bims-camemi 2019-12-29 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2019–12–29
27 papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit

A Variant of SLC1A5 Is a Mitochondrial Glutamine Transporter for Metabolic Reprogramming in Cancer Cells.
Oncogenic K-ras Induces Mitochondrial OPA3 Expression to Promote Energy Metabolism in Pancreatic Cancer Cells.
OPA1 regulates respiratory supercomplexes assembly: the role of mitochondrial swelling.
Podocytes maintain high basal levels of autophagy independent of mtor signaling.
Glutamine Skipping the Q into Mitochondria.
Ketogenesis-generated β-hydroxybutyrate is an epigenetic regulator of CD8+ T-cell memory development.
Hypoxia Inducible Factor 1α Inhibits the Expression of Immunosuppressive Tryptophan-2,3-Dioxygenase in Glioblastoma.
Mitochondrial fission regulates germ cell differentiation by suppressing ROS-mediated activation of Epidermal Growth Factor Signaling in the Drosophila larval testis.
Bioenergetics underlying single cell migration on aligned nanofiber scaffolds.
The activation loop and substrate-binding cleft of glutaminase C are allosterically coupled.
Sideroflexin 4 affects Fe-S cluster biogenesis, iron metabolism, mitochondrial respiration and heme biosynthetic enzymes.
Metabolism, Epigenetics, and Causal Inference in Heart Failure.
Mitochondrial nucleoid morphology and respiratory function are altered in Drp1-deficient HeLa cells.
Spatiotemporal regulation of NADP(H) phosphatase Nocturnin and its role in oxidative stress response.
Low-Level Saturated Fatty Acid Palmitate Benefits Liver Cells by Boosting Mitochondrial Metabolism via CDK1-SIRT3-CPT2 Cascade.
Glutamine Links Obesity to Inflammation in Human White Adipose Tissue.
HOPS/TMUB1 retains p53 in the cytoplasm and sustains p53-dependent mitochondrial apoptosis.
Crebl2 regulates cell metabolism in muscle and liver cells.
Label-free metabolic imaging by mid-infrared optoacoustic microscopy in living cells.
Redox-mediated kick-start of mitochondrial energy metabolism drives resource-efficient seed germination.
Microbial bile acid metabolites modulate gut RORγ+ regulatory T cell homeostasis.
Molecular basis for acetyl-CoA production by ATP-citrate lyase.
GDF15 mediates the effects of metformin on body weight and energy balance.
Suppression of the SLC7A11/glutathione axis causes synthetic lethality in KRAS-mutant lung adenocarcinoma.
Differential regulation of autophagy during metabolic stress in astrocytes and neurons.
Metabolic changes in the kidney.
Archaic mitochondrial DNA inserts in modern day nuclear genomes.

Cell Metab. 2019 Dec 13. pii: S1550-4131(19)30664-3. [Epub ahead of print]

A Variant of SLC1A5 Is a Mitochondrial Glutamine Transporter for Metabolic Reprogramming in Cancer Cells.

Hee Chan Yoo, Seung Joon Park, Miso Nam, Juwon Kang, Kibum Kim, Joo Hye Yeo, Joon-Ki Kim, Yunkyung Heo, Hee Seung Lee, Myeong Youl Lee, Chang Woo Lee, Jong Soon Kang, Yun-Hee Kim, Jinu Lee, Junjeong Choi, Geum-Sook Hwang, Seungmin Bang, Jung Min Han.

  Glutamine is an essential nutrient that regulates energy production, redox homeostasis, and signaling in cancer cells. Despite the importance of glutamine in mitochondrial metabolism, the mitochondrial glutamine transporter has long been unknown. Here, we show that the SLC1A5 variant plays a critical role in cancer metabolic reprogramming by transporting glutamine into mitochondria. The SLC1A5 variant has an N-terminal targeting signal for mitochondrial localization. Hypoxia-induced gene expression of the SLC1A5 variant is mediated by HIF-2α. Overexpression of the SLC1A5 variant mediates glutamine-induced ATP production and glutathione synthesis and confers gemcitabine resistance to pancreatic cancer cells. SLC1A5 variant knockdown and overexpression alter cancer cell and tumor growth, supporting an oncogenic role. This work demonstrates that the SLC1A5 variant is a mitochondrial glutamine transporter for cancer metabolic reprogramming.

Keywords:  ASCT2; HIF-2α; SLC1A5; SLC1A5 variant; cancer metabolism; gemcitabine resistance; glutamine; hypoxia; metabolic reprogramming; mitochondrial glutamine transporter

DOI:  https://doi.org/10.1016/j.cmet.2019.11.020
Cancers (Basel). 2019 Dec 25. pii: E65. [Epub ahead of print]12(1):

Oncogenic K-ras Induces Mitochondrial OPA3 Expression to Promote Energy Metabolism in Pancreatic Cancer Cells.

Ning Meng, Christophe Glorieux, Yanyu Zhang, Liyun Liang, Peiting Zeng, Wenhua Lu, Peng Huang.

  K-ras (Kirsten ras GTPase) mutations are oncogenic events frequently observed in many cancer types especially in pancreatic cancer. Although mitochondrial dysfunction has been associated with K-ras mutation, the molecular mechanisms by which K-ras impacts mitochondria and maintains metabolic homeostasis are not fully understood. In this study, we used two K-ras inducible cell systems, human pancreatic epithelial/ K-rasG12D (HPNE/K-rasG12D) and human embryonic kidney cells with tetracycline repressorT-Rex/K-rasG12V, to evaluate the role of oncogenic K-ras in regulating mitochondrial function. Among a panel of genes known to affect mitochondria, only the expression of OPA3 (optic atrophy protein 3) was consistently up-regulated by K-ras activation in both cell lines. Importantly, high expression of OPA3 was also observed in clinical pancreatic cancer tissues. Genetic knockdown of OPA3 caused a significant decrease of energy metabolism, manifested by a suppression of oxygen consumption rate (OCR) and a decrease in cellular ATP content, leading to inhibition of cell proliferation capacity and reduced expression of epithelial-mesenchymal transition (EMT) markers. Our study suggests that OPA3 may promote cellular energy metabolism and its up-regulation in K-ras-driven cancer is likely a mechanism to offset the negative impact of K-ras on mitochondria to maintain energy homeostasis. As such, OPA3 could be a potential target to kill cancer cells with K-ras mutations.

