bims-camemi 2020-10-04 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2020–10–04
25 papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit

Mitochondrial DNA Haplotypes as Genetic Modifiers of Cancer.
Extreme heterogeneity of human mitochondrial DNA from organelles to populations.
Acid enhancement of ROS generation by complex-I reverse electron transport is balanced by acid inhibition of complex-II: Relevance for tissue reperfusion injury.
Role of succinate dehydrogenase deficiency and oncometabolites in gastrointestinal stromal tumors.
Nox4 regulates InsP3 receptor-dependent Ca2+ release into mitochondria to promote cell survival.
Tumoural activation of TLR3-SLIT2 axis in endothelium drives metastasis.
Metabolic characterization of aggressive breast cancer cells exhibiting invasive phenotype: impact of non-cytotoxic doses of 2-DG on diminishing invasiveness.
Disruption of redox homeostasis for combinatorial drug efficacy in K-Ras tumors as revealed by metabolic connectivity profiling.
SIRT1 is downregulated by autophagy in senescence and ageing.
RIPK1 gene variants associate with obesity in humans and can be therapeutically silenced to reduce obesity in mice.
MITO-FIND: A study in 390 patients to determine a diagnostic strategy for mitochondrial disease.
Metabolic dysfunction in human skin: Restoration of mitochondrial integrity and metabolic output by nicotinamide (niacinamide) in primary dermal fibroblasts from older aged donors.
Sperm-specific COX6B2 enhances oxidative phosphorylation, proliferation, and survival in human lung adenocarcinoma.
Metabolic precision labeling enables selective probing of O-linked N-acetylgalactosamine glycosylation.
Regulation of glycolysis by the hypoxia-inducible factor (HIF): implications for cellular physiology.
LC3 lipidation is essential for TFEB activation during the lysosomal damage response to kidney injury.
Reducing NADPH Synthesis Counteracts Diabetic Nephropathy through Restoration of AMPK Activity in Type 1 Diabetic Rats.
Local targeting of NAD+ salvage pathway alters the immune tumor microenvironment and enhances checkpoint immunotherapy in glioblastoma.
Methylarginine metabolites are associated with attenuated muscle protein synthesis in cancer-associated muscle wasting.
A pathogen branched-chain amino acid catabolic pathway subverts host survival by impairing energy metabolism and the mitochondrial UPR.
Coupling of Peptidoglycan Synthesis to Central Metabolism in Mycobacteria: Post-transcriptional Control of CwlM by Aconitase.
Utilizing tandem mass spectrometry for metabolic flux analysis.
PINCH-1 regulates mitochondrial dynamics to promote proline synthesis and tumor growth.
SARS-CoV2-mediated suppression of NRF2-signaling reveals potent antiviral and anti-inflammatory activity of 4-octyl-itaconate and dimethyl fumarate.
Metformin and Systemic Metabolism.

Trends Cancer. 2020 Sep 23. pii: S2405-8033(20)30236-3. [Epub ahead of print]

Mitochondrial DNA Haplotypes as Genetic Modifiers of Cancer.

Alpaslan Tasdogan, David G McFadden, Prashant Mishra.

  Mitochondria play an essential role in cellular metabolism, generation of reactive oxygen species (ROS), and the initiation of apoptosis. These properties enable mitochondria to be crucial integrators in the pathways of tumorigenesis. An open question is to what extent variation in the mitochondrial genome (mtDNA) contributes to the biological heterogeneity observed in human tumors. In this review, we summarize our current understanding of the role of mtDNA genetics in relation to human cancers.

Keywords:  cancer; haplotypes; mitochondria; mtDNA; oncocytoma

DOI:  https://doi.org/10.1016/j.trecan.2020.08.004
Nat Rev Genet. 2020 Sep 28.

Extreme heterogeneity of human mitochondrial DNA from organelles to populations.

James B Stewart, Patrick F Chinnery.

Contrary to the long-held view that most humans harbour only identical mitochondrial genomes, deep resequencing has uncovered unanticipated extreme genetic variation within mitochondrial DNA (mtDNA). Most, if not all, humans contain multiple mtDNA genotypes (heteroplasmy); specific patterns of variants accumulate in different tissues, including cancers, over time; and some variants are preferentially passed down or suppressed in the maternal germ line. These findings cast light on the origin and spread of mtDNA mutations at multiple scales, from the organelle to the human population, and challenge the conventional view that high percentages of a mutation are required before a new variant has functional consequences.

DOI: https://doi.org/10.1038/s41576-020-00284-x
Redox Biol. 2020 Sep 19. pii: S2213-2317(20)30938-1. [Epub ahead of print]37 101733

Acid enhancement of ROS generation by complex-I reverse electron transport is balanced by acid inhibition of complex-II: Relevance for tissue reperfusion injury.

Alexander S Milliken, Chaitanya A Kulkarni, Paul S Brookes.

  Generation of mitochondrial reactive oxygen species (ROS) is an important process in triggering cellular necrosis and tissue infarction during ischemia-reperfusion (IR) injury. Ischemia results in accumulation of the metabolite succinate. Rapid oxidation of this succinate by mitochondrial complex II (Cx-II) during reperfusion reduces the co-enzyme Q (Co-Q) pool, thereby driving electrons backward into complex-I (Cx-I), a process known as reverse electron transport (RET), which is thought to be a major source of ROS. During ischemia, enhanced glycolysis results in an acidic cellular pH at the onset of reperfusion. While the process of RsET within Cx-I is known to be enhanced by a high mitochondrial trans-membrane ΔpH, the impact of pH itself on the integrated process of Cx-II to Cx-I RET has not been fully studied. Using isolated mouse heart and liver mitochondria under conditions which mimic the onset of reperfusion (i.e., high [ADP]), we show that mitochondrial respiration (state 2 and state 3) as well as isolated Cx-II activity are impaired at acidic pH, whereas the overall generation of ROS by Cx-II to Cx-I RET was insensitive to pH. Together these data indicate that the acceleration of Cx-I RET ROS by ΔpH appears to be cancelled out by the impact of pH on the source of electrons, i.e. Cx-II. Implications for the role of Cx-II to Cx-I RET derived ROS in IR injury are discussed.

