bims-camemi 2021-08-29 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2021–08–29
39 papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit

A cancer ubiquitome landscape identifies metabolic reprogramming as target of Parkin tumor suppression.
First we eat, then we do everything else: The dynamic metabolic regulation of efferocytosis.
MitoPhen database: a human phenotype ontology-based approach to identify mitochondrial DNA diseases.
The mitochondrial coenzyme Q junction and complex III: biochemistry and pathophysiology.
Mitochondrial DNA variants modulate N-formylmethionine, proteostasis and risk of late-onset human diseases.
Dysregulated cholesterol homeostasis results in resistance to ferroptosis increasing tumorigenicity and metastasis in cancer.
A Single LC-MS/MS Analysis to Quantify CoA Biosynthetic Intermediates and Short-Chain Acyl CoAs.
Alkaline intracellular pHi (pHi) activates AMPK-mTORC2 signaling to promote cell survival during growth factor limitation.
The Yoga of Rag GTPases: Dynamic structural poses confer amino acid sensing by mTORC1.
Routes for Potassium Ions across Mitochondrial Membranes: A Biophysical Point of View with Special Focus on the ATP-Sensitive K+ Channel.
The pleiotropic functions of autophagy in metastasis.
Metabolic Adaptation of Macrophages as Mechanism of Defense against Crystalline Silica.
Crosstalk between Drp1 phosphorylation sites during mitochondrial remodeling and their impact on metabolic adaptation.
NAD(H) Regulates the Permeability Transition Pore in Mitochondria through an External Site.
Metformin Is a Pyridoxal-5'-phosphate (PLP)-Competitive Inhibitor of SHMT2.
Miro1 functions as an inhibitory regulator of MFN at elevated mitochondrial Ca2+ levels.
Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment.
Mitochondrial Carriers and Substrates Transport Network: A Lesson from Saccharomyces cerevisiae.
Metabolic plasticity drives development during mammalian embryogenesis.
Mitochondrial dysfunction governs immunometabolism in leukocytes of patients with acute-on-chronic liver failure.
SLC-30A9 is required for Zn2+ homeostasis, Zn2+ mobilization, and mitochondrial health.
Loss of tyrosine catabolic enzyme HPD promotes glutamine anaplerosis through mTOR signaling in liver cancer.
Metabolomics and lipidomics in Caenorhabditis elegans using a single-sample preparation.
Metabolic Outcomes of Anaplerotic Dodecanedioic Acid Supplementation in Very Long Chain Acyl-CoA Dehydrogenase (VLCAD) Deficient Fibroblasts.
mTORC1 Promotes ARID1A Degradation and Oncogenic Chromatin Remodeling in Hepatocellular Carcinoma.
Quality control of protein import into mitochondria.
Urinary 2-Hydroxyglutarate Enantiomers Are Markedly Elevated in a Murine Model of Type 2 Diabetic Kidney Disease.
Mechano-energetic aspects of Barth Syndrome.
A Sweet Story of Metabolic Innovation in the Naked Mole-Rat.
METTL14 facilitates global genome repair and suppresses skin tumorigenesis.
Metabolic Controls on Epigenetic Reprogramming in Regulatory T Cells.
Aspartate availability limits hematopoietic stem cell function during hematopoietic regeneration.
The role of 5-HT metabolism in cancer.
Establishment of Patient-derived Succinate Dehydrogenase-deficient Gastrointestinal Stromal Tumor Models For Predicting Therapeutic Response.
COVID-19 provides an opportunity to transform cancer research.
Metformin Decreases 2-HG Production through the MYC-PHGDH Pathway in Suppressing Breast Cancer Cell Proliferation.
Hexosamine Biosynthetic Pathway-Derived O-GlcNAcylation Is Critical for RANKL-Mediated Osteoclast Differentiation.
Synthetic biosensor accelerates evolution by rewiring carbon metabolism toward a specific metabolite.
A body map of somatic mutagenesis in morphologically normal human tissues.

Sci Adv. 2021 Aug;pii: eabg7287. [Epub ahead of print]7(35):

A cancer ubiquitome landscape identifies metabolic reprogramming as target of Parkin tumor suppression.

Ekta Agarwal, Aaron R Goldman, Hsin-Yao Tang, Andrew V Kossenkov, Jagadish C Ghosh, Lucia R Languino, Valentina Vaira, David W Speicher, Dario C Altieri.

Changes in metabolism that affect mitochondrial and glycolytic networks are hallmarks of cancer, but their impact in disease is still elusive. Using global proteomics and ubiquitome screens, we now show that Parkin, an E3 ubiquitin ligase and key effector of mitophagy altered in Parkinson's disease, shuts off mitochondrial dynamics and inhibits the non-oxidative phase of the pentose phosphate pathway. This blocks tumor cell movements, creates metabolic and oxidative stress, and inhibits primary and metastatic tumor growth. Uniformly down-regulated in cancer patients, Parkin tumor suppression requires its E3 ligase function, is reversed by antioxidants, and is independent of mitophagy. These data demonstrate that cancer metabolic networks are potent oncogenes directly targeted by endogenous tumor suppression.

DOI: https://doi.org/10.1126/sciadv.abg7287
Cell Metab. 2021 Aug 17. pii: S1550-4131(21)00364-8. [Epub ahead of print]

First we eat, then we do everything else: The dynamic metabolic regulation of efferocytosis.

Alissa Trzeciak, Ya-Ting Wang, Justin Shaun Arnold Perry.

Clearance of apoptotic cells, or "efferocytosis," is essential for diverse processes including embryonic development, tissue turnover, organ regeneration, and immune cell development. The human body is estimated to remove approximately 1% of its body mass via apoptotic cell clearance daily. This poses several intriguing cell metabolism problems. For instance, phagocytes such as macrophages must induce or suppress metabolic pathways to find, engulf, and digest apoptotic cells. Then, phagocytes must manage the potentially burdensome biomass of the engulfed apoptotic cell. Finally, phagocytes reside in complex tissue architectures that vary in nutrient availability, the types of dying cells or debris that require clearance, and the neighboring cells they interact with. Here, we review advances in our understanding of these three key areas of phagocyte metabolism. We end by proposing a model of efferocytosis that integrates recent findings and establishes a new paradigm for testing how efferocytosis prevents chronic inflammatory disease and autoimmunity.

DOI: https://doi.org/10.1016/j.cmet.2021.08.001
Nucleic Acids Res. 2021 Aug 24. pii: gkab726. [Epub ahead of print]

MitoPhen database: a human phenotype ontology-based approach to identify mitochondrial DNA diseases.

Thiloka E Ratnaike, Daniel Greene, Wei Wei, Alba Sanchis-Juan, Katherine R Schon, Jelle van den Ameele, Lucy Raymond, Rita Horvath, Ernest Turro, Patrick F Chinnery.

Diagnosing mitochondrial disorders remains challenging. This is partly because the clinical phenotypes of patients overlap with those of other sporadic and inherited disorders. Although the widespread availability of genetic testing has increased the rate of diagnosis, the combination of phenotypic and genetic heterogeneity still makes it difficult to reach a timely molecular diagnosis with confidence. An objective, systematic method for describing the phenotypic spectra for each variant provides a potential solution to this problem. We curated the clinical phenotypes of 6688 published individuals with 89 pathogenic mitochondrial DNA (mtDNA) mutations, collating 26 348 human phenotype ontology (HPO) terms to establish the MitoPhen database. This enabled a hypothesis-free definition of mtDNA clinical syndromes, an overview of heteroplasmy-phenotype relationships, the identification of under-recognized phenotypes, and provides a publicly available reference dataset for objective clinical comparison with new patients using the HPO. Studying 77 patients with independently confirmed positive mtDNA diagnoses and 1083 confirmed rare disease cases with a non-mitochondrial nuclear genetic diagnosis, we show that HPO-based phenotype similarity scores can distinguish these two classes of rare disease patients with a false discovery rate <10% at a sensitivity of 80%. Enriching the MitoPhen database with more patients will improve predictions for increasingly rare variants.

DOI: https://doi.org/10.1093/nar/gkab726
FEBS J. 2021 Aug 24.

The mitochondrial coenzyme Q junction and complex III: biochemistry and pathophysiology.

Rishi Banerjee, Janne Purhonen, Jukka Kallijärvi.