Keywords:  K-ras; OPA3; energy metabolism; mitochondria; pancreatic cancer

DOI:  https://doi.org/10.3390/cancers12010065
Mitochondrion. 2019 Dec 20. pii: S1567-7249(19)30143-6. [Epub ahead of print]

OPA1 regulates respiratory supercomplexes assembly: the role of mitochondrial swelling.

Sehwan Jang, Sabzali Javadov.

  Optic atrophy type 1 protein (OPA1), a dynamin-related GTPase, that, in addition to mitochondrial fusion, plays an important role in maintaining the structural organization and integrity of the inner mitochondrial membrane (IMM). OPA1 exists in two forms: IMM-bound long-OPA1 (L-OPA1) and soluble short-OPA1 (S-OPA1), a product of L-OPA1 proteolytic cleavage localized in the intermembrane space. In addition to OPA1, the structural and functional integrity of IMM can be regulated by changes in the matrix volume due to the opening/closure of permeability transition pores (PTP). Herein, we investigated the crosstalk between the PTP and OPA1 to clarify whether PTP opening is involved in OPA1-mediated regulation of respiratory chain supercomplexes (RCS) assembly using cardiac mitochondria and cell line. We found that: 1) Proteolytic cleavage of L-OPA1 is stimulated by PTP-induced mitochondrial swelling, 2) OPA1 knockdown reduces PTP-induced mitochondrial swelling but enhances ROS production, 3) OPA1 deficiency impairs the RCS assembly associated with diminished ETC activity and oxidative phosphorylation, 4) OPA1 has no physical interaction with phospholipid scramblase 3 although OPA1 downregulation increases expression of the scramblase. Thus, this study demonstrates that L-OPA1 cleavage depends on the PTP-induced mitochondrial swelling suggesting a regulatory role of the PTP-OPA1 axis in RCS assembly and mitochondrial bioenergetics.

Keywords:  mitochondria; mitochondrial swelling; optic atrophy type 1 protein; permeability transition pore; respiratory supercomplexes

DOI:  https://doi.org/10.1016/j.mito.2019.11.006
Autophagy. 2019 Dec 23. 1-17

Podocytes maintain high basal levels of autophagy independent of mtor signaling.

Tillmann Bork, Wei Liang, Kosuke Yamahara, Philipp Lee, Zhejia Tian, Shuya Liu, Christoph Schell, Kathrin Thedieck, Bjoern Hartleben, Ketan Patel, Pierre-Louis Tharaux, Olivia Lenoir, Tobias B Huber.

  While constant basal levels of macroautophagy/autophagy are a prerequisite to preserve long-lived podocytes at the filtration barrier, MTOR regulates at the same time podocyte size and compensatory hypertrophy. Since MTOR is known to generally suppress autophagy, the apparently independent regulation of these two key pathways of glomerular maintenance remained puzzling. We now report that long-term genetic manipulation of MTOR activity does in fact not influence high basal levels of autophagy in podocytes either in vitro or in vivo. Instead we present data showing that autophagy in podocytes is mainly controlled by AMP-activated protein kinase (AMPK) and ULK1 (unc-51 like kinase 1). Pharmacological inhibition of MTOR further shows that the uncoupling of MTOR activity and autophagy is time dependent. Together, our data reveal a novel and unexpected cell-specific mechanism, which permits concurrent MTOR activity as well as high basal autophagy rates in podocytes. Thus, these data indicate manipulation of the AMPK-ULK1 axis rather than inhibition of MTOR as a promising therapeutic intervention to enhance autophagy and preserve podocyte homeostasis in glomerular diseases.Abbreviations: AICAR: 5-aminoimidazole-4-carboxamide ribonucleotide; AMPK: AMP-activated protein kinase; ATG: autophagy related; BW: body weight; Cq: chloroquine; ER: endoplasmic reticulum; ESRD: end stage renal disease; FACS: fluorescence activated cell sorting; GFP: green fluorescent protein; i.p.: intra peritoneal; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; NPHS1: nephrosis 1, nephrin; NPHS2: nephrosis 2, podocin; PLA: proximity-ligation assay; PRKAA: 5'-AMP-activated protein kinase catalytic subunit alpha; RPTOR/RAPTOR: regulatory associated protein of MTOR, complex 1; RFP: red fluorescent protein; TSC1: tuberous sclerosis 1; ULK1: unc-51 like kinase 1.

Keywords:  AMPK; LC3; MTOR; Raptor; Tsc1; autophagy; glomerulus; kidney; podocyte; rapamycin; signaling

DOI:  https://doi.org/10.1080/15548627.2019.1705007
Trends Mol Med. 2019 Dec 02. pii: S1471-4914(19)30295-3. [Epub ahead of print]

Glutamine Skipping the Q into Mitochondria.

Zachary E Stine, Chi V Dang.

  Imported across the plasma membrane by SLC1A5, glutamine has emerged as a metabolic fuel that is catabolized by mitochondrial glutaminase to support tumor growth. The missing link between cytoplasmic and mitochondrial glutamine metabolism is now provided by Yoo et al., identifying the mitochondrial glutamine importer as a variant of SLC1A5.

Keywords:  alternative promoter; glutamine; hypoxia; metabolism; mitochondria; transporter

DOI:  https://doi.org/10.1016/j.molmed.2019.11.004
Nat Cell Biol. 2019 Dec 23.

Ketogenesis-generated β-hydroxybutyrate is an epigenetic regulator of CD8+ T-cell memory development.

