bims-camemi 2020-04-05 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2020–04–05
38 papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit

Cysteine depletion induces pancreatic tumor ferroptosis in mice.
Cystine transporter regulation of pentose phosphate pathway dependency and disulfide stress exposes a targetable metabolic vulnerability in cancer.
Adipose Tissue and FoxO1: Bridging Physiology and Mechanisms.
The Function of Tafazzin, a Mitochondrial Phospholipid-Lysophospholipid Acyltransferase.
Cryo-EM structures of S-OPA1 reveal its interactions with membrane and changes upon nucleotide binding.
Oncogenic KrasG12D causes myeloproliferation via NLRP3 inflammasome activation.
Mitochondrial quality control in cardiac microvascular ischemia-reperfusion injury: New insights into the mechanisms and therapeutic potentials.
Mitochondrial Diseases: Hope for the Future.
OTULIN protects the liver against cell death, inflammation, fibrosis, and cancer.
Single-cell chromatin accessibility maps reveal regulatory programs driving early mouse organogenesis.
Regulation of coenzyme A levels by degradation: the 'Ins and Outs'.
Mitochondrial fragmentation enables localized signaling required for cell repair.
Immunomodulatory drugs activate NK cells via both Zap-70 and cereblon-dependent pathways.
Selective covalent targeting of GPX4 using masked nitrile-oxide electrophiles.
CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities.
Pan-Cancer Analysis of Mitochondria Chaperone-Client Co-Expression Reveals Chaperone Functional Partitioning.
Metabolic Reprogramming Promotes Neural Crest Migration via Yap/Tead Signaling.
Increased mitochondrial fragmentation in polycystic kidney disease acts as a modifier of disease progression.
Mitochondria-Endoplasmic Reticulum Contacts in Reactive Astrocytes Promote Vascular Remodeling.
Low Levels of Serum Tryptophan Underlie Skeletal Muscle Atrophy.
Exercise-Mediated Lowering of Glutamine Availability Suppresses Tumor Growth and Attenuates Muscle Wasting.
Redox Modifications of Proteins of the Mitochondrial Fusion and Fission Machinery.
TET-Mediated Hypermethylation Primes SDH-Deficient Cells for HIF2α-Driven Mesenchymal Transition.
Activation of AMP-activated protein kinase during sepsis/inflammation improves survival by preserving cellular metabolic fitness.
Cell-intrinsic metabolic regulation of mononuclear phagocyte activation: Findings from the tip of the iceberg.
Metabolites released from apoptotic cells act as tissue messengers.
MitoPlex: A targeted multiple reaction monitoring assay for quantification of a curated set of mitochondrial proteins.
Succinate Dehydrogenase-Regulated Phosphoenolpyruvate Carboxykinase Sustains Copulation Fitness in Aging C. elegans Males.
KMT2D Deficiency Impairs Super-Enhancers to Confer a Glycolytic Vulnerability in Lung Cancer.
Reactive oxygen species (ROS) as pleiotropic physiological signalling agents.
Senescence-Induced Vascular Remodeling Creates Therapeutic Vulnerabilities in Pancreas Cancer.
The Chemical Biology of Ferroptosis in the Central Nervous System.
A salvage pathway maintains highly functional respiratory complex I.
The short variant of optic atrophy 1 (OPA1) improves cell survival under oxidative stress.
The Role of D-3-Phosphoglycerate Dehydrogenase in Cancer.
A Metformin-Responsive Metabolic Pathway Controls Distinct Steps in Gastric Progenitor Fate Decisions and Maturation.
Understanding cachexia in the context of metastatic progression.
Mitochondrial fission factor (MFF) is a critical regulator of peroxisome maturation.

Science. 2020 Apr 03. 368(6486): 85-89

Cysteine depletion induces pancreatic tumor ferroptosis in mice.

Michael A Badgley, Daniel M Kremer, H Carlo Maurer, Kathleen E DelGiorno, Ho-Joon Lee, Vinee Purohit, Irina R Sagalovskiy, Alice Ma, Jonathan Kapilian, Christina E M Firl, Amanda R Decker, Steve A Sastra, Carmine F Palermo, Leonardo R Andrade, Peter Sajjakulnukit, Li Zhang, Zachary P Tolstyka, Tal Hirschhorn, Candice Lamb, Tong Liu, Wei Gu, E Scott Seeley, Everett Stone, George Georgiou, Uri Manor, Alina Iuga, Geoffrey M Wahl, Brent R Stockwell, Costas A Lyssiotis, Kenneth P Olive.

Ferroptosis is a form of cell death that results from the catastrophic accumulation of lipid reactive oxygen species (ROS). Oncogenic signaling elevates lipid ROS production in many tumor types and is counteracted by metabolites that are derived from the amino acid cysteine. In this work, we show that the import of oxidized cysteine (cystine) via system xC - is a critical dependency of pancreatic ductal adenocarcinoma (PDAC), which is a leading cause of cancer mortality. PDAC cells used cysteine to synthesize glutathione and coenzyme A, which, together, down-regulated ferroptosis. Studying genetically engineered mice, we found that the deletion of a system xC - subunit, Slc7a11, induced tumor-selective ferroptosis and inhibited PDAC growth. This was replicated through the administration of cyst(e)inase, a drug that depletes cysteine and cystine, demonstrating a translatable means to induce ferroptosis in PDAC.

DOI: https://doi.org/10.1126/science.aaw9872
Nat Cell Biol. 2020 Mar 30.

Cystine transporter regulation of pentose phosphate pathway dependency and disulfide stress exposes a targetable metabolic vulnerability in cancer.

Xiaoguang Liu, Kellen Olszewski, Yilei Zhang, Esther W Lim, Jiejun Shi, Xiaoshan Zhang, Jie Zhang, Hyemin Lee, Pranavi Koppula, Guang Lei, Li Zhuang, M James You, Bingliang Fang, Wei Li, Christian M Metallo, Masha V Poyurovsky, Boyi Gan.

SLC7A11-mediated cystine uptake is critical for maintaining redox balance and cell survival. Here we show that this comes at a significant cost for cancer cells with high levels of SLC7A11. Actively importing cystine is potentially toxic due to its low solubility, forcing cancer cells with high levels of SLC7A11 (SLC7A11high) to constitutively reduce cystine to the more soluble cysteine. This presents a significant drain on the cellular NADPH pool and renders such cells dependent on the pentose phosphate pathway. Limiting glucose supply to SLC7A11high cancer cells results in marked accumulation of intracellular cystine, redox system collapse and rapid cell death, which can be rescued by treatments that prevent disulfide accumulation. We further show that inhibitors of glucose transporters selectively kill SLC7A11high cancer cells and suppress SLC7A11high tumour growth. Our results identify a coupling between SLC7A11-associated cystine metabolism and the pentose phosphate pathway, and uncover an accompanying metabolic vulnerability for therapeutic targeting in SLC7A11high cancers.

DOI: https://doi.org/10.1038/s41556-020-0496-x
Cells. 2020 Mar 31. pii: E849. [Epub ahead of print]9(4):

Adipose Tissue and FoxO1: Bridging Physiology and Mechanisms.

Laura Ioannilli, Fabio Ciccarone, Maria Rosa Ciriolo.

  Forkhead box O class proteins (FoxOs) are expressed nearly in all tissues and are involved in different functions such as energy metabolism, redox homeostasis, differentiation, and cell cycle arrest. The plasticity of FoxOs is demonstrated by post-translational modifications that determine diverse levels of transcriptional regulations also controlled by their subcellular localization. Among the different members of the FoxO family, we will focus on FoxO1 in adipose tissue, where it is abundantly expressed and is involved in differentiation and transdifferentiation processes. The capability of FoxO1 to respond differently in dependence of adipose tissue subtype underlines the specific involvement of the transcription factor in energy metabolism and the "browning" process of adipocytes. FoxO1 can localize to nuclear, cytoplasm, and mitochondrial compartments of adipocytes responding to different availability of nutrients and source of reactive oxygen species (ROS). Specifically, fasted state produced-ROS enhance the nuclear activity of FoxO1, triggering the transcription of lipid catabolism and antioxidant response genes. The enhancement of lipid catabolism, in combination with ROS buffering, allows systemic energetic homeostasis and metabolic adaptation of white/beige adipocytes. On the contrary, a fed state induces FoxO1 to accumulate in the cytoplasm, but also in the mitochondria where it affects mitochondrial DNA gene expression. The importance of ROS-mediated signaling in FoxO1 subcellular localization and retrograde communication will be discussed, highlighting key aspects of FoxO1 multifaceted regulation in adipocytes.