  Coenzyme Q (CoQ, ubiquinone) is the electron-carrying lipid in the mitochondrial electron transport system (ETS). In mammals, it serves as the electron acceptor for nine mitochondrial inner membrane dehydrogenases. These include the NADH-dehydrogenase (complex I, CI) and succinate dehydrogenase (complex II, CII) but also several others that are often omitted in the context of respiratory enzymes: dihydroorotate dehydrogenase, choline dehydrogenase, electron-transferring flavoprotein dehydrogenase, mitochondrial glycerol-3-phosphate dehydrogenase, proline dehydrogenases 1 and 2, and sulfide:quinone oxidoreductase. The metabolic pathways these enzymes are involved in range from amino acid and fatty acid oxidation to nucleotide biosynthesis, methylation, and hydrogen sulfide detoxification, among many others. The CoQ-linked metabolism depends on CoQ re-oxidation by the mitochondrial complex III (cytochrome bc1 complex, CIII). However, the literature is surprisingly limited as for the role of the CoQ-linked metabolism in the pathogenesis of human diseases of oxidative phosphorylation (OXPHOS), in which the CoQ homeostasis is directly or indirectly affected. In this review, we give an introduction to CIII function, and an overview of the pathological consequences of CIII dysfunction in humans and mice and of the CoQ-dependent metabolic processes potentially affected in these pathological states. Finally, we discuss some experimental tools to dissect the various aspects of compromised CoQ oxidation.

Keywords:  coenzyme Q; complex III; mitochondrial disease; oxidative phosphorylation; ubiquinone

DOI:  https://doi.org/10.1111/febs.16164
Nat Med. 2021 Aug 23.

Mitochondrial DNA variants modulate N-formylmethionine, proteostasis and risk of late-onset human diseases.

ICICLE-PD Study Group

Mitochondrial DNA (mtDNA) variants influence the risk of late-onset human diseases, but the reasons for this are poorly understood. Undertaking a hypothesis-free analysis of 5,689 blood-derived biomarkers with mtDNA variants in 16,220 healthy donors, here we show that variants defining mtDNA haplogroups Uk and H4 modulate the level of circulating N-formylmethionine (fMet), which initiates mitochondrial protein translation. In human cytoplasmic hybrid (cybrid) lines, fMet modulated both mitochondrial and cytosolic proteins on multiple levels, through transcription, post-translational modification and proteolysis by an N-degron pathway, abolishing known differences between mtDNA haplogroups. In a further 11,966 individuals, fMet levels contributed to all-cause mortality and the disease risk of several common cardiovascular disorders. Together, these findings indicate that fMet plays a key role in common age-related disease through pleiotropic effects on cell proteostasis.

DOI: https://doi.org/10.1038/s41591-021-01441-3
Nat Commun. 2021 08 24. 12(1): 5103

Dysregulated cholesterol homeostasis results in resistance to ferroptosis increasing tumorigenicity and metastasis in cancer.

Wen Liu, Binita Chakraborty, Rachid Safi, Dmitri Kazmin, Ching-Yi Chang, Donald P McDonnell.

Hypercholesterolemia and dyslipidemia are associated with an increased risk for many cancer types and with poor outcomes in patients with established disease. Whereas the mechanisms by which this occurs are multifactorial we determine that chronic exposure of cells to 27-hydroxycholesterol (27HC), an abundant circulating cholesterol metabolite, selects for cells that exhibit increased cellular uptake and/or lipid biosynthesis. These cells exhibit substantially increased tumorigenic and metastatic capacity. Notably, the metabolic stress imposed upon cells by the accumulated lipids requires sustained expression of GPX4, a negative regulator of ferroptotic cell death. We show that resistance to ferroptosis is a feature of metastatic cells and further demonstrate that GPX4 knockdown attenuates the enhanced tumorigenic and metastatic activity of 27HC resistant cells. These findings highlight the general importance of ferroptosis in tumor growth and metastasis and suggest that dyslipidemia/hypercholesterolemia impacts cancer pathogenesis by selecting for cells that are resistant to ferroptotic cell death.

DOI: https://doi.org/10.1038/s41467-021-25354-4
Metabolites. 2021 Jul 21. pii: 468. [Epub ahead of print]11(8):

A Single LC-MS/MS Analysis to Quantify CoA Biosynthetic Intermediates and Short-Chain Acyl CoAs.

Anthony E Jones, Nataly J Arias, Aracely Acevedo, Srinivasa T Reddy, Ajit S Divakaruni, David Meriwether.

  Coenzyme A (CoA) is an essential cofactor for dozens of reactions in intermediary metabolism. Dysregulation of CoA synthesis or acyl CoA metabolism can result in metabolic or neurodegenerative disease. Although several methods use liquid chromatography coupled with mass spectrometry/mass spectrometry (LC-MS/MS) to quantify acyl CoA levels in biological samples, few allow for simultaneous measurement of intermediates in the CoA biosynthetic pathway. Here we describe a simple sample preparation and LC-MS/MS method that can measure both short-chain acyl CoAs and biosynthetic precursors of CoA. The method does not require use of a solid phase extraction column during sample preparation and exhibits high sensitivity, precision, and accuracy. It reproduces expected changes from known effectors of cellular CoA homeostasis and helps clarify the mechanism by which excess concentrations of etomoxir reduce intracellular CoA levels.

Keywords:  CoA biosynthesis; LC-MS/MS; etomoxir; mitochondria; short-chain acyl CoAs

DOI:  https://doi.org/10.3390/metabo11080468
J Biol Chem. 2021 Aug 18. pii: S0021-9258(21)00903-0. [Epub ahead of print] 101100

Alkaline intracellular pHi (pHi) activates AMPK-mTORC2 signaling to promote cell survival during growth factor limitation.

D Kazyken, S I Lentz, D C Fingar.

  mTOR complex 2 (mTORC2) signaling controls cell metabolism, promotes cell survival, and contributes to tumorigenesis, yet its upstream regulation remains poorly defined. While considerable evidence supports the prevailing view that amino acids activate mTOR complex 1 (mTORC1) but not mTORC2, several studies reported paradoxical activation of mTORC2 signaling by amino acids. We noted that after amino acid starvation of cells in culture, addition of an amino acid solution increased mTORC2 signaling. Interestingly, we found the pH of the amino acid solution to be alkaline, ∼pH 10. These observations led us to discover and demonstrate here that alkaline intracellular pH (pHi) represents a previously unknown activator of mTORC2. Using a fluorescent pH-sensitive dye (cSNARF1-AM) coupled with live-cell imaging, we demonstrate that culturing cells in media at alkaline pH induces a rapid rise in pHi, which increases mTORC2 catalytic activity and downstream signaling to the pro-growth and -survival kinase Akt. Alkaline pHi also activates AMPK, a canonical sensor of energetic stress. Functionally, alkaline pHi attenuates mTOR- and AMPK-mediated apoptosis caused by growth factor withdrawal. Collectively, these findings reveal that alkaline pHi increases mTORC2- and AMPK-mediated signaling to promote cell survival during conditions of growth factor limitation, analogous to the demonstrated ability of energetic stress to activate AMPK-mTORC2 and promote cell survival. As elevated pHi represents an under-appreciated hallmark of cancer cells, we propose that alkaline pHi stress sensing by AMPK-mTORC2 may contribute to tumorigenesis by enabling cancer cells at the core of a growing tumor to evade apoptosis and survive.

Keywords:  AMPK; Akt; intracellular pH (pHi); mTORC2

DOI:  https://doi.org/10.1016/j.jbc.2021.101100
J Biol Chem. 2021 Aug 19. pii: S0021-9258(21)00906-6. [Epub ahead of print] 101103

The Yoga of Rag GTPases: Dynamic structural poses confer amino acid sensing by mTORC1.

Diane C Fingar.

Heterodimeric Rag GTPases play a critical role in relaying fluctuating levels of cellular amino acids to the sensor mTOR complex 1 (mTORC1). Important mechanistic questions remain unresolved, however, regarding how guanine nucleotide binding enables Rag GTPases to transition dynamically between distinct Yoga-like structural poses that control activation state. Egri et al. identify a critical interdomain hydrogen bond within RagA and RagC that stabilizes their GDP-bound states. They demonstrate that this long-distance interaction controls Rag structure and function to confer appropriate amino acid sensing by mTORC1.

