blair, Hannah Hagen, Melanie R McReynolds, Emily Sullivan, Kyra Majors, Christina Roberts, Joon Ho Kang, Joachim D Steiner, Teemu P Miettinen, Scott R Manalis, Adam Antebi, Sean J Morrison, Jacqueline A Lees, Laurie A Boyer, Ömer H Yilmaz, Angelika Amon.
      [Figure: see text].
    DOI:  https://doi.org/10.1126/sciadv.abk0271
  42. Nature. 2021 Nov 10.
    Dietary palmitic acid promotes a prometastatic memory via Schwann cells.
    Gloria Pascual, Diana Domínguez, Marc Elosúa-Bayes, Felipe Beckedorff, Carmelo Laudanna, Claudia Bigas, Delphine Douillet, Carolina Greco, Aikaterini Symeonidi, Inmaculada Hernández, Sara Ruiz Gil, Neus Prats, Coro Bescós, Ramin Shiekhattar, Moran Amit, Holger Heyn, Ali Shilatifard, Salvador Aznar Benitah.
      Fatty acid uptake and altered metabolism constitute hallmarks of metastasis1,2, yet evidence of the underlying biology, as well as whether all dietary fatty acids are prometastatic, is lacking. Here we show that dietary palmitic acid (PA), but not oleic acid or linoleic acid, promotes metastasis in oral carcinomas and melanoma in mice. Tumours from mice that were fed a short-term palm-oil-rich diet (PA), or tumour cells that were briefly exposed to PA in vitro, remained highly metastatic even after being serially transplanted (without further exposure to high levels of PA). This PA-induced prometastatic memory requires the fatty acid transporter CD36 and is associated with the stable deposition of histone H3 lysine 4 trimethylation by the methyltransferase Set1A (as part of the COMPASS complex (Set1A/COMPASS)). Bulk, single-cell and positional RNA-sequencing analyses indicate that genes with this prometastatic memory predominantly relate to a neural signature that stimulates intratumoural Schwann cells and innervation, two parameters that are strongly correlated with metastasis but are aetiologically poorly understood3,4. Mechanistically, tumour-associated Schwann cells secrete a specialized proregenerative extracellular matrix, the ablation of which inhibits metastasis initiation. Both the PA-induced memory of this proneural signature and its long-term boost in metastasis require the transcription factor EGR2 and the glial-cell-stimulating peptide galanin. In summary, we provide evidence that a dietary metabolite induces stable transcriptional and chromatin changes that lead to a long-term stimulation of metastasis, and that this is related to a proregenerative state of tumour-activated Schwann cells.
    DOI:  https://doi.org/10.1038/s41586-021-04075-0
  43. Nat Commun. 2021 Nov 08. 12(1): 6448
    MMAB promotes negative feedback control of cholesterol homeostasis.
    Leigh Goedeke, Alberto Canfrán-Duque, Noemi Rotllan, Balkrishna Chaube, Bonne M Thompson, Richard G Lee, Gary W Cline, Jeffrey G McDonald, Gerald I Shulman, Miguel A Lasunción, Yajaira Suárez, Carlos Fernández-Hernando.
      Intricate regulatory networks govern the net balance of cholesterol biosynthesis, uptake and efflux; however, the mechanisms surrounding cholesterol homeostasis remain incompletely understood. Here, we develop an integrative genomic strategy to detect regulators of LDLR activity and identify 250 genes whose knockdown affects LDL-cholesterol uptake and whose expression is modulated by intracellular cholesterol levels in human hepatic cells. From these hits, we focus on MMAB, an enzyme which catalyzes the conversion of vitamin B12 to adenosylcobalamin, and whose expression has previously been linked with altered levels of circulating cholesterol in humans. We demonstrate that hepatic levels of MMAB are modulated by dietary and cellular cholesterol levels through SREBP2, the master transcriptional regulator of cholesterol homeostasis. Knockdown of MMAB decreases intracellular cholesterol levels and augments SREBP2-mediated gene expression and LDL-cholesterol uptake in human and mouse hepatic cell lines. Reductions in total sterol content were attributed to increased intracellular levels of propionic and methylmalonic acid and subsequent inhibition of HMGCR activity and cholesterol biosynthesis. Moreover, mice treated with antisense inhibitors of MMAB display a significant reduction in hepatic HMGCR activity, hepatic sterol content and increased expression of SREBP2-mediated genes. Collectively, these findings reveal an unexpected role for the adenosylcobalamin pathway in regulating LDLR expression and identify MMAB as an additional control point by which cholesterol biosynthesis is regulated by its end product.
    DOI:  https://doi.org/10.1038/s41467-021-26787-7
  44. iScience. 2021 Nov 19. 24(11): 103244
    Acetyl-CoA derived from hepatic mitochondrial fatty acid β-oxidation aggravates inflammation by enhancing p65 acetylation.