Keywords:  ROS; adipogenesis; browning; fasted state; mitochondria

DOI:  https://doi.org/10.3390/cells9040849
J Mol Biol. 2020 Mar 28. pii: S0022-2836(20)30259-X. [Epub ahead of print]

The Function of Tafazzin, a Mitochondrial Phospholipid-Lysophospholipid Acyltransferase.

Michael Schlame, Yang Xu.

  Tafazzin is a mitochondrial enzyme that exchanges fatty acids between phospholipids by phospholipid-lysophospholipid transacylation. The reaction alters the molecular species composition and, as a result, the physical properties of lipids. In vivo, the most important substrate of tafazzin is the mitochondria-specific lipid cardiolipin. Tafazzin mutations cause the human disease Barth syndrome, which presents with cardiomyopathy, skeletal muscle weakness, fatigue, and other symptoms, probably all related to mitochondrial dysfunction. The reason why mitochondria require tafazzin is still not known but recent evidence suggests that tafazzin may lower the energy cost associated with protein crowding in the inner mitochondrial membrane.

Keywords:  Barth syndrome; Cardiolipin; Membrane lipids; Mitochondria

DOI:  https://doi.org/10.1016/j.jmb.2020.03.026
Elife. 2020 Mar 31. pii: e50294. [Epub ahead of print]9

Cryo-EM structures of S-OPA1 reveal its interactions with membrane and changes upon nucleotide binding.

Danyang Zhang, Yan Zhang, Jun Ma, Chunmei Zhu, Tongxin Niu, Wenbo Chen, Xiaoyun Pang, Yujia Zhai, Fei Sun.

  Mammalian mitochondrial inner membrane fusion is mediated by optic atrophy 1 (OPA1). Under physiological conditions, OPA1 undergoes proteolytic processing to form a membrane-anchored long isoform (L-OPA1) and a soluble short isoform (S-OPA1). A combination of L-OPA1 and S-OPA1 is essential for efficient membrane fusion; however, the relevant mechanism is not well understood. In this study, we investigate the cryo-electron microscopic structures of S-OPA1-coated liposomes in nucleotide-free and GTPγS-bound states. S-OPA1 exhibits a general dynamin-like structure and can assemble onto membranes in a helical array with a dimer building block. We reveal that hydrophobic residues in its extended membrane-binding domain are critical for its tubulation activity. The binding of GTPγS triggers a conformational change and results in a rearrangement of the helical lattice and tube expansion similar to that of S-Mgm1. These observations indicate that S-OPA1 adopts a dynamin-like power stroke membrane remodeling mechanism during mitochondrial inner membrane fusion.

Keywords:  human; molecular biophysics; structural biology

DOI:  https://doi.org/10.7554/eLife.50294
Nat Commun. 2020 Apr 03. 11(1): 1659

Oncogenic KrasG12D causes myeloproliferation via NLRP3 inflammasome activation.

Shaima'a Hamarsheh, Lena Osswald, Benedikt S Saller, Susanne Unger, Donatella De Feo, Janaki Manoja Vinnakota, Martina Konantz, Franziska M Uhl, Heiko Becker, Michael Lübbert, Khalid Shoumariyeh, Christoph Schürch, Geoffroy Andrieux, Nils Venhoff, Annette Schmitt-Graeff, Sandra Duquesne, Dietmar Pfeifer, Matthew A Cooper, Claudia Lengerke, Melanie Boerries, Justus Duyster, Charlotte M Niemeyer, Miriam Erlacher, Bruce R Blazar, Burkard Becher, Olaf Groß, Tilman Brummer, Robert Zeiser.

Oncogenic Ras mutations occur in various leukemias. It was unclear if, besides the direct transforming effect via constant RAS/MEK/ERK signaling, an inflammation-related effect of KRAS contributes to the disease. Here, we identify a functional link between oncogenic KrasG12D and NLRP3 inflammasome activation in murine and human cells. Mice expressing active KrasG12D in the hematopoietic system developed myeloproliferation and cytopenia, which is reversed in KrasG12D mice lacking NLRP3 in the hematopoietic system. Therapeutic IL-1-receptor blockade or NLRP3-inhibition reduces myeloproliferation and improves hematopoiesis. Mechanistically, KrasG12D-RAC1 activation induces reactive oxygen species (ROS) production causing NLRP3 inflammasome-activation. In agreement with our observations in mice, patient-derived myeloid leukemia cells exhibit KRAS/RAC1/ROS/NLRP3/IL-1β axis activity. Our findings indicate that oncogenic KRAS not only act via its canonical oncogenic driver function, but also enhances the activation of the pro-inflammatory RAC1/ROS/NLRP3/IL-1β axis. This paves the way for a therapeutic approach based on immune modulation via NLRP3 blockade in KRAS-mutant myeloid malignancies.

DOI: https://doi.org/10.1038/s41467-020-15497-1
Pharmacol Res. 2020 Mar 28. pii: S1043-6618(20)30302-9. [Epub ahead of print] 104771

Mitochondrial quality control in cardiac microvascular ischemia-reperfusion injury: New insights into the mechanisms and therapeutic potentials.

Jin Wang, Sam Toan, Hao Zhou.

  Thrombolytic therapy and revascularization strategies create a complete recanalization of the occluded epicardial coronary artery in patients with myocardial infarction (MI). However, about 35% of patients still experience an impaired myocardial reperfusion, which is termed a no-reflow phenomenon mainly caused by cardiac microvascular ischemia-reperfusion (I/R) injury. Mitochondria are essential for microvascular endothelial cells' survival, both because of their roles as metabolic energy producers and as regulators of programmed cell death. Mitochondrial structure and function are regulated by a mitochondrial quality control (MQC) system, a series of processes including mitochondrial biogenesis, mitochondrial dynamics/mitophagy, mitochondrial proteostasis, and mitochondria-mediated cell death. Our review discusses the MQC mechanisms and how they are linked to cardiac microvascular I/R injury. Additionally, we will summarize the molecular basis that results in defective MQC mechanisms and present potential therapeutic interventions for improving MQC in cardiac microvascular I/R injury.

Keywords:  mitochondria-mediated cell death; mitochondrial biogenesis; mitochondrial dynamics/mitophagy; mitochondrial proteostasis; mitochondrial quality control

DOI:  https://doi.org/10.1016/j.phrs.2020.104771
Cell. 2020 Apr 02. pii: S0092-8674(20)30228-2. [Epub ahead of print]181(1): 168-188

Mitochondrial Diseases: Hope for the Future.

Oliver M Russell, Gráinne S Gorman, Robert N Lightowlers, Doug M Turnbull.

Mitochondrial diseases are clinically heterogeneous disorders caused by a wide spectrum of mutations in genes encoded by either the nuclear or the mitochondrial genome. Treatments for mitochondrial diseases are currently focused on symptomatic management rather than improving the biochemical defect caused by a particular mutation. This review focuses on the latest advances in the development of treatments for mitochondrial disease, both small molecules and gene therapies, as well as methods to prevent transmission of mitochondrial disease through the germline.

DOI: https://doi.org/10.1016/j.cell.2020.02.051
Cell Death Differ. 2020 Mar 30.

OTULIN protects the liver against cell death, inflammation, fibrosis, and cancer.

Rune Busk Damgaard, Helen E Jolin, Michael E D Allison, Susan E Davies, Hannah L Titheradge, Andrew N J McKenzie, David Komander.

Methionine-1 (M1)-linked polyubiquitin chains conjugated by the linear ubiquitin chain assembly complex (LUBAC) control NF-κB activation, immune homoeostasis, and prevents tumour necrosis factor (TNF)-induced cell death. The deubiquitinase OTULIN negatively regulates M1-linked polyubiquitin signalling by removing the chains conjugated by LUBAC, and OTULIN deficiency causes OTULIN-related autoinflammatory syndrome (ORAS) in humans. However, the cellular pathways and physiological functions controlled by OTULIN remain poorly understood. Here, we show that OTULIN prevents development of liver disease in mice and humans. In an ORAS patient, OTULIN deficiency caused spontaneous and progressive steatotic liver disease at 10-13 months of age. Similarly, liver-specific deletion of OTULIN in mice leads to neonatally onset steatosis and hepatitis, akin to the ORAS patient. OTULIN deficiency triggers metabolic alterations, apoptosis, and inflammation in the liver. In mice, steatosis progresses to steatohepatitis, fibrosis and pre-malignant tumour formation by 8 weeks of age, and by the age of 7-12 months the phenotype has advanced to malignant hepatocellular carcinoma. Surprisingly, the pathology in OTULIN-deficient livers is independent of TNFR1 signalling. Instead, we find that steatohepatitis in OTULIN-deficient livers is associated with aberrant mTOR activation, and inhibition of mTOR by rapamycin administration significantly reduces the liver pathology. Collectively, our results reveal that OTULIN is critical for maintaining liver homoeostasis and suggest that M1-linked polyubiquitin chains may play a role in regulation of mTOR signalling and metabolism in the liver.