DOI: https://doi.org/10.1016/j.jbc.2021.101103
Biomolecules. 2021 Aug 08. pii: 1172. [Epub ahead of print]11(8):

Routes for Potassium Ions across Mitochondrial Membranes: A Biophysical Point of View with Special Focus on the ATP-Sensitive K+ Channel.

Yevheniia Kravenska, Vanessa Checchetto, Ildiko Szabo.

  Potassium ions can cross both the outer and inner mitochondrial membranes by means of multiple routes. A few potassium-permeable ion channels exist in the outer membrane, while in the inner membrane, a multitude of different potassium-selective and potassium-permeable channels mediate K+ uptake into energized mitochondria. In contrast, potassium is exported from the matrix thanks to an H+/K+ exchanger whose molecular identity is still debated. Among the K+ channels of the inner mitochondrial membrane, the most widely studied is the ATP-dependent potassium channel, whose pharmacological activation protects cells against ischemic damage and neuronal injury. In this review, we briefly summarize and compare the different hypotheses regarding the molecular identity of this patho-physiologically relevant channel, taking into account the electrophysiological characteristics of the proposed components. In addition, we discuss the characteristics of the other channels sharing localization to both the plasma membrane and mitochondria.

Keywords:  ATP-dependent potassium channel; electrophysiology; ion channels; mitochondria

DOI:  https://doi.org/10.3390/biom11081172
J Cell Sci. 2021 Jan 15. pii: jcs247056. [Epub ahead of print]134(2):

The pleiotropic functions of autophagy in metastasis.

Timothy Marsh, Bhairavi Tolani, Jayanta Debnath.

  Autophagy is deregulated in many cancers and represents an attractive target for therapeutic intervention. However, the precise contributions of autophagy to metastatic progression, the principle cause of cancer-related mortality, is only now being uncovered. While autophagy promotes primary tumor growth, metabolic adaptation and resistance to therapy, recent studies have unexpectedly revealed that autophagy suppresses the proliferative outgrowth of disseminated tumor cells into overt and lethal macrometastases. These studies suggest autophagy plays unexpected and complex roles in the initiation and progression of metastases, which will undoubtedly impact therapeutic approaches for cancer treatment. Here, we discuss the intricacies of autophagy in metastatic progression, highlighting and integrating the pleiotropic roles of autophagy on diverse cell biological processes involved in metastasis.

Keywords:  Autophagy; Cancer; Metastasis; Selective Autophagy

DOI:  https://doi.org/10.1242/jcs.247056
J Immunol. 2021 Aug 25. pii: ji2000628. [Epub ahead of print]

Metabolic Adaptation of Macrophages as Mechanism of Defense against Crystalline Silica.

Antonella Marrocco, Krystin Frawley, Linda L Pearce, James Peterson, James P O'Brien, Steven J Mullett, Stacy G Wendell, Claudette M St Croix, Steven E Mischler, Luis A Ortiz.

Silicosis is a lethal pneumoconiosis for which no therapy is available. Silicosis is a global threat, and more than 2.2 million people per year are exposed to silica in the United States. The initial response to silica is mediated by innate immunity. Phagocytosis of silica particles by macrophages is followed by recruitment of mitochondria to phagosomes, generation of mitochondrial reactive oxygen species, and cytokine (IL-1β, TNF-α, IFN-β) release. In contrast with LPS, the metabolic remodeling of silica-exposed macrophages is unclear. This study contrasts mitochondrial and metabolic alterations induced by LPS and silica on macrophages and correlates them with macrophage viability and cytokine production, which are central to the pathogenesis of silicosis. Using high-resolution respirometer and liquid chromatography-high-resolution mass spectrometry, we determined the effects of silica and LPS on mitochondrial respiration and determined changes in central carbon metabolism of murine macrophage cell lines RAW 264.7 and IC-21. We show that silica induces metabolic reprogramming of macrophages. Silica, as well as LPS, enhances glucose uptake and increases aerobic glycolysis in macrophages. In contrast with LPS, silica affects mitochondria respiration, reducing complex I and enhancing complex II activity, to sustain cell viability. These mitochondrial alterations are associated in silica, but not in LPS-exposed macrophages, with reductions of tricarboxylic acid cycle intermediates, including succinate, itaconate, glutamate, and glutamine. Furthermore, in contrast with LPS, these silica-induced metabolic adaptations do not correlate with IL-1β or TNF-α production, but with the suppressed release of IFN-β. Our data highlight the importance of complex II activity and tricarboxylic acid cycle remodeling to macrophage survival and cytokine-mediated inflammation in silicosis.

DOI: https://doi.org/10.4049/jimmunol.2000628
Cell Rep. 2021 Aug 24. pii: S2211-1247(21)00999-2. [Epub ahead of print]36(8): 109565

Crosstalk between Drp1 phosphorylation sites during mitochondrial remodeling and their impact on metabolic adaptation.

Miriam Valera-Alberni, Magali Joffraud, Joan Miro-Blanch, Jordi Capellades, Alexandra Junza, Loïc Dayon, Antonio Núñez Galindo, Jose L Sanchez-Garcia, Armand Valsesia, Angelique Cercillieux, Flavia Söllner, Andreas G Ladurner, Oscar Yanes, Carles Cantó.

  Mitochondria constantly undergo fusion and fission events, referred as mitochondrial dynamics, which determine mitochondrial architecture and bioenergetics. Cultured cell studies demonstrate that mitochondrial dynamics are acutely regulated by phosphorylation of the mitochondrial fission orchestrator dynamin-related protein 1 (Drp1) at S579 or S600. However, the physiological impact and crosstalk of these phosphorylation sites is poorly understood. Here, we describe the functional interrelation between S579 and S600 phosphorylation sites in vivo and their role on mitochondrial remodeling. Mice carrying a homozygous Drp1 S600A knockin (Drp1 KI) mutation display larger mitochondria and enhanced lipid oxidation and respiratory capacities, granting improved glucose tolerance and thermogenic response upon high-fat feeding. Housing mice at thermoneutrality blunts these differences, suggesting a role for the brown adipose tissue in the protection of Drp1 KI mice against metabolic damage. Overall, we demonstrate crosstalk between Drp1 phosphorylation sites and provide evidence that their modulation could be used in the treatment and prevention of metabolic diseases.

Keywords:  Drp1; brown adipose tissue; insulin resistance; metabolic syndrome; mitochondrial dynamics; mitochondrial respiration; phosphorylation; thermoneutrality

DOI:  https://doi.org/10.1016/j.celrep.2021.109565
Int J Mol Sci. 2021 Aug 09. pii: 8560. [Epub ahead of print]22(16):

NAD(H) Regulates the Permeability Transition Pore in Mitochondria through an External Site.

Ekaterina Kharechkina, Anna Nikiforova, Alexey Kruglov.

  The opening of the permeability transition pore (mPTP) in mitochondria initiates cell death in numerous diseases. The regulation of mPTP by NAD(H) in the mitochondrial matrix is well established; however, the role of extramitochondrial (cytosolic) NAD(H) is still unclear. We studied the effect of added NADH and NAD+ on: (1) the Ca2+-retention capacity (CRC) of isolated rat liver, heart, and brain mitochondria; (2) the Ca2+-dependent mitochondrial swelling in media whose particles can (KCl) or cannot (sucrose) be extruded from the matrix by mitochondrial carriers; (3) the Ca2+-dependent mitochondrial depolarization and the release of entrapped calcein from mitochondria of permeabilized hepatocytes; and (4) the Ca2+-dependent mitochondrial depolarization and subsequent repolarization. NADH and NAD+ increased the CRC of liver, heart, and brain mitochondria 1.5-2.5 times, insignificantly affecting the rate of Ca2+-uptake and the free Ca2+ concentration in the medium. NAD(H) suppressed the Ca2+-dependent mitochondrial swelling both in KCl- and sucrose-based media but did not induce the contraction and repolarization of swollen mitochondria. By contrast, EGTA caused mitochondrial repolarization in both media and the contraction in KCl-based medium only. NAD(H) delayed the Ca2+-dependent depolarization and the release of calcein from individual mitochondria in hepatocytes. These data unambiguously demonstrate the existence of an external NAD(H)-dependent site of mPTP regulation.

Keywords:  NAD+; NADH; calcium retention capacity; cytosolic; external regulatory site; permeability transition pore; pore closure

DOI:  https://doi.org/10.3390/ijms22168560
Cancers (Basel). 2021 Aug 09. pii: 4009. [Epub ahead of print]13(16):

Metformin Is a Pyridoxal-5'-phosphate (PLP)-Competitive Inhibitor of SHMT2.