Keywords:  Acidosis; Complex I; Ischemia; Metabolism; Mitochondria; ROS

DOI:  https://doi.org/10.1016/j.redox.2020.101733
World J Gastroenterol. 2020 Sep 14. 26(34): 5074-5089

Role of succinate dehydrogenase deficiency and oncometabolites in gastrointestinal stromal tumors.

Yue Zhao, Fei Feng, Qing-Hong Guo, Yu-Ping Wang, Rui Zhao.

  Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. At the molecular level, GISTs can be categorized into two groups based on the causative oncogenic mutations. Approximately 85% of GISTs are caused by gain-of-function mutations in the tyrosine kinase receptor KIT or platelet-derived growth factor receptor alpha (PDGFRA). The remaining GISTs, referred to as wild-type (WT) GISTs, are often deficient in succinate dehydrogenase complex (SDH), a key metabolic enzyme complex in the tricarboxylic acid (TCA) cycle and electron transport chain. SDH deficiency leads to the accumulation of succinate, a metabolite produced by the TCA cycle. Succinate inhibits α-ketoglutarate-dependent dioxygenase family enzymes, which comprise approximately 60 members and regulate key aspects of tumorigenesis such as DNA and histone demethylation, hypoxia responses, and m6A mRNA modification. For this reason, succinate and metabolites with similar structures, such as D-2-hydroxyglutarate and fumarate, are considered oncometabolites. In this article, we review recent advances in the understanding of how metabolic enzyme mutations and oncometabolites drive human cancer with an emphasis on SDH mutations and succinate in WT GISTs.

Keywords:  Epigenetics; Gastrointestinal stromal tumors; Oncometabolite; Succinate; Succinate dehydrogenase; α-ketoglutarate-dependent dioxygenase

DOI:  https://doi.org/10.3748/wjg.v26.i34.5074
EMBO J. 2020 Oct 01. 39(19): e103530

Nox4 regulates InsP3 receptor-dependent Ca2+ release into mitochondria to promote cell survival.

Matteo Beretta, Celio Xc Santos, Chris Molenaar, Anne D Hafstad, Chris Cj Miller, Aram Revazian, Kai Betteridge, Katrin Schröder, Katrin Streckfuß-Bömeke, James H Doroshow, Roland A Fleck, Tsung-Ping Su, Vsevolod V Belousov, Maddy Parsons, Ajay M Shah.

  Cells subjected to environmental stresses undergo regulated cell death (RCD) when homeostatic programs fail to maintain viability. A major mechanism of RCD is the excessive calcium loading of mitochondria and consequent triggering of the mitochondrial permeability transition (mPT), which is especially important in post-mitotic cells such as cardiomyocytes and neurons. Here, we show that stress-induced upregulation of the ROS-generating protein Nox4 at the ER-mitochondria contact sites (MAMs) is a pro-survival mechanism that inhibits calcium transfer through InsP3 receptors (InsP3 R). Nox4 mediates redox signaling at the MAM of stressed cells to augment Akt-dependent phosphorylation of InsP3 R, thereby inhibiting calcium flux and mPT-dependent necrosis. In hearts subjected to ischemia-reperfusion, Nox4 limits infarct size through this mechanism. These results uncover a hitherto unrecognized stress pathway, whereby a ROS-generating protein mediates pro-survival effects through spatially confined signaling at the MAM to regulate ER to mitochondria calcium flux and triggering of the mPT.

Keywords:  InsP3 receptor; NADPH oxidase-4; calcium signaling; cell death; mitochondria-associated membrane

DOI:  https://doi.org/10.15252/embj.2019103530
Nature. 2020 Sep 30.

Tumoural activation of TLR3-SLIT2 axis in endothelium drives metastasis.

Bernardo Tavora, Tobias Mederer, Kai J Wessel, Simon Ruffing, Mahan Sadjadi, Marc Missmahl, Benjamin N Ostendorf, Xuhang Liu, Ji-Young Kim, Olav Olsen, Alana L Welm, Hani Goodarzi, Sohail F Tavazoie.

Blood vessels support tumours by providing nutrients and oxygen, while also acting as conduits for the dissemination of cancer1. Here we use mouse models of breast and lung cancer to investigate whether endothelial cells also have active 'instructive' roles in the dissemination of cancer. We purified genetically tagged endothelial ribosomes and their associated transcripts from highly and poorly metastatic tumours. Deep sequencing revealed that metastatic tumours induced expression of the axon-guidance gene Slit2 in endothelium, establishing differential expression between the endothelial (high Slit2 expression) and tumoural (low Slit2 expression) compartments. Endothelial-derived SLIT2 protein and its receptor ROBO1 promoted the migration of cancer cells towards endothelial cells and intravasation. Deleting endothelial Slit2 suppressed metastatic dissemination in mouse models of breast and lung cancer. Conversely, deletion of tumoural Slit2 enhanced metastatic progression. We identified double-stranded RNA derived from tumour cells as an upstream signal that induces expression of endothelial SLIT2 by acting on the RNA-sensing receptor TLR3. Accordingly, a set of endogenous retroviral element RNAs were upregulated in metastatic cells and detected extracellularly. Thus, cancer cells co-opt innate RNA sensing to induce a chemotactic signalling pathway in endothelium that drives intravasation and metastasis. These findings reveal that endothelial cells have a direct instructive role in driving metastatic dissemination, and demonstrate that a single gene (Slit2) can promote or suppress cancer progression depending on its cellular source.

DOI: https://doi.org/10.1038/s41586-020-2774-y
BMC Cancer. 2020 Sep 29. 20(1): 929

Metabolic characterization of aggressive breast cancer cells exhibiting invasive phenotype: impact of non-cytotoxic doses of 2-DG on diminishing invasiveness.

