bims-camemi 2021-01-03 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2021–01–03
35 papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit

Non-canonical Glutamate-Cysteine Ligase Activity Protects against Ferroptosis.
Pressure-Driven Mitochondrial Transfer Pipeline Generates Mammalian Cells of Desired Genetic Combinations and Fates.
High Fructose Drives the Serine Synthesis Pathway in Acute Myeloid Leukemic Cells.
Reductive TCA cycle metabolism fuels glutamine- and glucose-stimulated insulin secretion.
Mitochondrial Transfer and Regulators of Mesenchymal Stromal Cell Function and Therapeutic Efficacy.
The influence of aerobic exercise on mitochondrial quality control in skeletal muscle.
Abrogating GPT2 in triple negative breast cancer inhibits tumor growth and promotes autophagy.
Amino Acid Transporters Are a Vital Focal Point in the Control of mTORC1 Signaling and Cancer.
Endogenous retroelement activation by epigenetic therapy reverses the Warburg effect and elicits mitochondrial-mediated cancer cell death.
NAD+ metabolism and its roles in cellular processes during ageing.
Electrophysiological properties of the mitochondrial permeability transition pores: channel diversity and disease implication.
mTORC2 Assembly Is Regulated by USP9X-Mediated Deubiquitination of RICTOR.
Genome-scale reconstruction of Gcn4/ATF4 networks driving a growth program.
Regulation of autophagosome biogenesis by OFD1-mediated selective autophagy.
Not all mitochondrial DNAs are made equal and the nucleus knows it.
TRIB3 Promotes Lung Adenocarcinoma Progression via an Enhanced Warburg Effect.
Recruitment of pro-IL-1α to mitochondrial cardiolipin, via shared LC3 binding domain, inhibits mitophagy and drives maximal NLRP3 activation.
Coenzyme Q Depletion Reshapes MCF-7 Cells Metabolism.
How Autophagy Shapes the Tumor Microenvironment in Ovarian Cancer.
Mitochondria form contact sites with the nucleus to couple prosurvival retrograde response.
Stimulation of cholesterol biosynthesis in mitochondrial complex I-deficiency lowers reductive stress and improves motor function and survival in mice.
Regulation of ATP hydrolysis by the ε subunit, ζ subunit and Mg-ADP in the ATP synthase of Paracoccus denitrificans.
Differential expression of the BCAT isoforms between breast cancer subtypes.
Mitochondria-lysosome membrane contacts are defective in GDAP1-related Charcot-Marie-Tooth disease.
TMEM70 forms oligomeric scaffolds within mitochondrial cristae promoting in situ assembly of mammalian ATP synthase proton channel.
Phenotypic mapping of pathological crosstalk between glioblastoma and innate immune cells by synthetic genetic tracing.
Ribosome 18S m6A Methyltransferase METTL5 Promotes Translation Initiation and Breast Cancer Cell Growth.
Increased demand for NAD+ relative to ATP drives aerobic glycolysis.
Metastasis and immune evasion from extracellular cGAMP hydrolysis.
The Metabolic Importance of the Glutaminase II Pathway in Normal and Cancerous Cells.
Mitochondrial OPA1 cleavage is reversibly activated by differentiation of H9c2 cardiomyoblasts.
Gene expression regulates metabolite homeostasis during the Crabtree effect: Implications for the adaptation and evolution of Metabolism.
Functionally distinct roles for TET-oxidized 5-methylcytosine bases in somatic reprogramming to pluripotency.
The plasticity of the pyruvate dehydrogenase complex confers a labile structure that is associated with its catalytic activity.
Sugar-induced dysregulation of purine metabolism impacts lifespan.

Cell Metab. 2020 Dec 17. pii: S1550-4131(20)30662-8. [Epub ahead of print]

Non-canonical Glutamate-Cysteine Ligase Activity Protects against Ferroptosis.

Yun Pyo Kang, Andrea Mockabee-Macias, Chang Jiang, Aimee Falzone, Nicolas Prieto-Farigua, Everett Stone, Isaac S Harris, Gina M DeNicola.

  Cysteine is required for maintaining cellular redox homeostasis in both normal and transformed cells. Deprivation of cysteine induces the iron-dependent form of cell death known as ferroptosis; however, the metabolic consequences of cysteine starvation beyond impairment of glutathione synthesis are poorly characterized. Here, we find that cystine starvation of non-small-cell lung cancer cell lines induces an unexpected accumulation of γ-glutamyl-peptides, which are produced due to a non-canonical activity of glutamate-cysteine ligase catalytic subunit (GCLC). This activity is enriched in cell lines with high levels of NRF2, a key transcriptional regulator of GCLC, but is also inducible in healthy murine tissues following cysteine limitation. γ-glutamyl-peptide synthesis limits the accumulation of glutamate, thereby protecting against ferroptosis. These results indicate that GCLC has a glutathione-independent, non-canonical role in the protection against ferroptosis by maintaining glutamate homeostasis under cystine starvation.

Keywords:  GCLC; NRF2; cysteine; cystine; ferroptosis; glutamate; γ-glutamyl

DOI:  https://doi.org/10.1016/j.cmet.2020.12.007
Cell Rep. 2020 Dec 29. pii: S2211-1247(20)31551-5. [Epub ahead of print]33(13): 108562

Pressure-Driven Mitochondrial Transfer Pipeline Generates Mammalian Cells of Desired Genetic Combinations and Fates.

Alexander N Patananan, Alexander J Sercel, Ting-Hsiang Wu, Fasih M Ahsan, Alejandro Torres, Stephanie A L Kennedy, Amy Vandiver, Amanda J Collier, Artin Mehrabi, Jon Van Lew, Lise Zakin, Noe Rodriguez, Marcos Sixto, Wael Tadros, Adam Lazar, Peter A Sieling, Thang L Nguyen, Emma R Dawson, Daniel Braas, Justin Golovato, Luis Cisneros, Charles Vaske, Kathrin Plath, Shahrooz Rabizadeh, Kayvan R Niazi, Pei-Yu Chiou, Michael A Teitell.