Angela Tramonti, Elisabet Cuyàs, José Antonio Encinar, Matthias Pietzke, Alessio Paone, Sara Verdura, Aina Arbusà, Begoña Martin-Castillo, Giorgio Giardina, Jorge Joven, Alexei Vazquez, Roberto Contestabile, Francesca Cutruzzolà, Javier A Menendez.

  The anticancer actions of the biguanide metformin involve the functioning of the serine/glycine one-carbon metabolic network. We report that metformin directly and specifically targets the enzymatic activity of mitochondrial serine hydroxymethyltransferase (SHMT2). In vitro competitive binding assays with human recombinant SHMT1 and SHMT2 isoforms revealed that metformin preferentially inhibits SHMT2 activity by a non-catalytic mechanism. Computational docking coupled with molecular dynamics simulation predicted that metformin could occupy the cofactor pyridoxal-5'-phosphate (PLP) cavity and destabilize the formation of catalytically active SHMT2 oligomers. Differential scanning fluorimetry-based biophysical screening confirmed that metformin diminishes the capacity of PLP to promote the conversion of SHMT2 from an inactive, open state to a highly ordered, catalytically competent closed state. CRISPR/Cas9-based disruption of SHMT2, but not of SHMT1, prevented metformin from inhibiting total SHMT activity in cancer cell lines. Isotope tracing studies in SHMT1 knock-out cells confirmed that metformin decreased the SHMT2-channeled serine-to-formate flux and restricted the formate utilization in thymidylate synthesis upon overexpression of the metformin-unresponsive yeast equivalent of mitochondrial complex I (mCI). While maintaining its capacity to inhibit mitochondrial oxidative phosphorylation, metformin lost its cytotoxic and antiproliferative activity in SHMT2-null cancer cells unable to produce energy-rich NADH or FADH2 molecules from tricarboxylic acid cycle (TCA) metabolites. As currently available SHMT2 inhibitors have not yet reached the clinic, our current data establishing the structural and mechanistic bases of metformin as a small-molecule, PLP-competitive inhibitor of the SHMT2 activating oligomerization should benefit future discovery of biguanide skeleton-based novel SHMT2 inhibitors in cancer prevention and treatment.

Keywords:  folate; glycine; one-carbon metabolism; serine; serine hydroxymethyltransferase

DOI:  https://doi.org/10.3390/cancers13164009
J Cell Biochem. 2021 Aug 25.

Miro1 functions as an inhibitory regulator of MFN at elevated mitochondrial Ca2+ levels.

Ferdinand F Fatiga, Li-Jie Wang, Tian Hsu, Jenica Irish Capuno, Chi-Yu Fu.

  Mitochondria function as an integrated network that moves along the microtubules within cells and changes the morphology through membrane fusion and fission events. Mitofusin (MFN) mediates membrane tethering and subsequent fusion of the mitochondrial outer membrane. Understanding the regulatory mechanisms of MFN function is critical to tackling the pathology related to mitochondrial network imbalance. Here, we reveal a novel inhibitory mechanism of MFN-mediated fusion by mitochondrial Rho GTPase (Miro1) in response to elevated mitochondrial Ca2+ concentration ([Ca2+ ]m ). We showed that elevated [Ca2+ ]m prevents the fusion between mitochondria forming the outer membrane tether by ectopically expressing MFN. Lowering [Ca2+ ]m by treating cells with an inhibitor of mitochondrial calcium uniporter or knocking down Miro1/2 induces more fused networks. Miro1 interacts with MFN as supported by co-immunoprecipitation and protein association identified by proximity labeling proteomics. It suggests that Miro1 functions as a Ca2+ -sensor and inhibits MFN function at elevated [Ca2+ ]m. Miro1 EF-hand mutant has a compromised inhibitory effect, which reiterates Ca2+ -modulated regulation. Dysregulated Ca2+ -handling and mitochondrial network imbalance are highly relevant in the pathology of cancers, cardiovascular, and neurodegenerative diseases. Miro1 functions as a coordinated Ca2+ -responder by pausing mitochondrial transport while reducing network fusion and cooperating with Drp1-mediated fission. It likely prevents the detrimental effect of Ca2+ m overload and facilitates mitophagy. Our finding reveals a novel regulation of mitochondrial network dynamics responding to [Ca2+ ]m through the interplay of Miro1 and MFN. Modulation of Miro1 and MFN interaction is a potential intervention to promote network homeostasis.

Keywords:  mitochondrial Rho GTPase (Miro); mitochondrial calcium; mitochondrial fusion; mitochondrial network homeostasis; mitofusin (MFN)

DOI:  https://doi.org/10.1002/jcb.30138
Nat Commun. 2021 08 24. 12(1): 5086

Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment.

NCI PDXNet Consortium

Development of candidate cancer treatments is a resource-intensive process, with the research community continuing to investigate options beyond static genomic characterization. Toward this goal, we have established the genomic landscapes of 536 patient-derived xenograft (PDX) models across 25 cancer types, together with mutation, copy number, fusion, transcriptomic profiles, and NCI-MATCH arms. Compared with human tumors, PDXs typically have higher purity and fit to investigate dynamic driver events and molecular properties via multiple time points from same case PDXs. Here, we report on dynamic genomic landscapes and pharmacogenomic associations, including associations between activating oncogenic events and drugs, correlations between whole-genome duplications and subclone events, and the potential PDX models for NCI-MATCH trials. Lastly, we provide a web portal having comprehensive pan-cancer PDX genomic profiles and source code to facilitate identification of more druggable events and further insights into PDXs' recapitulation of human tumors.

DOI: https://doi.org/10.1038/s41467-021-25177-3
Int J Mol Sci. 2021 Aug 07. pii: 8496. [Epub ahead of print]22(16):

Mitochondrial Carriers and Substrates Transport Network: A Lesson from Saccharomyces cerevisiae.

Alessandra Ferramosca, Vincenzo Zara.

  The yeast Saccharomyces cerevisiae is one of the most widely used model organisms for investigating various aspects of basic cellular functions that are conserved in human cells. This organism, as well as human cells, can modulate its metabolism in response to specific growth conditions, different environmental changes, and nutrient depletion. This adaptation results in a metabolic reprogramming of specific metabolic pathways. Mitochondrial carriers play a fundamental role in cellular metabolism, connecting mitochondrial with cytosolic reactions. By transporting substrates across the inner membrane of mitochondria, they contribute to many processes that are central to cellular function. The genome of Saccharomyces cerevisiae encodes 35 members of the mitochondrial carrier family, most of which have been functionally characterized. The aim of this review is to describe the role of the so far identified yeast mitochondrial carriers in cell metabolism, attempting to show the functional connections between substrates transport and specific metabolic pathways, such as oxidative phosphorylation, lipid metabolism, gluconeogenesis, and amino acids synthesis. Analysis of the literature reveals that these proteins transport substrates involved in the same metabolic pathway with a high degree of flexibility and coordination. The understanding of the role of mitochondrial carriers in yeast biology and metabolism could be useful for clarifying unexplored aspects related to the mitochondrial carrier network. Such knowledge will hopefully help in obtaining more insight into the molecular basis of human diseases.

Keywords:  Saccharomyces cerevisiae; metabolism; mitochondria; mitochondrial carrier; transport

DOI:  https://doi.org/10.3390/ijms22168496
Dev Cell. 2021 Aug 23. pii: S1534-5807(21)00603-1. [Epub ahead of print]56(16): 2329-2347.e6

Metabolic plasticity drives development during mammalian embryogenesis.

Mark S Sharpley, Fangtao Chi, Johanna Ten Hoeve, Utpal Banerjee.

  Mammalian preimplantation embryos follow a stereotypic pattern of development from zygotes to blastocysts. Here, we use labeled nutrient isotopologue analysis of small numbers of embryos to track downstream metabolites. Combined with transcriptomic analysis, we assess the capacity of the embryo to reprogram its metabolism through development. Early embryonic metabolism is rigid in its nutrient requirements, sensitive to reductive stress and has a marked disequilibrium between two halves of the TCA cycle. Later, loss of maternal LDHB and transcription of zygotic products favors increased activity of bioenergetic shuttles, fatty-acid oxidation and equilibration of the TCA cycle. As metabolic plasticity peaks, blastocysts can develop without external nutrients. Normal developmental metabolism of the early embryo is distinct from cancer metabolism. However, similarities emerge upon reductive stress. Increased metabolic plasticity with maturation is due to changes in redox control mechanisms and to transcriptional reprogramming of later-stage embryos during homeostasis or upon adaptation to environmental changes.