Mayumi Fujita, Kaori Imadome, Veena Somasundaram, Miki Kawanishi, Kumiko Karasawa, David A Wink.

   BACKGROUND: Metabolic reprogramming is being recognized as a fundamental hallmark of cancer, and efforts to identify drugs that can target cancer metabolism are underway. In this study, we used human breast cancer (BC) cell lines and established their invading phenotype (INV) collected from transwell inserts to compare metabolome differences and evaluate prognostic significance of the metabolome in aggressive BC invasiveness.
METHODS: The invasiveness of seven human BC cell lines were compared using the transwell invasion assay. Among these, INV was collected from SUM149, which exhibited the highest invasiveness. Levels of metabolites in INV were compared with those of whole cultured SUM149 cells (WCC) using CE-TOFMS. The impact of glycolysis in INV was determined by glucose uptake assay using fluorescent derivative of glucose (2-NBDG), and significance of glycolysis, or tricarboxylic acid cycle (TCA) and electron transport chain (ETC) in the invasive process were further determined in aggressive BC cell lines, SUM149, MDA-MB-231, HCC1937, using invasion assays in the presence or absence of inhibitors of glycolysis, TCA cycle or ETC.
RESULTS: SUM149 INV sub-population exhibited a persistent hyperinvasive phenotype. INV were hyper-glycolytic with increased glucose (2-NBDG) uptake; diminished glucose-6-phosphate (G6P) levels but elevated pyruvate and lactate, along with higher expression of phosphorylated-pyruvate dehydrogenase (pPDH) compared to WCC. Notably, inhibiting of glycolysis with lower doses of 2-DG (1 mM), non-cytotoxic to MDA-MB-231 and HCC1937, was effective in diminishing invasiveness of aggressive BC cell lines. In contrast, 3-Nitropropionic acid (3-NA), an inhibitor of succinate dehydrogenase, the enzyme that oxidizes succinate to fumarate in TCA cycle, and functions as complex II of ETC, had no significant effect on their invasiveness, although levels of TCA metabolites or detection of mitochondrial membrane potential with JC-1 staining, indicated that INV cells originally had functional TCA cycles and membrane potential.
CONCLUSIONS: Hyper-glycolytic phenotype of invading cells caters to rapid energy production required for invasion while TCA cycle/ETC cater to cellular energy needs for sustenance in aggressive BC. Lower, non-cytotoxic doses of 2-DG can hamper invasion and can potentially be used as an adjuvant with other anti-cancer therapies without the usual side-effects associated with cytotoxic doses.

Keywords:  2-DG; Breast cancer; ETC; Glycolysis; Invasion; Metabolism; TCA cycle

DOI:  https://doi.org/10.1186/s12885-020-07414-y
Cancer Metab. 2020 ;8 22

Disruption of redox homeostasis for combinatorial drug efficacy in K-Ras tumors as revealed by metabolic connectivity profiling.

Daniela Gaglio, Marcella Bonanomi, Silvia Valtorta, Rohit Bharat, Marilena Ripamonti, Federica Conte, Giulia Fiscon, Nicole Righi, Elisabetta Napodano, Federico Papa, Isabella Raccagni, Seth J Parker, Ingrid Cifola, Tania Camboni, Paola Paci, Anna Maria Colangelo, Marco Vanoni, Christian M Metallo, Rosa Maria Moresco, Lilia Alberghina.

   Abstract:
Background: Rewiring of metabolism induced by oncogenic K-Ras in cancer cells involves both glucose and glutamine utilization sustaining enhanced, unrestricted growth. The development of effective anti-cancer treatments targeting metabolism may be facilitated by the identification and rational combinatorial targeting of metabolic pathways.
Methods: We performed mass spectrometric metabolomics analysis in vitro and in vivo experiments to evaluate the efficacy of drugs and identify metabolic connectivity.
Results: We show that K-Ras-mutant lung and colon cancer cells exhibit a distinct metabolic rewiring, the latter being more dependent on respiration. Combined treatment with the glutaminase inhibitor CB-839 and the PI3K/aldolase inhibitor NVP-BKM120 more consistently reduces cell growth of tumor xenografts. Maximal growth inhibition correlates with the disruption of redox homeostasis, involving loss of reduced glutathione regeneration, redox cofactors, and a decreased connectivity among metabolites primarily involved in nucleic acid metabolism.
Conclusions: Our findings open the way to develop metabolic connectivity profiling as a tool for a selective strategy of combined drug repositioning in precision oncology.

Keywords:  Combinatorial drug treatment; Glutamine; Glycolysis; Metabolic cancer therapy; Metabolic connectivity; Metabolic rewiring; Metabolic signature; Precision oncology

DOI:  https://doi.org/10.1186/s40170-020-00227-4
Nat Cell Biol. 2020 Oct;22(10): 1170-1179

SIRT1 is downregulated by autophagy in senescence and ageing.

Caiyue Xu, Lu Wang, Parinaz Fozouni, Gry Evjen, Vemika Chandra, Jing Jiang, Congcong Lu, Michael Nicastri, Corey Bretz, Jeffrey D Winkler, Ravi Amaravadi, Benjamin A Garcia, Peter D Adams, Melanie Ott, Wei Tong, Terje Johansen, Zhixun Dou, Shelley L Berger.

SIRT1 (Sir2) is an NAD+-dependent deacetylase that plays critical roles in a broad range of biological events, including metabolism, the immune response and ageing1-5. Although there is strong interest in stimulating SIRT1 catalytic activity, the homeostasis of SIRT1 at the protein level is poorly understood. Here we report that macroautophagy (hereafter referred to as autophagy), a catabolic membrane trafficking pathway that degrades cellular components through autophagosomes and lysosomes, mediates the downregulation of mammalian SIRT1 protein during senescence and in vivo ageing. In senescence, nuclear SIRT1 is recognized as an autophagy substrate and is subjected to cytoplasmic autophagosome-lysosome degradation, via the autophagy protein LC3. Importantly, the autophagy-lysosome pathway contributes to the loss of SIRT1 during ageing of several tissues related to the immune and haematopoietic system in mice, including the spleen, thymus, and haematopoietic stem and progenitor cells, as well as in CD8+CD28- T cells from aged human donors. Our study reveals a mechanism in the regulation of the protein homeostasis of SIRT1 and suggests a potential strategy to stabilize SIRT1 to promote productive ageing.

