bims-camemi 2019-10-06 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2019‒10‒06
38 papers selected by
Christian Frezza,

Dissociation of mitochondrial HK-II elicits mitophagy and confers cardioprotection against ischemia.
Mitochondrial calcium exchange links metabolism with the epigenome to control cellular differentiation.
PINK1/Parkin Influences Cell Cycle by Sequestering TBK1 at Damaged Mitochondria, Inhibiting Mitosis.
NAD+ in Brain Aging and Neurodegenerative Disorders.
Dietary Sugars Alter Hepatic Fatty Acid Oxidation via Transcriptional and Post-translational Modifications of Mitochondrial Proteins.
Phosphoethanolamine Accumulation Protects Cancer Cells under Glutamine Starvation through Downregulation of PCYT2.
Crosstalk between Mitochondrial Ca2+ Uptake and Autophagy in Skeletal Muscle.
Breathe: Your Mitochondria Will Do the Rest… If They Are Healthy!
Oxidative stress mediates ethanol-induced skeletal muscle mitochondrial dysfunction and dysregulated protein synthesis and autophagy.
Differential contribution of pyruvate carboxylation to anaplerosis and cataplerosis during non-gluconeogenic and gluconeogenic conditions in HepG2 cells.
Manipulating mtDNA in vivo reprograms metabolism via novel response mechanisms.
Metabolic Diversity in Human Non-Small Cell Lung Cancer Cells.
MFF REGULATION OF MITOCHONDRIAL CELL DEATH IS A THERAPEUTIC TARGET IN CANCER.
Liver-Type Glutaminase GLS2 Is a Druggable Metabolic Node in Luminal-Subtype Breast Cancer.
Mitochondrial phosphoenolpyruvate carboxykinase (PCK2) regulates osteogenic differentiation by modulating AMPK/ULK1-dependent autophagy.
Mitochondrial Dynamics and Its Involvement in Disease.
United They Stand, Divided They Fall.
Thioredoxin-1 maintains mitochondrial function via mTOR signaling in the heart.
PI3K/Akt pathway-mediated HO-1 induction regulates mitochondrial quality control and attenuates endotoxin-induced acute lung injury.
In Vivo Microdialysis of Endogenous and 13C-labeled TCA Metabolites in Rat Brain: Reversible and Persistent Effects of Mitochondrial Inhibition and Transient Cerebral Ischemia.
Dynamic Incorporation of Histone H3 Variants into Chromatin Is Essential for Acquisition of Aggressive Traits and Metastatic Colonization.
Prolonged hypoxia decreases nuclear pyruvate dehydrogenase complex and regulates the gene expression.
RORα is crucial for attenuated inflammatory response to maintain intestinal homeostasis.
Distinct Alterations in Tricarboxylic Acid Cycle Metabolites Associate with Cancer and Autism Phenotypes in Cowden Syndrome and Bannayan-Riley-Ruvalcaba Syndrome.
Oncogenic Rag GTPase signaling enhances B cell activation and drives follicular lymphoma sensitive to pharmacological inhibition of mTOR.
Functional expression of a bacterial α-ketoglutarate dehydrogenase in the cytosol of Saccharomyces cerevisiae.
PRDM16 Maintains Homeostasis of the Intestinal Epithelium by Controlling Region-Specific Metabolism.
Fifty Shades of α-Ketoglutarate on Cellular Programming.
Bile acid-induced "Minority MOMP" promotes esophageal carcinogenesis while maintaining apoptotic resistance via Mcl-1.
ZNF281 is recruited on DNA breaks to facilitate DNA repair by non-homologous end joining.
Germline NPM1 mutations lead to altered rRNA 2'-O-methylation and cause dyskeratosis congenita.
CD98hc (SLC3A2) sustains amino acid and nucleotide availability for cell cycle progression.
Metabolic Consequences of T-cell Costimulation in Anticancer Immunity.
Miro1 Marks Parkinson's Disease Subset and Miro1 Reducer Rescues Neuron Loss in Parkinson's Models.
MK5 regulates YAP stability and is a molecular target in YAP-driven cancers.
Systematic identification of metabolites controlling gene expression in E. coli.
Absence of HIF1A leads to glycogen accumulation and an inflammatory response that enables pancreatic tumor growth.
Histone lysine methyltransferases in biology and disease.

Cell Death Dis. 2019 Sep 30. 10(10): 730

Dissociation of mitochondrial HK-II elicits mitophagy and confers cardioprotection against ischemia.

Valerie P Tan, Jeffrey M Smith, Michelle Tu, Justin D Yu, Eric Y Ding, Shigeki Miyamoto.

Preservation of mitochondrial integrity is critical for maintaining cellular homeostasis. Mitophagy is a mitochondria-specific type of autophagy which eliminates damaged mitochondria thereby contributing to mitochondrial quality control. Depolarization of the mitochondrial membrane potential is an established mechanism for inducing mitophagy, mediated through PINK1 stabilization and Parkin recruitment to mitochondria. Hexokinase-II (HK-II) which catalyzes the first step in glucose metabolism, also functions as a signaling molecule to regulate cell survival, and a significant fraction of cellular HK-II is associated with mitochondria (mitoHK-II). We demonstrate here that pharmacological interventions and adenoviral expression of a mitoHK-II dissociating peptide which reduce mitoHK-II levels lead to robust increases in mitochondrial Parkin and ubiquitination of mitochondrial proteins in cardiomyocytes and in a human glioblastoma cell line 1321N1, independent of mitochondrial membrane depolarization or PINK1 accumulation. MitoHK-II dissociation-induced mitophagy was demonstrated using Mito-Keima in cardiomyocytes and in 1321N1 cells. Subjecting cardiomyocytes or the in vivo heart to ischemia leads to modest dissociation of mitoHK-II. This response is potentiated by expression of the mitoHK-II dissociating peptide, which increases Parkin recruitment to mitochondria and, importantly, provides cardioprotection against ischemic stress. These results suggest that mitoHK-II dissociation is a physiologically relevant cellular event that is induced by ischemic stress, the enhancement of which protects against ischemic damage. The mechanism which underlies the effects of mitoHK-II dissociation can be attributed to the ability of Bcl2-associated athanogene 5 (BAG5), an inhibitor of Parkin, to localize to mitochondria and form a molecular complex with HK-II. Overexpression of BAG5 attenuates while knockdown of BAG5 sensitizes the effect of mitoHK-II dissociation on mitophagy. We suggest that HK-II, a glycolytic molecule, can function as a sensor for metabolic derangements at mitochondria to trigger mitophagy, and modulating the intracellular localization of HK-II could be a novel way of regulating mitophagy to prevent cell death induced by ischemic stress.

DOI: https://doi.org/10.1038/s41419-019-1965-7
Nat Commun. 2019 Oct 04. 10(1): 4509

Mitochondrial calcium exchange links metabolism with the epigenome to control cellular differentiation.

Alyssa A Lombardi, Andrew A Gibb, Ehtesham Arif, Devin W Kolmetzky, Dhanendra Tomar, Timothy S Luongo, Pooja Jadiya, Emma K Murray, Pawel K Lorkiewicz, György Hajnóczky, Elizabeth Murphy, Zoltan P Arany, Daniel P Kelly, Kenneth B Margulies, Bradford G Hill, John W Elrod.

Fibroblast to myofibroblast differentiation is crucial for the initial healing response but excessive myofibroblast activation leads to pathological fibrosis. Therefore, it is imperative to understand the mechanisms underlying myofibroblast formation. Here we report that mitochondrial calcium (mCa2+) signaling is a regulatory mechanism in myofibroblast differentiation and fibrosis. We demonstrate that fibrotic signaling alters gating of the mitochondrial calcium uniporter (mtCU) in a MICU1-dependent fashion to reduce mCa2+ uptake and induce coordinated changes in metabolism, i.e., increased glycolysis feeding anabolic pathways and glutaminolysis yielding increased α-ketoglutarate (αKG) bioavailability. mCa2+-dependent metabolic reprogramming leads to the activation of αKG-dependent histone demethylases, enhancing chromatin accessibility in loci specific to the myofibroblast gene program, resulting in differentiation. Our results uncover an important role for the mtCU beyond metabolic regulation and cell death and demonstrate that mCa2+ signaling regulates the epigenome to influence cellular differentiation.

DOI: https://doi.org/10.1038/s41467-019-12103-x
Cell Rep. 2019 Oct 01. pii: S2211-1247(19)31147-7. [Epub ahead of print]29(1): 225-235.e5

PINK1/Parkin Influences Cell Cycle by Sequestering TBK1 at Damaged Mitochondria, Inhibiting Mitosis.

Shireen A Sarraf, Dionisia P Sideris, Nikolaos Giagtzoglou, Lina Ni, Mark W Kankel, Anindya Sen, Lauren E Bochicchio, Chiu-Hui Huang, Samuel C Nussenzweig, Stuart H Worley, Paul D Morton, Spyros Artavanis-Tsakonas, Richard J Youle, Alicia M Pickrell.