  Generating mammalian cells with desired mitochondrial DNA (mtDNA) sequences is enabling for studies of mitochondria, disease modeling, and potential regenerative therapies. MitoPunch, a high-throughput mitochondrial transfer device, produces cells with specific mtDNA-nuclear DNA (nDNA) combinations by transferring isolated mitochondria from mouse or human cells into primary or immortal mtDNA-deficient (ρ0) cells. Stable isolated mitochondrial recipient (SIMR) cells isolated in restrictive media permanently retain donor mtDNA and reacquire respiration. However, SIMR fibroblasts maintain a ρ0-like cell metabolome and transcriptome despite growth in restrictive media. We reprogrammed non-immortal SIMR fibroblasts into induced pluripotent stem cells (iPSCs) with subsequent differentiation into diverse functional cell types, including mesenchymal stem cells (MSCs), adipocytes, osteoblasts, and chondrocytes. Remarkably, after reprogramming and differentiation, SIMR fibroblasts molecularly and phenotypically resemble unmanipulated control fibroblasts carried through the same protocol. Thus, our MitoPunch "pipeline" enables the production of SIMR cells with unique mtDNA-nDNA combinations for additional studies and applications in multiple cell types.

Keywords:  cell engineering; differentiation, MitoPunch, mitochondrial transplantation, mitochondrial replacement, mitonuclear communication, isolated mitochondria; mitochondrial transfer; mtDNA; reprogramming

DOI:  https://doi.org/10.1016/j.celrep.2020.108562
Cell Metab. 2020 Dec 17. pii: S1550-4131(20)30660-4. [Epub ahead of print]

High Fructose Drives the Serine Synthesis Pathway in Acute Myeloid Leukemic Cells.

Sangmoo Jeong, Angela Maria Savino, Rachel Chirayil, Ersilia Barin, Yuanming Cheng, Sun-Mi Park, Alexandra Schurer, Edouard Mullarky, Lewis C Cantley, Michael G Kharas, Kayvan R Keshari.

  A significant increase in dietary fructose consumption has been implicated as a potential driver of cancer. Metabolic adaptation of cancer cells to utilize fructose confers advantages for their malignant growth, but compelling therapeutic targets have not been identified. Here, we show that fructose metabolism of leukemic cells can be inhibited by targeting the de novo serine synthesis pathway (SSP). Leukemic cells, unlike their normal counterparts, become significantly dependent on the SSP in fructose-rich conditions as compared to glucose-rich conditions. This metabolic program is mediated by the ratio of redox cofactors, NAD+/NADH, and the increased SSP flux is beneficial for generating alpha-ketoglutarate from glutamine, which allows leukemic cells to proliferate even in the absence of glucose. Inhibition of PHGDH, a rate-limiting enzyme in the SSP, dramatically reduces leukemia engraftment in mice in the presence of high fructose, confirming the essential role of the SSP in the metabolic plasticity of leukemic cells.

Keywords:  in vivo isotope tracing; metabolic flux; redox; serine synthesis pathway

DOI:  https://doi.org/10.1016/j.cmet.2020.12.005
Cell Metab. 2020 Dec 08. pii: S1550-4131(20)30655-0. [Epub ahead of print]

Reductive TCA cycle metabolism fuels glutamine- and glucose-stimulated insulin secretion.

Guo-Fang Zhang, Mette V Jensen, Sarah M Gray, Kimberley El, You Wang, Danhong Lu, Thomas C Becker, Jonathan E Campbell, Christopher B Newgard.

  Metabolic fuels regulate insulin secretion by generating second messengers that drive insulin granule exocytosis, but the biochemical pathways involved are incompletely understood. Here we demonstrate that stimulation of rat insulinoma cells or primary rat islets with glucose or glutamine + 2-aminobicyclo-(2,2,1)-heptane-2-carboxylic acid (Gln + BCH) induces reductive, "counter-clockwise" tricarboxylic acid (TCA) cycle flux of glutamine to citrate. Molecular or pharmacologic suppression of isocitrate dehydrogenase-2 (IDH2), which catalyzes reductive carboxylation of 2-ketoglutarate to isocitrate, results in impairment of glucose- and Gln + BCH-stimulated reductive TCA cycle flux, lowering of NADPH levels, and inhibition of insulin secretion. Pharmacologic suppression of IDH2 also inhibits insulin secretion in living mice. Reductive TCA cycle flux has been proposed as a mechanism for generation of biomass in cancer cells. Here we demonstrate that reductive TCA cycle flux also produces stimulus-secretion coupling factors that regulate insulin secretion, including in non-dividing cells.

Keywords:  NADPH; anaplerosis; insulin secretion; isocitrate dehydrogenase-2; metabolic flux; pancreatic islet β cells; reductive TCA cycle; stable isotopes

DOI:  https://doi.org/10.1016/j.cmet.2020.11.020
Front Cell Dev Biol. 2020 ;8 603292

Mitochondrial Transfer and Regulators of Mesenchymal Stromal Cell Function and Therapeutic Efficacy.

Amina Mohammadalipour, Sandeep P Dumbali, Pamela L Wenzel.