Huafeng Zhang, Ke Tang, Jingwei Ma, Li Zhou, Jincheng Liu, Liping Zeng, Liyan Zhu, Pingwei Xu, Jie Chen, Keke Wei, Xiaoyu Liang, Jiadi Lv, Jing Xie, Yuying Liu, Yonghong Wan, Bo Huang.

Glycogen has long been considered to have a function in energy metabolism. However, our recent study indicated that glycogen metabolism, directed by cytosolic phosphoenolpyruvate carboxykinase Pck1, controls the formation and maintenance of CD8+ memory T (Tmem) cells by regulating redox homeostasis1. This unusual metabolic program raises the question of how Pck1 is upregulated in CD8+ Tmem cells. Here, we show that mitochondrial acetyl coenzyme A is diverted to the ketogenesis pathway, which indirectly regulates Pck1 expression. Mechanistically, ketogenesis-derived β-hydroxybutyrate is present in CD8+ Tmem cells; β-hydroxybutyrate epigenetically modifies Lys 9 of histone H3 (H3K9) of Foxo1 and Ppargc1a (which encodes PGC-1α) with β-hydroxybutyrylation, upregulating the expression of these genes. As a result, FoxO1 and PGC-1α cooperatively upregulate Pck1 expression, therefore directing the carbon flow along the gluconeogenic pathway to glycogen and the pentose phosphate pathway. These results reveal that ketogenesis acts as an unusual metabolic pathway in CD8+ Tmem cells, linking epigenetic modification required for memory development.

DOI: https://doi.org/10.1038/s41556-019-0440-0
Front Immunol. 2019 ;10 2762

Hypoxia Inducible Factor 1α Inhibits the Expression of Immunosuppressive Tryptophan-2,3-Dioxygenase in Glioblastoma.

Soumya R Mohapatra, Ahmed Sadik, Lars-Oliver Tykocinski, Jørn Dietze, Gernot Poschet, Ines Heiland, Christiane A Opitz.

  Abnormal circulation in solid tumors results in hypoxia, which modulates both tumor intrinsic malignant properties as well as anti-tumor immune responses. Given the importance of hypoxia in glioblastoma (GBM) biology and particularly in shaping anti-tumor immunity, we analyzed which immunomodulatory genes are differentially regulated in response to hypoxia in GBM cells. Gene expression analyses identified the immunosuppressive enzyme tryptophan-2,3-dioxygenase (TDO2) as the second most downregulated gene in GBM cells cultured under hypoxic conditions. TDO2 catalyses the oxidation of tryptophan to N-formyl kynurenine, which is the first and rate-limiting step of Trp degradation along the kynurenine pathway (KP). In multiple GBM cell lines hypoxia reduced TDO2 expression both at mRNA and protein levels. The downregulation of TDO2 through hypoxia was reversible as re-oxygenation rescued TDO2 expression. Computational modeling of tryptophan metabolism predicted reduced flux through the KP and lower intracellular concentrations of kynurenine and its downstream metabolite 3-hydroxyanthranilic acid under hypoxia. Metabolic measurements confirmed the predicted changes, thus demonstrating the ability of the mathematical model to infer intracellular tryptophan metabolite concentrations. Moreover, we identified hypoxia inducible factor 1α (HIF1α) to regulate TDO2 expression under hypoxic conditions, as the HIF1α-stabilizing agents dimethyloxalylglycine (DMOG) and cobalt chloride reduced TDO2 expression. Knockdown of HIF1α restored the expression of TDO2 upon cobalt chloride treatment, confirming that HIF1α controls TDO2 expression. To investigate the immunoregulatory effects of this novel mechanism of TDO2 regulation, we co-cultured isolated T cells with TDO2-expressing GBM cells under normoxic and hypoxic conditions. Under normoxia TDO2-expressing GBM cells suppressed T cell proliferation, while hypoxia restored the proliferation of the T cells, likely due to the reduction in kynurenine levels produced by the GBM cells. Taken together, our data suggest that the regulation of TDO2 expression by HIF1α may be involved in modulating anti-tumor immunity in GBM.

Keywords:  HIF1α; TDO2; hypoxia; immunosuppression; tryptophan

DOI:  https://doi.org/10.3389/fimmu.2019.02762
Sci Rep. 2019 Dec 23. 9(1): 19695

Mitochondrial fission regulates germ cell differentiation by suppressing ROS-mediated activation of Epidermal Growth Factor Signaling in the Drosophila larval testis.

Rafael Sênos Demarco, D Leanne Jones.

Mitochondria are essential organelles that have recently emerged as hubs for several metabolic and signaling pathways in the cell. Mitochondrial morphology is regulated by constant fusion and fission events to maintain a functional mitochondrial network and to remodel the mitochondrial network in response to external stimuli. Although the role of mitochondria in later stages of spermatogenesis has been investigated in depth, the role of mitochondrial dynamics in regulating early germ cell behavior is relatively less-well understood. We previously demonstrated that mitochondrial fusion is required for germline stem cell (GSC) maintenance in the Drosophila testis. Here, we show that mitochondrial fission is also important for regulating the maintenance of early germ cells in larval testes. Inhibition of Drp1 in early germ cells resulted in the loss of GSCs and spermatogonia due to the accumulation of reactive oxygen species (ROS) and activation of the EGFR pathway in adjacent somatic cyst cells. EGFR activation contributed to premature germ cell differentiation. Our data provide insights into how mitochondrial dynamics can impact germ cell maintenance and differentiation via distinct mechanisms throughout development.

DOI: https://doi.org/10.1038/s41598-019-55728-0
Am J Physiol Cell Physiol. 2019 Dec 25.

Bioenergetics underlying single cell migration on aligned nanofiber scaffolds.

Abinash Padhi, Alexander H Thomson, Justin B Perry, Grace N Davis, Ryan P McMillan, Sandra Loesgen, Elizabeth N Kaweesa, Rakesh Kapania, Amrinder S Nain, David A Brown.