    Qiang Chen, Jianlong Du, Kun Cui, Wei Fang, Zengqi Zhao, Qiuchi Chen, Kangsen Mai, Qinghui Ai.
      Acetylation coordinates many biological processes to ensure cells respond appropriately to nutrients. However, how acetylation regulates lipid surplus-induced inflammation remains poorly understood. Here, we found that a high-fat diet (HFD) enhanced mitochondrial fatty acid β-oxidation, which enhanced acetyl-CoA levels in the liver of the large yellow croaker. The HFD activated ACLY to govern the "citrate transport" to transfer acetyl-CoA from the mitochondria to the nucleus. Elevated acetyl-CoA activated CBP to increase p65 acetylation and then aggravated inflammation. SIRT1 was deactivated with a decline in NAD+/NADH, which further aggravated inflammation. Therefore, acetylation-dependent regulation of transcription factor activity is an adaptation to proinflammatory stimuli under nutrient stress, which was also confirmed in AML12 hepatocytes. In vitro octanoate stimulation further verified that acetyl-CoA derived from fatty acid β-oxidation mediated acetylation homeostasis in the nucleus. The broad therapeutic prospects of intermediate metabolites and acetyltransferases/deacetylases might provide critical insights for the treatment of metabolic diseases in vertebrates.
    Keywords:  Cellular physiology; Immunology; Pathophysiology
    DOI:  https://doi.org/10.1016/j.isci.2021.103244
  45. Nat Commun. 2021 Nov 10. 12(1): 6479
    Evolutionary metabolic landscape from preneoplasia to invasive lung adenocarcinoma.
    Meng Nie, Ke Yao, Xinsheng Zhu, Na Chen, Nan Xiao, Yi Wang, Bo Peng, LiAng Yao, Peng Li, Peng Zhang, Zeping Hu.
      Metabolic reprogramming evolves during cancer initiation and progression. However, thorough understanding of metabolic evolution from preneoplasia to lung adenocarcinoma (LUAD) is still limited. Here, we perform large-scale targeted metabolomics on resected lesions and plasma obtained from invasive LUAD and its precursors, and decipher the metabolic trajectories from atypical adenomatous hyperplasia (AAH) to adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA) and invasive adenocarcinoma (IAC), revealing that perturbed metabolic pathways emerge early in premalignant lesions. Furthermore, three panels of plasma metabolites are identified as non-invasive predictive biomarkers to distinguish IAC and its precursors with benign diseases. Strikingly, metabolomics clustering defines three metabolic subtypes of IAC patients with distinct clinical characteristics. We identify correlation between aberrant bile acid metabolism in subtype III with poor clinical features and demonstrate dysregulated bile acid metabolism promotes migration of LUAD, which could be exploited as potential targetable vulnerability and for stratifying patients. Collectively, the comprehensive landscape of the metabolic evolution along the development of LUAD will improve early detection and provide impactful therapeutic strategies.
    DOI:  https://doi.org/10.1038/s41467-021-26685-y
  46. Nat Commun. 2021 Nov 11. 12(1): 6522
    Deciphering intratumoral heterogeneity using integrated clonal tracking and single-cell transcriptome analyses.
    Humberto Contreras-Trujillo, Jiya Eerdeng, Samir Akre, Du Jiang, Jorge Contreras, Basia Gala, Mary C Vergel-Rodriguez, Yeachan Lee, Aparna Jorapur, Areen Andreasian, Lisa Harton, Charles S Bramlett, Anna Nogalska, Gang Xiao, Jae-Woong Lee, Lai N Chan, Markus Müschen, Akil A Merchant, Rong Lu.
      Cellular heterogeneity is a major cause of treatment resistance in cancer. Despite recent advances in single-cell genomic and transcriptomic sequencing, it remains difficult to relate measured molecular profiles to the cellular activities underlying cancer. Here, we present an integrated experimental system that connects single cell gene expression to heterogeneous cancer cell growth, metastasis, and treatment response. Our system integrates single cell transcriptome profiling with DNA barcode based clonal tracking in patient-derived xenograft models. We show that leukemia cells exhibiting unique gene expression respond to different chemotherapies in distinct but consistent manners across multiple mice. In addition, we uncover a form of leukemia expansion that is spatially confined to the bone marrow of single anatomical sites and driven by cells with distinct gene expression. Our integrated experimental system can interrogate the molecular and cellular basis of the intratumoral heterogeneity underlying disease progression and treatment resistance.
    DOI:  https://doi.org/10.1038/s41467-021-26771-1
  47. Biol Direct. 2021 Nov 07. 16(1): 22
    Rab32 uses its effector reticulon 3L to trigger autophagic degradation of mitochondria-associated membrane (MAM) proteins.
    Maria Sol Herrera-Cruz, Megan C Yap, Nasser Tahbaz, Keelie Phillips, Laurel Thomas, Gary Thomas, Thomas Simmen.