  Mesenchymal stromal cell (MSC) metabolism plays a crucial role in the surrounding microenvironment in both normal physiology and pathological conditions. While MSCs predominantly utilize glycolysis in their native hypoxic niche within the bone marrow, new evidence reveals the importance of upregulation in mitochondrial activity in MSC function and differentiation. Mitochondria and mitochondrial regulators such as sirtuins play key roles in MSC homeostasis and differentiation into mature lineages of the bone and hematopoietic niche, including osteoblasts and adipocytes. The metabolic state of MSCs represents a fine balance between the intrinsic needs of the cellular state and constraints imposed by extrinsic conditions. In the context of injury and inflammation, MSCs respond to reactive oxygen species (ROS) and damage-associated molecular patterns (DAMPs), such as damaged mitochondria and mitochondrial products, by donation of their mitochondria to injured cells. Through intercellular mitochondria trafficking, modulation of ROS, and modification of nutrient utilization, endogenous MSCs and MSC therapies are believed to exert protective effects by regulation of cellular metabolism in injured tissues. Similarly, these same mechanisms can be hijacked in malignancy whereby transfer of mitochondria and/or mitochondrial DNA (mtDNA) to cancer cells increases mitochondrial content and enhances oxidative phosphorylation (OXPHOS) to favor proliferation and invasion. The role of MSCs in tumor initiation, growth, and resistance to treatment is debated, but their ability to modify cancer cell metabolism and the metabolic environment suggests that MSCs are centrally poised to alter malignancy. In this review, we describe emerging evidence for adaptations in MSC bioenergetics that orchestrate developmental fate decisions and contribute to cancer progression. We discuss evidence and potential strategies for therapeutic targeting of MSC mitochondria in regenerative medicine and tissue repair. Lastly, we highlight recent progress in understanding the contribution of MSCs to metabolic reprogramming of malignancies and how these alterations can promote immunosuppression and chemoresistance. Better understanding the role of metabolic reprogramming by MSCs in tissue repair and cancer progression promises to broaden treatment options in regenerative medicine and clinical oncology.

Keywords:  MSC differentiation; cancer metabolism; hematological malignancy; mesenchymal stromal cells (MSCs); metabolic reprogramming; mitochondrial biogenesis; mitochondrial dynamics; mitochondrial transfer

DOI:  https://doi.org/10.3389/fcell.2020.603292
J Physiol. 2020 Dec 28.

The influence of aerobic exercise on mitochondrial quality control in skeletal muscle.

Ashleigh M Philp, Nicholas J Saner, Michael Lazarou, Ian G Ganley, Andrew Philp.

Mitochondria are dynamic organelles, intricately designed to meet cellular energy requirements. To accommodate alterations in energy demand, mitochondria have a high degree of plasticity, changing in response to transient activation of numerous stress-related pathways. This adaptive response is particularly relevant in highly metabolic tissues such as skeletal muscle, where mitochondria support numerous biological processes related to metabolism, growth and regeneration. Aerobic exercise is a potent stimulus for skeletal muscle remodeling, leading to alterations in substrate utilisation, fibre-type composition and performance. Underlying these physiological responses is a change in mitochondrial quality control (MQC), a term encompassing the co-ordination of mitochondrial synthesis (biogenesis), remodeling (dynamics) and degradation (mitophagy) pathways. Understanding of MQC in skeletal muscle and the regulatory role of aerobic exercise of this process are rapidly advancing, as are the molecular techniques allowing the study of MQC in vivo. Given the emerging link between MQC and the onset of numerous non-communicable diseases, understanding the molecular regulation of MQC and the role of aerobic exercise in this process, will have substantial future impact on therapeutic approaches to manipulate MQC and maintain mitochondrial function across healthspan. This article is protected by copyright. All rights reserved.

DOI: https://doi.org/10.1113/JP279411
Int J Cancer. 2020 Dec 24.

Abrogating GPT2 in triple negative breast cancer inhibits tumor growth and promotes autophagy.

Devina Mitra, Silvia Vega-Rubin-de-Celis, Nadine Royla, Stephan Bernhardt, Heike Wilhelm, Nooraldeen Tarade, Gernot Poschet, Michael Buettner, Ilona Binenbaum, Simone Borgoni, Martina Vetter, Eva Johanna Kantelhardt, Christoph Thomssen, Aristotelis Chatziioannou, Rüdiger Hell, Stefan Kempa, Karin Müller-Decker, Stefan Wiemann.

  Uncontrolled proliferation and altered metabolic reprogramming are hallmarks of cancer. Active glycolysis and glutaminolysis are characteristic features of these hallmarks and required for tumorigenesis. A fine balance between cancer metabolism and autophagy is a prerequisite of homeostasis within cancer cells. Here we show that glutamate pyruvate transaminase 2 (GPT2), which serves as a pivot between glycolysis and glutaminolysis, is highly upregulated in aggressive breast cancers, particularly the triple negative breast cancer (TNBC) subtype. Abrogation of this enzyme results in decreased TCA cycle intermediates, which promotes the rewiring of glucose carbon atoms and alterations in nutrient levels. Concordantly, loss of GPT2 results in an impairment of mechanistic target of rapamycin complex 1 (mTORC1) activity as well as the induction of autophagy. Furthermore, in vivo xenografts studies have shown that autophagy induction correlates with decreased tumor growth and that markers of induced autophagy correlate with low GPT2 levels in patient samples. Taken together, these findings indicate that cancer cells have a close network between metabolic and nutrient sensing pathways necessary to sustain tumorigenesis, and that aminotransferase reactions play an important role in maintaining this balance.

Keywords:  Autophagy; Breast Cancer; Cancer metabolism; GPT2; mTORC1

DOI:  https://doi.org/10.1002/ijc.33456
Int J Mol Sci. 2020 Dec 22. pii: E23. [Epub ahead of print]22(1):

Amino Acid Transporters Are a Vital Focal Point in the Control of mTORC1 Signaling and Cancer.

Yann Cormerais, Milica Vučetić, Scott K Parks, Jacques Pouyssegur.