  Cell migration is centrally involved in a myriad of physiological processes, including morphogenesis, wound healing, tissue repair, and metastatic growth. The bioenergetics that underlie migratory behavior are not fully understood, in part due to variations in cell culture media and utilization of experimental cell culture systems that do not model physiological connective extracellular fibrous networks. In this study, we evaluated the bioenergetics of C2C12 myoblast migration and force production on fibronectin-coated nanofiber scaffolds of controlled diameter and alignment fabricated using non-electrospinning spinneret-based tunable engineered parameters (STEP) platform. The contribution of various metabolic pathways to cellular migration was determined using inhibitors of cellular respiration, ATP synthesis, glycolysis, or glucose uptake. Despite immediate effects on oxygen consumption, mitochondrial inhibition only modestly reduced cell migration velocity, whereas inhibitors of glycolysis and cellular glucose uptake led to striking decreases in migration. The migratory metabolic sensitivity was modifiable based on the substrates present in cell culture media. Cells cultured in galactose (instead of glucose) showed substantial migratory sensitivity to mitochondrial inhibition. We utilized Nanonet Force Microscopy to determine the bioenergetic factors responsible for single-cell force production, and observed that neither mitochondrial nor glycolytic inhibition altered single-cell force production. These data suggest that myoblast migration is heavily reliant on glycolysis in cells grown in conventional media. These studies have wide-ranging implications for the causes, consequences, and putative therapeutic treatments aimed at cellular migration.

Keywords:  bioenergetics; glycolysis; migration; mitochondria; single cell

DOI:  https://doi.org/10.1152/ajpcell.00221.2019
J Biol Chem. 2019 Dec 23. pii: jbc.RA119.010314. [Epub ahead of print]

The activation loop and substrate-binding cleft of glutaminase C are allosterically coupled.

Yunxing Li, Sekar Ramachandran, Thuy-Tien T Nguyen, Clint A Stalnecker, Richard A Cerione, Jon W Erickson.

  The glutaminase C (GAC) isoform of mitochondrial glutaminase is overexpressed in many cancer cells and therefore represents a potential therapeutic target. Understanding the regulation of GAC activity has been guided by the development of spectroscopic approaches that measure glutaminase activity in real time. Previously, we engineered a GAC protein (GAC(F327W)) in which a tryptophan residue is substituted for phenylalanine in an activation loop to explore the role of this loop in enzyme activity. We showed that the fluorescence emission of Trp-327 is enhanced in response to activator binding, but quenched by inhibitors of the BPTES class that bind to the GAC tetramer and contact the activation loop, thereby constraining it in an inactive conformation. In the present work, we took advantage of a tryptophan substitution at position 471, proximal to the GAC catalytic site, to examine the conformational coupling between the activation loop and the substrate-binding cleft, separated by approximately 16 Å. Comparison of glutamine binding in the presence or absence of the BPTES analog CB-839 revealed a reciprocal relationship between the constraints imposed on the activation loop position and the affinity of GAC for substrate. Binding of the inhibitor weakened the affinity of GAC for glutamine, whereas activating anions such as inorganic phosphate increased this affinity. These results indicate that the conformations of the activation loop and the substrate-binding cleft in GAC are allosterically coupled and that this coupling determines substrate affinity and enzymatic activity and explains the activities of CB-839, which is currently in clinical trials.

Keywords:  CB-839; cancer; conformational change; fluorescence; fluorescence quenching; glutaminase; glutamine metabolism; glutaminolysis; protein self-assembly; quaternary structure; small molecule; substrate specificity; tryptophan

DOI:  https://doi.org/10.1074/jbc.RA119.010314
Sci Rep. 2019 Dec 23. 9(1): 19634

Sideroflexin 4 affects Fe-S cluster biogenesis, iron metabolism, mitochondrial respiration and heme biosynthetic enzymes.

Bibbin T Paul, Lia Tesfay, C R Winkler, Frank M Torti, Suzy V Torti.

Sideroflexin4 (SFXN4) is a member of a family of nuclear-encoded mitochondrial proteins. Rare germline mutations in SFXN4 lead to phenotypic characteristics of mitochondrial disease including impaired mitochondrial respiration and hematopoetic abnormalities. We sought to explore the function of this protein. We show that knockout of SFXN4 has profound effects on Fe-S cluster formation. This in turn diminishes mitochondrial respiratory chain complexes and mitochondrial respiration and causes a shift to glycolytic metabolism. SFXN4 knockdown reduces the stability and activity of cellular Fe-S proteins, affects iron metabolism by influencing the cytosolic aconitase-IRP1 switch, redistributes iron from the cytosol to mitochondria, and impacts heme synthesis by reducing levels of ferrochelatase and inhibiting translation of ALAS2. We conclude that SFXN4 is essential for normal functioning of mitochondria, is necessary for Fe-S cluster biogenesis and iron homeostasis, and plays a critical role in mitochondrial respiration and synthesis of heme.

DOI: https://doi.org/10.1038/s41598-019-55907-z
Trends Endocrinol Metab. 2019 Dec 19. pii: S1043-2760(19)30234-6. [Epub ahead of print]

Metabolism, Epigenetics, and Causal Inference in Heart Failure.

Todd H Kimball, Thomas M Vondriska.

  Eukaryotes must balance the metabolic and cell death actions of mitochondria via control of gene expression and cell fate by chromatin, thereby functionally binding the metabolome and epigenome. This interaction has far-reaching implications for chronic diseases in humans, the most common of which are those of the cardiovascular system. The most devastating consequence of cardiovascular disease, heart failure, is not a single disease, diagnosis, or endpoint. Human and animal studies have revealed that, regardless of etiology and symptoms, heart failure is universally associated with abnormal metabolism and gene expression - to frame this as cause or consequence, however, may be to wrongfoot the question. This essay aims to challenge current thinking on metabolic-epigenetic crosstalk in heart failure, presenting hypotheses for how chronic diseases arise, take hold, and persist. We unpack assumptions about the order of operations for gene expression and metabolism, exploring recent findings in noncardiac systems that link metabolic intermediates directly to chromatin remodeling. Lastly, we discuss potential mechanisms by which chromatin may serve as a substrate for metabolic memory, and how changes in cellular transcriptomes (and hence in cellular behavior) in response to stress correspond to global changes in chromatin accessibility and structure.