DOI: https://doi.org/10.1038/s41556-020-00579-5
Nat Metab. 2020 Sep 28.

RIPK1 gene variants associate with obesity in humans and can be therapeutically silenced to reduce obesity in mice.

Denuja Karunakaran, Adam W Turner, Anne-Claire Duchez, Sebastien Soubeyrand, Adil Rasheed, David Smyth, David P Cook, Majid Nikpay, Joshua W Kandiah, Calvin Pan, Michele Geoffrion, Richard Lee, Ludovic Boytard, Hailey Wyatt, My-Anh Nguyen, Paulina Lau, Markku Laakso, Bhama Ramkhelawon, Marcus Alvarez, Kirsi H Pietiläinen, Päivi Pajukanta, Barbara C Vanderhyden, Peter Liu, Scott B Berger, Peter J Gough, John Bertin, Mary-Ellen Harper, Aldons J Lusis, Ruth McPherson, Katey J Rayner.

Obesity is a major public health burden worldwide and is characterized by chronic low-grade inflammation driven by the cooperation of the innate immune system and dysregulated metabolism in adipose tissue and other metabolic organs. Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) is a central regulator of inflammatory cell function that coordinates inflammation, apoptosis and necroptosis in response to inflammatory stimuli. Here we show that genetic polymorphisms near the human RIPK1 locus associate with increased RIPK1 gene expression and obesity. We show that one of these single nucleotide polymorphisms is within a binding site for E4BP4 and increases RIPK1 promoter activity and RIPK1 gene expression in adipose tissue. Therapeutic silencing of RIPK1 in vivo in a mouse model of diet-induced obesity dramatically reduces fat mass, total body weight and improves insulin sensitivity, while simultaneously reducing macrophage and promoting invariant natural killer T cell accumulation in adipose tissue. These findings demonstrate that RIPK1 is genetically associated with obesity, and reducing RIPK1 expression is a potential therapeutic approach to target obesity and related diseases.

DOI: https://doi.org/10.1038/s42255-020-00279-2
Mol Genet Metab. 2020 Sep 18. pii: S1096-7192(20)30191-8. [Epub ahead of print]

MITO-FIND: A study in 390 patients to determine a diagnostic strategy for mitochondrial disease.

Marina Kerr, Stacey Hume, Fadya Omar, Desmond Koo, Heather Barnes, Maida Khan, Suhaib Aman, Xing-Chang Wei, Hanen Alfuhaid, Roman McDonald, Liam McDonald, Christopher Newell, Rebecca Sparkes, Dustin Hittel, Aneal Khan.

Mitochondrial diseases, due to nuclear or mitochondrial genome mutations causing mitochondrial dysfunction, have a wide range of clinical features involving neurologic, muscular, cardiac, hepatic, visual, and auditory symptoms. Making a diagnosis of a mitochondrial disease is often challenging since there is no gold standard and traditional testing methods have required tissue biopsy which presents technical challenges and most patients prefer a non-invasive approach. Since a diagnosis invariably involves finding a disease-causing DNA variant, new approaches such as next generation sequencing (NGS) have the potential to make it easier to make a diagnosis. We evaluated the ability of our traditional diagnostic pathway (metabolite analysis, tissue neuropathology and respiratory chain enzyme activity) in 390 patients. The traditional diagnostic pathway provided a diagnosis of mitochondrial disease in 115 patients (29.50%). Analysis of mtDNA, tissue neuropathology, skin electron microscopy, respiratory chain enzyme analysis using inhibitor assays, blue native polyacrylamide gel electrophoresis were all statistically significant in distinguishing patients between a mitochondrial and non-mitochondrial diagnosis. From these 390 patients who underwent traditional analysis, we recruited 116 patients for the NGS part of the study (36 patients who had a mitochondrial diagnosis (MITO) and 80 patients who had no diagnosis (No-Dx)). In the group of 36 MITO patients, nuclear whole exome sequencing (nWES) provided a second diagnosis in 2 cases who already had a pathogenic variant in mtDNA, and a revised diagnosis (GLUL) in one case that had abnormal pathology but no pathogenic mtDNA variant. In the 80 NO-Dx patients, nWES found non-mitochondrial diagnosis in 26 patients and a mitochondrial diagnosis in 1 patient. A genetic diagnosis was obtained in 53/116 (45.70%) cases that were recruited for NGS, but not in 11/116 (9.48%) of cases with abnormal mitochondrial neuropathology. Our results show that a non-invasive, bigenomic sequencing (BGS) approach (using both a nWES and optimized mtDNA analysis to include large deletions) should be the first step in investigating for mitochondrial diseases. There may still be a role for tissue biopsy in unsolved cases or when the diagnosis is still not clear after NGS studies.

DOI: https://doi.org/10.1016/j.ymgme.2020.08.009
Aging Cell. 2020 Sep 29. e13248

Metabolic dysfunction in human skin: Restoration of mitochondrial integrity and metabolic output by nicotinamide (niacinamide) in primary dermal fibroblasts from older aged donors.

John E Oblong, Amy Bowman, Holly A Rovito, Bradley B Jarrold, Joseph D Sherrill, Markaisa R Black, Glyn Nelson, Alexa B Kimball, Mark A Birch-Machin.