  The mechanistic target of rapamycin complex 1 (mTORC1) integrates signals from growth factors and nutrients to control biosynthetic processes, including protein, lipid, and nucleic acid synthesis. Dysregulation in the mTORC1 network underlies a wide array of pathological states, including metabolic diseases, neurological disorders, and cancer. Tumor cells are characterized by uncontrolled growth and proliferation due to a reduced dependency on exogenous growth factors. The genetic events underlying this property, such as mutations in the PI3K-Akt and Ras-Erk signaling networks, lead to constitutive activation of mTORC1 in nearly all human cancer lineages. Aberrant activation of mTORC1 has been shown to play a key role for both anabolic tumor growth and resistance to targeted therapeutics. While displaying a growth factor-independent mTORC1 activity and proliferation, tumors cells remain dependent on exogenous nutrients such as amino acids (AAs). AAs are an essential class of nutrients that are obligatory for the survival of any cell. Known as the building blocks of proteins, AAs also act as essential metabolites for numerous biosynthetic processes such as fatty acids, membrane lipids and nucleotides synthesis, as well as for maintaining redox homeostasis. In most tumor types, mTORC1 activity is particularly sensitive to intracellular AA levels. This dependency, therefore, creates a targetable vulnerability point as cancer cells become dependent on AA transporters to sustain their homeostasis. The following review will discuss the role of AA transporters for mTORC1 signaling in cancer cells and their potential as therapeutic drug targets.

Keywords:  ASCT2; LAT1; SNAT2; amino acid transporters; cancer; growth factors; mTORC1; nutrients; xCT

DOI:  https://doi.org/10.3390/ijms22010023
Cancer Discov. 2020 Dec 18. pii: CD-20-1065. [Epub ahead of print]

Endogenous retroelement activation by epigenetic therapy reverses the Warburg effect and elicits mitochondrial-mediated cancer cell death.

Vicente Fresquet, Maria J Garcia-Barchino, Marta J Larrayoz, Jon Celay, Carmen Vicente, Marta Fernandez-Galilea, Maria Jose Larrayoz, Maria J Calasanz, Carlos Panizo, Alexandra Junza, Jiahuai Han, Celia Prior, Puri Fortes, Ruben Pio, Julen Oyarzabal, Álvaro Martínez-Baztán, Bruno Paiva, Maria J Moreno-Aliaga, Maria D Odero, Xabier Agirre, Oscar Yanes, Felipe Prósper, Jose A Martinez-Climent.

During millions of years, endogenous retroelements have remained transcriptionally silent within mammalian genomes by epigenetic mechanisms. Modern anti-cancer therapies targeting the epigenetic machinery awaken retroelement expression, inducing anti-viral responses that eliminate tumors through mechanisms not completely understood. Here we find that massive binding of epigenetically-activated retroelements by RIG-I and MDA5 viral sensors promotes ATP hydrolysis and depletes intracellular energy, driving tumor killing independently of immune signaling. Energy depletion boosts compensatory ATP production by switching glycolysis to mitochondrial oxidative phosphorylation, thereby reversing the Warburg effect. However, hyperfunctional succinate dehydrogenase in mitochondrial electron transport chain generates excessive oxidative stress that unleashes RIP1-mediated necroptosis. To maintain ATP generation, hyperactive mitochondrial membrane blocks intrinsic apoptosis by increasing BCL2 dependency. Accordingly, drugs targeting BCL2-family proteins and epigenetic inhibitors yield synergistic responses in multiple cancer types. Thus, epigenetic therapy kills cancer cells by rewiring mitochondrial metabolism upon retroelement activation, which primes mitochondria to apoptosis by BH3-mimetics.

DOI: https://doi.org/10.1158/2159-8290.CD-20-1065
Nat Rev Mol Cell Biol. 2020 Dec 22.

NAD+ metabolism and its roles in cellular processes during ageing.

Anthony J Covarrubias, Rosalba Perrone, Alessia Grozio, Eric Verdin.

Nicotinamide adenine dinucleotide (NAD+) is a coenzyme for redox reactions, making it central to energy metabolism. NAD+ is also an essential cofactor for non-redox NAD+-dependent enzymes, including sirtuins, CD38 and poly(ADP-ribose) polymerases. NAD+ can directly and indirectly influence many key cellular functions, including metabolic pathways, DNA repair, chromatin remodelling, cellular senescence and immune cell function. These cellular processes and functions are critical for maintaining tissue and metabolic homeostasis and for healthy ageing. Remarkably, ageing is accompanied by a gradual decline in tissue and cellular NAD+ levels in multiple model organisms, including rodents and humans. This decline in NAD+ levels is linked causally to numerous ageing-associated diseases, including cognitive decline, cancer, metabolic disease, sarcopenia and frailty. Many of these ageing-associated diseases can be slowed down and even reversed by restoring NAD+ levels. Therefore, targeting NAD+ metabolism has emerged as a potential therapeutic approach to ameliorate ageing-related disease, and extend the human healthspan and lifespan. However, much remains to be learnt about how NAD+ influences human health and ageing biology. This includes a deeper understanding of the molecular mechanisms that regulate NAD+ levels, how to effectively restore NAD+ levels during ageing, whether doing so is safe and whether NAD+ repletion will have beneficial effects in ageing humans.

DOI: https://doi.org/10.1038/s41580-020-00313-x
Biochim Biophys Acta Bioenerg. 2020 Dec 23. pii: S0005-2728(20)30207-3. [Epub ahead of print] 148357

Electrophysiological properties of the mitochondrial permeability transition pores: channel diversity and disease implication.

M A Neginskaya, E V Pavlov, S-S Sheu.

  The mitochondrial permeability transition pore (mPTP) is a channel that, when open, is responsible for a dramatic increase in the permeability of the mitochondrial inner membrane, a process known as the mitochondrial permeability transition (mPT). mPTP activation during Ca2+ dyshomeostasis and oxidative stress disrupts normal mitochondrial function and induces cell death. mPTP opening has been implicated as a critical event in many diseases, including hypoxic injuries, neurodegeneration, and diabetes. Discoveries of recent years indicate that mPTP demonstrates very complicated behavior and regulation, and depending on specific induction or stress conditions, it can function as a high-conductance pore, a small channel, or a non-specific membrane leak. The focus of this review is to summarize the literature on the electrophysiological properties of the mPTP and to evaluate the evidence that it has multiple molecular identities. This review also provides perspective on how an electrophysiological approach can be used to quantitatively investigate the biophysical properties of the mPTP under physiological, pharmacological, pathophysiological, and disease conditions.