Keywords:  cardiovascular disease; chromatin; epigenome; metabolism; mitochondria

DOI:  https://doi.org/10.1016/j.tem.2019.11.009
J Biochem. 2019 Dec 24. pii: mvz112. [Epub ahead of print]

Mitochondrial nucleoid morphology and respiratory function are altered in Drp1-deficient HeLa cells.

Azusa Ota, Takaya Ishihara, Naotada Ishihara.

  Mitochondria are dynamic organelles that frequently divide and fuse with each other. The dynamin-related GTPase protein Drp1 has a key role in mitochondrial fission. To analyze the physiological roles of Drp1 in cultured human cells, we analyzed Drp1-deficient HeLa cells established by genome editing using CRISPR/Cas9. Under fluorescent microscopy, not only mitochondria were elongated but their DNA (mtDNA) nucleoids were extremely enlarged in bulb-like mitochondrial structures ("mito-bulbs") in the Drp1-deficient HeLa cells. We further found that respiratory activity, as measured by oxygen consumption rates, was severely repressed in Drp1-deficient HeLa cells and that this was reversible by the co-repression of mitochondrial fusion factors. Although mtDNA copy number was not affected, several respiratory subunits were repressed in Drp1-deficient HeLa cells. These results suggest that mitochondrial fission is required for the maintenance of active respiratory activity and the morphology of mtDNA nucleoids in human cells.

Keywords:  GTPase; membrane dynamics; mitochondria; mtDNA; respiratory complex

DOI:  https://doi.org/10.1093/jb/mvz112
Proc Natl Acad Sci U S A. 2019 Dec 26. pii: 201913712. [Epub ahead of print]

Spatiotemporal regulation of NADP(H) phosphatase Nocturnin and its role in oxidative stress response.

Isara Laothamatas, Peng Gao, Anushka Wickramaratne, Carlo G Quintanilla, Arianna Dino, Crystal A Khan, Jen Liou, Carla B Green.

  An intimate link exists between circadian clocks and metabolism with nearly every metabolic pathway in the mammalian liver under circadian control. Circadian regulation of metabolism is largely driven by rhythmic transcriptional activation of clock-controlled genes. Among these output genes, Nocturnin (Noct) has one of the highest amplitude rhythms at the mRNA level. The Noct gene encodes a protein (NOC) that is highly conserved with the endonuclease/exonuclease/phosphatase (EEP) domain-containing CCR4 family of deadenylases, but highly purified NOC possesses little or no ribonuclease activity. Here, we show that NOC utilizes the dinucleotide NADP(H) as a substrate, removing the 2' phosphate to generate NAD(H), and is a direct regulator of oxidative stress response through its NADPH 2' phosphatase activity. Furthermore, we describe two isoforms of NOC in the mouse liver. The cytoplasmic form of NOC is constitutively expressed and associates externally with membranes of other organelles, including the endoplasmic reticulum, via N-terminal glycine myristoylation. In contrast, the mitochondrial form of NOC possesses high-amplitude circadian rhythmicity with peak expression level during the early dark phase. These findings suggest that NOC regulates local intracellular concentrations of NADP(H) in a manner that changes over the course of the day.

Keywords:  NADPH; Nocturnin; circadian; mitochondria; oxidative stress

DOI:  https://doi.org/10.1073/pnas.1913712117
Dev Cell. 2019 Dec 13. pii: S1534-5807(19)30943-8. [Epub ahead of print]

Low-Level Saturated Fatty Acid Palmitate Benefits Liver Cells by Boosting Mitochondrial Metabolism via CDK1-SIRT3-CPT2 Cascade.

Lin Liu, Bowen Xie, Ming Fan, Demet Candas-Green, Joy X Jiang, Ryan Wei, Yinsheng Wang, Hong-Wu Chen, Yiyang Hu, Jian Jian Li.

  Saturated fatty acids (SFAs) (the "bad" fat), especially palmitate (PA), in the human diet are blamed for potential health risks such as obesity and cancer because of SFA-induced lipotoxicity. However, epidemiological results demonstrate a latent benefit of SFAs, and it remains elusive whether a certain low level of SFAs is physiologically essential for maintaining cell metabolic hemostasis. Here, we demonstrate that although high-level PA (HPA) indeed induces lipotoxic effects in liver cells, low-level PA (LPA) increases mitochondrial functions and alleviates the injuries induced by HPA or hepatoxic agent carbon tetrachloride (CCl4). LPA treatment in mice enhanced liver mitochondrial activity and reduced CCl4 hepatotoxicity with improved blood levels of aspartate aminotransferase (AST), alanine transaminase (ALT), and mitochondrial aspartate transaminase (m-AST). LPA-mediated mitochondrial homeostasis is regulated by CDK1-mediated SIRT3 phosphorylation, which in turn deacetylates and dimerizes CPT2 to enhance fatty acid oxidation. Thus, an advantageous effect is suggested by the consumption of LPA that augments mitochondrial metabolic homeostasis via CDK1-SIRT3-CPT2 cascade.

Keywords:  CCl(4); CDK1; CPT2; SIRT3; fatty acid oxidation; hepatotoxicity; metabolism; mitochondria; palmitate; saturated fatty acid

DOI:  https://doi.org/10.1016/j.devcel.2019.11.012
Cell Metab. 2019 Dec 12. pii: S1550-4131(19)30663-1. [Epub ahead of print]

Glutamine Links Obesity to Inflammation in Human White Adipose Tissue.