Alterations in metabolism in skin are accelerated by environmental stressors such as solar radiation, leading to premature aging. The impact of aging on mitochondria is of interest given their critical role for metabolic output and the finding that environmental stressors cause lowered energy output, particularly in fibroblasts where damage accumulates. To better understand these metabolic changes with aging, we performed an in-depth profiling of the expression patterns of dermal genes in face, forearm, and buttock biopsies from females of 20-70 years of age that encode for all subunits comprising complexes I-V of the mitochondrial electron transport chain. This complements previous preliminary analyses of these changes. "Oxidative phosphorylation" was the top canonical pathway associated with aging in the face, and genes encoding for numerous subunits had decreased expression patterns with age. Investigations on fibroblasts from older aged donors also showed decreased gene expression of numerous subunits from complexes I-V, oxidative phosphorylation rates, spare respiratory capacity, and mitochondrial number and membrane potential compared to younger cells. Treatment of older fibroblasts with nicotinamide (Nam) restored these measures to younger cell levels. Nam increased complexes I, IV, and V activity and gene expression of representative subunits. Elevated mt-Keima staining suggests a possible mechanism of action for these restorative effects via mitophagy. Nam also improved mitochondrial number and membrane potential in younger fibroblasts. These findings show there are significant changes in mitochondrial functionality with aging and that Nam treatment can restore bioenergetic efficiency and capacity in older fibroblasts with an amplifying effect in younger cells.

DOI: https://doi.org/10.1111/acel.13248
Elife. 2020 Sep 29. pii: e58108. [Epub ahead of print]9

Sperm-specific COX6B2 enhances oxidative phosphorylation, proliferation, and survival in human lung adenocarcinoma.

Chun-Chun Cheng, Joshua Wooten, Zane A Gibbs, Kathleen McGlynn, Prashant Mishra, Angelique W Whitehurst.

  Cancer testis antigens (CTAs) are proteins whose expression is normally restricted to the testis but anomalously activated in human cancer. In sperm, a number of CTAs support energy generation, however whether they contribute to tumor metabolism is not understood. We describe human COX6B2, a component of cytochrome c oxidase (complex IV). COX6B2 is expressed in human lung adenocarcinoma (LUAD) and expression correlates with reduced survival time. COX6B2, but not its somatic isoform COX6B1, enhances activity of complex IV, increasing oxidative phosphorylation (OXPHOS) and NAD+ generation. Consequently, COX6B2-expressing cancer cells display a proliferative advantage, particularly in low oxygen. Conversely, depletion of COX6B2 attenuates OXPHOS and collapses mitochondrial membrane potential leading to cell death or senescence. COX6B2 is both necessary and sufficient for growth of human tumor xenografts in mice. Our findings reveal a previously unappreciated, tumor specific metabolic pathway hijacked from one of the most ATP-intensive processes in the animal kingdom: sperm motility.

Keywords:  cancer biology; human

DOI:  https://doi.org/10.7554/eLife.58108
Proc Natl Acad Sci U S A. 2020 Sep 28. pii: 202007297. [Epub ahead of print]

Metabolic precision labeling enables selective probing of O-linked N-acetylgalactosamine glycosylation.

Marjoke F Debets, Omur Y Tastan, Simon P Wisnovsky, Stacy A Malaker, Nikolaos Angelis, Leonhard K R Moeckl, Junwon Choi, Helen Flynn, Lauren J S Wagner, Ganka Bineva-Todd, Aristotelis Antonopoulos, Anna Cioce, William M Browne, Zhen Li, David C Briggs, Holly L Douglas, Gaelen T Hess, Anthony J Agbay, Chloe Roustan, Svend Kjaer, Stuart M Haslam, Ambrosius P Snijders, Michael C Bassik, W E Moerner, Vivian S W Li, Carolyn R Bertozzi, Benjamin Schumann.

  Protein glycosylation events that happen early in the secretory pathway are often dysregulated during tumorigenesis. These events can be probed, in principle, by monosaccharides with bioorthogonal tags that would ideally be specific for distinct glycan subtypes. However, metabolic interconversion into other monosaccharides drastically reduces such specificity in the living cell. Here, we use a structure-based design process to develop the monosaccharide probe N-(S)-azidopropionylgalactosamine (GalNAzMe) that is specific for cancer-relevant Ser/Thr(O)-linked N-acetylgalactosamine (GalNAc) glycosylation. By virtue of a branched N-acylamide side chain, GalNAzMe is not interconverted by epimerization to the corresponding N-acetylglucosamine analog by the epimerase N-acetylgalactosamine-4-epimerase (GALE) like conventional GalNAc-based probes. GalNAzMe enters O-GalNAc glycosylation but does not enter other major cell surface glycan types including Asn(N)-linked glycans. We transfect cells with the engineered pyrophosphorylase mut-AGX1 to biosynthesize the nucleotide-sugar donor uridine diphosphate (UDP)-GalNAzMe from a sugar-1-phosphate precursor. Tagged with a bioorthogonal azide group, GalNAzMe serves as an O-glycan-specific reporter in superresolution microscopy, chemical glycoproteomics, a genome-wide CRISPR-knockout (CRISPR-KO) screen, and imaging of intestinal organoids. Additional ectopic expression of an engineered glycosyltransferase, "bump-and-hole" (BH)-GalNAc-T2, boosts labeling in a programmable fashion by increasing incorporation of GalNAzMe into the cell surface glycoproteome. Alleviating the need for GALE-KO cells in metabolic labeling experiments, GalNAzMe is a precision tool that allows a detailed view into the biology of a major type of cancer-relevant protein glycosylation.

Keywords:  bioorthogonal; glycosylation; glycosyltransferase; mucin

DOI:  https://doi.org/10.1073/pnas.2007297117
J Physiol. 2020 Oct 02.

Regulation of glycolysis by the hypoxia-inducible factor (HIF): implications for cellular physiology.

S J Kierans, C T Taylor.