Keywords:  ROS; calcium; ion channel; mitochondria; mitochondrial permeability transition pore; patch-clamp

DOI:  https://doi.org/10.1016/j.bbabio.2020.148357
Cell Rep. 2020 Dec 29. pii: S2211-1247(20)31553-9. [Epub ahead of print]33(13): 108564

mTORC2 Assembly Is Regulated by USP9X-Mediated Deubiquitination of RICTOR.

Lidia Wrobel, Farah H Siddiqi, Sandra M Hill, Sung Min Son, Cansu Karabiyik, Hyunjeong Kim, David C Rubinsztein.

  The mechanistic target of rapamycin complex 2 (mTORC2) controls cell metabolism and survival in response to environmental inputs. Dysregulation of mTORC2 signaling has been linked to diverse human diseases, including cancer and metabolic disorders, highlighting the importance of a tightly controlled mTORC2. While mTORC2 assembly is a critical determinant of its activity, the factors regulating this event are not well understood, and it is unclear whether this process is regulated by growth factors. Here, we present data, from human cell lines and mice, describing a mechanism by which growth factors regulate ubiquitin-specific protease 9X (USP9X) deubiquitinase to stimulate mTORC2 assembly and activity. USP9X removes Lys63-linked ubiquitin from RICTOR to promote its interaction with mTOR, thereby facilitating mTORC2 signaling. As mTORC2 is central for cellular homeostasis, understanding the mechanisms regulating mTORC2 activation toward its downstream targets is vital for our understanding of physiological processes and for developing new therapeutic strategies in pathology.

Keywords:  RICTOR; USP9X; growth factor signaling; mTORC2; mechanistic target of rapamycin complex 2; posttranslational modification; ubiquitin-specific protease 9X

DOI:  https://doi.org/10.1016/j.celrep.2020.108564
PLoS Genet. 2020 Dec;16(12): e1009252

Genome-scale reconstruction of Gcn4/ATF4 networks driving a growth program.

Rajalakshmi Srinivasan, Adhish S Walvekar, Zeenat Rashida, Aswin Seshasayee, Sunil Laxman.

Growth and starvation are considered opposite ends of a spectrum. To sustain growth, cells use coordinated gene expression programs and manage biomolecule supply in order to match the demands of metabolism and translation. Global growth programs complement increased ribosomal biogenesis with sufficient carbon metabolism, amino acid and nucleotide biosynthesis. How these resources are collectively managed is a fundamental question. The role of the Gcn4/ATF4 transcription factor has been best studied in contexts where cells encounter amino acid starvation. However, high Gcn4 activity has been observed in contexts of rapid cell proliferation, and the roles of Gcn4 in such growth contexts are unclear. Here, using a methionine-induced growth program in yeast, we show that Gcn4/ATF4 is the fulcrum that maintains metabolic supply in order to sustain translation outputs. By integrating matched transcriptome and ChIP-Seq analysis, we decipher genome-wide direct and indirect roles for Gcn4 in this growth program. Genes that enable metabolic precursor biosynthesis indispensably require Gcn4; contrastingly ribosomal genes are partly repressed by Gcn4. Gcn4 directly binds promoter-regions and transcribes a subset of metabolic genes, particularly driving lysine and arginine biosynthesis. Gcn4 also globally represses lysine and arginine enriched transcripts, which include genes encoding the translation machinery. The Gcn4 dependent lysine and arginine supply thereby maintains the synthesis of the translation machinery. This is required to maintain translation capacity. Gcn4 consequently enables metabolic-precursor supply to bolster protein synthesis, and drive a growth program. Thus, we illustrate how growth and starvation outcomes are both controlled using the same Gcn4 transcriptional outputs that function in distinct contexts.

DOI: https://doi.org/10.1371/journal.pgen.1009252
EMBO J. 2020 Dec 28. e105120

Regulation of autophagosome biogenesis by OFD1-mediated selective autophagy.

Manuela Morleo, Simona Brillante, Umberto Formisano, Luigi Ferrante, Fabrizia Carbone, Daniela Iaconis, Alessandro Palma, Viviana Buonomo, Angela Serena Maione, Paolo Grumati, Carmine Settembre, Brunella Franco.

  Autophagy is a lysosome-dependent degradation pathway essential to maintain cellular homeostasis. Therefore, either defective or excessive autophagy may be detrimental for cells and tissues. The past decade was characterized by significant advances in molecular dissection of stimulatory autophagy inputs; however, our understanding of the mechanisms that restrain autophagy is far from complete. Here, we describe a negative feedback mechanism that limits autophagosome biogenesis based on the selective autophagy-mediated degradation of ATG13, a component of the ULK1 autophagy initiation complex. We demonstrate that the centrosomal protein OFD1 acts as bona fide autophagy receptor for ATG13 via direct interaction with the Atg8/LC3/GABARAP family of proteins. We also show that patients with Oral-Facial-Digital type I syndrome, caused by mutations in the OFD1 gene, display excessive autophagy and that genetic inhibition of autophagy in a mouse model of the disease, significantly ameliorates polycystic kidney, a clinical manifestation of the disorder. Collectively, our data report the discovery of an autophagy self-regulated mechanism and implicate dysregulated autophagy in the pathogenesis of renal cystic disease in mammals.

Keywords:  OFD1; autophagy receptor; polycystic kidney; selective autophagy

DOI:  https://doi.org/10.15252/embj.2020105120
IUBMB Life. 2020 Dec 25.

Not all mitochondrial DNAs are made equal and the nucleus knows it.

Ana Victoria Lechuga-Vieco, Raquel Justo-Méndez, José Antonio Enríquez.