  PINK1 and Parkin are established mediators of mitophagy, the selective removal of damaged mitochondria by autophagy. PINK1 and Parkin have been proposed to act as tumor suppressors, as loss-of-function mutations are correlated with enhanced tumorigenesis. However, it is unclear how PINK1 and Parkin act in coordination during mitophagy to influence the cell cycle. Here we show that PINK1 and Parkin genetically interact with proteins involved in cell cycle regulation, and loss of PINK1 and Parkin accelerates cell growth. PINK1- and Parkin-mediated activation of TBK1 at the mitochondria during mitophagy leads to a block in mitosis due to the sequestration of TBK1 from its physiological role at centrosomes during mitosis. Our study supports a diverse role for the far-reaching, regulatory effects of mitochondrial quality control in cellular homeostasis and demonstrates that the PINK1/Parkin pathway genetically interacts with the cell cycle, providing a framework for understanding the molecular basis linking PINK1 and Parkin to mitosis.

Keywords:  ATM; PINK1; Parkin; TBK1; cell cycle; centrosome; ik2; mitophagy; mitosis; tank binding kinase 1

DOI:  https://doi.org/10.1016/j.celrep.2019.08.085
Cell Metab. 2019 Oct 01. pii: S1550-4131(19)30502-9. [Epub ahead of print]30(4): 630-655

NAD+ in Brain Aging and Neurodegenerative Disorders.

Sofie Lautrup, David A Sinclair, Mark P Mattson, Evandro F Fang.

  NAD+ is a pivotal metabolite involved in cellular bioenergetics, genomic stability, mitochondrial homeostasis, adaptive stress responses, and cell survival. Multiple NAD+-dependent enzymes are involved in synaptic plasticity and neuronal stress resistance. Here, we review emerging findings that reveal key roles for NAD+ and related metabolites in the adaptation of neurons to a wide range of physiological stressors and in counteracting processes in neurodegenerative diseases, such as those occurring in Alzheimer's, Parkinson's, and Huntington diseases, and amyotrophic lateral sclerosis. Advances in understanding the molecular and cellular mechanisms of NAD+-based neuronal resilience will lead to novel approaches for facilitating healthy brain aging and for the treatment of a range of neurological disorders.

Keywords:  Alzheimer’s disease; NAD+; Parkinson’s disease; brain aging; mitochondria; mitophagy; neurodegeneration; neuronal plasticity; sirtuins

DOI:  https://doi.org/10.1016/j.cmet.2019.09.001
Cell Metab. 2019 Oct 01. pii: S1550-4131(19)30504-2. [Epub ahead of print]30(4): 735-753.e4

Dietary Sugars Alter Hepatic Fatty Acid Oxidation via Transcriptional and Post-translational Modifications of Mitochondrial Proteins.

Samir Softic, Jesse G Meyer, Guo-Xiao Wang, Manoj K Gupta, Thiago M Batista, Hans P M M Lauritzen, Shiho Fujisaka, Dolors Serra, Laura Herrero, Jennifer Willoughby, Kevin Fitzgerald, Olga Ilkayeva, Christopher B Newgard, Bradford W Gibson, Birgit Schilling, David E Cohen, C Ronald Kahn.

  Dietary sugars, fructose and glucose, promote hepatic de novo lipogenesis and modify the effects of a high-fat diet (HFD) on the development of insulin resistance. Here, we show that fructose and glucose supplementation of an HFD exert divergent effects on hepatic mitochondrial function and fatty acid oxidation. This is mediated via three different nodes of regulation, including differential effects on malonyl-CoA levels, effects on mitochondrial size/protein abundance, and acetylation of mitochondrial proteins. HFD- and HFD plus fructose-fed mice have decreased CTP1a activity, the rate-limiting enzyme of fatty acid oxidation, whereas knockdown of fructose metabolism increases CPT1a and its acylcarnitine products. Furthermore, fructose-supplemented HFD leads to increased acetylation of ACADL and CPT1a, which is associated with decreased fat metabolism. In summary, dietary fructose, but not glucose, supplementation of HFD impairs mitochondrial size, function, and protein acetylation, resulting in decreased fatty acid oxidation and development of metabolic dysregulation.

Keywords:  acetylation; fatty acid oxidation; fatty liver disease; fructose; glucose; ketohexokinase; mass spectrometry; mitochondria; obesity; sugar

DOI:  https://doi.org/10.1016/j.cmet.2019.09.003
Cell Rep. 2019 Oct 01. pii: S2211-1247(19)31149-0. [Epub ahead of print]29(1): 89-103.e7

Phosphoethanolamine Accumulation Protects Cancer Cells under Glutamine Starvation through Downregulation of PCYT2.

Tsuyoshi Osawa, Teppei Shimamura, Kyoko Saito, Yoko Hasegawa, Naoko Ishii, Miyuki Nishida, Ritsuko Ando, Ayano Kondo, Muyassar Anwar, Rika Tsuchida, Shinjiro Hino, Akihisa Sakamoto, Kaori Igarashi, Kaori Saitoh, Keiko Kato, Keiko Endo, Shotaro Yamano, Yasuharu Kanki, Yoshihiro Matsumura, Takashi Minami, Toshiya Tanaka, Motonobu Anai, Youichiro Wada, Hideki Wanibuchi, Mitsuhiro Hayashi, Akinobu Hamada, Masayuki Yoshida, Shinichi Yachida, Mitsuyoshi Nakao, Juro Sakai, Hiroyuki Aburatani, Masabumi Shibuya, Kentaro Hanada, Satoru Miyano, Tomoyoshi Soga, Tatsuhiko Kodama.

  Tolerance to severe tumor microenvironments, including hypoxia and nutrient starvation, is a common feature of aggressive cancer cells and can be targeted. However, metabolic alterations that support cancer cells upon nutrient starvation are not well understood. Here, by comprehensive metabolome analyses, we show that glutamine deprivation leads to phosphoethanolamine (PEtn) accumulation in cancer cells via the downregulation of PEtn cytidylyltransferase (PCYT2), a rate-limiting enzyme of phosphatidylethanolamine biosynthesis. PEtn accumulation correlated with tumor growth under nutrient starvation. PCYT2 suppression was partially mediated by downregulation of the transcription factor ELF3. Furthermore, PCYT2 overexpression reduced PEtn levels and tumor growth. In addition, PEtn accumulation and PCYT2 downregulation in human breast tumors correlated with poor prognosis. Thus, we show that glutamine deprivation leads to tumor progression by regulating PE biosynthesis via the ELF3-PCYT2 axis. Furthermore, manipulating glutamine-responsive genes could be a therapeutic approach to limit cancer progression.

Keywords:  PCYT2; PE biosynthesis; amino acids; cancer metabolism; glutamine deprivation; hypoxia; nutrient starvation; phosphoethanolamine; tumor microenvironments

DOI:  https://doi.org/10.1016/j.celrep.2019.08.087
Oxid Med Cell Longev. 2019 ;2019 1845321

Crosstalk between Mitochondrial Ca2+ Uptake and Autophagy in Skeletal Muscle.

Gaia Gherardi, Giulia Di Marco, Rosario Rizzuto, Cristina Mammucari.

Autophagy is responsible for the maintenance of skeletal muscle homeostasis, thanks to the removal of aberrant and dysfunctional macromolecules and organelles. During fasting, increased autophagy ensures the maintenance of the amino acid pool required for energy production. The activity of the mitochondrial Ca2+ uniporter (MCU), the highly selective channel responsible for mitochondrial Ca2+ uptake, controls skeletal muscle size, force, and nutrient utilization. Thus, both autophagy and mitochondrial Ca2+ accumulation play a pivotal role to maintain muscle homeostasis and to sustain muscle function. Here, we address whether, in skeletal muscle, mitochondrial Ca2+ uptake and autophagy are mutually related. Muscle-restricted MCU silencing partially inhibits the autophagy flux. Moreover, skeletal muscle-specific deletion of the essential autophagy gene Atg7, known to cause the accumulation of dysfunctional mitochondria, drastically reduces mitochondrial Ca2+ accumulation. Thus, a vicious cycle takes place, in which reduced MCU activity hampers the autophagic flux, and loss of autophagy further impairs mitochondrial Ca2+ signaling.

DOI: https://doi.org/10.1155/2019/1845321
Cell Metab. 2019 Oct 01. pii: S1550-4131(19)30507-8. [Epub ahead of print]30(4): 628-629

Breathe: Your Mitochondria Will Do the Rest… If They Are Healthy!

Carlo Viscomi, Massimo Zeviani.

Dysfunctions of the mitochondrial electron transport chain cause severe, currently untreatable, diseases in humans. A new study by Jain et al. (2019) reports increased oxygen levels in the brain of complex-I-deficient mice. Reducing the O2 levels by hypoxia, carbon monoxide, or anemia, improved the clinical phenotype and prolonged the lifespan of the mouse model.

DOI: https://doi.org/10.1016/j.cmet.2019.09.004
Free Radic Biol Med. 2019 Sep 28. pii: S0891-5849(19)31297-3. [Epub ahead of print]

Oxidative stress mediates ethanol-induced skeletal muscle mitochondrial dysfunction and dysregulated protein synthesis and autophagy.