  Under conditions of hypoxia, most eukaryotic cells can shift their primary metabolic strategy from predominantly mitochondrial respiration towards increased glycolysis to maintain ATP levels. This hypoxia-induced reprogramming of metabolism is key to satisfying cellular energetic requirements during acute hypoxic stress. At a transcriptional level, this metabolic switch can be regulated by several pathways including the hypoxia inducible factor-1α (HIF-1α) which induces an increased expression of glycolytic enzymes. While this increase in glycolytic flux is beneficial for maintaining bioenergetic homeostasis during hypoxia, the pathways mediating this increase can also be exploited by cancer cells to promote tumor survival and growth, an area which has been extensively studied. It has recently become appreciated that increased glycolytic metabolism in hypoxia may also have profound effects on cellular physiology in hypoxic immune and endothelial cells. Therefore, understanding the mechanisms central to mediating this reprogramming are of importance from both physiologic and pathophysiologic standpoints. In this review, we highlight the role of HIF-1α in the regulation of hypoxic glycolysis and its implications for physiological processes such as angiogenesis and immune cell effector function. Abstract figure legend Schematic outlining the functional physiological consequences of enhanced glycolytic metabolism in endothelial cells and immune cells. This article is protected by copyright. All rights reserved.

Keywords:  HIF; glycolysis; hypoxia; metabolism

DOI:  https://doi.org/10.1113/JP280572
Nat Cell Biol. 2020 Oct;22(10): 1252-1263

LC3 lipidation is essential for TFEB activation during the lysosomal damage response to kidney injury.

Shuhei Nakamura, Saki Shigeyama, Satoshi Minami, Takayuki Shima, Shiori Akayama, Tomoki Matsuda, Alessandra Esposito, Gennaro Napolitano, Akiko Kuma, Tomoko Namba-Hamano, Jun Nakamura, Kenichi Yamamoto, Miwa Sasai, Ayaka Tokumura, Mika Miyamoto, Yukako Oe, Toshiharu Fujita, Seigo Terawaki, Atsushi Takahashi, Maho Hamasaki, Masahiro Yamamoto, Yukinori Okada, Masaaki Komatsu, Takeharu Nagai, Yoshitsugu Takabatake, Haoxing Xu, Yoshitaka Isaka, Andrea Ballabio, Tamotsu Yoshimori.

Sensing and clearance of dysfunctional lysosomes is critical for cellular homeostasis. Here we show that transcription factor EB (TFEB)-a master transcriptional regulator of lysosomal biogenesis and autophagy-is activated during the lysosomal damage response, and its activation is dependent on the function of the ATG conjugation system, which mediates LC3 lipidation. In addition, lysosomal damage triggers LC3 recruitment on lysosomes, where lipidated LC3 interacts with the lysosomal calcium channel TRPML1, facilitating calcium efflux essential for TFEB activation. Furthermore, we demonstrate the presence and importance of this TFEB activation mechanism in kidneys in a mouse model of oxalate nephropathy accompanying lysosomal damage. A proximal tubule-specific TFEB-knockout mouse exhibited progression of kidney injury induced by oxalate crystals. Together, our results reveal unexpected mechanisms of TFEB activation by LC3 lipidation and their physiological relevance during the lysosomal damage response.

DOI: https://doi.org/10.1038/s41556-020-00583-9
Cell Rep. 2020 Sep 29. pii: S2211-1247(20)31196-7. [Epub ahead of print]32(13): 108207

Reducing NADPH Synthesis Counteracts Diabetic Nephropathy through Restoration of AMPK Activity in Type 1 Diabetic Rats.

Xiao Wei, Zongshi Lu, Li Li, Hexuan Zhang, Fang Sun, Huan Ma, Lijuan Wang, Yingru Hu, Zhencheng Yan, Hongting Zheng, Gangyi Yang, Daoyan Liu, Martin Tepel, Peng Gao, Zhiming Zhu.

  Diabetic nephropathy (DN) is a major complication of diabetes mellitus and a primary cause of end-stage renal failure. Clinical studies indicate that metabolic surgery improves DN; however, the mechanism remains unclear. Here, we report that Roux-en-Y Gastric Bypass (RYGB) surgery significantly blocked and reversed DN without affecting the insulin signaling pathway. This protective role of RYGB surgery is almost blocked by either inhibition or knockout of 5'AMP-activated protein kinase (AMPK) in podocytes. Furthermore, mRNA microarray data reveal that RYGB surgery obviously reduced the gene expression involved in nicotinamide adenine dinucleotide phosphate (NAPDH) synthesis. The expression of a key NADPH synthase, hexose-6-phosphate dehydrogenase (H6PD), was inhibited by the low plasma corticosterone level after surgery. In addition, blocking NAPDH synthesis by knocking down H6PD mimicked the beneficial role of RYGB surgery through activation of AMPK in podocytes. Therefore, this study demonstrates that reducing NADPH production is critical for renal AMPK activation in response to RYGB surgery.

Keywords:  AMPK; NADPH; RYGB surgery; diabetic nephropathy; podocyte

DOI:  https://doi.org/10.1016/j.celrep.2020.108207
Cancer Res. 2020 Sep 30. pii: canres.1094.2020. [Epub ahead of print]

Local targeting of NAD+ salvage pathway alters the immune tumor microenvironment and enhances checkpoint immunotherapy in glioblastoma.

Ming Li, Ameya R Kirtane, Juri Kiyokawa, Hiroaki Nagashima, Aaron Lopes, Zain A Tirmizi, Christine K Lee, Giovanni Traverso, Daniel P Cahill, Hiroaki Wakimoto.

The aggressive primary brain tumor glioblastoma (GBM) is characterized by aberrant metabolism that fuels its malignant phenotype. Diverse genetic subtypes of malignant glioma are sensitive to selective inhibition of the NAD+ salvage pathway enzyme nicotinamide phosphoribosyltransferase (NAMPT). However, the potential impact of NAD+ depletion on the brain tumor microenvironment has not been elaborated. In addition, systemic toxicity of NAMPT inhibition remains a significant concern. Here we show that microparticle-mediated intratumoral delivery of NAMPT inhibitor GMX1778 induces specific immunological changes in the tumor microenvironment of murine GBM, characterized by upregulation of immune checkpoint PD-L1, recruitment of CD3+, CD4+, and CD8+ T cells, and reduction of M2-polarized immunosuppressive macrophages. NAD+ depletion and autophagy induced by NAMPT inhibitors mediated the upregulation of PD-L1 transcripts and cell surface protein levels in GBM cells. NAMPT inhibitor modulation of the tumor immune microenvironment was therefore combined with PD-1 checkpoint blockade in vivo, significantly increasing the survival of GBM bearing animals. Thus, the therapeutic impacts of NAMPT inhibition extended beyond neoplastic cells, shaping surrounding immune effectors. Microparticle delivery and release of NAMPT inhibitor at the tumor site offers a safe and robust means to alter an immune tumor microenvironment that could potentiate checkpoint immunotherapy for glioblastoma.