DOI: https://doi.org/10.1038/s41418-020-0532-1
Nat Cell Biol. 2020 Mar 30.

Single-cell chromatin accessibility maps reveal regulatory programs driving early mouse organogenesis.

Blanca Pijuan-Sala, Nicola K Wilson, Jun Xia, Xiaomeng Hou, Rebecca L Hannah, Sarah Kinston, Fernando J Calero-Nieto, Olivier Poirion, Sebastian Preissl, Feng Liu, Berthold Göttgens.

During mouse embryonic development, pluripotent cells rapidly divide and diversify, yet the regulatory programs that define the cell repertoire for each organ remain ill-defined. To delineate comprehensive chromatin landscapes during early organogenesis, we mapped chromatin accessibility in 19,453 single nuclei from mouse embryos at 8.25 days post-fertilization. Identification of cell-type-specific regions of open chromatin pinpointed two TAL1-bound endothelial enhancers, which we validated using transgenic mouse assays. Integrated gene expression and transcription factor motif enrichment analyses highlighted cell-type-specific transcriptional regulators. Subsequent in vivo experiments in zebrafish revealed a role for the ETS factor FEV in endothelial identity downstream of ETV2 (Etsrp in zebrafish). Concerted in vivo validation experiments in mouse and zebrafish thus illustrate how single-cell open chromatin maps, representative of a mammalian embryo, provide access to the regulatory blueprint for mammalian organogenesis.

DOI: https://doi.org/10.1038/s41556-020-0489-9
Prog Lipid Res. 2020 Mar 29. pii: S0163-7827(20)30008-4. [Epub ahead of print] 101028

Regulation of coenzyme A levels by degradation: the 'Ins and Outs'.

Philippe Naquet, Evan W Kerr, Schuyler D Vickers, Roberta Leonardi.

  Coenzyme A (CoA) is the predominant acyl carrier in mammalian cells and a cofactor that plays a key role in energy and lipid metabolism. CoA and its thioesters (acyl-CoAs) regulate a multitude of metabolic processes at different levels: as substrates, allosteric modulators, and via post-translational modification of histones and other non-histone proteins. Evidence is emerging that synthesis and degradation of CoA are regulated in a manner that enables metabolic flexibility in different subcellular compartments. Degradation of CoA occurs through distinct intra- and extracellular pathways that rely on the activity of specific hydrolases. The pantetheinase enzymes specifically hydrolyze pantetheine to cysteamine and pantothenate, the last step in the extracellular degradation pathway for CoA. This reaction releases pantothenate in the bloodstream, making this CoA precursor available for cellular uptake and de novo CoA synthesis. Intracellular degradation of CoA depends on specific mitochondrial and peroxisomal Nudix hydrolases. These enzymes are also active against a subset of acyl-CoAs and play a key role in the regulation of subcellular (acyl-)CoA pools and CoA-dependent metabolic reactions. The evidence currently available indicates that the extracellular and intracellular (acyl-)CoA degradation pathways are regulated in a coordinated and opposite manner by the nutritional state and maximize the changes in the total intracellular CoA levels that support the metabolic switch between fed and fasted states in organs like the liver. The objective of this review is to update the contribution of these pathways to the regulation of metabolism, physiology and pathology and to highlight the many questions that remain open.

Keywords:  Coenzyme A; Metabolic regulation; Nudix hydrolase; Pantetheinases; Pantothenate/organelles

DOI:  https://doi.org/10.1016/j.plipres.2020.101028
J Cell Biol. 2020 May 04. pii: e201909154. [Epub ahead of print]219(5):

Mitochondrial fragmentation enables localized signaling required for cell repair.

Adam Horn, Shreya Raavicharla, Sonna Shah, Dan Cox, Jyoti K Jaiswal.

Plasma membrane injury can cause lethal influx of calcium, but cells survive by mounting a polarized repair response targeted to the wound site. Mitochondrial signaling within seconds after injury enables this response. However, as mitochondria are distributed throughout the cell in an interconnected network, it is unclear how they generate a spatially restricted signal to repair the plasma membrane wound. Here we show that calcium influx and Drp1-mediated, rapid mitochondrial fission at the injury site help polarize the repair response. Fission of injury-proximal mitochondria allows for greater amplitude and duration of calcium increase in these mitochondria, allowing them to generate local redox signaling required for plasma membrane repair. Drp1 knockout cells and patient cells lacking the Drp1 adaptor protein MiD49 fail to undergo injury-triggered mitochondrial fission, preventing polarized mitochondrial calcium increase and plasma membrane repair. Although mitochondrial fission is considered to be an indicator of cell damage and death, our findings identify that mitochondrial fission generates localized signaling required for cell survival.

DOI: https://doi.org/10.1083/jcb.201909154
Leukemia. 2020 Apr 01.

Immunomodulatory drugs activate NK cells via both Zap-70 and cereblon-dependent pathways.

Teru Hideshima, Daisuke Ogiya, Jiye Liu, Takeshi Harada, Keiji Kurata, Jooeun Bae, Walter Massefski, Kenneth C Anderson.

Immunomodulatory drugs (IMiDs) lenalidomide and pomalidomide show remarkable antitumor activity in multiple myeloma (MM) via directly inhibiting MM-cell growth in the bone marrow (BM) microenvironment and promoting immune effector cell function. They are known to bind to the ubiquitin 3 ligase CRBN complex and thereby triggering degradation of IKZF1/3. In this study, we demonstrate that IMiDs also directly bind and activate zeta-chain-associated protein kinase-70 (Zap-70) via its tyrosine residue phosphorylation in T cells. IMiDs also triggered phosphorylation of Zap-70 in natural killer (NK) cells. Importantly, increased granzyme-B (GZM-B) expression and NK-cell activity triggered by IMiDs is associated with Zap-70 activation and inhibited by Zap-70 knockdown (KD), independent of CRBN. We also demonstrate a second mechanism whereby IMiDs trigger GZM-B and NK cytotoxicity which is CRBN and IKZF3 mediated, and inhibited or enhanced by KD of CRBN or IKZF3, respectively, independent of Zap-70. Our studies therefore show that IMiDs can enhance NK and T-cell cytotoxicity in (1) ZAP-70-mediated CRBN independent, as well as (2) CRBN-mediated ZAP-70 independent mechanisms; and provide the framework for developing novel therapeutics to activate Zap-70 and thereby enhance T and NK anti-MM cytotoxicity.

DOI: https://doi.org/10.1038/s41375-020-0809-x
Nat Chem Biol. 2020 Mar 30.

Selective covalent targeting of GPX4 using masked nitrile-oxide electrophiles.

John K Eaton, Laura Furst, Richard A Ruberto, Dieter Moosmayer, André Hilpmann, Matthew J Ryan, Katja Zimmermann, Luke L Cai, Michael Niehues, Volker Badock, Anneke Kramm, Sixun Chen, Roman C Hillig, Paul A Clemons, Stefan Gradl, Claire Montagnon, Kiel E Lazarski, Sven Christian, Besnik Bajrami, Roland Neuhaus, Ashley L Eheim, Vasanthi S Viswanathan, Stuart L Schreiber.

We recently described glutathione peroxidase 4 (GPX4) as a promising target for killing therapy-resistant cancer cells via ferroptosis. The onset of therapy resistance by multiple types of treatment results in a stable cell state marked by high levels of polyunsaturated lipids and an acquired dependency on GPX4. Unfortunately, all existing inhibitors of GPX4 act covalently via a reactive alkyl chloride moiety that confers poor selectivity and pharmacokinetic properties. Here, we report our discovery that masked nitrile-oxide electrophiles, which have not been explored previously as covalent cellular probes, undergo remarkable chemical transformations in cells and provide an effective strategy for selective targeting of GPX4. The new GPX4-inhibiting compounds we describe exhibit unexpected proteome-wide selectivity and, in some instances, vastly improved physiochemical and pharmacokinetic properties compared to existing chloroacetamide-based GPX4 inhibitors. These features make them superior tool compounds for biological interrogation of ferroptosis and constitute starting points for development of improved inhibitors of GPX4.