Avinash Kumar, Gangarao Davuluri, Nicole Welch, Adam Kim, Mahesha Gangadhariah, Allawy Allawy, Anupama Priyadarshini, Megan R McMullen, Yana Sandlers, Belinda Willard, Charles L Hoppel, Laura E Nagy, Srinivasan Dasarathy.

  Protein synthesis and autophagy are regulated by cellular ATP content. We tested the hypothesis that mitochondrial dysfunction, including generation of reactive oxygen species (ROS), contributes to impaired protein synthesis and increased proteolysis resulting in tissue atrophy in a comprehensive array of models. In myotubes treated with ethanol, using unbiased approaches, we identified defects in mitochondrial electron transport chain components, endogenous antioxidants, and enzymes regulating the tricarboxylic acid (TCA) cycle. Using high sensitivity respirometry, we observed impaired cellular respiration, decreased function of complexes I, II, and IV, and a reduction in oxidative phosphorylation in ethanol-treated myotubes and muscle from ethanol-fed mice. These perturbations resulted in lower skeletal muscle ATP content and redox ratio (NAD+/NADH). Ethanol also caused a leak of electrons, primarily from complex III, with generation of mitochondrial ROS and reverse electron transport. Oxidant stress with lipid peroxidation (thiobarbituric acid reactive substances) and protein oxidation (carbonylated proteins) were increased in myotubes and skeletal muscle from mice and humans with alcoholic liver disease. Ethanol also impaired succinate oxidation in the TCA cycle with decreased metabolic intermediates. MitoTEMPO, a mitochondrial specific antioxidant, reversed ethanol-induced mitochondrial perturbations (including reduced oxygen consumption, generation of ROS and oxidative stress), increased TCA cycle intermediates, and reversed impaired protein synthesis and the sarcopenic phenotype. We show that ethanol causes skeletal muscle mitochondrial dysfunction, decreased protein synthesis, and increased autophagy, and that these perturbations are reversed by targeting mitochondrial ROS.

Keywords:  ATP; Ethanol; Mitochondria; Oxidative stress; Skeletal muscle

DOI:  https://doi.org/10.1016/j.freeradbiomed.2019.09.031
Arch Biochem Biophys. 2019 Oct 01. pii: S0003-9861(19)30468-0. [Epub ahead of print] 108124

Differential contribution of pyruvate carboxylation to anaplerosis and cataplerosis during non-gluconeogenic and gluconeogenic conditions in HepG2 cells.

Siriluck Wattanavanitchakorn, Israr-Ul H Ansari, Mahmoud El Azzouny, Melissa J Longacre, Scott W Stoker, Sarawut Jitrapakdee, Michael J MacDonald.

  Pyruvate carboxylase (PC) is an anaplerotic enzyme that supplies oxaloacetate to mitochondria enabling the maintenance of other metabolic intermediates consumed by cataplerosis. Using liquid chromatography mass spectrometry (LC-MS) to measure metabolic intermediates derived from uniformly labeled 13C6-glucose or [3-13C]l-lactate, we investigated the contribution of PC to anaplerosis and cataplerosis in the liver cell line HepG2. Suppression of PC expression by short hairpin RNA lowered incorporation of 13C glucose incorporation into tricarboxylic acid cycle intermediates, aspartate, glutamate and sugar derivatives, indicating impaired cataplerosis. The perturbation of these biosynthetic pathways is accompanied by a marked decrease of cell viability and proliferation. In contrast, under gluconeogenic conditions where the HepG2 cells use lactate as a carbon source, pyruvate carboxylation contributed very little to the maintenance of these metabolites. Suppression of PC did not affect the percent incorporation of 13C-labeled carbon from lactate into citrate, α-ketoglutarate, malate, succinate as well as aspartate and glutamate, suggesting that under gluconeogenic condition, PC does not support cataplerosis from lactate.

Keywords:  Anaplerosis; Cataplerosis; Gluconeogenesis; Metabolic flux; PC; PEPCK; Phosphoenolpyruvate carboxykinase; Pyruvate carboxylase; TCA; TCA cycle; Tricarboxylic acid cycle

DOI:  https://doi.org/10.1016/j.abb.2019.108124
PLoS Genet. 2019 Oct 04. 15(10): e1008410

Manipulating mtDNA in vivo reprograms metabolism via novel response mechanisms.

Diana Bahhir, Cagri Yalgin, Liina Ots, Sampsa Järvinen, Jack George, Alba Naudí, Tatjana Krama, Indrikis Krams, Mairi Tamm, Ana Andjelković, Eric Dufour, Jose M González de Cózar, Mike Gerards, Mikael Parhiala, Reinald Pamplona, Howard T Jacobs, Priit Jõers.

Mitochondria have been increasingly recognized as a central regulatory nexus for multiple metabolic pathways, in addition to ATP production via oxidative phosphorylation (OXPHOS). Here we show that inducing mitochondrial DNA (mtDNA) stress in Drosophila using a mitochondrially-targeted Type I restriction endonuclease (mtEcoBI) results in unexpected metabolic reprogramming in adult flies, distinct from effects on OXPHOS. Carbohydrate utilization was repressed, with catabolism shifted towards lipid oxidation, accompanied by elevated serine synthesis. Cleavage and translocation, the two modes of mtEcoBI action, repressed carbohydrate rmetabolism via two different mechanisms. DNA cleavage activity induced a type II diabetes-like phenotype involving deactivation of Akt kinase and inhibition of pyruvate dehydrogenase, whilst translocation decreased post-translational protein acetylation by cytonuclear depletion of acetyl-CoA (AcCoA). The associated decease in the concentrations of ketogenic amino acids also produced downstream effects on physiology and behavior, attributable to decreased neurotransmitter levels. We thus provide evidence for novel signaling pathways connecting mtDNA to metabolism, distinct from its role in supporting OXPHOS.

DOI: https://doi.org/10.1371/journal.pgen.1008410
Mol Cell. 2019 Sep 24. pii: S1097-2765(19)30683-5. [Epub ahead of print]

Metabolic Diversity in Human Non-Small Cell Lung Cancer Cells.

Pei-Hsuan Chen, Ling Cai, Kenneth Huffman, Chendong Yang, Jiyeon Kim, Brandon Faubert, Lindsey Boroughs, Bookyung Ko, Jessica Sudderth, Elizabeth A McMillan, Luc Girard, Dong Chen, Michael Peyton, Misty D Shields, Bo Yao, David S Shames, Hyun Seok Kim, Brenda Timmons, Ikuo Sekine, Rebecca Britt, Stephanie Weber, Lauren A Byers, John V Heymach, Jing Chen, Michael A White, John D Minna, Guanghua Xiao, Ralph J DeBerardinis.

  Intermediary metabolism in cancer cells is regulated by diverse cell-autonomous processes, including signal transduction and gene expression patterns, arising from specific oncogenotypes and cell lineages. Although it is well established that metabolic reprogramming is a hallmark of cancer, we lack a full view of the diversity of metabolic programs in cancer cells and an unbiased assessment of the associations between metabolic pathway preferences and other cell-autonomous processes. Here, we quantified metabolic features, mostly from the 13C enrichment of molecules from central carbon metabolism, in over 80 non-small cell lung cancer (NSCLC) cell lines cultured under identical conditions. Because these cell lines were extensively annotated for oncogenotype, gene expression, protein expression, and therapeutic sensitivity, the resulting database enables the user to uncover new relationships between metabolism and these orthogonal processes.

Keywords:  (13)C stable isotope labeling; cancer metabolism; cell lines; gene expression; glucose; glutamine; non-small cell lung cancer; oncogenotypes; protein expression; therapeutic sensitivity

DOI:  https://doi.org/10.1016/j.molcel.2019.08.028
Cancer Res. 2019 Oct 03. pii: canres.1982.2019. [Epub ahead of print]

MFF REGULATION OF MITOCHONDRIAL CELL DEATH IS A THERAPEUTIC TARGET IN CANCER.

Jae Ho Seo, Young Chan Chae, Andrew V Kossenkov, Yu Geon Lee, Hsin-Yao Tang, Ekta Agarwal, Dmitry I Gabrilovich, Lucia R Languino, David W Speicher, Prashanth K Shastrula, Alessandra Maria Storaci, Stefano Ferrero, Gabriella Gaudioso, Manuela Caroli, Davide Tosi, Massimo Giroda, Valentina Vaira, Vito W Rebecca, Meenhard Herlyn, Min Xiao, Dylan Fingerman, Alessandra Martorella, Emmanuel Skordalakes, Dario C Altieri.

The regulators of mitochondrial cell death in cancer have remained elusive, hampering the development of new therapies. Here, we showed that protein isoforms of Mitochondrial Fission Factor (MFF1 and MFF2), a molecule that controls mitochondrial size and shape, i.e. mitochondrial dynamics, were overexpressed in patients with non-small cell lung cancer and formed homo- and heterodimeric complexes with the voltage-dependent anion channel-1 (VDAC1), a key regulator of mitochondrial outer membrane permeability. MFF inserted into the interior hole of the VDAC1 ring using Arg225, Arg236 and Gln241 as key contact sites. A cell-permeable MFF Ser223-Leu243 D-enantiomeric peptidomimetic disrupted the MFF-VDAC1 complex, acutely depolarized mitochondria and triggered cell death in heterogeneous tumor types, including drug-resistant melanoma, but had no effect on normal cells. In preclinical models, treatment with the MFF peptidomimetic was well-tolerated and demonstrated anticancer activity in patient-derived xenografts, primary breast and lung adenocarcinoma 3D organoids and glioblastoma neurospheres. These data identify the MFF-VDAC1 complex as a novel regulator of mitochondrial cell death and an actionable therapeutic target in cancer.