  The oxidative phosphorylation (OXPHOS) system is the only structure in animal cells with components encoded by two genomes, maternally transmitted mitochondrial DNA (mtDNA), and biparentally transmitted nuclear DNA (nDNA). MtDNA-encoded genes have to physically assemble with their counterparts encoded in the nucleus to build together the functional respiratory complexes. Therefore, structural and functional matching requirements between the protein subunits of these molecular complexes are rigorous. The crosstalk between nDNA and mtDNA needs to overcome some challenges, as the nuclear-encoded factors have to be imported into the mitochondria in a correct quantity and match the high number of organelles and genomes per mitochondria that encode and synthesize their own components locally. The cell is able to sense the mito-nuclear match through changes in the activity of the OXPHOS system, modulation of the mitochondrial biogenesis, or reactive oxygen species production. This implies that a complex signaling cascade should optimize OXPHOS performance to the cellular-specific requirements, which will depend on cell type, environmental conditions, and life stage. Therefore, the mitochondria would function as a cellular metabolic information hub integrating critical information that would feedback the nucleus for it to respond accordingly. Here, we review the current understanding of the complex interaction between mtDNA and nDNA.

Keywords:  cytoplasmic communication; intergenomic coadaptation; mito-nuclear interactions; mitochondrial DNA; mitochondrial haplotypes; nucleo-mitochondrial mismatch; respiratory complexes and supercomplexes; retrograde responses

DOI:  https://doi.org/10.1002/iub.2434
Cancer Manag Res. 2020 ;12 13195-13206

TRIB3 Promotes Lung Adenocarcinoma Progression via an Enhanced Warburg Effect.

Yutong Xing, Peng Luo, Rui Hu, Duanduan Wang, Gang Zhou, Jie Jiang.

   Background: The pseudokinase Tribbles 3 (TRIB3) is involved in many cellular processes and various cancers. In recent years, the importance of metabolic transformation in the maintenance of malignant tumors has become increasingly prominent. Abnormal metabolism of cancer cells is considered a hallmark of cancer. However, the exact role and molecular mechanism of TRIB3 in lung adenocarcinoma (LUAD) cell reprogramming is largely unknown.
Methods: The oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) of cells were examined with a Seahorse XF Extracellular Flux Analyzer. In vitro and in vivo RT-qPCR, Western blotting, and functional assays were performed to explore the functional roles of TRIB3 in LUAD.
Results: In the present study, we demonstrated that TRIB3 is remarkably upregulated in LUAD cell lines as well as tissues. TRIB3 knockdown significantly inhibited LUAD cell growth and suppressed LUAD cell invasion, while TRIB3 overexpression conferred the opposite effects. Moreover, silencing TRIB3 suppressed the tumorigenesis and metastatic ability of LUAD cells. Mechanistically, we demonstrated that silencing TRIB3 significantly impaired aerobic glycolysis ability in LUAD cells. Furthermore, our data indicated that TRIB3 knockdown decreased hypoxia-inducible factor (HIF)1α levels and targeted the glycolytic genes regulated by HIF1α.
Conclusion: Together, our findings revealed a previously unappreciated function of TRIB3 in cancer cell metabolism and tumor progression, illustrating that TRIB3 could be considered a valuable therapeutic target for LUAD patients.

Keywords:  HIF1α; LUAD; TRIB3; aerobic glycolysis

DOI:  https://doi.org/10.2147/CMAR.S287956
Proc Natl Acad Sci U S A. 2021 Jan 05. pii: e2015632118. [Epub ahead of print]118(1):

Recruitment of pro-IL-1α to mitochondrial cardiolipin, via shared LC3 binding domain, inhibits mitophagy and drives maximal NLRP3 activation.

Jargalsaikhan Dagvadorj, Karolina Mikulska-Ruminska, Gantsetseg Tumurkhuu, Rojo A Ratsimandresy, Jessica Carriere, Allen M Andres, Stefanie Marek-Iannucci, Yang Song, Shuang Chen, Malcolm Lane, Andrea Dorfleutner, Roberta A Gottlieb, Christian Stehlik, Suzanne Cassel, Fayyaz S Sutterwala, Ivet Bahar, Timothy R Crother, Moshe Arditi.

  The balance between NLRP3 inflammasome activation and mitophagy is essential for homeostasis and cellular health, but this relationship remains poorly understood. Here we found that interleukin-1α (IL-1α)-deficient macrophages have reduced caspase-1 activity and diminished IL-1β release, concurrent with reduced mitochondrial damage, suggesting a role for IL-1α in regulating this balance. LPS priming of macrophages induced pro-IL-1α translocation to mitochondria, where it directly interacted with mitochondrial cardiolipin (CL). Computational modeling revealed a likely CL binding motif in pro-IL-1α, similar to that found in LC3b. Thus, binding of pro-IL-1α to CL in activated macrophages may interrupt CL-LC3b-dependent mitophagy, leading to enhanced Nlrp3 inflammasome activation and more robust IL-1β production. Mutation of pro-IL-1α residues predicted to be involved in CL binding resulted in reduced pro-IL-1α-CL interaction, a reduction in NLRP3 inflammasome activity, and increased mitophagy. These data identify a function for pro-IL-1α in regulating mitophagy and the potency of NLRP3 inflammasome activation.

Keywords:  IL-1α; autophagy; cardiolipin; inflammasome; mitochondria

DOI:  https://doi.org/10.1073/pnas.2015632118
Int J Mol Sci. 2020 Dec 28. pii: E198. [Epub ahead of print]22(1):

Coenzyme Q Depletion Reshapes MCF-7 Cells Metabolism.

Wenping Wang, Irene Liparulo, Nicola Rizzardi, Paola Bolignano, Natalia Calonghi, Christian Bergamini, Romana Fato.