DOI: https://doi.org/10.1038/s41589-020-0501-5
Nature. 2020 Apr;580(7801): 136-141

CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities.

Kyuho Han, Sarah E Pierce, Amy Li, Kaitlyn Spees, Grace R Anderson, Jose A Seoane, Yuan-Hung Lo, Michael Dubreuil, Micah Olivas, Roarke A Kamber, Michael Wainberg, Kaja Kostyrko, Marcus R Kelly, Maryam Yousefi, Scott W Simpkins, David Yao, Keonil Lee, Calvin J Kuo, Peter K Jackson, Alejandro Sweet-Cordero, Anshul Kundaje, Andrew J Gentles, Christina Curtis, Monte M Winslow, Michael C Bassik.

Cancer genomics studies have identified thousands of putative cancer driver genes1. Development of high-throughput and accurate models to define the functions of these genes is a major challenge. Here we devised a scalable cancer-spheroid model and performed genome-wide CRISPR screens in 2D monolayers and 3D lung-cancer spheroids. CRISPR phenotypes in 3D more accurately recapitulated those of in vivo tumours, and genes with differential sensitivities between 2D and 3D conditions were highly enriched for genes that are mutated in lung cancers. These analyses also revealed drivers that are essential for cancer growth in 3D and in vivo, but not in 2D. Notably, we found that carboxypeptidase D is responsible for removal of a C-terminal RKRR motif2 from the α-chain of the insulin-like growth factor 1 receptor that is critical for receptor activity. Carboxypeptidase D expression correlates with patient outcomes in patients with lung cancer, and loss of carboxypeptidase D reduced tumour growth. Our results reveal key differences between 2D and 3D cancer models, and establish a generalizable strategy for performing CRISPR screens in spheroids to reveal cancer vulnerabilities.

DOI: https://doi.org/10.1038/s41586-020-2099-x
Cancers (Basel). 2020 Mar 30. pii: E825. [Epub ahead of print]12(4):

Pan-Cancer Analysis of Mitochondria Chaperone-Client Co-Expression Reveals Chaperone Functional Partitioning.

Geut Galai, Hila Ben-David, Liron Levin, Martin F Orth, Thomas G P Grünewald, Shai Pilosof, Shimon Berstein, Barak Rotblat.

  Metabolic reprogramming is a hallmark of cancer. Such reprogramming entails the up-regulation of the expression of specific mitochondrial proteins, thus increasing the burden on the mitochondrial protein quality control. However, very little is known about the specificity of interactions between mitochondrial chaperones and their clients, or to what extent the mitochondrial chaperone-client co-expression is coordinated. We hypothesized that a physical interaction between a chaperone and its client in mitochondria ought to be manifested in the co-expression pattern of both transcripts. Using The Cancer Genome Atlas (TCGA) gene expression data from 13 tumor entities, we constructed the mitochondrial chaperone-client co-expression network. We determined that the network is comprised of three distinct modules, each populated with unique chaperone-clients co-expression pairs belonging to distinct functional groups. Surprisingly, chaperonins HSPD1 and HSPE1, which are known to comprise a functional complex, each occupied a different module: HSPD1 co-expressed with tricarboxylic acid cycle cycle enzymes, while HSPE1 co-expressed with proteins involved in oxidative phosphorylation. Importantly, we found that the genes in each module were enriched for discrete transcription factor binding sites, suggesting the mechanism for the coordinated co-expression. We propose that our mitochondrial chaperone-client interactome can facilitate the identification of chaperones supporting specific mitochondrial pathways and bring forth a fundamental principle in metabolic adaptation.

Keywords:  bioinformatics analysis; cancer; chaperone; co-expression; mitochondria

DOI:  https://doi.org/10.3390/cancers12040825
Dev Cell. 2020 Apr 01. pii: S1534-5807(20)30189-1. [Epub ahead of print]

Metabolic Reprogramming Promotes Neural Crest Migration via Yap/Tead Signaling.

Debadrita Bhattacharya, Ana Paula Azambuja, Marcos Simoes-Costa.

  The Warburg effect is one of the metabolic hallmarks of cancer cells, characterized by enhanced glycolysis even under aerobic conditions. This physiological adaptation is associated with metastasis , but we still have a superficial understanding of how it affects cellular processes during embryonic development. Here we report that the neural crest, a migratory stem cell population in vertebrate embryos, undergoes an extensive metabolic remodeling to engage in aerobic glycolysis prior to delamination. This increase in glycolytic flux promotes Yap/Tead signaling, which activates the expression of a set of transcription factors to drive epithelial-to-mesenchymal transition. Our results demonstrate how shifts in carbon metabolism can trigger the gene regulatory circuits that control complex cell behaviors. These findings support the hypothesis that the Warburg effect is a precisely regulated developmental mechanism that is anomalously reactivated during tumorigenesis and metastasis.

Keywords:  Warburg effect; Yap/Tead signaling; cell metabolism; cell migration; epithelial to mesenchymal transition; glycolysis; neural crest

DOI:  https://doi.org/10.1016/j.devcel.2020.03.005
FASEB J. 2020 Apr 02.

Increased mitochondrial fragmentation in polycystic kidney disease acts as a modifier of disease progression.

Laura Cassina, Marco Chiaravalli, Alessandra Boletta.

  Autosomal dominant polycystic kidney disease (ADPKD) is a common monogenic disorder, characterized by bilateral renal cyst formation. Multiple pathways are de-regulated in cystic epithelia offering good opportunities for therapy. Others and we have previously reported that metabolic reprogramming, including alterations of the TCA cycle, are prominent features of ADPKD. Several lines of evidence suggest that mitochondrial impairment might be responsible for the metabolic alterations. Here, we performed morphologic and morphometric evaluation of mitochondria by TEM in an orthologous mouse model of PKD caused by mutations in the Pkd1 gene (Ksp-Cre;Pkd1flox/- ). Furthermore, we measured mitochondrial respiration by COX and SDH enzymatic activity in situ. We found several alterations including reduced mitochondrial mass, altered structure and fragmentation of the mitochondrial network in cystic epithelia of Ksp-Cre;Pkd1flox/- mice. At the molecular level, we found reduced expression of the pro-fusion proteins OPA1 and MFN1 and up-regulation of the pro-fission protein DRP1. Importantly, administration of Mdivi-1, which interferes with DRP1 rescuing mitochondrial fragmentation, significantly reduced kidney/body weight, cyst formation, and improved renal function in Ksp-Cre;Pkd1flox/- mice. Our data indicate that impaired mitochondrial structure and function play a role in disease progression, and that their improvement can significantly modify the course of the disease.

Keywords:  Mdivi-1; cellular respiration; mitochondrial fragmentation; polycystic kidney disease

DOI:  https://doi.org/10.1096/fj.201901739RR
Cell Metab. 2020 Mar 20. pii: S1550-4131(20)30120-0. [Epub ahead of print]

Mitochondria-Endoplasmic Reticulum Contacts in Reactive Astrocytes Promote Vascular Remodeling.

Jana Gӧbel, Esther Engelhardt, Patric Pelzer, Vignesh Sakthivelu, Hannah M Jahn, Milica Jevtic, Kat Folz-Donahue, Christian Kukat, Astrid Schauss, Christian K Frese, Patrick Giavalisco, Alexander Ghanem, Karl-Klaus Conzelmann, Elisa Motori, Matteo Bergami.

  Astrocytes have emerged for playing important roles in brain tissue repair; however, the underlying mechanisms remain poorly understood. We show that acute injury and blood-brain barrier disruption trigger the formation of a prominent mitochondrial-enriched compartment in astrocytic endfeet, which enables vascular remodeling. Integrated imaging approaches revealed that this mitochondrial clustering is part of an adaptive response regulated by fusion dynamics. Astrocyte-specific conditional deletion of Mitofusin 2 (Mfn2) suppressed perivascular mitochondrial clustering and disrupted mitochondria-endoplasmic reticulum (ER) contact sites. Functionally, two-photon imaging experiments showed that these structural changes were mirrored by impaired mitochondrial Ca2+ uptake leading to abnormal cytosolic transients within endfeet in vivo. At the tissue level, a compromised vascular complexity in the lesioned area was restored by boosting mitochondrial-ER perivascular tethering in MFN2-deficient astrocytes. These data unmask a crucial role for mitochondrial dynamics in coordinating astrocytic local domains and have important implications for repairing the injured brain.