DOI: https://doi.org/10.1158/0008-5472.CAN-19-1982
Cell Rep. 2019 Oct 01. pii: S2211-1247(19)31131-3. [Epub ahead of print]29(1): 76-88.e7

Liver-Type Glutaminase GLS2 Is a Druggable Metabolic Node in Luminal-Subtype Breast Cancer.

Michael J Lukey, Ahmad A Cluntun, William P Katt, Miao-Chong J Lin, Joseph E Druso, Sekar Ramachandran, Jon W Erickson, Henry H Le, Zhihan-Emily Wang, Bryant Blank, Kai Su Greene, Richard A Cerione.

  Efforts to target glutamine metabolism for cancer therapy have focused on the glutaminase isozyme GLS. The importance of the other isozyme, GLS2, in cancer has remained unclear, and it has been described as a tumor suppressor in some contexts. Here, we report that GLS2 is upregulated and essential in luminal-subtype breast tumors, which account for >70% of breast cancer incidence. We show that GLS2 expression is elevated by GATA3 in luminal-subtype cells but suppressed by promoter methylation in basal-subtype cells. Although luminal breast cancers resist GLS-selective inhibitors, we find that they can be targeted with a dual-GLS/GLS2 inhibitor. These results establish a critical role for GLS2 in mammary tumorigenesis and advance our understanding of how to target glutamine metabolism in cancer.

Keywords:  968; BPTES; CB-839; GLS; breast cancer; glutaminase; glutamine metabolism GLS2

DOI:  https://doi.org/10.1016/j.celrep.2019.08.076
Stem Cells. 2019 Oct 01.

Mitochondrial phosphoenolpyruvate carboxykinase (PCK2) regulates osteogenic differentiation by modulating AMPK/ULK1-dependent autophagy.

Zheng Li, Xuenan Liu, Yuan Zhu, Yangge Du, Xuejiao Liu, Longwei Lv, Xiao Zhang, Yunsong Liu, Ping Zhang, Yongsheng Zhou.

  Mitochondrial phosphoenolpyruvate carboxykinase (PCK2) is a rate-limiting enzyme that plays critical roles in multiple physiological processes. The decompensation of PCK2 leads to various energy metabolic disorders. However, little is known regarding the effects of PCK2 on osteogenesis by human adipose-derived mesenchymal stem cells (hMSCs). Here, we report a novel function of PCK2 as a positive regulator of MSCs osteogenic differentiation. In addition to its well-known role in anabolism, we demonstrate that PCK2 regulates autophagy. PCK2 deficiency significantly suppressed autophagy, leading to the impairment of osteogenic capacity of MSCs. On the other hand, autophagy was promoted by PCK2 overexpression; this was accompanied by increased osteogenic differentiation of MSCs. Moreover, PCK2 regulated osteogenic differentiation of MSCs via AMPK/ULK1-dependent autophagy. Collectively, our present study unveiled a novel role for PCK2 in integrating autophagy and bone formation, providing a potential target for stem-cell-based bone tissue engineering that may lead to improved therapies for metabolic bone diseases. © AlphaMed Press 2019 SIGNIFICANCE STATEMENT: The degradation substances from autophagy can be used as an optional nutrient supply for cell survival and differentiation, making autophagy a suitable energy-refuelling process during osteogenesis by MSCs. Although mitochondrial phosphoenolpyruvate carboxykinase (PCK2) has been suggested as a critical enzyme for anabolism, it has been unclear whether PCK2 play critical roles in autophagy. The study first determines that PCK2 promotes osteogenic differentiation by positively regulating autophagy in MSCs, which facilities better application of bone tissue engineering and maintenance of bone homeostasis.

Keywords:  Autophagy; mesenchymal stem cells; mitochondrial phosphoenolpyruvate carboxykinase; osteogenic differentiation

DOI:  https://doi.org/10.1002/stem.3091
Annu Rev Pathol. 2019 Oct 04.

Mitochondrial Dynamics and Its Involvement in Disease.

David C Chan.

The dynamic properties of mitochondria-including their fusion, fission, and degradation-are critical for their optimal function in energy generation. The interplay of fusion and fission confers widespread benefits on mitochondria, including efficient transport, increased homogenization of the mitochondrial population, and efficient oxidative phosphorylation. These benefits arise through control of morphology, content exchange, equitable inheritance of mitochondria, maintenance of high-quality mitochondrial DNA, and segregation of damaged mitochondria for degradation. The key components of the machinery mediating mitochondrial fusion and fission belong to the dynamin family of GTPases that utilize GTP hydrolysis to drive mechanical work on biological membranes. Defects in this machinery cause a range of diseases that especially affect the nervous system. In addition, several common diseases, including neurodegenerative diseases and cancer, strongly affect mitochondrial dynamics. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 15 is January 24, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI: https://doi.org/10.1146/annurev-pathmechdis-012419-032711
Cell Metab. 2019 Oct 01. pii: S1550-4131(19)30511-X. [Epub ahead of print]30(4): 624-625

United They Stand, Divided They Fall.

Isaac S Harris, Joan S Brugge.

Cancer cells that leave their natural environment during metastatic spread must adapt to numerous stresses to survive. In this issue, Labuschagne et al. (2019) highlight one adaptive mechanism to overcome these stresses that involves cell clustering, which induces a hypoxic environment and metabolic rewiring to buffer oxidative stress.

DOI: https://doi.org/10.1016/j.cmet.2019.09.008
Cardiovasc Res. 2019 Oct 04. pii: cvz251. [Epub ahead of print]

Thioredoxin-1 maintains mitochondrial function via mTOR signaling in the heart.

Shin-Ichi Oka, Adave Chin, Ji Yeon Park, Shohei Ikeda, Wataru Mizushima, Guersom Ralda, Peiyong Zhai, Mingming Tong, Jaemin Byun, Fan Tang, Yudai Einaga, Chun-Yang Huang, Toshihide Kashihara, Mengyuan Zhao, Jihoon Nah, Bin Tian, Yoko Hirabayashi, Junji Yodoi, Junichi Sadoshima.

  AIMS: Thioredoxin 1 (Trx1) is an evolutionarily conserved oxidoreductase that cleaves disulfide bonds in oxidized substrate proteins such as mechanistic target of rapamycin (mTOR) and maintains nuclear-encoded mitochondrial gene expression. The cardioprotective effect of Trx1 has been demonstrated via cardiac-specific overexpression of Trx1 and dominant negative Trx1. However, the pathophysiological role of endogenous Trx1 has not been defined with a loss-of-function model. To address this, we have generated cardiac-specific Trx1 knockout (Trx1cKO) mice.METHODS AND RESULTS: Trx1cKO mice were viable but died with a median survival age of 25.5 days. They developed heart failure, evidenced by contractile dysfunction, hypertrophy, and increased fibrosis and apoptotic cell death. Multiple markers consistently indicated increased oxidative stress and RNA-sequencing revealed downregulation of genes involved in energy production in Trx1cKO mice. Mitochondrial morphological abnormality was evident in these mice. Although heterozygous Trx1cKO mice did not show any significant baseline phenotype, pressure-overload-induced cardiac dysfunction and downregulation of metabolic genes were exacerbated in these mice. mTOR was more oxidized and phosphorylation of mTOR substrates such as S6K and 4EBP1 was impaired in Trx1cKO mice. In cultured cardiomyocytes, Trx1 knockdown inhibited mitochondrial respiration and metabolic gene promoter activity, suggesting that Trx1 maintains mitochondrial function in a cell autonomous manner. Importantly, mTOR-C1483F, an oxidation resistant mutation, prevented Trx1 knockdown-induced mTOR oxidation and inhibition and attenuated suppression of metabolic gene promoter activity.
CONCLUSION(S): Endogenous Trx1 is essential for maintaining cardiac function and metabolism, partly through mTOR regulation via Cys1483.
TRANSLATIONAL PERSPECTIVE: Although cell protective effects of Trx1 have been demonstrated previously, the in vivo function and the direct target of endogenous Trx1 remain to be elucidated. Using cardiac-specific Trx1 KO mice, this study demonstrates that endogenous Trx1 plays an essential role in maintaining cardiac function and redox homeostasis and confers stress resistance to the heart. The salutary effect of Trx1 in the heart is primarily mediated through reduction of mTOR in vivo.

Keywords:  Heart; Redox; Thioredoxin-1(Trx1); mechanistic target of rapamycin (mTOR); metabolism

DOI:  https://doi.org/10.1093/cvr/cvz251
Lab Invest. 2019 Sep 30.

PI3K/Akt pathway-mediated HO-1 induction regulates mitochondrial quality control and attenuates endotoxin-induced acute lung injury.