  Mitochondrial dysfunction plays a significant role in the metabolic flexibility of cancer cells. This study aimed to investigate the metabolic alterations due to Coenzyme Q depletion in MCF-7 cells.
METHOD: The Coenzyme Q depletion was induced by competitively inhibiting with 4-nitrobenzoate the coq2 enzyme, which catalyzes one of the final reactions in the biosynthetic pathway of CoQ. The bioenergetic and metabolic characteristics of control and coenzyme Q depleted cells were investigated using polarographic and spectroscopic assays. The effect of CoQ depletion on cell growth was analyzed in different metabolic conditions.
RESULTS: we showed that cancer cells could cope from energetic and oxidative stress due to mitochondrial dysfunction by reshaping their metabolism. In CoQ depleted cells, the glycolysis was upregulated together with increased glucose consumption, overexpression of GLUT1 and GLUT3, as well as activation of pyruvate kinase (PK). Moreover, the lactate secretion rate was reduced, suggesting that the pyruvate flux was redirected, toward anabolic pathways. Finally, we found a different expression pattern in enzymes involved in glutamine metabolism, and TCA cycle in CoQ depleted cells in comparison to controls.
CONCLUSION: This work elucidated the metabolic alterations in CoQ-depleted cells and provided an insightful understanding of cancer metabolism targeting.

Keywords:  bioenergetics; cancer metabolism targeting; coenzyme Q; glutamine metabolism; glycolysis; metabolic reprogramming; mitochondrial dysfunction; spheroids

DOI:  https://doi.org/10.3390/ijms22010198
Front Oncol. 2020 ;10 599915

How Autophagy Shapes the Tumor Microenvironment in Ovarian Cancer.

Alessandra Ferraresi, Carlo Girone, Andrea Esposito, Chiara Vidoni, Letizia Vallino, Eleonora Secomandi, Danny N Dhanasekaran, Ciro Isidoro.

  Ovarian cancer (OC) is characterized by a high mortality rate due to the late diagnosis and the elevated metastatic potential. Autophagy, a lysosomal-driven catabolic process, contributes to the macromolecular turnover, cell homeostasis, and survival, and as such, it represents a pathway targetable for anti-cancer therapies. It is now recognized that the vascularization and the cellular composition of the tumor microenvironment influence the development and progression of OC by controlling the availability of nutrients, oxygen, growth factors, and inflammatory and immune-regulatory soluble factors that ultimately impinge on autophagy regulation in cancer cells. An increasing body of evidence indicates that OC carcinogenesis is associated, at least in the early stages, to insufficient autophagy. On the other hand, when the tumor is already established, autophagy activation provides a survival advantage to the cancer cells that face metabolic stress and protects from the macromolecules and organelles damages induced by chemo- and radiotherapy. Additionally, upregulation of autophagy may lead cancer cells to a non-proliferative dormant state that protects the cells from toxic injuries while preserving their stem-like properties. Further to complicate the picture, autophagy is deregulated also in stromal cells. Thus, changes in the tumor microenvironment reflect on the metabolic crosstalk between cancer and stromal cells impacting on their autophagy levels and, consequently, on cancer progression. Here, we present a brief overview of the role of autophagy in OC hallmarks, including tumor dormancy, chemoresistance, metastasis, and cell metabolism, with an emphasis on the bidirectional metabolic crosstalk between cancer cells and stromal cells in shaping the OC microenvironment.

Keywords:  autophagy; cancer; cancer associated fibroblasts; cell metabolism; chemoresistance; cytokines; dormancy; inflammatory stroma

DOI:  https://doi.org/10.3389/fonc.2020.599915
Sci Adv. 2020 Dec;pii: eabc9955. [Epub ahead of print]6(51):

Mitochondria form contact sites with the nucleus to couple prosurvival retrograde response.

Radha Desai, Daniel A East, Liana Hardy, Danilo Faccenda, Manuel Rigon, James Crosby, María Soledad Alvarez, Aarti Singh, Marta Mainenti, Laura Kuhlman Hussey, Robert Bentham, Gyorgy Szabadkai, Valentina Zappulli, Gurtej K Dhoot, Lisa E Romano, Dong Xia, Isabelle Coppens, Anne Hamacher-Brady, J Paul Chapple, Rosella Abeti, Roland A Fleck, Gema Vizcay-Barrena, Kenneth Smith, Michelangelo Campanella.

Mitochondria drive cellular adaptation to stress by retro-communicating with the nucleus. This process is known as mitochondrial retrograde response (MRR) and is induced by mitochondrial dysfunction. MRR results in the nuclear stabilization of prosurvival transcription factors such as the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). Here, we demonstrate that MRR is facilitated by contact sites between mitochondria and the nucleus. The translocator protein (TSPO) by preventing the mitophagy-mediated segregation o mitochonria is required for this interaction. The complex formed by TSPO with the protein kinase A (PKA), via the A-kinase anchoring protein acyl-CoA binding domain containing 3 (ACBD3), established the tethering. The latter allows for cholesterol redistribution of cholesterol in the nucleus to sustain the prosurvival response by blocking NF-κB deacetylation. This work proposes a previously unidentified paradigm in MRR: the formation of contact sites between mitochondria and nucleus to aid communication.

DOI: https://doi.org/10.1126/sciadv.abc9955
Biochim Biophys Acta Mol Basis Dis. 2020 Dec 29. pii: S0925-4439(20)30410-5. [Epub ahead of print] 166062

Stimulation of cholesterol biosynthesis in mitochondrial complex I-deficiency lowers reductive stress and improves motor function and survival in mice.

Tom J J Schirris, Sergio Rossell, Ria de Haas, Sanne J C M Frambach, Charlotte A Hoogstraten, G Herma Renkema, Julien D Beyrath, Peter H G M Willems, Martijn A Huynen, Jan A M Smeitink, Frans G M Russel, Richard A Notebaart.

  The majority of cellular energy is produced by the mitochondrial oxidative phosphorylation (OXPHOS) system. Failure of the first OXPHOS enzyme complex, NADH:ubiquinone oxidoreductase or complex I (CI), is associated with multiple signs and symptoms presenting at variable ages of onset. There is no approved drug treatment yet to slow or reverse the progression of CI-deficient disorders. Here, we present a comprehensive human metabolic network model of genetically characterized CI-deficient patient-derived fibroblasts. Model calculations predicted that increased cholesterol production, export, and utilization can counterbalance the surplus of reducing equivalents in patient-derived fibroblasts, as these pathways consume considerable amounts of NAD(P)H. We show that fibrates attenuated increased NAD(P)H levels and improved CI-deficient fibroblast growth by stimulating the production of cholesterol via enhancement of its cellular efflux. In CI-deficient (Ndufs4-/-) mice, fibrate treatment resulted in prolonged survival and improved motor function, which was accompanied by an increased cholesterol efflux from peritoneal macrophages. Our results shine a new light on the use of compensatory biological pathways in mitochondrial dysfunction which may lead to novel therapeutic interventions for mitochondrial diseases for which currently no cure exists.