DOI: https://doi.org/10.1158/0008-5472.CAN-20-1094
J Biol Chem. 2020 Oct 01. pii: jbc.RA120.014884. [Epub ahead of print]

Methylarginine metabolites are associated with attenuated muscle protein synthesis in cancer-associated muscle wasting.

Hawley E Kunz, Jessica M Dorschner, Taylor E Berent, Thomas Meyer, Xuewei Wang, Aminah Jatoi, Rajiv Kumar, Ian R Lanza.

  Cancer cachexia is characterized by reductions in peripheral lean muscle mass. Prior studies have primarily focused on increased protein breakdown as the driver of cancer-associated muscle wasting. Therapeutic interventions targeting catabolic pathways have, however, largely failed to preserve muscle mass in cachexia, suggesting that other mechanisms might be involved. In pursuit of novel pathways, we used untargeted metabolomics to search for metabolite signatures that may be linked with muscle atrophy. We injected seven-week old C57/BL6 mice with LLC1 tumor cells or vehicle. After 21 days, tumor-bearing mice exhibited reduced body and muscle mass and impaired grip strength compared to controls, which was accompanied by lower synthesis rates of mixed muscle protein and the myofibrillar and sarcoplasmic muscle fractions. Reductions in protein synthesis were accompanied by mitochondrial enlargement and reduced coupling efficiency in tumor-bearing mice. To generate mechanistic insights into impaired protein synthesis, we performed untargeted metabolomic analyses of plasma and muscle and found increased concentrations of two methylarginines, asymmetric dimethylarginine (ADMA) and NG-monomethyl-L-arginine, in tumor-bearing mice compared to control mice. Compared to healthy controls, human cancer patients were also found to have higher levels of ADMA in the skeletal muscle. Treatment of C2C12 myotubes with ADMA impaired protein synthesis and reduced mitochondrial protein quality. These results suggest that increased levels of ADMA and mitochondrial changes may contribute to impaired muscle protein synthesis in cancer cachexia and could point to novel therapeutic targets by which to mitigate cancer cachexia.

Keywords:  cachexia; cancer; metabolomics; methylarginines; mitochondria; protein synthesis; skeletal muscle

DOI:  https://doi.org/10.1074/jbc.RA120.014884
PLoS Pathog. 2020 Sep 30. 16(9): e1008918

A pathogen branched-chain amino acid catabolic pathway subverts host survival by impairing energy metabolism and the mitochondrial UPR.

Siraje Arif Mahmud, Mohammed Adnan Qureshi, Madhab Sapkota, Mark W Pellegrino.

The mitochondrial unfolded protein response (UPRmt) is a stress-activated pathway promoting mitochondrial recovery and defense against infection. In C. elegans, the UPRmt is activated during infection with the pathogen Pseudomonas aeruginosa-but only transiently. As this may reflect a pathogenic strategy to target a pathway required for host survival, we conducted a P. aeruginosa genetic screen to uncover mechanisms associated with this temporary activation. Here, we find that loss of the P. aeruginosa acyl-CoA dehydrogenase FadE2 prolongs UPRmt activity and extends host survival. FadE2 shows substrate preferences for the coenzyme A intermediates produced during the breakdown of the branched-chain amino acids valine and leucine. Our data suggests that during infection, FadE2 restricts the supply of these catabolites to the host hindering host energy metabolism in addition to the UPRmt. Thus, a metabolic pathway in P. aeruginosa contributes to pathogenesis during infection through manipulation of host energy status and mitochondrial stress signaling potential.

DOI: https://doi.org/10.1371/journal.ppat.1008918
Cell Rep. 2020 Sep 29. pii: S2211-1247(20)31198-0. [Epub ahead of print]32(13): 108209

Coupling of Peptidoglycan Synthesis to Central Metabolism in Mycobacteria: Post-transcriptional Control of CwlM by Aconitase.

Peter J Bancroft, Obolbek Turapov, Heena Jagatia, Kristine B Arnvig, Galina V Mukamolova, Jeffrey Green.

  Mycobacterium tuberculosis causes human tuberculosis, and a better understanding of its biology is required to identify vulnerabilities that might be exploited in developing new therapeutics. The iron-sulfur cluster of the essential M. tuberculosis central metabolic enzyme, aconitase (AcnA), disassembles when exposed to oxidative/nitrosative stress or iron chelators. The catalytically inactive apo-AcnA interacts with a sequence resembling an iron-responsive element (IRE) located within the transcript of another essential protein, CwlM, a regulator of peptidoglycan synthesis. A Mycobacterium smegmatis cwlM conditional mutant complemented with M. tuberculosis cwlM with a disrupted IRE is unable to recover from combinations of oxidative, nitrosative, and iron starvation stresses. An equivalent M. tuberculosis cwlM conditional mutant complemented with the cwlM gene lacking a functional IRE exhibits a growth defect in THP-1 macrophages. It appears that AcnA acts to couple peptidoglycan synthesis and central metabolism, and disruption of this coupling potentially leaves mycobacteria vulnerable to attack by macrophages.

Keywords:  CwlM; Mycobacterium tuberculosis; aconitase; iron-responsive element; macrophage infection; nitrosative stress; oxidative stress; peptidoglycan; post-transcriptional regulation; protein kinase B (PknB)

DOI:  https://doi.org/10.1016/j.celrep.2020.108209
Lab Invest. 2020 Sep 29.

Utilizing tandem mass spectrometry for metabolic flux analysis.