       BACKGROUND: Rab32 is a small GTPase associated with multiple organelles but is particularly enriched at the endoplasmic reticulum (ER). Here, it controls targeting to mitochondria-ER contacts (MERCs), thus influencing composition of the mitochondria-associated membrane (MAM). Moreover, Rab32 regulates mitochondrial membrane dynamics via its effector dynamin-related protein 1 (Drp1). Rab32 has also been reported to induce autophagy, an essential pathway targeting intracellular components for their degradation. However, no autophagy-specific effectors have been identified for Rab32. Similarly, the identity of the intracellular membrane targeted by this small GTPase and the type of autophagy it induces are not known yet.
    RESULTS: To investigate the target of autophagic degradation mediated by Rab32, we tested a large panel of organellar proteins. We found that a subset of MERC proteins, including the thioredoxin-related transmembrane protein TMX1, are specifically targeted for degradation in a Rab32-dependent manner. We also identified the long isoform of reticulon-3 (RTN3L), a known ER-phagy receptor, as a Rab32 effector.
    CONCLUSIONS: Rab32 promotes degradation of mitochondrial-proximal ER membranes through autophagy with the help of RTN3L. We propose to call this type of selective autophagy "MAM-phagy".
    Keywords:  Autophagy; ER-phagy; Mitochondria-associated membrane (MAM); Rab32
    DOI:  https://doi.org/10.1186/s13062-021-00311-9
  48. Adv Exp Med Biol. 2021 ;1344 43-53
    Linking Depression to Epigenetics: Role of the Circadian Clock.
    Shogo Sato, Paolo Sassone-Corsi.
      The circadian clock governs multiple biological functions at the molecular level and plays an essential role in providing temporal diversity of behavior and physiology including neuronal activity. Studies spanning the past two decades have deciphered the molecular mechanisms of the circadian clock, which appears to operate as an essential interface in linking cellular metabolism to epigenetic control. Accumulating evidence illustrates that disruption of circadian rhythms through jet lag, shift work, and temporary irregular life-style could lead to depression-like symptoms. Remarkably, abnormal neuronal activity and depression-like behavior appear in animals lacking elements of the molecular clock. Recent studies demonstrate that neuronal and synaptic gene induction is under epigenetic control, and robust epigenetic remodeling is observed under depression and related psychiatric disorders. Thus, the intertwined links between the circadian clock and epigenetics may point to novel approaches for antidepressant treatments, epigenetic therapy, and chronotherapy. In this chapter we summarize how the circadian clock is involved in neuronal functions and depressive-like behavior and propose that potential strategies for antidepressant therapy by incorporating circadian genomic and epigenetic rewiring of neuronal signaling pathways.
    Keywords:  Chronotherapy; Clock; Depression; Epigenetics; Metabolism
    DOI:  https://doi.org/10.1007/978-3-030-81147-1_3
  49. Science. 2021 Nov 11. eabm4805
    Computed structures of core eukaryotic protein complexes.
    Ian R Humphreys, Jimin Pei, Minkyung Baek, Aditya Krishnakumar, Ivan Anishchenko, Sergey Ovchinnikov, Jing Zhang, Travis J Ness, Sudeep Banjade, Saket R Bagde, Viktoriya G Stancheva, Xiao-Han Li, Kaixian Liu, Zhi Zheng, Daniel J Barrero, Upasana Roy, Jochen Kuper, Israel S Fernández, Barnabas Szakal, Dana Branzei, Josep Rizo, Caroline Kisker, Eric C Greene, Sue Biggins, Scott Keeney, Elizabeth A Miller, J Christopher Fromme, Tamara L Hendrickson, Qian Cong, David Baker.
      [Figure: see text].
    DOI:  https://doi.org/10.1126/science.abm4805
  50. Front Mol Neurosci. 2021 ;14 767219
    Mitochondrial Extracellular Vesicles - Origins and Roles.
    Lydia Amari, Marc Germain.
      Extracellular vesicles (EVs) have emerged in the last decade as critical cell-to-cell communication devices used to carry nucleic acids and proteins between cells. EV cargo includes plasma membrane and endosomal proteins, but EVs also contain material from other cellular compartments, including mitochondria. Within cells, mitochondria are responsible for a large range of metabolic reactions, but they can also produce damaging levels of reactive oxygen species and induce inflammation when damaged. Consistent with this, recent evidence suggests that EV-mediated transfer of mitochondrial content alters metabolic and inflammatory responses of recipient cells. As EV mitochondrial content is also altered in some pathologies, this could have important implications for their diagnosis and treatment. In this review, we will discuss the nature and roles of mitochondrial EVs, with a special emphasis on the nervous system.
    Keywords:  extracellular vesicle; inflammation; metabolism; mitochondria; mitochondrial quality control
    DOI:  https://doi.org/10.3389/fnmol.2021.767219
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