Keywords:  Mitofusin 2; angiogenesis; brain injury; brain repair; calcium imaging; contact sites; metabolism; mitochondrial dynamics; perivascular endfeet; proteomics; synthetic linker

DOI:  https://doi.org/10.1016/j.cmet.2020.03.005
Nutrients. 2020 Apr 01. pii: E978. [Epub ahead of print]12(4):

Low Levels of Serum Tryptophan Underlie Skeletal Muscle Atrophy.

Soranobu Ninomiya, Nobuhiko Nakamura, Hiroshi Nakamura, Taku Mizutani, Yuto Kaneda, Kimihiro Yamaguchi, Takuro Matsumoto, Junichi Kitagawa, Nobuhiro Kanemura, Makoto Shiraki, Takeshi Hara, Masahito Shimizu, Hisashi Tsurumi.

  Sarcopenia is a poor prognosis factor in some cancer patients, but little is known about the mechanisms by which malignant tumors cause skeletal muscle atrophy. Tryptophan metabolism mediated by indoleamine 2,3-dioxygenase is one of the most important amino acid changes associated with cancer progression. Herein, we demonstrate the relationship between skeletal muscles and low levels of tryptophan. A positive correlation was observed between the volume of skeletal muscles and serum tryptophan levels in patients with diffuse large B-cell lymphoma. Low levels of tryptophan reduced C2C12 myoblast cell proliferation and differentiation. Fiber diameters in the tibialis anterior of C57BL/6 mice fed a tryptophan-deficient diet were smaller than those in mice fed a standard diet. Metabolomics analysis revealed that tryptophan-deficient diet downregulated glycolysis in the gastrocnemius and upregulated the concentrations of amino acids associated with the tricarboxylic acid cycle. The weights and muscle fiber diameters of mice fed the tryptophan-deficient diet recovered after switching to the standard diet. Our data showed a critical role for tryptophan in regulating skeletal muscle mass. Thus, the tryptophan metabolism pathway may be a promising target for preventing or treating skeletal muscle atrophies.

Keywords:  cancer; glycolysis; indoleamine 2,3-dioxygenase; sarcopenia; tryptophan

DOI:  https://doi.org/10.3390/nu12040978
iScience. 2020 Mar 12. pii: S2589-0042(20)30162-0. [Epub ahead of print]23(4): 100978

Exercise-Mediated Lowering of Glutamine Availability Suppresses Tumor Growth and Attenuates Muscle Wasting.

Katrine S Pedersen, Francesco Gatto, Bo Zerahn, Jens Nielsen, Bente K Pedersen, Pernille Hojman, Julie Gehl.

  Glutamine is a central nutrient for many cancers, contributing to the generation of building blocks and energy-promoting signaling necessary for neoplastic proliferation. In this study, we hypothesized that lowering systemic glutamine levels by exercise may starve tumors, thereby contributing to the inhibitory effect of exercise on tumor growth. We demonstrate that limiting glutamine availability, either pharmacologically or physiologically by voluntary wheel running, significantly attenuated the growth of two syngeneic murine tumor models of breast cancer and lung cancer, respectively, and decreased markers of atrophic signaling in muscles from tumor-bearing mice. In continuation, wheel running completely abolished tumor-induced loss of weight and lean body mass, independently of the effect of wheel running on tumor growth. Moreover, wheel running abolished tumor-induced upregulation of muscular glutamine transporters and myostatin signaling. In conclusion, our data suggest that voluntary wheel running preserves muscle mass by counteracting muscular glutamine release and tumor-induced atrophic signaling.

Keywords:  Cancer; Physiology; Specialized Functions of Cells

DOI:  https://doi.org/10.1016/j.isci.2020.100978
Cells. 2020 Mar 27. pii: E815. [Epub ahead of print]9(4):

Redox Modifications of Proteins of the Mitochondrial Fusion and Fission Machinery.

Christina Wolf, Víctor López Del Amo, Sabine Arndt, Diones Bueno, Stefan Tenzer, Eva-Maria Hanschmann, Carsten Berndt, Axel Methner.

  Mitochondrial fusion and fission tailors the mitochondrial shape to changes in cellular homeostasis. Players of this process are the mitofusins, which regulate fusion of the outer mitochondrial membrane, and the fission protein DRP1. Upon specific stimuli, DRP1 translocates to the mitochondria, where it interacts with its receptors FIS1, MFF, and MID49/51. Another fission factor of clinical relevance is GDAP1. Here, we identify and discuss cysteine residues of these proteins that are conserved in phylogenetically distant organisms and which represent potential sites of posttranslational redox modifications. We reveal that worms and flies possess only a single mitofusin, which in vertebrates diverged into MFN1 and MFN2. All mitofusins contain four conserved cysteines in addition to cysteine 684 in MFN2, a site involved in mitochondrial hyperfusion. DRP1 and FIS1 are also evolutionarily conserved but only DRP1 contains four conserved cysteine residues besides cysteine 644, a specific site of nitrosylation. MFF and MID49/51 are only present in the vertebrate lineage. GDAP1 is missing in the nematode genome and contains no conserved cysteine residues. Our analysis suggests that the function of the evolutionarily oldest proteins of the mitochondrial fusion and fission machinery, the mitofusins and DRP1 but not FIS1, might be altered by redox modifications.

Keywords:  fission; fusion; metabolism; mitochondria; redox; thiol switch

DOI:  https://doi.org/10.3390/cells9040815
Cell Rep. 2020 Mar 31. pii: S2211-1247(20)30329-6. [Epub ahead of print]30(13): 4551-4566.e7

TET-Mediated Hypermethylation Primes SDH-Deficient Cells for HIF2α-Driven Mesenchymal Transition.

Aurélie Morin, Judith Goncalves, Sophie Moog, Luis-Jaime Castro-Vega, Sylvie Job, Alexandre Buffet, Marie-Joséphine Fontenille, Justine Woszczyk, Anne-Paule Gimenez-Roqueplo, Eric Letouzé, Judith Favier.

  Loss-of-function mutations in the SDHB subunit of succinate dehydrogenase predispose patients to aggressive tumors characterized by pseudohypoxic and hypermethylator phenotypes. The mechanisms leading to DNA hypermethylation and its contribution to SDH-deficient cancers remain undemonstrated. We examine the genome-wide distribution of 5-methylcytosine and 5-hydroxymethylcytosine and their correlation with RNA expression in SDHB-deficient tumors and murine Sdhb-/- cells. We report that DNA hypermethylation results from TET inhibition. Although it preferentially affects PRC2 targets and known developmental genes, PRC2 activity does not contribute to the DNA hypermethylator phenotype. We also prove, in vitro and in vivo, that TET silencing, although recapitulating the methylation profile of Sdhb-/- cells, is not sufficient to drive their EMT-like phenotype, which requires additional HIF2α activation. Altogether, our findings reveal synergistic roles of TET repression and pseudohypoxia in the acquisition of metastatic traits, providing a rationale for targeting HIF2α and DNA methylation in SDH-associated malignancies.

Keywords:  SDH; SDHB; epithelial-to-mesenchymal transition; hydroxymethylation; hypoxia; methylation; paraganglioma; pheochromocytoma; succinate dehydrogenase

DOI:  https://doi.org/10.1016/j.celrep.2020.03.022
FASEB J. 2020 Apr 04.

Activation of AMP-activated protein kinase during sepsis/inflammation improves survival by preserving cellular metabolic fitness.

Kui Jin, Yujie Ma, Carlos L Manrique-Caballero, Hui Li, David R Emlet, Shengnan Li, Catherine J Baty, Xiaoyan Wen, Nahmah Kim-Campbell, Alicia Frank, Elizabeth V Menchikova, Nuria M Pastor-Soler, Kenneth R Hallows, Edwin K Jackson, Sruti Shiva, Michael R Pinsky, Brian S Zuckerbraun, John A Kellum, Hernando Gómez.