Yujue Wang, Sheng Hui, Fredric E Wondisford, Xiaoyang Su.

Metabolic flux analysis (MFA) aims at revealing the metabolic reaction rates in a complex biochemical network. To do so, MFA uses the input of stable isotope labeling patterns of the intracellular metabolites. Elementary metabolic unit (EMU) is the computational framework to simulate the metabolite labeling patterns in a network, which was originally designed for simulating mass isotopomer distributions (MIDs) at the MS1 level. Recently, the EMU framework is expanded to simulate tandem mass spectrometry data. Tandem mass spectrometry has emerged as a new experimental approach to provide information on the positional isotope labeling of metabolites and therefore greatly improves the precision of MFA. In this review, we will discuss the new EMU framework that can accommodate the tandem mass isotopomer distributions (TMIDs) data. We will also analyze the improvement on the MFA precision by using TMID. Our analysis shows that combining the MIDs of the parent and daughter ions and the TMID for the MFA is more powerful than using TMID alone.

DOI: https://doi.org/10.1038/s41374-020-00488-z
Nat Commun. 2020 10 01. 11(1): 4913

PINCH-1 regulates mitochondrial dynamics to promote proline synthesis and tumor growth.

Ling Guo, Chunhong Cui, Jiaxin Wang, Jifan Yuan, Qingyang Yang, Ping Zhang, Wen Su, Ruolu Bao, Jingchao Ran, Chuanyue Wu.

Reprograming of proline metabolism is critical for tumor growth. Here we show that PINCH-1 is highly expressed in lung adenocarcinoma and promotes proline synthesis through regulation of mitochondrial dynamics. Knockout (KO) of PINCH-1 increases dynamin-related protein 1 (DRP1) expression and mitochondrial fragmentation, which suppresses kindlin-2 mitochondrial translocation and interaction with pyrroline-5-carboxylate reductase 1 (PYCR1), resulting in inhibition of proline synthesis and cell proliferation. Depletion of DRP1 reverses PINCH-1 deficiency-induced defects on mitochondrial dynamics, proline synthesis and cell proliferation. Furthermore, overexpression of PYCR1 in PINCH-1 KO cells restores proline synthesis and cell proliferation, and suppresses DRP1 expression and mitochondrial fragmentation. Finally, ablation of PINCH-1 from lung adenocarcinoma in mouse increases DRP1 expression and inhibits PYCR1 expression, proline synthesis, fibrosis and tumor growth. Our results identify a signaling axis consisting of PINCH-1, DRP1 and PYCR1 that regulates mitochondrial dynamics and proline synthesis, and suggest an attractive strategy for alleviation of tumor growth.

DOI: https://doi.org/10.1038/s41467-020-18753-6
Nat Commun. 2020 Oct 02. 11(1): 4938

SARS-CoV2-mediated suppression of NRF2-signaling reveals potent antiviral and anti-inflammatory activity of 4-octyl-itaconate and dimethyl fumarate.

David Olagnier, Ensieh Farahani, Jacob Thyrsted, Julia Blay-Cadanet, Angela Herengt, Manja Idorn, Alon Hait, Bruno Hernaez, Alice Knudsen, Marie Beck Iversen, Mirjam Schilling, Sofie E Jørgensen, Michelle Thomsen, Line S Reinert, Michael Lappe, Huy-Dung Hoang, Victoria H Gilchrist, Anne Louise Hansen, Rasmus Ottosen, Camilla G Nielsen, Charlotte Møller, Demi van der Horst, Suraj Peri, Siddharth Balachandran, Jinrong Huang, Martin Jakobsen, Esben B Svenningsen, Thomas B Poulsen, Lydia Bartsch, Anne L Thielke, Yonglun Luo, Tommy Alain, Jan Rehwinkel, Antonio Alcamí, John Hiscott, Trine Mogensen, Søren R Paludan, Christian K Holm.

Antiviral strategies to inhibit Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) and the pathogenic consequences of COVID-19 are urgently required. Here, we demonstrate that the NRF2 antioxidant gene expression pathway is suppressed in biopsies obtained from COVID-19 patients. Further, we uncover that NRF2 agonists 4-octyl-itaconate (4-OI) and the clinically approved dimethyl fumarate (DMF) induce a cellular antiviral program that potently inhibits replication of SARS-CoV2 across cell lines. The inhibitory effect of 4-OI and DMF extends to the replication of several other pathogenic viruses including Herpes Simplex Virus-1 and-2, Vaccinia virus, and Zika virus through a type I interferon (IFN)-independent mechanism. In addition, 4-OI and DMF limit host inflammatory responses to SARS-CoV2 infection associated with airway COVID-19 pathology. In conclusion, NRF2 agonists 4-OI and DMF induce a distinct IFN-independent antiviral program that is broadly effective in limiting virus replication and in suppressing the pro-inflammatory responses of human pathogenic viruses, including SARS-CoV2.

DOI: https://doi.org/10.1038/s41467-020-18764-3
Trends Pharmacol Sci. 2020 Sep 26. pii: S0165-6147(20)30204-2. [Epub ahead of print]

Metformin and Systemic Metabolism.

Ling He.

  Metformin can improve patients' hyperglycemia through significant suppression of hepatic glucose production. However, up to 300 times higher concentrations of metformin accumulate in the intestine than in the circulation, where it alters nutrient metabolism in intestinal epithelial cells and microbiome, leading to increased lactate production. Hepatocytes use lactate to make glucose at the cost of energy expenditure, creating a futile intestine-liver cycle. Furthermore, metformin reduces blood lipopolysaccharides and its initiated low-grade inflammation and increased oxidative phosphorylation in liver and adipose tissues. These metformin effects result in the improvement of insulin sensitivity and glucose utilization in extrahepatic tissues. In this review, I discuss the current understanding of the impact of metformin on systemic metabolism and its molecular mechanisms of action in various tissues.

Keywords:  Metformin; insulin resistance; mitochondria; nutrient metabolism

DOI:  https://doi.org/10.1016/j.tips.2020.09.001