Keywords:  MYC; NAD+/NADH; developmental metabolism; embryo; metabolic plasticity; metabolic reprogramming; preimplantation; redox; reductive stress; zygotic genome activation

DOI:  https://doi.org/10.1016/j.devcel.2021.07.020
J Hepatol. 2021 Aug 24. pii: S0168-8278(21)02004-3. [Epub ahead of print]

Mitochondrial dysfunction governs immunometabolism in leukocytes of patients with acute-on-chronic liver failure.

Ingrid W Zhang, Anna Curto, Cristina López-Vicario, Mireia Casulleras, Marta Duran-Güell, Roger Flores-Costa, Benoit Colsch, Ferran Aguilar, Ana M Aransay, Juan José Lozano, María Hernández-Tejero, David Toapanta, Javier Fernández, Vicente Arroyo, Joan Clària.

   BACKGROUND&AIMS: Patients with acute decompensation (AD) of cirrhosis progressing to acute-on-chronic liver failure (ACLF) present a systemic hyperinflammatory response associated with increased circulating levels of small-molecule metabolites. To investigate whether these alterations reflect inadequate cell energy output, we assessed mitochondrial morphology and central metabolic pathways with emphasis on the tricarboxylic acid (TCA) cycle in peripheral leukocytes from AD patients with and without ACLF.
METHODS: The study included samples from AD patients (108 without and 128 with ACLF) and 41 healthy subjects. Leukocyte mitochondrial ultrastructure was visualized by transmission electron microscopy and cytosolic and mitochondrial metabolic fluxes were determined by assessing NADH/FADH2 production from various substrates. Plasma GDF15 and FGF21 were determined by Luminex and acylcarnitines by LC-MS/MS. Gene expression was analyzed by RNA-sequencing and PCR-based glucose metabolism profiler array.
RESULTS: Mitochondrial ultrastructure in patients with advanced cirrhosis was distinguished by cristae rarefication and swelling. The number of mitochondria per leukocyte was higher in patients, accompanied by a reduction in their size. Increased FGF21 and C6:0- and C8:0-carnitine predicted mortality whereas GDF15 strongly correlated with a gene set signature related to leukocyte activation. Metabolic flux analyses revealed increased energy production in mononuclear leukocytes from patients with preferential involvement of extra-mitochondrial pathways, supported by upregulated expression of genes encoding enzymes of the glycolytic and pentose phosphate pathways. In ACLF patients, mitochondrial function analysis uncovered two break-points in the TCA cycle at the isocitrate dehydrogenase and succinate dehydrogenase level, which were bridged by anaplerotic reactions involving glutaminolysis and nucleoside metabolism.
CONCLUSIONS: Our findings provide evidence at the cellular, organelle and biochemical levels that severe mitochondrial dysfunction governs immunometabolism in leukocytes from patients with AD cirrhosis and ACLF.
LAY SUMMARY: Patients at advanced stages of liver disease have dismal prognosis due to vital organ failures and the lack of treatment options. In this study, we report that the functioning of mitochondria, which are known as the cell powerhouse, is severely impaired in leukocytes of these patients, probably as the consequence of intense inflammation. Mitochondrial dysfunction is therefore a hallmark of advanced liver disease.

Keywords:  ACLF; RNA-seq; acute decompensated cirrhosis; immune cells; metabolic phenotype; mitochondria

DOI:  https://doi.org/10.1016/j.jhep.2021.08.009
Proc Natl Acad Sci U S A. 2021 Aug 31. pii: e2023909118. [Epub ahead of print]118(35):

SLC-30A9 is required for Zn2+ homeostasis, Zn2+ mobilization, and mitochondrial health.

Huichao Deng, Xinhua Qiao, Ting Xie, Wenfeng Fu, Hang Li, Yanmei Zhao, Miaomiao Guo, Yaqian Feng, Ligong Chen, Yan Zhao, Long Miao, Chang Chen, Kang Shen, Xiangming Wang.

  The trace element zinc is essential for many aspects of physiology. The mitochondrion is a major Zn2+ store, and excessive mitochondrial Zn2+ is linked to neurodegeneration. How mitochondria maintain their Zn2+ homeostasis is unknown. Here, we find that the SLC-30A9 transporter localizes on mitochondria and is required for export of Zn2+ from mitochondria in both Caenorhabditis elegans and human cells. Loss of slc-30a9 leads to elevated Zn2+ levels in mitochondria, a severely swollen mitochondrial matrix in many tissues, compromised mitochondrial metabolic function, reductive stress, and induction of the mitochondrial stress response. SLC-30A9 is also essential for organismal fertility and sperm activation in C. elegans, during which Zn2+ exits from mitochondria and acts as an activation signal. In slc-30a9-deficient neurons, misshapen mitochondria show reduced distribution in axons and dendrites, providing a potential mechanism for the Birk-Landau-Perez cerebrorenal syndrome where an SLC30A9 mutation was found.

Keywords:  Birk–Landau–Perez cerebrorenal syndrome; SLC-30A9; Zn2+ transporters; mitochondria

DOI:  https://doi.org/10.1073/pnas.2023909118
Cell Rep. 2021 Aug 24. pii: S2211-1247(21)01055-X. [Epub ahead of print]36(8): 109617

Loss of tyrosine catabolic enzyme HPD promotes glutamine anaplerosis through mTOR signaling in liver cancer.

Man Tong, Tin-Lok Wong, Hongzhi Zhao, Yuanyuan Zheng, Yu-Nong Xie, Cheuk-Hin Li, Lei Zhou, Noélia Che, Jing-Ping Yun, Kwan Man, Terence Kin-Wah Lee, Zongwei Cai, Stephanie Ma.

  The liver plays central roles in coordinating different metabolic processes, such as the catabolism of amino acids. In this study, we identify a loss of tyrosine catabolism and a concomitant increase in serum tyrosine levels during liver cancer development. Liver cells with disordered tyrosine catabolism, as exemplified by the suppression of a tyrosine catabolic enzyme 4-hydroxyphenylpyruvate dioxygenase (HPD), display augmented tumorigenic and proliferative potentials. Metabolomics profiling and isotope tracing reveal the metabolic reliance of HPD-silenced cells on glutamine, coupled with increased tricarboxylic acid cycle metabolites and their associated amino acid pools. Mechanistically, HPD silencing reduces ketone bodies, which regulate the proliferative and metabolic phenotypes via the AMPK/mTOR/p70S6 kinase pathway and mTOR-dependent glutaminase (GLS) activation. Collectively, our results demonstrate a metabolic link between tyrosine and glutamine metabolism, which could be exploited as a potentially promising anticancer therapy for liver cancer.

Keywords:  HPD; glutamine metabolism; liver cancer; mTOR signaling; tyrosine catabolism

DOI:  https://doi.org/10.1016/j.celrep.2021.109617
Dis Model Mech. 2021 Apr 01. pii: dmm047746. [Epub ahead of print]14(4):

Metabolomics and lipidomics in Caenorhabditis elegans using a single-sample preparation.

Marte Molenaars, Bauke V Schomakers, Hyung L Elfrink, Arwen W Gao, Martin A T Vervaart, Mia L Pras-Raves, Angela C Luyf, Reuben L Smith, Mark G Sterken, Jan E Kammenga, Antoine H C van Kampen, Georges E Janssens, Frédéric M Vaz, Michel van Weeghel, Riekelt H Houtkooper.

  Comprehensive metabolomic and lipidomic mass spectrometry methods are in increasing demand; for instance, in research related to nutrition and aging. The nematode Caenorhabditis elegans is a key model organism in these fields, owing to the large repository of available C. elegans mutants and their convenient natural lifespan. Here, we describe a robust and sensitive analytical method for the semi-quantitative analysis of >100 polar (metabolomics) and >1000 apolar (lipidomics) metabolites in C. elegans, using a single-sample preparation. Our method is capable of reliably detecting a wide variety of biologically relevant metabolic aberrations in, for example, glycolysis and the tricarboxylic acid cycle, pyrimidine metabolism and complex lipid biosynthesis. In conclusion, we provide a powerful analytical tool that maximizes metabolic data yield from a single sample. This article has an associated First Person interview with the joint first authors of the paper.