Paul Petrus, Simon Lecoutre, Lucile Dollet, Clotilde Wiel, André Sulen, Hui Gao, Beatriz Tavira, Jurga Laurencikiene, Olav Rooyackers, Antonio Checa, Iyadh Douagi, Craig E Wheelock, Peter Arner, Mark McCarthy, Martin O Bergo, Laurienne Edgar, Robin P Choudhury, Myriam Aouadi, Anna Krook, Mikael Rydén.

  While obesity and associated metabolic complications are linked to inflammation of white adipose tissue (WAT), the causal factors remain unclear. We hypothesized that the local metabolic environment could be an important determinant. To this end, we compared metabolites released from WAT of 81 obese and non-obese women. This identified glutamine to be downregulated in obesity and inversely associated with a pernicious WAT phenotype. Glutamine administration in vitro and in vivo attenuated both pro-inflammatory gene and protein levels in adipocytes and WAT and macrophage infiltration in WAT. Metabolomic and bioenergetic analyses in human adipocytes suggested that glutamine attenuated glycolysis and reduced uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) levels. UDP-GlcNAc is the substrate for the post-translational modification O-linked β-N-acetylglucosamine (O-GlcNAc) mediated by the enzyme O-GlcNAc transferase. Functional studies in human adipocytes established a mechanistic link between reduced glutamine, O-GlcNAcylation of nuclear proteins, and a pro-inflammatory transcriptional response. Altogether, glutamine metabolism is linked to WAT inflammation in obesity.

Keywords:  adipocyte; adipokine; epigenetics; inflammation; leukocyte; macrophage; metabolomics; obesity

DOI:  https://doi.org/10.1016/j.cmet.2019.11.019
EMBO Rep. 2019 Dec 23. e48073

HOPS/TMUB1 retains p53 in the cytoplasm and sustains p53-dependent mitochondrial apoptosis.

Marilena Castelli, Danilo Piobbico, Martina Chiacchiaretta, Cinzia Brunacci, Stefania Pieroni, Daniela Bartoli, Marco Gargaro, Francesca Fallarino, Paolo Puccetti, Silvia Soddu, Maria Agnese Della-Fazia, Giuseppe Servillo.

  Apoptotic signalling by p53 occurs at both transcriptional and non-transcriptional levels, as p53 may act as a direct apoptogenic stimulus via activation of the intrinsic mitochondrial pathway. HOPS is a highly conserved, ubiquitously expressed shuttling protein with an ubiquitin-like domain. We generated Hops-/- mice and observed that they are viable with no apparent phenotypic defects. However, when treated with chemotherapeutic agents, Hops-/- mice display a significant reduction in apoptosis, suggesting an impaired ability to respond to genotoxic stressors. We show that HOPS acts as a regulator of cytoplasmic p53 levels and function. By binding p53, HOPS inhibits p53 proteasomal degradation and favours p53 recruitment to mitochondria and apoptosis induction. By interfering with importin α, HOPS further increases p53 cytoplasmic levels. Thus, HOPS promotes the p53-dependent mitochondrial apoptosis pathway by preserving cytoplasmic p53 from both degradation and nuclear uptake.

Keywords:   HOPS ; TMUB1; apoptosis; mitochondria; p53; ubiquitin like

DOI:  https://doi.org/10.15252/embr.201948073
Sci Rep. 2019 Dec 27. 9(1): 19869

Crebl2 regulates cell metabolism in muscle and liver cells.

Marcel Tiebe, Marilena Lutz, Deniz Senyilmaz Tiebe, Aurelio A Teleman.

We previously identified Drosophila REPTOR and REPTOR-BP as transcription factors downstream of mTORC1 that play an important role in regulating organismal metabolism. We study here the mammalian ortholog of REPTOR-BP, Crebl2. We find that Crebl2 mediates part of the transcriptional induction caused by mTORC1 inhibition. In C2C12 myoblasts, Crebl2 knockdown leads to elevated glucose uptake, elevated glycolysis as observed by lactate secretion, and elevated triglyceride biosynthesis. In Hepa1-6 hepatoma cells, Crebl2 knockdown also leads to elevated triglyceride levels. In sum, this works identifies Crebl2 as a regulator of cellular metabolism that can link nutrient sensing via mTORC1 to the metabolic response of cells.

DOI: https://doi.org/10.1038/s41598-019-56407-w
Nat Biotechnol. 2019 Dec 23.

Label-free metabolic imaging by mid-infrared optoacoustic microscopy in living cells.

Miguel A Pleitez, Asrar Ali Khan, Alice Soldà, Andriy Chmyrov, Josefine Reber, Francesca Gasparin, Markus R Seeger, Benedikt Schätz, Stephan Herzig, Marcel Scheideler, Vasilis Ntziachristos.

We develop mid-infrared optoacoustic microscopy (MiROM) for label-free, bond-selective, live-cell metabolic imaging, enabling spatiotemporal monitoring of carbohydrates, lipids and proteins in cells and tissues. Using acoustic detection of optical absorption, MiROM converts mid-infrared sensing into a positive-contrast imaging modality with negligible photodamage and high sensitivity. We use MiROM to observe changes in intrinsic carbohydrate distribution from a diffusive spatial pattern to tight co-localization with lipid droplets during adipogenesis.

DOI: https://doi.org/10.1038/s41587-019-0359-9
Proc Natl Acad Sci U S A. 2019 Dec 23. pii: 201910501. [Epub ahead of print]

Redox-mediated kick-start of mitochondrial energy metabolism drives resource-efficient seed germination.

Thomas Nietzel, Jörg Mostertz, Cristina Ruberti, Guillaume Née, Philippe Fuchs, Stephan Wagner, Anna Moseler, Stefanie J Müller-Schüssele, Abdelilah Benamar, Gernot Poschet, Michael Büttner, Ian Max Møller, Christopher H Lillig, David Macherel, Markus Wirtz, Rüdiger Hell, Iris Finkemeier, Andreas J Meyer, Falko Hochgräfe, Markus Schwarzländer.