Jia Shi, Jianbo Yu, Yuan Zhang, Lili Wu, Shuan Dong, Lina Wu, Lingzhi Wu, Shihan Du, Yanfang Zhang, Daqing Ma.

Sepsis-related acute lung injury (ALI) remains a major cause of mortality in critically ill patients and lacks specific therapy. Mitochondrial dysfunction is involved in the progression of septic lung injury. Mitochondrial dynamics, mitophagy, and biogenesis converge to constitute the assiduous quality control of mitochondria (MQC). Heme oxygenase-1 (HO-1) protects against sepsis-induced ALI through the modulation of mitochondrial dynamics. However, the causal relationship between HO-1 and the general processes of MQC, and their associated cellular pathways in sepsis-related ALI remain ill-defined. Herein, lipopolysaccharide (LPS)-induced ALI in Sprague-Dawley rats together with LPS-induced oxidative injury in RAW264.7 macrophages were used to investigate whether the PI3K/Akt pathway-mediated induction of HO-1 preserves MQC and alleviates septic lung injury. After pretreatment with hemin, a potent inducer of HO-1, LPS-induced cell apoptosis, enhanced mitochondrial fragmentation, and mitochondrial membrane potential damage were significantly reduced in macrophages. In rats, these effects were accompanied by a higher survival rate, less damage to lung tissue, a 28.5% elevation in lung mitochondria MnSOD activity, and a 39.2% increase in respiratory control ratios. Concomitantly, HO-1 induction preserved the dynamic process of mitochondrial fusion/fission (Mfn2, OPA1, Drp1), promoted mitochondrial biogenesis (NRF1, PGC1α, Tfam), and facilitated the key mediators of mitochondrial mitophagy (Parkin, PINK1) at mRNA and protein levels. Notably, LY294002, a PI3K inhibitor, or knockdown of PI3K by small interfering RNA significantly suppressed Akt phosphorylation, attenuated HO-1 induction, and further reversed these beneficial effects evoked by hemin pretreatment in RAW264.7 cells or rats received LPS, indicating a direct involvement of PI3K/Akt pathway. Taken together, our results indicated that HO-1 activation, through PI3K/Akt pathway, plays a critical role in protecting lung from oxidative injury in the setting of sepsis by regulating MQC. HO-1 may therefore be a therapeutic target for the prevention sepsis-related lung injury.

DOI: https://doi.org/10.1038/s41374-019-0286-x
Metabolites. 2019 Sep 27. pii: E204. [Epub ahead of print]9(10):

In Vivo Microdialysis of Endogenous and 13C-labeled TCA Metabolites in Rat Brain: Reversible and Persistent Effects of Mitochondrial Inhibition and Transient Cerebral Ischemia.

Jesper F Havelund, Kevin H Nygaard, Troels H Nielsen, Carl-Henrik Nordström, Frantz R Poulsen, Nils J Færgeman, Axel Forsse, Jan Bert Gramsbergen.

  Cerebral micro-dialysis allows continuous sampling of extracellular metabolites, including glucose, lactate and pyruvate. Transient ischemic events cause a rapid drop in glucose and a rise in lactate levels. Following such events, the lactate/pyruvate (L/P) ratio may remain elevated for a prolonged period of time. In neurointensive care clinics, this ratio is considered a metabolic marker of ischemia and/or mitochondrial dysfunction. Here we propose a novel, sensitive microdialysis liquid chromatography-mass spectrometry (LC-MS) approach to monitor mitochondrial dysfunction in living brain using perfusion with 13C-labeled succinate and analysis of 13C-labeled tricarboxylic acid cycle (TCA) intermediates. This approach was evaluated in rat brain using malonate-perfusion (10-50 mM) and endothelin-1 (ET-1)-induced transient cerebral ischemia. In the malonate model, the expected changes upon inhibition of succinate dehydrogenase (SDH) were observed, i.e., an increase in endogenous succinate and decreases in fumaric acid and malic acid. The inhibition was further elaborated by incorporation of 13C into specific TCA intermediates from 13C-labeled succinate. In the ET-1 model, increases in non-labeled TCA metabolites (reflecting release of intracellular compounds) and decreases in 13C-labeled TCA metabolites (reflecting inhibition of de novo synthesis) were observed. The analysis of 13C incorporation provides further layers of information to identify metabolic disturbances in experimental models and neuro-intensive care patients.

Keywords:  13C-labeled succinate; LC-MS; cerebral ischemia; endothelin-1; energy metabolism; malonate; micro-dialysis; mitochondrial dysfunction; reperfusion; tricarboxylic acid cycle

DOI:  https://doi.org/10.3390/metabo9100204
Cancer Cell. 2019 Sep 04. pii: S1535-6108(19)30374-5. [Epub ahead of print]

Dynamic Incorporation of Histone H3 Variants into Chromatin Is Essential for Acquisition of Aggressive Traits and Metastatic Colonization.

Ana P Gomes, Didem Ilter, Vivien Low, Adam Rosenzweig, Zih-Jie Shen, Tanya Schild, Martin A Rivas, Ekrem E Er, Dylan R McNally, Anders P Mutvei, Julie Han, Yi-Hung Ou, Paola Cavaliere, Edouard Mullarky, Michal Nagiec, Sejeong Shin, Sang-Oh Yoon, Noah Dephoure, Joan Massagué, Ari M Melnick, Lewis C Cantley, Jessica K Tyler, John Blenis.

  Metastasis is the leading cause of cancer mortality. Chromatin remodeling provides the foundation for the cellular reprogramming necessary to drive metastasis. However, little is known about the nature of this remodeling and its regulation. Here, we show that metastasis-inducing pathways regulate histone chaperones to reduce canonical histone incorporation into chromatin, triggering deposition of H3.3 variant at the promoters of poor-prognosis genes and metastasis-inducing transcription factors. This specific incorporation of H3.3 into chromatin is both necessary and sufficient for the induction of aggressive traits that allow for metastasis formation. Together, our data clearly show incorporation of histone variant H3.3 into chromatin as a major regulator of cell fate during tumorigenesis, and histone chaperones as valuable therapeutic targets for invasive carcinomas.

Keywords:  CAF-1 complex; HIRA; chromatin remodeling; epigenetics; histone H3.3; histone chaperones; metastasis; tumor progression

DOI:  https://doi.org/10.1016/j.ccell.2019.08.006
Biochem Biophys Res Commun. 2019 Sep 30. pii: S0006-291X(19)31847-9. [Epub ahead of print]

Prolonged hypoxia decreases nuclear pyruvate dehydrogenase complex and regulates the gene expression.

Kayoko Eguchi, Koh Nakayama.

  Cells require proper regulation of energy metabolism to maintain cellular homeostasis. Pyruvate dehydrogenase (PDH) is a metabolic enzyme that converts pyruvate into acetyl-CoA, connecting glycolysis to the TCA cycle, thus regulating cellular energy metabolism. PDH is involved in multiple cellular processes, such as glucose metabolism, fatty acid synthesis, and protein acetylation, all of which are mediated by acetyl-CoA. We previously demonstrated that PDH-E1β is downregulated in prolonged hypoxia and inhibits PDH activity, which serves as machinery to securely inhibit PDH activity together with PDH-E1α phosphorylation. PDH has been identified to localize to the nucleus in addition to mitochondria, but its precise regulatory mechanisms in the nucleus remain elusive. In the present study, we characterized nuclear PDH during prolonged hypoxia. Nuclear PDH complex was downregulated under hypoxic conditions, and PDH activity was reduced. Depletion of HIF-1α partly recovered nuclear levels of the PDH complex. Furthermore, decreased nuclear PDH activity resulted in reduced histone H3 acetylation, altering the gene expression profile of cells exposed to prolonged hypoxia. Taken together, these findings indicate that nuclear PDH complex is downregulated under prolonged hypoxic conditions and controls gene expression.

Keywords:  Histone acetylation; Hypoxia; Nucleus; PDH complex; Pyruvate dehydrogenase

DOI:  https://doi.org/10.1016/j.bbrc.2019.09.109
Proc Natl Acad Sci U S A. 2019 Sep 30. pii: 201907595. [Epub ahead of print]

RORα is crucial for attenuated inflammatory response to maintain intestinal homeostasis.

Se Kyu Oh, Dongha Kim, Kyeongkyu Kim, Kyungjin Boo, Young Suk Yu, Ik Soo Kim, Yoon Jeon, Sun-Kyoung Im, Su-Hyung Lee, Ji Min Lee, Younhee Ko, Ho Lee, Daechan Park, Sungsoon Fang, Sung Hee Baek.