Keywords:   C. elegans ; Lipidomics; Metabolism; Metabolomics

DOI:  https://doi.org/10.1242/dmm.047746
Metabolites. 2021 Aug 13. pii: 538. [Epub ahead of print]11(8):

Metabolic Outcomes of Anaplerotic Dodecanedioic Acid Supplementation in Very Long Chain Acyl-CoA Dehydrogenase (VLCAD) Deficient Fibroblasts.

Igor Radzikh, Erica Fatica, Jillian Kodger, Rohan Shah, Ryan Pearce, Yana I Sandlers.

  Very long-chain acyl-CoA dehydrogenase deficiency (VLCADD, OMIM 609575) is associated with energy deficiency and mitochondrial dysfunction and may lead to rhabdomyolysis and cardiomyopathy. Under physiological conditions, there is a fine balance between the utilization of different carbon nutrients to maintain the Krebs cycle. The maintenance of steady pools of Krebs cycle intermediates is critical formitochondrial energy homeostasis especially in high-energy demanding organs such as muscle and heart. Even-chain dicarboxylic acids are established as alternative energy carbon sources that replenish the Krebs cycle by bypassing a defective β-oxidation pathway. Despite this, even-chain dicarboxylic acids are eliminated in the urine of VLCAD-affected individuals. In this study, we explore dodecanedioic acid (C12; DODA) supplementation and investigate its metabolic effect on Krebs cycle intermediates, glucose uptake, and acylcarnitine profiles in VLCAD-deficient fibroblasts. Our findings indicate that DODA supplementation replenishes the Krebs cycle by increasing the succinate pool, attenuates glycolytic flux, and reduces levels of toxic very long-chain acylcarnitines.

Keywords:  Krebs cycle; VLCAD deficiency; acylcarnitines; dodecandioic acid

DOI:  https://doi.org/10.3390/metabo11080538
Cancer Res. 2021 Aug 24. pii: canres.0206.2021. [Epub ahead of print]

mTORC1 Promotes ARID1A Degradation and Oncogenic Chromatin Remodeling in Hepatocellular Carcinoma.

Shanshan Zhang, Yu-Feng Zhou, Jian Cao, Stephen K Burley, Hui-Yun Wang, X F Steven Zheng.

The SWI/SNF chromatin remodeling complexes control accessibility of chromatin to transcriptional and co-regulatory machineries. Chromatin remodeling plays important roles in normal physiology and diseases, particularly cancer. The ARID1A-containing SWI/SNF complex is commonly mutated and thought to be a key tumor suppressor in hepatocellular carcinoma (HCC), but its regulation in response to oncogenic signals remains poorly understood. mTOR is a conserved central controller of cell growth and an oncogenic driver of HCC. Remarkably, cancer mutations in mTOR and SWI/SNF complex are mutually exclusive in human HCC tumors, suggesting that they share a common oncogenic function. Here we report that mTOR complex 1 (mTORC1) interact with ARID1A and regulates ubiquitination and proteasomal degradation of ARID1A protein. The mTORC1-ARID1A axis promoted oncogenic chromatin remodeling and YAP-dependent transcription, thereby enhancing liver cancer cell growth in vitro and tumor development in vivo. Conversely, excessive ARID1A expression counteracted AKT-driven liver tumorigenesis in vivo. Moreover, dysregulation of this axis conferred resistance to mTOR-targeted therapies. These findings demonstrate that the ARID1A-SWI/SNF complex is a regulatory target for oncogenic mTOR signaling, which is important for mTORC1-driven hepatocarcinogenesis with implications for therapeutic interventions in HCC.

DOI: https://doi.org/10.1158/0008-5472.CAN-21-0206
Biochem J. 2021 Aug 27. 478(16): 3125-3143

Quality control of protein import into mitochondria.

Fabian den Brave, Jeannine Engelke, Thomas Becker.

  Mitochondria import about 1000 proteins that are produced as precursors on cytosolic ribosomes. Defects in mitochondrial protein import result in the accumulation of non-imported precursor proteins and proteotoxic stress. The cell is equipped with different quality control mechanisms to monitor protein transport into mitochondria. First, molecular chaperones guide unfolded proteins to mitochondria and deliver non-imported proteins to proteasomal degradation. Second, quality control factors remove translocation stalled precursor proteins from protein translocases. Third, protein translocases monitor protein sorting to mitochondrial subcompartments. Fourth, AAA proteases of the mitochondrial subcompartments remove mislocalized or unassembled proteins. Finally, impaired efficiency of protein transport is an important sensor for mitochondrial dysfunction and causes the induction of cellular stress responses, which could eventually result in the removal of the defective mitochondria by mitophagy. In this review, we summarize our current understanding of quality control mechanisms that govern mitochondrial protein transport.

Keywords:  TIM23 complex; TOM complex; mitochondria; protein sorting; protein transport

DOI:  https://doi.org/10.1042/BCJ20190584
Metabolites. 2021 Jul 21. pii: 469. [Epub ahead of print]11(8):

Urinary 2-Hydroxyglutarate Enantiomers Are Markedly Elevated in a Murine Model of Type 2 Diabetic Kidney Disease.

Judy Baek, Subramaniam Pennathur.

  Metabolic reprogramming is a hallmark of diabetic kidney disease (DKD); nutrient overload leads to increased production of metabolic byproducts that may become toxic at high levels. One metabolic byproduct may be 2-hydroxyglutarate (2-HG), a metabolite with many regulatory functions that exists in both enantiomeric forms physiologically. We quantitatively determined the levels of L and D-2HG enantiomers in the urine, plasma, and kidney cortex of db/db mice, a pathophysiologically relevant murine model of type 2 diabetes and DKD. We found increased fractional excretion of both L and D-2HG enantiomers, suggesting increased tubular secretion and/or production of the two metabolites in DKD. Quantitation of TCA cycle metabolites in db/db cortex suggests that TCA cycle overload and an increase in 2-HG precursor substrate, α-ketoglutarate, drive the increased L and D-2HG production in DKD. In conclusion, we demonstrated increased 2-HG enantiomer production and urinary excretion in murine type 2 DKD, which may contribute to metabolic reprogramming and progression of diabetic kidney disease.

Keywords:  2-hydroxyglutarate; TCA cycle; biomarker; diabetic kidney disease; mitochondria

DOI:  https://doi.org/10.3390/metabo11080469
J Inherit Metab Dis. 2021 Aug 23.

Mechano-energetic aspects of Barth Syndrome.

Jan Dudek, Christoph Maack.

Energy-demanding organs like the heart are strongly dependent on oxidative phosphorylation in mitochondria. Oxidative phosphorylation is governed by the respiratory chain located in the inner mitochondrial membrane. The inner mitochondrial membrane is the only cellular membrane with significant amounts of the phospholipid cardiolipin, and cardiolipin was found to directly interact with a number of essential protein complexes, including respiratory chain complexes I to V. An inherited defect in the biogenesis of cardiolipin causes Barth syndrome, which is associated with cardiomyopathy, skeletal myopathy, neutropenia and growth retardation. Energy conversion is dependent on reducing equivalents, which are replenished by oxidative metabolism in the Krebs cycle. Cardiolipin deficiency in Barth syndrome also affects Krebs cycle activity, metabolite transport and mitochondrial morphology. During excitation-contraction coupling, calcium (Ca2+ ) released from the sarcoplasmic reticulum drives sarcomeric contraction. At the same time, Ca2+ influx into mitochondria drives the activation of Krebs cycle dehydrogenases and the regeneration of reducing equivalents. Reducing equivalents are essential not only for energy conversion, but also for maintaining a redox buffer, which is required to detoxify reactive oxygen species (ROS). Defects in CL may also affect Ca2+ uptake into mitochondria and thereby hamper energy supply and demand matching, but also detoxification of ROS. Here, we review the impact of cardiolipin deficiency on mitochondrial function in Barth syndrome and discuss potential therapeutic strategies. This article is protected by copyright. All rights reserved.

DOI: https://doi.org/10.1002/jimd.12427
Adv Exp Med Biol. 2021 ;1319 271-286

A Sweet Story of Metabolic Innovation in the Naked Mole-Rat.

Jane Reznick, Thomas J Park, Gary R Lewin.