  Seeds preserve a far developed plant embryo in a quiescent state. Seed metabolism relies on stored resources and is reactivated to drive germination when the external conditions are favorable. Since the switchover from quiescence to reactivation provides a remarkable case of a cell physiological transition we investigated the earliest events in energy and redox metabolism of Arabidopsis seeds at imbibition. By developing fluorescent protein biosensing in intact seeds, we observed ATP accumulation and oxygen uptake within minutes, indicating rapid activation of mitochondrial respiration, which coincided with a sharp transition from an oxidizing to a more reducing thiol redox environment in the mitochondrial matrix. To identify individual operational protein thiol switches, we captured the fast release of metabolic quiescence in organello and devised quantitative iodoacetyl tandem mass tag (iodoTMT)-based thiol redox proteomics. The redox state across all Cys peptides was shifted toward reduction from 27.1% down to 13.0% oxidized thiol. A large number of Cys peptides (412) were redox switched, representing central pathways of mitochondrial energy metabolism, including the respiratory chain and each enzymatic step of the tricarboxylic acid (TCA) cycle. Active site Cys peptides of glutathione reductase 2, NADPH-thioredoxin reductase a/b, and thioredoxin-o1 showed the strongest responses. Germination of seeds lacking those redox proteins was associated with markedly enhanced respiration and deregulated TCA cycle dynamics suggesting decreased resource efficiency of energy metabolism. Germination in aged seeds was strongly impaired. We identify a global operation of thiol redox switches that is required for optimal usage of energy stores by the mitochondria to drive efficient germination.

Keywords:  in vivo biosensing; mitochondria; redox proteomics; redox regulation; seed germination

DOI:  https://doi.org/10.1073/pnas.1910501117
Nature. 2019 Dec 25.

Microbial bile acid metabolites modulate gut RORγ+ regulatory T cell homeostasis.

Xinyang Song, Ximei Sun, Sungwhan F Oh, Meng Wu, Yanbo Zhang, Wen Zheng, Naama Geva-Zatorsky, Ray Jupp, Diane Mathis, Christophe Benoist, Dennis L Kasper.

The metabolic pathways encoded by the human gut microbiome constantly interact with host gene products through numerous bioactive molecules1. Primary bile acids (BAs) are synthesized within hepatocytes and released into the duodenum to facilitate absorption of lipids or fat-soluble vitamins2. Some BAs (approximately 5%) escape into the colon, where gut commensal bacteria convert them into various intestinal BAs2 that are important hormones that regulate host cholesterol metabolism and energy balance via several nuclear receptors and/or G-protein-coupled receptors3,4. These receptors have pivotal roles in shaping host innate immune responses1,5. However, the effect of this host-microorganism biliary network on the adaptive immune system remains poorly characterized. Here we report that both dietary and microbial factors influence the composition of the gut BA pool and modulate an important population of colonic FOXP3+ regulatory T (Treg) cells expressing the transcription factor RORγ. Genetic abolition of BA metabolic pathways in individual gut symbionts significantly decreases this Treg cell population. Restoration of the intestinal BA pool increases colonic RORγ+ Treg cell counts and ameliorates host susceptibility to inflammatory colitis via BA nuclear receptors. Thus, a pan-genomic biliary network interaction between hosts and their bacterial symbionts can control host immunological homeostasis via the resulting metabolites.

DOI: https://doi.org/10.1038/s41586-019-1865-0
Nat Struct Mol Biol. 2019 Dec 23.

Molecular basis for acetyl-CoA production by ATP-citrate lyase.

Xuepeng Wei, Kollin Schultz, Gleb A Bazilevsky, Austin Vogt, Ronen Marmorstein.

ATP-citrate lyase (ACLY) synthesizes cytosolic acetyl coenzyme A (acetyl-CoA), a fundamental cellular building block. Accordingly, aberrant ACLY activity is observed in many diseases. Here we report cryo-EM structures of human ACLY, alone or bound to substrates or products. ACLY forms a homotetramer with a rigid citrate synthase homology (CSH) module, flanked by four flexible acetyl-CoA synthetase homology (ASH) domains; CoA is bound at the CSH-ASH interface in mutually exclusive productive or unproductive conformations. The structure of a catalytic mutant of ACLY in the presence of ATP, citrate and CoA substrates reveals a phospho-citryl-CoA intermediate in the ASH domain. ACLY with acetyl-CoA and oxaloacetate products shows the products bound in the ASH domain, with an additional oxaloacetate in the CSH domain, which could function in ACLY autoinhibition. These structures, which are supported by biochemical and biophysical data, challenge previous proposals of the ACLY catalytic mechanism and suggest additional therapeutic possibilities for ACLY-associated metabolic disorders.

DOI: https://doi.org/10.1038/s41594-019-0351-6
Nature. 2019 Dec 25.

GDF15 mediates the effects of metformin on body weight and energy balance.

Anthony P Coll, Michael Chen, Pranali Taskar, Debra Rimmington, Satish Patel, John Tadross, Irene Cimino, Ming Yang, Paul Welsh, Samuel Virtue, Deborah A Goldspink, Emily L Miedzybrodzka, Adam R Konopka, Raul Ruiz Esponda, Jeffrey T-J Huang, Y C Loraine Tung, Sergio Rodriguez-Cuenca, Rute A Tomaz, Heather P Harding, Audrey Melvin, Giles S H Yeo, David Preiss, Antonio Vidal-Puig, Ludovic Vallier, K Sreekumaran Nair, Nicholas J Wareham, David Ron, Fiona M Gribble, Frank Reimann, Naveed Sattar, David B Savage, Bernard B Allan, Stephen O'Rahilly.