  Retinoic acid-related orphan receptor α (RORα) functions as a transcription factor for various biological processes, including circadian rhythm, cancer, and metabolism. Here, we generate intestinal epithelial cell (IEC)-specific RORα-deficient (RORαΔIEC) mice and find that RORα is crucial for maintaining intestinal homeostasis by attenuating nuclear factor κB (NF-κB) transcriptional activity. RORαΔIEC mice exhibit excessive intestinal inflammation and highly activated inflammatory responses in the dextran sulfate sodium (DSS) mouse colitis model. Transcriptome analysis reveals that deletion of RORα leads to up-regulation of NF-κB target genes in IECs. Chromatin immunoprecipitation analysis reveals corecruitment of RORα and histone deacetylase 3 (HDAC3) on NF-κB target promoters and subsequent dismissal of CREB binding protein (CBP) and bromodomain-containing protein 4 (BRD4) for transcriptional repression. Together, we demonstrate that RORα/HDAC3-mediated attenuation of NF-κB signaling controls the balance of inflammatory responses, and therapeutic strategies targeting this epigenetic regulation could be beneficial to the treatment of chronic inflammatory diseases, including inflammatory bowel disease (IBD).

Keywords:  HDAC3; NF-kB signaling; RORα; epigenetic regulation; inflammation

DOI:  https://doi.org/10.1073/pnas.1907595116
Am J Hum Genet. 2019 Oct 03. pii: S0002-9297(19)30343-X. [Epub ahead of print]105(4): 813-821

Distinct Alterations in Tricarboxylic Acid Cycle Metabolites Associate with Cancer and Autism Phenotypes in Cowden Syndrome and Bannayan-Riley-Ruvalcaba Syndrome.

Lamis Yehia, Ying Ni, Fang Feng, Marilyn Seyfi, Tammy Sadler, Thomas W Frazier, Charis Eng.

  Germline heterozygous PTEN mutations cause subsets of Cowden syndrome (CS) and Bannayan-Riley-Ruvalcaba syndrome (BRRS); these subsets are characterized by high risks of breast, thyroid, and other cancers and, in one subset, autism spectrum disorder (ASD). Up to 10% of individuals with PTENMUT CS, CS-like syndrome, or BRRS have germline SDHx (succinate dehydrogenase, mitochondrial complex II) variants, which modify cancer risk. PTEN contributes to metabolic reprogramming; this is a well-established role in a cancer context. Relatedly, SDH sits at the crossroad of the electron transport chain and tricarboxylic acid (TCA) cycle, two central bioenergetic pathways. Intriguingly, PTENMUT and SDHMUT individuals have reduced SDH catalytic activity, resulting in succinate accumulation; this indicates a common genotype-independent biochemical alteration. Here, we conducted a TCA targeted metabolomics study on 511 individuals with CS, CS-like syndrome, or BRRS with various genotypes (PTEN or SDHx, mutant or wild type [WT]) and phenotypes (cancer or ASD) and a series of 187 population controls. We found consistent TCA cycle metabolite alterations in cases with various genotypes and phenotypes compared to controls, and we found unique correlations of individual metabolites with particular genotype-phenotype combinations. Notably, increased isocitrate (p = 1.2 × 10-3), but reduced citrate (p = 5.0 × 10-4), were found to be associated with breast cancer in individuals with PTENMUT/SDHxWT. Conversely, increased lactate was associated with neurodevelopmental disorders regardless of genotype (p = 9.7 × 10-3); this finding was replicated in an independent validation series (n = 171) enriched for idiopathic ASD (PTENWT, p = 5.6 × 10-4). Importantly, we identified fumarate (p = 1.9 × 10-2) as a pertinent metabolite, distinguishing individuals who develop ASD from those who develop cancer. Our observations suggest that TCA cycle metabolite alterations are germane to the pathobiology of PTEN-related CS and BRRS, as well as genotype-independent ASD, with implications for potential biomarker and/or therapeutic value.

Keywords:  Krebs cycle; PTEN hamartoma tumor syndrome; autism spectrum disorder; hereditary cancer; neurodevelopmental disorders; targeted metabolomics

DOI:  https://doi.org/10.1016/j.ajhg.2019.09.004
Nat Metab. 2019 Aug;1(8): 775-789

Oncogenic Rag GTPase signaling enhances B cell activation and drives follicular lymphoma sensitive to pharmacological inhibition of mTOR.

Ana Ortega-Molina, Nerea Deleyto-Seldas, Joaquim Carreras, Alba Sanz, Cristina Lebrero-Fernández, Camino Menéndez, Andrew Vandenberg, Beatriz Fernández-Ruiz, Leyre Marín-Arraiza, Celia de la Calle Arregui, Ana Belén Plata-Gómez, Eduardo Caleiras, Alba de Martino, Nuria Martínez-Martín, Kevin Troulé, Elena Piñeiro-Yáñez, Naoya Nakamura, Shamzah Araf, Gabriel D Victora, Jessica Okosun, Jude Fitzgibbon, Alejo Efeyan.

  The humoral immune response demands that B cells undergo a sudden anabolic shift and high cellular nutrient levels which are required to sustain the subsequent proliferative burst. Follicular lymphoma (FL) originates from B cells that have participated in the humoral response, and 15% of FL samples harbor point, activating mutations in RRAGC, an essential activator of mTORC1 downstream of the sensing of cellular nutrients. The impact of recurrent RRAGC mutations in B cell function and lymphoma is unexplored. RRAGC mutations, targeted to the endogenous locus in mice, confer a partial insensitivity to nutrient deprivation, but strongly exacerbate B cell responses and accelerate lymphomagenesis, while creating a selective vulnerability to pharmacological inhibition of mTORC1. This moderate increase in nutrient signaling synergizes with paracrine cues from the supportive T cell microenvironment that activates B cells via the PI3K-Akt-mTORC1 axis. Hence, Rragc mutations sustain induced germinal centers and murine and human FL in the presence of decreased T cell help. Our results support a model in which activating mutations in the nutrient signaling pathway foster lymphomagenesis by corrupting a nutrient-dependent control over paracrine signals from the T cell microenvironment.

Keywords:  B cell lymphoma; B lymphocytes; RRAGC; T follicular helper; apoptosis; cell growth; germinal center; mTOR; nutrient signaling; rapamycin

DOI:  https://doi.org/10.1038/s42255-019-0098-8
Metab Eng. 2019 Oct 01. pii: S1096-7176(19)30332-5. [Epub ahead of print]

Functional expression of a bacterial α-ketoglutarate dehydrogenase in the cytosol of Saccharomyces cerevisiae.

Nicolo Baldi, James C Dykstra, Marijke A H Luttik, Martin Pabst, Liang Wu, Kirsten R Benjamin, André Vente, Jack T Pronk, Robert Mans.

  Efficient production of fuels and chemicals by metabolically engineered micro-organisms requires availability of precursor molecules for product pathways. In eukaryotic cell factories, heterologous product pathways are usually expressed in the cytosol, which may limit availability of precursors that are generated in other cellular compartments. In Saccharomyces cerevisiae, synthesis of the precursor molecule succinyl-Coenzyme A is confined to the mitochondrial matrix. To enable cytosolic synthesis of succinyl-CoA, we expressed the structural genes for all three subunits of the Escherichia coli α-ketoglutarate dehydrogenase (αKGDH) complex in S. cerevisiae. The E. coli lipoic-acid scavenging enzyme was co-expressed to enable cytosolic lipoylation of the αKGDH complex, which is required for its enzymatic activity. Size-exclusion chromatography and mass spectrometry indicated that the heterologously expressed αKGDH complex contained all subunits and that its size was the same as in E. coli. Functional expression of the heterologous complex was evident from increased αKGDH activity in the cytosolic fraction of yeast cell homogenates. In vivo cytosolic activity of the αKGDH complex was tested by constructing a reporter strain in which the essential metabolite 5-aminolevulinic acid could only be synthetized from cytosolic, and not mitochondrial, succinyl-CoA. To this end HEM1, which encodes the succinyl-CoA-converting mitochondrial enzyme 5-aminolevulinic acid (ALA) synthase, was deleted and a bacterial ALA synthase was expressed in the cytosol. In the resulting strain, complementation of ALA auxotrophy depended on activation of the αKGDH complex by lipoic acid addition. Functional expression of a bacterial αKGDH complex in yeast represents a vital step towards efficient yeast-based production of compounds such as 1,4-butanediol and 4-aminobutyrate, whose product pathways use succinyl-CoA as a precursor.

Keywords:  5-Aminolevulinic acid; Compartmentalization; Lipoylation; Precursor supply; Proteomics; Succinyl-CoA

DOI:  https://doi.org/10.1016/j.ymben.2019.10.001
Cell Stem Cell. 2019 Sep 21. pii: S1934-5909(19)30384-4. [Epub ahead of print]

PRDM16 Maintains Homeostasis of the Intestinal Epithelium by Controlling Region-Specific Metabolism.

Rachel R Stine, Alexander P Sakers, Tara TeSlaa, Megan Kissig, Zachary E Stine, Chan Wook Kwon, Lan Cheng, Hee-Woong Lim, Klaus H Kaestner, Joshua D Rabinowitz, Patrick Seale.