  The purpose was to determine the role of AMPK activation in the renal metabolic response to sepsis, the development of sepsis-induced acute kidney injury (AKI) and on survival. In a prospective experimental study, 167 10- to 12-week-old C57BL/6 mice underwent cecal ligation and puncture (CLP) and human proximal tubule epithelial cells (TEC; HK2) were exposed to inflammatory mix (IM), a combination of lipopolysaccharide (LPS) and high mobility group box 1 (HMGB1). Renal/TEC metabolic fitness was assessed by monitoring the expression of drivers of oxidative phosphorylation (OXPHOS), the rates of utilization of OXPHOS/glycolysis in response to metabolic stress, and mitochondrial function by measuring O2 consumption rates (OCR) and the membrane potential (Δψm ). Sepsis/IM resulted in AKI, increased mortality, and in renal AMPK activation 6-24 hours after CLP/IM. Pharmacologic activation of AMPK with 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) or metformin during sepsis improved the survival, while AMPK inhibition with Compound C increased mortality, impaired mitochondrial respiration, decreased OCR, and disrupted TEC metabolic fitness. AMPK-driven protection was associated with increased Sirt 3 expression and restoration of metabolic fitness. Renal AMPK activation in response to sepsis/IM is an adaptive mechanism that protects TEC, organs, and the host by preserving mitochondrial function and metabolic fitness likely through Sirt3 signaling.

Keywords:  AMPK; Sirt3; metabolism; mitochondria; tubular epithelial cell

DOI:  https://doi.org/10.1096/fj.201901900R
Immunol Rev. 2020 Apr 03.

Cell-intrinsic metabolic regulation of mononuclear phagocyte activation: Findings from the tip of the iceberg.

Nikki van Teijlingen Bakker, Edward J Pearce.

  We have only recently started to appreciate the extent to which immune cell activation involves significant changes in cellular metabolism. We are now beginning to understand how commitment to specific metabolic pathways influences aspects of cellular biology that are the more usual focus of immunological studies, such as activation-induced changes in gene transcription, post-transcriptional regulation of transcription, post-translational modifications of proteins, cytokine secretion, etc. Here, we focus on metabolic reprogramming in mononuclear phagocytes downstream of stimulation with inflammatory signals (such as LPS and IFNγ) vs alternative activation signals (IL-4), with an emphasis on work on dendritic cells and macrophages from our laboratory, and related studies from others. We cover aspects of glycolysis and its branching pathways (glycogen synthesis, pentose phosphate, serine synthesis, hexose synthesis, and glycerol 3 phosphate shuttle), the tricarboxylic acid pathway, fatty acid synthesis and oxidation, and mitochondrial biology. Although our understanding of the metabolism of mononuclear phagocytes has progressed significantly over the last 10 years, major challenges remain, including understanding the effects of tissue residence on metabolic programming related to cellular activation, and the translatability of findings from mouse to human biology.

Keywords:  IL-4; LPS; TCA cycle; alternative activation; cytokines; dendritic cells; glycolysis; immunometabolism; inflammation; macrophages; metabolism; mitochondria

DOI:  https://doi.org/10.1111/imr.12848
Nature. 2020 Apr;580(7801): 130-135

Metabolites released from apoptotic cells act as tissue messengers.

Christopher B Medina, Parul Mehrotra, Sanja Arandjelovic, Justin S A Perry, Yizhan Guo, Sho Morioka, Brady Barron, Scott F Walk, Bart Ghesquière, Alexander S Krupnick, Ulrike Lorenz, Kodi S Ravichandran.

Caspase-dependent apoptosis accounts for approximately 90% of homeostatic cell turnover in the body1, and regulates inflammation, cell proliferation, and tissue regeneration2-4. How apoptotic cells mediate such diverse effects is not fully understood. Here we profiled the apoptotic metabolite secretome and determined its effects on the tissue neighbourhood. We show that apoptotic lymphocytes and macrophages release specific metabolites, while retaining their membrane integrity. A subset of these metabolites is also shared across different primary cells and cell lines after the induction of apoptosis by different stimuli. Mechanistically, the apoptotic metabolite secretome is not simply due to passive emptying of cellular contents and instead is a regulated process. Caspase-mediated opening of pannexin 1 channels at the plasma membrane facilitated the release of a select subset of metabolites. In addition, certain metabolic pathways continued to remain active during apoptosis, with the release of only select metabolites from a given pathway. Functionally, the apoptotic metabolite secretome induced specific gene programs in healthy neighbouring cells, including suppression of inflammation, cell proliferation, and wound healing. Furthermore, a cocktail of apoptotic metabolites reduced disease severity in mouse models of inflammatory arthritis and lung-graft rejection. These data advance the concept that apoptotic cells are not inert cells waiting for removal, but instead release metabolites as 'good-bye' signals to actively modulate outcomes in tissues.

DOI: https://doi.org/10.1038/s41586-020-2121-3
J Mol Cell Cardiol. 2020 Mar 28. pii: S0022-2828(20)30076-6. [Epub ahead of print]

MitoPlex: A targeted multiple reaction monitoring assay for quantification of a curated set of mitochondrial proteins.

Aleksandr B Stotland, Weston Spivia, Amanda Orosco, Allen M Andres, Roberta A Gottlieb, Jennifer E Van Eyk, Sarah J Parker.

  Mitochondria are the major source of cellular energy (ATP), as well as critical mediators of widespread functions such as cellular redox balance, apoptosis, and metabolic flux. The organelles play an especially important role in the maintenance of cardiac homeostasis; their inability to generate ATP following impairment due to ischemic damage has been directly linked to organ failure. Methods to quantify mitochondrial content are limited to low throughput immunoassays, measurement of mitochondrial DNA, or relative quantification by untargeted mass spectrometry. Here, we present a high throughput, reproducible and quantitative mass spectrometry multiple reaction monitoring based assay of 37 proteins critical to central carbon chain metabolism and overall mitochondrial function termed 'MitoPlex'. We coupled this protein multiplex with a parallel analysis of the central carbon chain metabolites (219 metabolite assay) extracted in tandem from the same sample, be it cells or tissue. In tests of its biological applicability in cells and tissues, "MitoPlex plus metabolites" indicated profound effects of HMG-CoA Reductase inhibition (e.g., statin treatment) on mitochondria of i) differentiating C2C12 skeletal myoblasts, as well as a clear opposite trend of statins to promote mitochondrial protein expression and metabolism in heart and liver, while suppressing mitochondrial protein and ii) aspects of metabolism in the skeletal muscle obtained from C57Bl6 mice. Our results not only reveal new insights into the metabolic effect of statins in skeletal muscle, but present a new high throughput, reliable MS-based tool to study mitochondrial dynamics in both cell culture and in vivo models.

Keywords:  Metabolomics; Mitochondria; Statins; Targeted mass spectrometry

DOI:  https://doi.org/10.1016/j.yjmcc.2020.03.011
iScience. 2020 Mar 19. pii: S2589-0042(20)30174-7. [Epub ahead of print]23(4): 100990

Succinate Dehydrogenase-Regulated Phosphoenolpyruvate Carboxykinase Sustains Copulation Fitness in Aging C. elegans Males.

Jimmy Goncalves, Yufeng Wan, Xiaoyan Guo, Kyoungsun Rha, Brigitte LeBoeuf, Liusuo Zhang, Kerolayne Estler, L René Garcia.

  Dysregulated metabolism accelerates reduced decision-making and locomotor ability during aging. To identify mechanisms for delaying behavioral decline, we investigated how C. elegans males sustain their copulatory behavior during early to mid-adulthood. We found that in mid-aged males, gluco-/glyceroneogenesis, promoted by phosphoenolpyruvate carboxykinase (PEPCK), sustains competitive reproductive behavior. C. elegans' PEPCK paralogs, pck-1 and pck-2, increase in expression during the first 2 days of adulthood. Insufficient PEPCK expression correlates with reduced egl-2-encoded ether-a-go-go K+ channel expression and premature hyper-excitability of copulatory circuits. For copulation, pck-1 is required in neurons, whereas pck-2 is required in the epidermis. However, PCK-2 is more essential, because we found that epidermal PCK-2 likely supplements the copulation circuitry with fuel. We identified the subunit A of succinate dehydrogenase SDHA-1 as a potent modulator of PEPCK expression. We postulate that during mid-adulthood, reduction in mitochondrial physiology signals the upregulation of cytosolic PEPCK to sustain the male's energy demands.

Keywords:  Animal Physiology; Behavior Genetics; Biological Sciences

DOI:  https://doi.org/10.1016/j.isci.2020.100990
Cancer Cell. 2020 Mar 23. pii: S1535-6108(20)30106-9. [Epub ahead of print]

KMT2D Deficiency Impairs Super-Enhancers to Confer a Glycolytic Vulnerability in Lung Cancer.

Hunain Alam, Ming Tang, Mayinuer Maitituoheti, Shilpa S Dhar, Manish Kumar, Chae Young Han, Chandrashekar R Ambati, Samir B Amin, Bingnan Gu, Tsai-Yu Chen, Yu-Hsi Lin, Jichao Chen, Florian L Muller, Nagireddy Putluri, Elsa R Flores, Francesco J DeMayo, Laura Baseler, Kunal Rai, Min Gyu Lee.