The naked mole-rat's (Heterocephalus glaber) social and subterranean lifestyle imposes several evolutionary pressures which have shaped its physiology. One example is low oxygen availability in a crowded burrow system which the naked mole-rat has adapted to via several mechanisms. Here we describe a metabolic rewiring which enables the naked mole-rat to switch substrates in glycolysis from glucose to fructose thereby circumventing feedback inhibition at phosphofructokinase (PFK1) to allow unrestrained glycolytic flux and ATP supply under hypoxia. Preferential shift to fructose metabolism occurs in other species and biological systems as a means to provide fuel, water or like in the naked mole-rat, protection in a low oxygen environment. We review fructose metabolism through an ecological lens and suggest that the metabolic adaptation to utilize fructose in the naked mole-rat may have evolved to simultaneously combat multiple challenges posed by its hostile environment.

DOI: https://doi.org/10.1007/978-3-030-65943-1_10
Proc Natl Acad Sci U S A. 2021 Aug 31. pii: e2025948118. [Epub ahead of print]118(35):

METTL14 facilitates global genome repair and suppresses skin tumorigenesis.

Zizhao Yang, Seungwon Yang, Yan-Hong Cui, Jiangbo Wei, Palak Shah, Gayoung Park, Xiaolong Cui, Chuan He, Yu-Ying He.

  Global genome repair (GGR), a subpathway of nucleotide excision repair, corrects bulky helix-distorting DNA lesions across the whole genome and is essential for preventing mutagenesis and skin cancer. Here, we show that METTL14 (methyltransferase-like 14), a critical component of the N6-methyladenosine (m6A) RNA methyltransferase complex, promotes GGR through regulating m6A mRNA methylation-mediated DDB2 translation and suppresses ultraviolet B (UVB) radiation-induced skin tumorigenesis. UVB irradiation down-regulates METTL14 protein through NBR1-dependent selective autophagy. METTL14 knockdown decreases GGR and DDB2 abundance. Conversely, overexpression of wild-type METTL14 but not its enzymatically inactive mutant increases GGR and DDB2 abundance. METTL14 knockdown decreases m6A methylation and translation of the DDB2 transcripts. Adding DDB2 reverses the GGR repair defect in METTL14 knockdown cells, indicating that METTL14 facilitates GGR through regulating DDB2 m6A methylation and translation. Similarly, knockdown of YTHDF1, an m6A reader promoting translation of m6A-modified transcripts, decreases DDB2 protein levels. Both METTL14 and YTHDF1 bind to the DDB2 transcript. In mice, skin-specific heterozygous METTL14 deletion increases UVB-induced skin tumorigenesis. Furthermore, METTL14 as well as DDB2 is down-regulated in human and mouse skin tumors and by chronic UVB irradiation in mouse skin, and METTL14 level is associated with the DDB2 level, suggesting a tumor-suppressive role of METTL14 in UVB-associated skin tumorigenesis in association with DDB2 regulation. Taken together, these findings demonstrate that METTL14 is a target for selective autophagy and acts as a critical epitranscriptomic mechanism to regulate GGR and suppress UVB-induced skin tumorigenesis.

Keywords:  METTL14; UVB; m6A RNA methylation; nucleotide excision repair; ultraviolet radiation

DOI:  https://doi.org/10.1073/pnas.2025948118
Front Immunol. 2021 ;12 728783

Metabolic Controls on Epigenetic Reprogramming in Regulatory T Cells.

Jingli Lu, Yan Liang, Haiyang Meng, Ailing Zhang, Junjie Zhao, Chengliang Zhang.

  Forkhead box protein 3 (Foxp3+)-expressing regulatory T (Treg) cells are a unique CD4+T cell subset that suppresses excessive immune responses. The epigenetic plasticity and metabolic traits of Treg cells are crucial for the acquisition of their phenotypic and functional characteristics. Therefore, alterations to the epigenetics and metabolism affect Treg cell development and function. Recent evidence reveals that altering the metabolic pathways and generation of metabolites can regulate the epigenetics of Treg cells. Specifically, some intermediates of cell metabolism can directly act as substrates or cofactors of epigenetic-modifying enzymes. Here, we describe the metabolic and epigenetic features during Treg cell development, and discuss how metabolites can contribute to epigenetic alterations of Treg cells, which affects Treg cell activation, differentiation, and function.

Keywords:  epigenetics; immune suppression; metabolism; metabolites; regulatory T cells

DOI:  https://doi.org/10.3389/fimmu.2021.728783
Cell Stem Cell. 2021 Aug 21. pii: S1934-5909(21)00296-4. [Epub ahead of print]

Aspartate availability limits hematopoietic stem cell function during hematopoietic regeneration.

Le Qi, Misty S Martin-Sandoval, Salma Merchant, Wen Gu, Matthias Eckhardt, Thomas P Mathews, Zhiyu Zhao, Michalis Agathocleous, Sean J Morrison.

  The electron transport chain promotes aspartate synthesis, which is required for cancer cell proliferation. However, it is unclear whether aspartate is limiting in normal stem cells. We found that mouse hematopoietic stem cells (HSCs) depend entirely on cell-autonomous aspartate synthesis, which increases upon HSC activation. Overexpression of the glutamate/aspartate transporter, Glast, or deletion of glutamic-oxaloacetic transaminase 1 (Got1) each increased aspartate levels in HSCs/progenitor cells and increased the function of HSCs but not colony-forming progenitors. Conversely, deletion of Got2 reduced aspartate levels and the function of HSCs but not colony-forming progenitors. Deletion of Got1 and Got2 eliminated HSCs. Isotope tracing showed aspartate was used to synthesize asparagine and purines. Both contributed to increased HSC function as deletion of asparagine synthetase or treatment with 6-mercaptopurine attenuated the increased function of GLAST-overexpressing HSCs. HSC function is thus limited by aspartate, purine, and asparagine availability during hematopoietic regeneration.

Keywords:  asparagine; aspartate; electron transport chain; hematopoietic stem cell; metabolism; mitochondria; purine; regeneration

DOI:  https://doi.org/10.1016/j.stem.2021.07.011
Biochim Biophys Acta Rev Cancer. 2021 Aug 21. pii: S0304-419X(21)00116-5. [Epub ahead of print] 188618

The role of 5-HT metabolism in cancer.

Di Ye, Huanji Xu, Qiulin Tang, Hongwei Xia, Chenliang Zhang, Feng Bi.

  Serotonin (5-hydroxytryptamine, 5-HT) metabolism has long been linked to tumorigenesis and tumor progression. Numerous studies have shown the functions of 5-HT and its metabolites in the regulation of tumor biological processes like cell proliferation, invasion, metastasis, tumor angiogenesis and immunomodulatory through multi-step complex mechanisms. Reprogramming of 5-HT metabolism has been revealed in various tumors paving way for development of drugs that target enzymes, metabolites or receptors involved in 5-HT metabolic pathway. However, information on the role of 5-HT metabolism in cancer is scanty. This review briefly describes the main metabolic routes of 5-HT, the role of 5-HT metabolism in cancer and systematically summarizes the most recent advances in 5-HT metabolism-targeted cancer therapy.

Keywords:  Cancer therapy; Metabolism; Serotonin

DOI:  https://doi.org/10.1016/j.bbcan.2021.188618
Clin Cancer Res. 2021 Aug 23. pii: clincanres.2092.2021. [Epub ahead of print]

Establishment of Patient-derived Succinate Dehydrogenase-deficient Gastrointestinal Stromal Tumor Models For Predicting Therapeutic Response.

Mayra Yebra, Shruti Bhargava, Avi Kumar, Adam M Burgoyne, Chih-Min Tang, Hyunho Yoon, Sudeep Banerjee, Joseph Aguilera, Thekla Cordes, Vipul Sheth, Sangkyu Noh, Rowan Ustoy, Sam Li, Sunil J Advani, Christopher L Corless, Michael C Heinrich, Razelle Kurzrock, Scott M Lippman, Paul T Fanta, Olivier Harismendy, Christian Metallo, Jason K Sicklick.