Metformin, the world's most prescribed anti-diabetic drug, is also effective in preventing type 2 diabetes in people at high risk1,2. Over 60% of this effect is attributable to the ability of metformin to lower body weight in a sustained manner3. The molecular mechanisms by which metformin lowers body weight are unknown. In two, independent randomised controlled clinical trials, circulating levels of GDF15, recently described to reduce food intake and lower body weight through a brain stem-restricted receptor, were increased by metformin. In wild-type mice, oral metformin increased circulating GDF15 with GDF15 expression increasing predominantly in the distal intestine and the kidney. Metformin prevented weight gain in response to a high-fat diet in wild-type mice but not in mice lacking GDF15 or its receptor GFRAL. In obese, high-fat-fed mice, the effects of metformin to reduce body weight were reversed by a GFRAL antagonist antibody. Metformin had effects on both energy intake and energy expenditure that required GDF15. Metformin retained its ability to lower circulating glucose levels in the absence of GDF15 action. In summary, metformin elevates circulating levels of GDF15, which are necessary for its beneficial effects on energy balance and body weight, major contributors to its action as a chemopreventive agent.

DOI: https://doi.org/10.1038/s41586-019-1911-y
J Clin Invest. 2019 Dec 24. pii: 124049. [Epub ahead of print]

Suppression of the SLC7A11/glutathione axis causes synthetic lethality in KRAS-mutant lung adenocarcinoma.

Kewen Hu, Kun Li, Jing Lv, Jie Feng, Jing Chen, Haigang Wu, Feixiong Cheng, Wenhao Jiang, Jieqiong Wang, Haixiang Pei, Paul J Chiao, Zhenyu Cai, Yihua Chen, Mingyao Liu, Xiufeng Pang.

  Oncogenic KRAS is a major driver in lung adenocarcinoma (LUAD) that has yet to be therapeutically conquered. Here we report that the SLC7A11/glutathione axis displays metabolic synthetic lethality with oncogenic KRAS. Through metabolomics approaches, we found that mutationally activated KRAS strikingly increased the intracellular cystine level and glutathione biosynthesis. SLC7A11, a cystine/glutamate antiporter conferring specificity for cystine uptake, was overexpressed in patients with KRAS-mutant LUAD and showed positive association with tumor progression. Furthermore, SLC7A11 inhibition either by genetic depletion or pharmacological inhibition by sulfasalazine resulted in selective killing across a panel of KRAS-mutant cancer cells in vitro and tumor growth inhibition in vivo, suggesting the functionality and specificity of SLC7A11 as a therapeutic target. Importantly, we further identified a potent SLC7A11 inhibitor, HG106 that markedly decreased cystine uptake and intracellular glutathione biosynthesis. Furthermore, HG106 exhibited selective cytotoxicity towards KRAS-mutant cells by increasing oxidative stress- and endoplasmic reticulum stress-mediated cell apoptosis. Of note, treatment of KRAS-mutant LUAD with HG106 in several lung cancer preclinical mouse models led to marked tumor suppression and prolonged mouse survival. Overall, our findings reveal that KRAS-mutant LUAD cells are vulnerable to SLC7A11 inhibition, providing promising therapeutic approaches to the treatment of this currently incurable disease.

Keywords:  Cancer; Drug therapy; Oncology

DOI:  https://doi.org/10.1172/JCI124049
Autophagy. 2019 Dec 26. 1-17

Differential regulation of autophagy during metabolic stress in astrocytes and neurons.

Aditi Kulkarni, Audrey Dong, Vineet Vinay Kulkarni, Jessica Chen, Olivia Laxton, Anip Anand, Sandra Maday.

  Macroautophagy/autophagy is a key homeostatic process that targets cytoplasmic components to the lysosome for breakdown and recycling. Autophagy plays critical roles in glia and neurons that affect development, functionality, and viability of the nervous system. The mechanisms that regulate autophagy in glia and neurons, however, are poorly understood. Here, we define the molecular underpinnings of autophagy in primary cortical astrocytes in response to metabolic stress, and perform a comparative study in primary hippocampal neurons. We find that inducing metabolic stress by nutrient deprivation or pharmacological inhibition of MTOR (mechanistic target of rapamycin kinase) robustly activates autophagy in astrocytes. While both paradigms of metabolic stress dampen MTOR signaling, they affect the autophagy pathway differently. Further, we find that starvation-induced autophagic flux is dependent on the buffering system of the starvation solution. Lastly, starvation conditions that strongly activate autophagy in astrocytes have less pronounced effects on autophagy in neurons. Combined, our study reveals the complexity of regulating autophagy in different paradigms of metabolic stress, as well as in different cell types of the brain. Our findings raise important implications for how neurons and glia may collaborate to maintain homeostasis in the brain.Abbreviations ACSF: artificial cerebrospinal fluid; baf A1: bafilomycin A1; EBSS: earle's balanced salt solution; GFAP: glial fibrillary acidic protein; Glc: glucose; GM: glial media; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; p-RPS6: phospho-RPS6; p-ULK1: phospho-ULK1; RPS6: ribosomal protein S6; SQSTM1/p62: sequestosome 1; ULK1: unc-51-like kinase 1.

Keywords:  Astrocytes; LC3; MTOR; SQSTM1; autophagy; glia; neurons; starvation

DOI:  https://doi.org/10.1080/15548627.2019.1703354
Nat Rev Nephrol. 2019 Dec 24.

Metabolic changes in the kidney.

Rebecca Kelsey.

DOI: https://doi.org/10.1038/s41581-019-0249-x
BMC Genomics. 2019 Dec 26. 20(1): 1017

Archaic mitochondrial DNA inserts in modern day nuclear genomes.

Robert Bücking, Murray P Cox, Georgi Hudjashov, Lauri Saag, Herawati Sudoyo, Mark Stoneking.

   BACKGROUND: Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Saharan Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs).
RESULTS: We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin, present in 15 analysed genomes; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male.
CONCLUSIONS: Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.

Keywords:  Archaic introgression; Denisovans; NUMTs

DOI:  https://doi.org/10.1186/s12864-019-6392-8