  Epigenetic modifiers frequently harbor loss-of-function mutations in lung cancer, but their tumor-suppressive roles are poorly characterized. Histone methyltransferase KMT2D (a COMPASS-like enzyme, also called MLL4) is among the most highly inactivated epigenetic modifiers in lung cancer. Here, we show that lung-specific loss of Kmt2d promotes lung tumorigenesis in mice and upregulates pro-tumorigenic programs, including glycolysis. Pharmacological inhibition of glycolysis preferentially impedes tumorigenicity of human lung cancer cells bearing KMT2D-inactivating mutations. Mechanistically, Kmt2d loss widely impairs epigenomic signals for super-enhancers/enhancers, including the super-enhancer for the circadian rhythm repressor Per2. Loss of Kmt2d decreases expression of PER2, which regulates multiple glycolytic genes. These findings indicate that KMT2D is a lung tumor suppressor and that KMT2D deficiency confers a therapeutic vulnerability to glycolytic inhibitors.

Keywords:  KMT2D; epigenetic modifier; glycolysis; histone methylation; histone methyltransferase; inhibitor; lung cancer; metabolism; super-enhancer; tumor suppressor

DOI:  https://doi.org/10.1016/j.ccell.2020.03.005
Nat Rev Mol Cell Biol. 2020 Mar 30.

Reactive oxygen species (ROS) as pleiotropic physiological signalling agents.

Helmut Sies, Dean P Jones.

'Reactive oxygen species' (ROS) is an umbrella term for an array of derivatives of molecular oxygen that occur as a normal attribute of aerobic life. Elevated formation of the different ROS leads to molecular damage, denoted as 'oxidative distress'. Here we focus on ROS at physiological levels and their central role in redox signalling via different post-translational modifications, denoted as 'oxidative eustress'. Two species, hydrogen peroxide (H2O2) and the superoxide anion radical (O2·-), are key redox signalling agents generated under the control of growth factors and cytokines by more than 40 enzymes, prominently including NADPH oxidases and the mitochondrial electron transport chain. At the low physiological levels in the nanomolar range, H2O2 is the major agent signalling through specific protein targets, which engage in metabolic regulation and stress responses to support cellular adaptation to a changing environment and stress. In addition, several other reactive species are involved in redox signalling, for instance nitric oxide, hydrogen sulfide and oxidized lipids. Recent methodological advances permit the assessment of molecular interactions of specific ROS molecules with specific targets in redox signalling pathways. Accordingly, major advances have occurred in understanding the role of these oxidants in physiology and disease, including the nervous, cardiovascular and immune systems, skeletal muscle and metabolic regulation as well as ageing and cancer. In the past, unspecific elimination of ROS by use of low molecular mass antioxidant compounds was not successful in counteracting disease initiation and progression in clinical trials. However, controlling specific ROS-mediated signalling pathways by selective targeting offers a perspective for a future of more refined redox medicine. This includes enzymatic defence systems such as those controlled by the stress-response transcription factors NRF2 and nuclear factor-κB, the role of trace elements such as selenium, the use of redox drugs and the modulation of environmental factors collectively known as the exposome (for example, nutrition, lifestyle and irradiation).

DOI: https://doi.org/10.1038/s41580-020-0230-3
Cell. 2020 Mar 30. pii: S0092-8674(20)30270-1. [Epub ahead of print]

Senescence-Induced Vascular Remodeling Creates Therapeutic Vulnerabilities in Pancreas Cancer.

Marcus Ruscetti, John P Morris, Riccardo Mezzadra, James Russell, Josef Leibold, Paul B Romesser, Janelle Simon, Amanda Kulick, Yu-Jui Ho, Myles Fennell, Jinyang Li, Robert J Norgard, John E Wilkinson, Direna Alonso-Curbelo, Ramya Sridharan, Daniel A Heller, Elisa de Stanchina, Ben Z Stanger, Charles J Sherr, Scott W Lowe.

  KRAS mutant pancreatic ductal adenocarcinoma (PDAC) is characterized by a desmoplastic response that promotes hypovascularity, immunosuppression, and resistance to chemo- and immunotherapies. We show that a combination of MEK and CDK4/6 inhibitors that target KRAS-directed oncogenic signaling can suppress PDAC proliferation through induction of retinoblastoma (RB) protein-mediated senescence. In preclinical mouse models of PDAC, this senescence-inducing therapy produces a senescence-associated secretory phenotype (SASP) that includes pro-angiogenic factors that promote tumor vascularization, which in turn enhances drug delivery and efficacy of cytotoxic gemcitabine chemotherapy. In addition, SASP-mediated endothelial cell activation stimulates the accumulation of CD8+ T cells into otherwise immunologically "cold" tumors, sensitizing tumors to PD-1 checkpoint blockade. Therefore, in PDAC models, therapy-induced senescence can establish emergent susceptibilities to otherwise ineffective chemo- and immunotherapies through SASP-dependent effects on the tumor vasculature and immune system.

Keywords:  T cells; chemotherapy resistance; endothelial cell activation; immunotherapy; pancreatic cancer; senescence; senescence-associated secretory phenotype; targeted therapy; tumor microenvironment; vascular biology

DOI:  https://doi.org/10.1016/j.cell.2020.03.008
Cell Chem Biol. 2020 Mar 24. pii: S2451-9456(20)30081-7. [Epub ahead of print]

The Chemical Biology of Ferroptosis in the Central Nervous System.

Rajiv R Ratan.

  Over the past five decades, thanatology has come to include the study of how individual cells in our bodies die appropriately and inappropriately in response to physiological and pathological stimuli. Morphological and biochemical criteria have been painstakingly established to create clarity around definitions of distinct types of cell death and mechanisms for their activation. Among these, ferroptosis has emerged as a unique, oxidative stress-induced cell death pathway with implications for diseases as diverse as traumatic brain injury, hemorrhagic stroke, Alzheimer's disease, cancer, renal ischemia, and heat stress in plants. In this review, I highlight some of the formative studies that fostered its recognition in the nervous system and describe how chemical biological tools have been essential in defining events necessary for its execution. Finally, I discuss emerging opportunities for antiferroptotic agents as therapeutic agents in neurological diseases.

Keywords:  ATF4; Chac1; Erk signaling; HIF prolyl hydroxylases; N-acetylcysteine; Nrf-2; Trib3; adaptaquin; c-Myc; cystine transport; ferroptosis; glutathione; glutathione peroxidase-4; iron; mithramycin; reactive lipid species; transglutaminase

DOI:  https://doi.org/10.1016/j.chembiol.2020.03.007
Nat Commun. 2020 Apr 02. 11(1): 1643

A salvage pathway maintains highly functional respiratory complex I.

Karolina Szczepanowska, Katharina Senft, Juliana Heidler, Marija Herholz, Alexandra Kukat, Michaela Nicole Höhne, Eduard Hofsetz, Christina Becker, Sophie Kaspar, Heiko Giese, Klaus Zwicker, Sergio Guerrero-Castillo, Linda Baumann, Johanna Kauppila, Anastasia Rumyantseva, Stefan Müller, Christian K Frese, Ulrich Brandt, Jan Riemer, Ilka Wittig, Aleksandra Trifunovic.

Regulation of the turnover of complex I (CI), the largest mitochondrial respiratory chain complex, remains enigmatic despite huge advancement in understanding its structure and the assembly. Here, we report that the NADH-oxidizing N-module of CI is turned over at a higher rate and largely independently of the rest of the complex by mitochondrial matrix protease ClpXP, which selectively removes and degrades damaged subunits. The observed mechanism seems to be a safeguard against the accumulation of dysfunctional CI arising from the inactivation of the N-module subunits due to attrition caused by its constant activity under physiological conditions. This CI salvage pathway maintains highly functional CI through a favorable mechanism that demands much lower energetic cost than de novo synthesis and reassembly of the entire CI. Our results also identify ClpXP activity as an unforeseen target for therapeutic interventions in the large group of mitochondrial diseases characterized by the CI instability.

DOI: https://doi.org/10.1038/s41467-020-15467-7
J Biol Chem. 2020 Apr 03. pii: jbc.RA119.010983. [Epub ahead of print]

The short variant of optic atrophy 1 (OPA1) improves cell survival under oxidative stress.

Hakjoo Lee, Sylvia B Smith, Shey-Shing Sheu, Yisang Yoon.