  Metabolic pathways dynamically regulate tissue development and maintenance. However, the mechanisms that govern the metabolic adaptation of stem or progenitor cells to their local niche are poorly understood. Here, we define the transcription factor PRDM16 as a region-specific regulator of intestinal metabolism and epithelial renewal. PRDM16 is selectively expressed in the upper intestine, with enrichment in crypt-resident progenitor cells. Acute Prdm16 deletion in mice triggered progenitor apoptosis, leading to diminished epithelial differentiation and severe intestinal atrophy. Genomic and metabolic analyses showed that PRDM16 transcriptionally controls fatty acid oxidation (FAO) in crypts. Expression of this PRDM16-driven FAO program was highest in the upper small intestine and declined distally. Accordingly, deletion of Prdm16 or inhibition of FAO selectively impaired the development and maintenance of upper intestinal enteroids, and these effects were rescued by acetate treatment. Collectively, these data reveal that regionally specified metabolic programs regulate intestinal maintenance.

Keywords:  PRDM16; apoptosis; differentiation; duodenum; fatty acid oxidation; intestinal stem cell; intestine; metabolism; transit amplifying cell

DOI:  https://doi.org/10.1016/j.stem.2019.08.017
Mol Cell. 2019 Oct 03. pii: S1097-2765(19)30687-2. [Epub ahead of print]76(1): 1-3

Fifty Shades of α-Ketoglutarate on Cellular Programming.

Giusy Di Conza, Chin-Hsien Tsai, Ping-Chih Ho.

High plasticity to utilize different nutrients to adapt metabolic stress is one of the hallmarks for cancer cells. However, the underlying mechanisms by which cancer cells reprogram metabolic machinery in response to metabolic stress remain largely unclear. In this issue of Molecular Cell, Wang et al. (2019) report that glutamate dehydrogenase 1 (GDH1) induces an unconventional regulation of the NF-κB pathway under glucose deprivation, thereby stimulating glycolysis in glioblastomas.

DOI: https://doi.org/10.1016/j.molcel.2019.09.002
Oncogene. 2019 Sep 30.

Bile acid-induced "Minority MOMP" promotes esophageal carcinogenesis while maintaining apoptotic resistance via Mcl-1.

Yuan Xu, Deborah R Surman, Laurence Diggs, Sichuan Xi, Shaojian Gao, Devikala Gurusamy, Kaitlin McLoughlin, Justin Drake, Paul Feingold, Kate Brown, Danny Wangsa, Darawalee Wangsa, Xi Zhang, Thomas Ried, Jeremy L Davis, Jonathan Hernandez, Chuong Hoang, Rhonda F Souza, David S Schrump, R Taylor Ripley.

Barrett's esophagus (BE) is associated with reflux and is implicated the development of esophageal adenocarcinoma (EAC). Apoptosis induces cell death through mitochondrial outer membrane permeabilization (MOMP), which is considered an irreversible step in apoptosis. Activation of MOMP to levels that fail to reach the apoptotic threshold may paradoxically promote cancer-a phenomenon called "Minority MOMP." We asked whether reflux-induced esophageal carcinogenesis occurred via minority MOMP and whether compensatory resistance mechanisms prevented cell death during this process. We exposed preneoplastic, hTERT-immortalized Barrett's cell, CP-C and CP-A, to the oncogenic bile acid, deoxycholic acid (DCA), for 1 year. Induction of minority MOMP was tested via comet assay, CyQuant, annexin V, JC-1, cytochrome C subcellular localization, caspase 3 activation, and immunoblots. We used bcl-2 homology domain-3 (BH3) profiling to test the mitochondrial apoptotic threshold. One-year exposure of Barrett's cells to DCA induced a malignant phenotype noted by clone and tumor formation. DCA promoted minority MOMP noted by minimal release of cytochrome C and limited caspase 3 activation, which resulted in DNA damage without apoptosis. Upregulation of the antiapoptotic protein, Mcl-1, ROS generation, and NF-κB activation occurred in conjunction with minority MOMP. Inhibition of ROS blocked minority MOMP and Mcl-1 upregulation. Knockdown of Mcl-1 shifted minority MOMP to complete MOMP as noted by dynamic BH3 profiling and increased apoptosis. Minority MOMP contributes to DCA induced carcinogenesis in preneoplastic BE. Mcl-1 provided a balance within the mitochondria that induced resistance complete MOMP and cell death. Targeting Mcl-1 may be a therapeutic strategy in EAC.

DOI: https://doi.org/10.1038/s41388-019-1029-6
Oncogene. 2019 Sep 30.

ZNF281 is recruited on DNA breaks to facilitate DNA repair by non-homologous end joining.

Sara Nicolai, Robert Mahen, Giuseppe Raschellà, Alberto Marini, Marco Pieraccioli, Michal Malewicz, Ashok R Venkitaraman, Gerry Melino.

Efficient repair of DNA double-strand breaks (DSBs) is of critical importance for cell survival. Although non-homologous end joining (NHEJ) is the most used DSBs repair pathway in the cells, how NHEJ factors are sequentially recruited to damaged chromatin remains unclear. Here, we identify a novel role for the zinc-finger protein ZNF281 in participating in the ordered recruitment of the NHEJ repair factor XRCC4 at damage sites. ZNF281 is recruited to DNA lesions within seconds after DNA damage through a mechanism dependent on its DNA binding domain and, at least in part, on poly-ADP ribose polymerase (PARP) activity. ZNF281 binds XRCC4 through its zinc-finger domain and facilitates its recruitment to damaged sites. Consequently, depletion of ZNF281 impairs the efficiency of the NHEJ repair pathway and decreases cell viability upon DNA damage. Survival analyses from datasets of commonly occurring human cancers show that higher levels of ZNF281 correlate with poor prognosis of patients treated with DNA-damaging therapies. Thus, our results define a late ZNF281-dependent regulatory step of NHEJ complex assembly at DNA lesions and suggest additional possibilities for cancer patients' stratification and for the development of personalised therapeutic strategies.

DOI: https://doi.org/10.1038/s41388-019-1028-7
Nat Genet. 2019 Sep 30.

Germline NPM1 mutations lead to altered rRNA 2'-O-methylation and cause dyskeratosis congenita.

Daphna Nachmani, Anne H Bothmer, Silvia Grisendi, Aldo Mele, Dietmar Bothmer, Jonathan D Lee, Emanuele Monteleone, Ke Cheng, Yang Zhang, Assaf C Bester, Alison Guzzetti, Caitlin A Mitchell, Lourdes M Mendez, Olga Pozdnyakova, Paolo Sportoletti, Maria-Paola Martelli, Tom J Vulliamy, Modi Safra, Schraga Schwartz, Lucio Luzzatto, Olivier Bluteau, Jean Soulier, Robert B Darnell, Brunangelo Falini, Inderjeet Dokal, Keisuke Ito, John G Clohessy, Pier Paolo Pandolfi.

RNA modifications are emerging as key determinants of gene expression. However, compelling genetic demonstrations of their relevance to human disease are lacking. Here, we link ribosomal RNA 2'-O-methylation (2'-O-Me) to the etiology of dyskeratosis congenita. We identify nucleophosmin (NPM1) as an essential regulator of 2'-O-Me on rRNA by directly binding C/D box small nucleolar RNAs, thereby modulating translation. We demonstrate the importance of 2'-O-Me-regulated translation for cellular growth, differentiation and hematopoietic stem cell maintenance, and show that Npm1 inactivation in adult hematopoietic stem cells results in bone marrow failure. We identify NPM1 germline mutations in patients with dyskeratosis congenita presenting with bone marrow failure and demonstrate that they are deficient in small nucleolar RNA binding. Mice harboring a dyskeratosis congenita germline Npm1 mutation recapitulate both hematological and nonhematological features of dyskeratosis congenita. Thus, our findings indicate that impaired 2'-O-Me can be etiological to human disease.

DOI: https://doi.org/10.1038/s41588-019-0502-z
Sci Rep. 2019 Oct 01. 9(1): 14065

CD98hc (SLC3A2) sustains amino acid and nucleotide availability for cell cycle progression.

Sara Cano-Crespo, Josep Chillarón, Alexandra Junza, Gonzalo Fernández-Miranda, Judit García, Christine Polte, Laura R de la Ballina, Zoya Ignatova, Óscar Yanes, Antonio Zorzano, Camille Stephan-Otto Attolini, Manuel Palacín.

CD98 heavy chain (CD98hc) forms heteromeric amino acid (AA) transporters by interacting with different light chains. Cancer cells overexpress CD98hc-transporters in order to meet their increased nutritional and antioxidant demands, since they provide branched-chain AA (BCAA) and aromatic AA (AAA) availability while protecting cells from oxidative stress. Here we show that BCAA and AAA shortage phenocopies the inhibition of mTORC1 signalling, protein synthesis and cell proliferation caused by CD98hc ablation. Furthermore, our data indicate that CD98hc sustains glucose uptake and glycolysis, and, as a consequence, the pentose phosphate pathway (PPP). Thus, loss of CD98hc triggers a dramatic reduction in the nucleotide pool, which leads to replicative stress in these cells, as evidenced by the enhanced DNA Damage Response (DDR), S-phase delay and diminished rate of mitosis, all recovered by nucleoside supplementation. In addition, proper BCAA and AAA availability sustains the expression of the enzyme ribonucleotide reductase. In this regard, BCAA and AAA shortage results in decreased content of deoxynucleotides that triggers replicative stress, also recovered by nucleoside supplementation. On the basis of our findings, we conclude that CD98hc plays a central role in AA and glucose cellular nutrition, redox homeostasis and nucleotide availability, all key for cell proliferation.