PURPOSE: Gastrointestinal stromal tumor (GIST) is the most common sarcoma of the gastrointestinal tract with mutant succinate dehydrogenase (SDH) subunits (A-D) comprising less than 7.5% (i.e. 150-200/year) of new cases annually in the United States. Contrary to GISTs harboring KIT or PDGFRA mutations, SDH-mutant GISTs affect adolescents/young adults, often metastasize, and are frequently resistant to tyrosine kinase inhibitors (TKIs). Lack of human models for any SDH-mutant tumors, including GIST, has limited molecular characterization and drug discovery.
EXPERIMENTAL DESIGN: We describe methods for establishing novel patient-derived SDH-mutant (mSDH) GIST models and interrogated the efficacy of temozolomide on these tumor models in vitro and in clinical trials of mSDH GIST patients.
RESULTS: Molecular and metabolic characterization of our patient-derived mSDH GIST models revealed that these models recapitulate the transcriptional and metabolic hallmarks of parent tumors and SDH-deficiency. We further demonstrate that temozolomide elicits DNA damage and apoptosis in our mSDH GIST models. Translating our in vitro discovery to the clinic, a cohort of SDH-mutant GIST patients treated with temozolomide (n=5) demonstrated a 40% objective response rate and 100% disease control rate suggesting that temozolomide represents a promising therapy for this subset of GIST.
CONCLUSION: We report the first methods to establish patient-derived mSDH tumor models, which can be readily employed for understanding patient-specific tumor biology and treatment strategies. We also demonstrate that temozolomide is effective in mSDH GIST patients who are refractory to existing chemotherapeutic drugs (namely TKIs) in clinic for GISTs, bringing a promising treatment option for these patients to clinic.

DOI: https://doi.org/10.1158/1078-0432.CCR-21-2092
Cancer Cell. 2021 Jul 29. pii: S1535-6108(21)00397-4. [Epub ahead of print]

COVID-19 provides an opportunity to transform cancer research.

Raffaella Casolino, Andrew V Biankin.

DOI: https://doi.org/10.1016/j.ccell.2021.07.018
Metabolites. 2021 Jul 26. pii: 480. [Epub ahead of print]11(8):

Metformin Decreases 2-HG Production through the MYC-PHGDH Pathway in Suppressing Breast Cancer Cell Proliferation.

Sehyun Oh, Youngup Cho, Minsun Chang, Sunghyouk Park, Hyuknam Kwon.

  The biguanide drug metformin has been widely used for the treatment of type 2 diabetes, and there is evidence supporting the anticancer effect of metformin despite some controversy. Here, we report the growth inhibitory activity of metformin in the breast cancer (MCF-7) cells, both in vitro and in vivo, and the associated metabolic changes. In particular, a decrease in a well-known oncometabolite 2-hydroxyglutarate (2-HG) was discovered by a metabolomics approach. The decrease in 2-HG by metformin was accompanied by the reduction in histone methylation, consistent with the known tumorigenic mechanism of 2-HG. The relevance of 2-HG inhibition in breast cancer was also supported by a higher level of 2-HG in human breast cancer tissues. Genetic knockdown of PHGDH identified the PHGDH pathway as the producer of 2-HG in the MCF-7 cells that do not carry isocitrate dehydrogenase 1 and 2 (IDH1/IDH2) mutations, the conventional producer of 2-HG. We also showed that metformin's inhibitory effect on the PHGDH-2HG axis may occur through the regulation of the AMPK-MYC pathway. Overall, our results provide an explanation for the coherent pathway from complex I inhibition to epigenetic changes for metformin's anticancer effect.

Keywords:  2-HG; PHGDH; anticancer effect; metabolomics; metformin

DOI:  https://doi.org/10.3390/metabo11080480
Int J Mol Sci. 2021 Aug 18. pii: 8888. [Epub ahead of print]22(16):

Hexosamine Biosynthetic Pathway-Derived O-GlcNAcylation Is Critical for RANKL-Mediated Osteoclast Differentiation.

Myoung Jun Kim, Hyuk Soon Kim, Sangyong Lee, Keun Young Min, Wahn Soo Choi, Jueng Soo You.

  O-linked-N-acetylglucosaminylation (O-GlcNAcylation) performed by O-GlcNAc transferase (OGT) is a nutrient-responsive post-translational modification (PTM) via the hexosamine biosynthetic pathway (HBP). Various transcription factors (TFs) are O-GlcNAcylated, affecting their activities and significantly contributing to cellular processes ranging from survival to cellular differentiation. Given the pleiotropic functions of O-GlcNAc modification, it has been studied in various fields; however, the role of O-GlcNAcylation during osteoclast differentiation remains to be explored. Kinetic transcriptome analysis during receptor activator of nuclear factor-kappaB (NF-κB) ligand (RANKL)-mediated osteoclast differentiation revealed that the nexus of major nutrient metabolism, HBP was critical for this process. We observed that the critical genes related to HBP activation, including Nagk, Gfpt1, and Ogt, were upregulated, while the global O-GlcNAcylation was increased concomitantly during osteoclast differentiation. The O-GlcNAcylation inhibition by the small-molecule inhibitor OSMI-1 reduced osteoclast differentiation in vitro and in vivo by disrupting the translocation of NF-κB p65 and nuclear factor of activated T cells c1 (NFATc1) into the nucleus by controlling their PTM O-GlcNAcylation. Furthermore, OSMI-1 had a synergistic effect with bone target therapy on osteoclastogenesis. Lastly, knocking down Ogt with shRNA (shOgt) mimicked OSMI-1's effect on osteoclastogenesis. Targeting O-GlcNAcylation during osteoclast differentiation may be a valuable therapeutic approach for osteoclast-activated bone diseases.

Keywords:  NFATc1; O-GlcNAc transferase; O-GlcNAcylation; osteoclast; osteoclastogenesis; p65

DOI:  https://doi.org/10.3390/ijms22168888
Cell Rep. 2021 Aug 24. pii: S2211-1247(21)01023-8. [Epub ahead of print]36(8): 109589

Synthetic biosensor accelerates evolution by rewiring carbon metabolism toward a specific metabolite.

Joo Yeon Seok, Yong Hee Han, Jae-Seong Yang, Jina Yang, Hyun Gyu Lim, Seong Gyeong Kim, Sang Woo Seo, Gyoo Yeol Jung.

  Proper carbon flux distribution between cell growth and production of a target compound is important for biochemical production because improper flux reallocation inhibits cell growth, thus adversely affecting production yield. Here, using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolve cells under the selective condition toward the acquisition of genotypes that optimally reallocate cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we determine that mutations in the conserved regions of proteins involved in global transcriptional regulation alter the expression of several genes associated with central carbon metabolism. These changes rewire central carbon flux toward the 3-HP production pathway, increasing 3-HP yield and reducing acetate accumulation by alleviating overflow metabolism. Our study provides a perspective on adaptive laboratory evolution (ALE) using synthetic biosensors, thereby supporting future efforts in metabolic pathway optimization.

Keywords:  3-hydroxypropionic acid; adaptive laboratory evolution; biosensor; evolutionary metabolic engineering; selection; synthetic biology

DOI:  https://doi.org/10.1016/j.celrep.2021.109589
Nature. 2021 Aug 25.

A body map of somatic mutagenesis in morphologically normal human tissues.

Ruoyan Li, Lin Di, Jie Li, Wenyi Fan, Yachen Liu, Wenjia Guo, Weiling Liu, Lu Liu, Qiong Li, Liping Chen, Yamei Chen, Chuanwang Miao, Hongjin Liu, Yuqian Wang, Yuling Ma, Deshu Xu, Dongxin Lin, Yanyi Huang, Jianbin Wang, Fan Bai, Chen Wu.

Somatic mutations that accumulate in normal tissues are associated with ageing and disease1,2. Here we performed a comprehensive genomic analysis of 1,737 morphologically normal tissue biopsies of 9 organs from 5 donors. We found that somatic mutation accumulations and clonal expansions were widespread, although to variable extents, in morphologically normal human tissues. Somatic copy number alterations were rarely detected, except for in tissues from the oesophagus and cardia. Endogenous mutational processes with the SBS1 and SBS5 mutational signatures are ubiquitous among normal tissues, although they exhibit different relative activities. Exogenous mutational processes operate in multiple tissues from the same donor. We reconstructed the spatial somatic clonal architecture with sub-millimetre resolution. In the oesophagus and cardia, macroscopic somatic clones that expanded to hundreds of micrometres were frequently seen, whereas in tissues such as the colon, rectum and duodenum, somatic clones were microscopic in size and evolved independently, possibly restricted by local tissue microstructures. Our study depicts a body map of somatic mutations and clonal expansions from the same individual.

DOI: https://doi.org/10.1038/s41586-021-03836-1