  Optic atrophy 1 (OPA1) is a dynamin protein that mediates mitochondrial fusion at the inner membrane. OPA1 is also necessary for maintaining the cristae, and thus essential for supporting cellular energetics. OPA1 exists as membrane-anchored long form (L-OPA1) and short form (S-OPA1) that lacks the transmembrane region and is generated by cleavage of L-OPA1. Mitochondrial dysfunction and cellular stresses activate the inner membrane-associated zinc metallopeptidase OMA1 that cleaves L-OPA1, causing S-OPA1 accumulation. The prevailing notion has been that L-OPA1 is the functional form while S-OPA1 is an inactive cleavage product in mammals, and that stress-induced OPA1 cleavage causes mitochondrial fragmentation and sensitizes cells to death. However, S-OPA1 contains all functional domains of dynamin proteins, suggesting that it has a physiological role. Indeed, we recently demonstrated that S-OPA1 can maintain cristae and energetics through its GTPase activity, despite lacking fusion activity. Here, applying oxidant insult that induces OPA1 cleavage, we show that cells unable to generate S-OPA1 are more sensitive to this stress under obligatory respiratory conditions, leading to necrotic death. These findings indicate that L-OPA1 and S-OPA1 differ in maintaining mitochondrial function. Mechanistically, we found that cells that exclusively express L-OPA1 generate more superoxide and are more sensitive to Ca2+-induced mitochondrial permeability transition, suggesting that S-OPA1, and not L-OPA1, protects against cellular stress. Importantly, silencing of OMA1 expression increased oxidant-induced cell death, indicating that stress-induced OPA1 cleavage supports cell survival. Our findings suggest that S-OPA1 generation by OPA1 cleavage is a survival mechanism in stressed cells.

Keywords:  OPA1; mitochondria; mitochondrial dynamics; mitochondrial permeability transition (MPT); necrosis (necrotic death); oxidative stress; reactive oxygen species (ROS)

DOI:  https://doi.org/10.1074/jbc.RA119.010983
Int J Biol Sci. 2020 ;16(9): 1495-1506

The Role of D-3-Phosphoglycerate Dehydrogenase in Cancer.

Xiaoya Zhao, Jianfei Fu, Jinlin Du, Wenxia Xu.

  Serine, a non-essential amino acid, can be imported from the extracellular environment by transporters and de novo synthesized from glycolytic 3-phosphoglycerate (3-PG) in the serine biosynthetic pathway (SSP). It has been reported that active serine synthesis might be needed for the synthesis of proteins, lipids, and nucleotides and the balance of folate metabolism and redox homeostasis, which are necessary for cancer cell proliferation. Human D-3-phosphoglycerate dehydrogenase (PHGDH), the first and only rate-limiting enzyme in the de novo serine biosynthetic pathway, catalyzes the oxidation of 3-PG derived from glycolysis to 3-phosphohydroxypyruvate (3-PHP). PHGDH is highly expressed in tumors as a result of amplification, transcription, or its degradation and stability alteration, which dysregulates the serine biosynthesis pathway via metabolic enzyme activity to nourish tumors. And some recent researches reported that PHGDH promoted some tumors growth via non-metabolic way by upregulating target cancer-promoting genes. In this article, we reviewed the type, structure, expression and inhibitors of PHGDH, as well as the role it plays in cancer and tumor resistance to chemotherapy.

Keywords:  SSP; cancer; expression of PHGDH; inhibitor of PHGDH; non-metabolic activity; serine metabolism; structure of PHGDH; tumor resistance

DOI:  https://doi.org/10.7150/ijbs.41051
Cell Stem Cell. 2020 Apr 02. pii: S1934-5909(20)30098-9. [Epub ahead of print]

A Metformin-Responsive Metabolic Pathway Controls Distinct Steps in Gastric Progenitor Fate Decisions and Maturation.

Zhi-Feng Miao, Mahliyah Adkins-Threats, Joseph R Burclaff, Luciana H Osaki, Jing-Xu Sun, Yan Kefalov, Zheng He, Zhen-Ning Wang, Jason C Mills.

  Cellular metabolism plays important functions in dictating stem cell behaviors, although its role in stomach epithelial homeostasis has not been evaluated in depth. Here, we show that the energy sensor AMP kinase (AMPK) governs gastric epithelial progenitor differentiation. Administering the AMPK activator metformin decreases epithelial progenitor proliferation and increases acid-secreting parietal cells (PCs) in mice and organoids. AMPK activation targets Krüppel-like factor 4 (KLF4), known to govern progenitor proliferation and PC fate choice, and PGC1α, which we show controls PC maturation after their specification. PC-specific deletion of AMPKα or PGC1α causes defective PC maturation, which could not be rescued by metformin. However, metformin treatment still increases KLF4 levels and suppresses progenitor proliferation. Thus, AMPK activates KLF4 in progenitors to reduce self-renewal and promote PC fate, whereas AMPK-PGC1α activation within the PC lineage promotes maturation, providing a potential suggestion for why metformin increases acid secretion and reduces gastric cancer risk in humans.

Keywords:  ADM; SPEM; mTORC1; metaplasia; mitochondria; paligenosis; ribosomes

DOI:  https://doi.org/10.1016/j.stem.2020.03.006
Nat Rev Cancer. 2020 Mar 31.

Understanding cachexia in the context of metastatic progression.

Anup K Biswas, Swarnali Acharyya.

Tumours reprogram host physiology, metabolism and immune responses during cancer progression. The release of soluble factors, exosomes and metabolites from tumours leads to systemic changes in distant organs, where cancer cells metastasize and grow. These tumour-derived circulating factors also profoundly impact tissues that are rarely inhabited by metastatic cancer cells such as skeletal muscle and adipose tissue. In fact, the majority of patients with metastatic cancer develop a debilitating muscle-wasting syndrome, known as cachexia, that is associated with decreased tolerance to antineoplastic therapy, poor prognosis and accelerated death, with no approved treatments. In this Perspective, we discuss the development of cachexia in the context of metastatic progression. We briefly discuss how circulating factors either directly or indirectly promote cachexia development and examine how signals from the metastatic process can trigger and amplify this process. Finally, we highlight promising therapeutic opportunities for targeting cachexia in the context of metastatic cancers.

DOI: https://doi.org/10.1038/s41568-020-0251-4
Biochim Biophys Acta Mol Cell Res. 2020 Mar 26. pii: S0167-4889(20)30067-7. [Epub ahead of print] 118709

Mitochondrial fission factor (MFF) is a critical regulator of peroxisome maturation.

Josiah B Passmore, Ruth E Carmichael, Tina A Schrader, Luis F Godinho, Sacha Ferdinandusse, Celien Lismont, Yunhong Wang, Christian Hacker, Markus Islinger, Marc Fransen, David M Richards, Peter Freisinger, Michael Schrader.

  Peroxisomes are highly dynamic subcellular compartments with important functions in lipid and ROS metabolism. Impaired peroxisomal function can lead to severe metabolic disorders with developmental defects and neurological abnormalities. Recently, a new group of disorders has been identified, characterised by defects in the membrane dynamics and division of peroxisomes rather than by loss of metabolic functions. However, the contribution of impaired peroxisome plasticity to the pathophysiology of those disorders is not well understood. Mitochondrial fission factor (MFF) is a key component of both the peroxisomal and mitochondrial division machinery. Patients with MFF deficiency present with developmental and neurological abnormalities. Peroxisomes (and mitochondria) in patient fibroblasts are highly elongated as a result of impaired organelle division. The majority of studies into MFF-deficiency have focused on mitochondrial dysfunction, but the contribution of peroxisomal alterations to the pathophysiology is largely unknown. Here, we show that MFF deficiency does not cause alterations to overall peroxisomal biochemical function. However, loss of MFF results in reduced import-competency of the peroxisomal compartment and leads to the accumulation of pre-peroxisomal membrane structures. We show that peroxisomes in MFF-deficient cells display alterations in peroxisomal redox state and intra-peroxisomal pH. Removal of elongated peroxisomes through induction of autophagic processes is not impaired. A mathematical model describing key processes involved in peroxisome dynamics sheds further light into the physical processes disturbed in MFF-deficient cells. The consequences of our findings for the pathophysiology of MFF-deficiency and related disorders with impaired peroxisome plasticity are discussed.

Keywords:  MFF; Mitochondria; Organelle division; PEX14; Peroxisomes; Pexophagy; Redox homeostasis

DOI:  https://doi.org/10.1016/j.bbamcr.2020.118709