DOI: https://doi.org/10.1038/s41598-019-50547-9
Cancer Immunol Res. 2019 Oct;7(10): 1564-1569

Metabolic Consequences of T-cell Costimulation in Anticancer Immunity.

Alvaro Teijeira, Saray Garasa, Inaki Etxeberria, Maria Gato-Cañas, Ignacio Melero, Greg M Delgoffe.

T-cell functional behavior and performance are closely regulated by nutrient availability and the control of metabolism within the T cell. T cells have distinct energetic and anabolic needs when nascently activated, actively proliferating, in naïveté, or in a resting, memory state. As a consequence, bioenergetics are key for T cells to mount adequate immune responses in health and disease. Solid tumors are particularly hostile metabolic environments, characterized by low glucose concentration, hypoxia, and low pH. These metabolic conditions in the tumor are known to hinder antitumor immune responses of T cells by limiting nutrient availability and energetic efficiency. In such immunosuppressive environments, artificial modulation of glycolysis, mitochondrial respiratory capabilities, and fatty acid β-oxidation are known to enhance antitumor performance. Reportedly, costimulatory molecules, such as CD28 and CD137, are important regulators of metabolic routes in T cells. In this sense, different costimulatory signals and cytokines induce diverse metabolic changes that critically involve mitochondrial mass and function. For instance, the efficacy of chimeric antigen receptors (CAR) encompassing costimulatory domains, agonist antibodies to costimulatory receptors, and checkpoint inhibitors depends on the associated metabolic events in immune cells. Here, we review the metabolic changes that costimulatory receptors can promote in T cells and the potential consequences for cancer immunotherapy. Our focus is mostly on discoveries regarding the physiology and pharmacology of IL15, CD28, PD-1, and CD137 (4-1BB).

DOI: https://doi.org/10.1158/2326-6066.CIR-19-0115
Cell Metab. 2019 Sep 23. pii: S1550-4131(19)30497-8. [Epub ahead of print]

Miro1 Marks Parkinson's Disease Subset and Miro1 Reducer Rescues Neuron Loss in Parkinson's Models.

Chung-Han Hsieh, Li Li, Roeland Vanhauwaert, Kong T Nguyen, Mary D Davis, Guojun Bu, Zbigniew K Wszolek, Xinnan Wang.

  The identification of molecular targets and pharmacodynamic markers for Parkinson's disease (PD) will empower more effective clinical management and experimental therapies. Miro1 is localized on the mitochondrial surface and mediates mitochondrial motility. Miro1 is removed from depolarized mitochondria to facilitate their clearance via mitophagy. Here, we explore the clinical utility of Miro1 for detecting PD and for gauging potential treatments. We measure the Miro1 response to mitochondrial depolarization using biochemical assays in skin fibroblasts from a broad spectrum of PD patients and discover that more than 94% of the patients' fibroblast cell lines fail to remove Miro1 following depolarization. We identify a small molecule that can repair this defect of Miro1 in PD fibroblasts. Treating patient-derived neurons and fly models with this compound rescues the locomotor deficits and dopaminergic neurodegeneration. Our results indicate that tracking this Miro1 marker and engaging in Miro1-based therapies could open new avenues to personalized medicine.

Keywords:  Miro1; Parkinson; biomarker; diet; fibroblast; fly; iPSC; mitochondria; mitophagy; neurons; small molecules; therapy

DOI:  https://doi.org/10.1016/j.cmet.2019.08.023
Cancer Res. 2019 Oct 02. pii: canres.1339.2019. [Epub ahead of print]

MK5 regulates YAP stability and is a molecular target in YAP-driven cancers.

Jimyung Seo, Min Hwan Kim, Hyowon Hong, Hyunsoo Cho, Seongyeol Park, Sang Kyum Kim, Joon Kim.

Transcriptional regulator YAP is activated in multiple human cancers and plays critical roles in tumor initiation, progression, metastasis, and drug resistance. However, therapeutic targeting of the Hippo-YAP pathway has been challenging due to its low druggability and limited knowledge of YAP regulation in cancer. Here we present a functional screen and identify a novel therapeutic target for YAP-driven tumorigenesis. RNAi screening using an oncogenic YAP activation model identified the serine/threonine kinase MK5 as a positive regulator of YAP. MK5 physically interacted with YAP and counteracted CK1δ/ε-mediated YAP ubiquitination and degradation independent of LATS1/2. MK5 kinase activity was essential for protecting YAP from ubiquitin-mediated degradation and cytoplasmic retention. Downregulating MK5 expression inhibited the survival of YAP-activated cancer cell lines and mouse xenograft models. MK5 upregulation was associated with high levels of YAP expression and poor prognosis in clinical tumor samples, confirming its important role for YAP activity in human cancer. These results uncover MK5 as a novel factor that regulates YAP stability and that targeting the YAP degradation pathway controlled by MK5 is a potential strategy for suppressing YAP activity in cancer.

DOI: https://doi.org/10.1158/0008-5472.CAN-19-1339
Nat Commun. 2019 Oct 02. 10(1): 4463

Systematic identification of metabolites controlling gene expression in E. coli.

Martin Lempp, Niklas Farke, Michelle Kuntz, Sven Andreas Freibert, Roland Lill, Hannes Link.

Metabolism controls gene expression through allosteric interactions between metabolites and transcription factors. These interactions are usually measured with in vitro assays, but there are no methods to identify them at a genome-scale in vivo. Here we show that dynamic transcriptome and metabolome data identify metabolites that control transcription factors in E. coli. By switching an E. coli culture between starvation and growth, we induce strong metabolite concentration changes and gene expression changes. Using Network Component Analysis we calculate the activities of 209 transcriptional regulators and correlate them with metabolites. This approach captures, for instance, the in vivo kinetics of CRP regulation by cyclic-AMP. By testing correlations between all pairs of transcription factors and metabolites, we predict putative effectors of 71 transcription factors, and validate five interactions in vitro. These results show that combining transcriptomics and metabolomics generates hypotheses about metabolism-transcription interactions that drive transitions between physiological states.

DOI: https://doi.org/10.1038/s41467-019-12474-1
Cancer Res. 2019 Oct 04. pii: canres.2994.2018. [Epub ahead of print]

Absence of HIF1A leads to glycogen accumulation and an inflammatory response that enables pancreatic tumor growth.

Marco Maruggi, Fabiana I A L Layng, Robert Lemos, Guillermina Garcia, Brian P James, Monica Sevilla, Ferran Soldevila, Bas J G Baaten, Petrus R de Jong, Mei Yee Koh, Garth Powis.

Cancer cells respond to hypoxia by upregulating the hypoxia-inducible factor 1α HIF1A) transcription factor, which drives survival mechanisms that include metabolic adaptation and induction of angiogenesis by vascular endothelial growth factor (VEGF). Pancreatic tumors are poorly vascularized and severely hypoxic. To study the angiogenic role of HIF1A, and specifically probe whether tumors are able to use alternative pathways in its absence, we created a xenograft mouse tumor model of pancreatic cancer lacking HIF1A. After an initial delay of about 30 days the HIF1A-deficient tumors grew as rapidly as the wild type tumors and had similar vascularization. These changes were maintained in subsequent passages of tumor xenografts in vivo and in cell lines ex vivo. There were many cancer cells with a "clear cell" phenotype in the HIF1A-deficient tumors; this was the result of accumulation of glycogen. Single-cell RNA sequencing (scRNAseq) of the tumors identified hypoxic cancer cells with inhibited glycogen breakdown which promoted glycogen accumulation, and the secretion of inflammatory cytokines including interleukins 1β (IL-1B) and 8 (IL-8). scRNAseq of the mouse tumor stroma showed enrichment of 2 subsets of myeloid dendritic cells (cDC), cDC1 and cDC2, that secreted pro-angiogenic cytokines. These results suggest that glycogen accumulation associated with a clear cell phenotype in hypoxic cancer cells lacking HIF1A can initiate an alternate pathway of cytokine and DC-driven angiogenesis. Inhibiting glycogen accumulation may provide a treatment for cancers with the clear cell phenotype.

DOI: https://doi.org/10.1158/0008-5472.CAN-18-2994
Nat Struct Mol Biol. 2019 Oct;26(10): 880-889

Histone lysine methyltransferases in biology and disease.

Dylan Husmann, Or Gozani.

The precise temporal and spatial coordination of histone lysine methylation dynamics across the epigenome regulates virtually all DNA-templated processes. A large number of histone lysine methyltransferase (KMT) enzymes catalyze the various lysine methylation events decorating the core histone proteins. Mutations, genetic translocations and altered gene expression involving these KMTs are frequently observed in cancer, developmental disorders and other pathologies. Therapeutic compounds targeting specific KMTs are currently being tested in the clinic, although overall drug discovery in the field is relatively underdeveloped. Here we review the biochemical and biological activities of histone KMTs and their connections to human diseases, focusing on cancer. We also discuss the scientific and clinical challenges and opportunities in studying KMTs.

DOI: https://doi.org/10.1038/s41594-019-0298-7