Keywords:  Leigh syndrome; NAD(P)H; Ndufs4(-/-) mice; cholesterol biosynthesis; complex I deficiency; metabolic network modelling

DOI:  https://doi.org/10.1016/j.bbadis.2020.166062
Biochim Biophys Acta Bioenerg. 2020 Dec 13. pii: S0005-2728(20)30205-X. [Epub ahead of print]1862(3): 148355

Regulation of ATP hydrolysis by the ε subunit, ζ subunit and Mg-ADP in the ATP synthase of Paracoccus denitrificans.

Owen D Jarman, Olivier Biner, Judy Hirst.

  F1FO-ATP synthase is a crucial metabolic enzyme that uses the proton motive force from respiration to regenerate ATP. For maximum thermodynamic efficiency ATP synthesis should be fully reversible, but the enzyme from Paracoccus denitrificans catalyzes ATP hydrolysis at far lower rates than it catalyzes ATP synthesis, an effect often attributed to its unique ζ subunit. Recently, we showed that deleting ζ increases hydrolysis only marginally, indicating that other common inhibitory mechanisms such as inhibition by the C-terminal domain of the ε subunit (ε-CTD) or Mg-ADP may be more important. Here, we created mutants lacking the ε-CTD, and double mutants lacking both the ε-CTD and ζ subunit. No substantial activation of ATP hydrolysis was observed in any of these strains. Instead, hydrolysis in even the double mutant strains could only be activated by oxyanions, the detergent lauryldimethylamine oxide, or a proton motive force, which are all considered to release Mg-ADP inhibition. Our results establish that P. denitrificans ATP synthase is regulated by a combination of the ε and ζ subunits and Mg-ADP inhibition.

Keywords:  ATP hydrolysis; F(1)F(O)-ATP synthase; Mg-ADP inhibition; P. denitrificans; ε subunit; ζ subunit

DOI:  https://doi.org/10.1016/j.bbabio.2020.148355
Breast Cancer. 2020 Dec 24.

Differential expression of the BCAT isoforms between breast cancer subtypes.

Mai Ahmed Shafei, Arwa Flemban, Carl Daly, Paul Kendrick, Paul White, Sarah Dean, David Qualtrough, Myra E Conway.

   BACKGROUND: Biological characterisation of breast cancer subtypes is essential as it informs treatment regimens especially as different subtypes have distinct locoregional patterns. This is related to metabolic phenotype, where altered cellular metabolism is a fundamental adaptation of cancer cells during rapid proliferation. In this context, the metabolism of the essential branched-chain amino acids (BCAAs), catalysed by the human branched-chain aminotransferase proteins (hBCAT), offers multiple benefits for tumour growth. Upregulation of the cytosolic isoform of hBCAT (hBCATc), regulated by c-Myc, has been demonstrated to increase cell migration, tumour aggressiveness and proliferation in gliomas, ovarian and colorectal cancer but the importance of the mitochondrial isoform, hBCATm has not been fully investigated.
METHODS: Using immunohistochemistry, the expression profile of metabolic proteins (hBCAT, IDH) was assessed between breast cancer subtypes, HER2 + , luminal A, luminal B and TNBC. Correlations between the percentage and the intensity of protein expression/co-expression with clinical parameters, such as hormone receptor status, tumour stage, lymph-node metastasis and survival, were determined.
RESULTS: We show that hBCATc expression was found to be significantly associated with the more aggressive HER2 + and luminal B subtypes, whilst hBCATm and IDH1 associated with luminal A subtype. This was concomitant with better prognosis indicating a differential metabolic reliance between these two subtypes, in which enhanced expression of IDH1 may replenish the α-ketoglutarate pool in cells with increased hBCATm expression.
CONCLUSION: The cytosolic isoform of BCAT is associated with tumours that express HER2 receptors, whereas the mitochondrial isoform is highly expressed in tumours that are ER + , indicating that the BCAT proteins are regulated through different signalling pathways, which may lead to the identification of novel targets for therapeutic applications targeting dysregulated cancer metabolism.

Keywords:  BCAT; Breast cancer; HER2 + ; IDH; Luminal A

DOI:  https://doi.org/10.1007/s12282-020-01197-7
Hum Mol Genet. 2020 Nov 06. pii: ddaa243. [Epub ahead of print]

Mitochondria-lysosome membrane contacts are defective in GDAP1-related Charcot-Marie-Tooth disease.

Lara Cantarero, Elena Juárez-Escoto, Azahara Civera-Tregón, María Rodríguez-Sanz, Mónica Roldán, Raúl Benítez, Janet Hoenicka, Francesc Palau.

Mutations in the GDAP1 gene cause Charcot-Marie-Tooth (CMT) neuropathy. GDAP1 is an atypical glutathione S-transferase (GST) of the outer mitochondrial membrane and the mitochondrial membrane contacts with the endoplasmic reticulum (MAMs). Here, we investigate the role of this GST in the autophagic flux and the membrane contact sites (MCSs) between mitochondria and lysosomes in the cellular pathophysiology of GDAP1 deficiency. We demonstrate that GDAP1 participates in basal autophagy and that its depletion affects LC3 and PI3P biology in autophagosome biogenesis and membrane trafficking from MAMs. GDAP1 also contributes to the maturation of lysosome by interacting with PYKfyve kinase, a pH-dependent master lysosomal regulator. GDAP1 deficiency causes giant lysosomes with hydrolytic activity, a delay in the autophagic lysosome reformation, and TFEB activation. Notably, we found that GDAP1 interacts with LAMP-1, which supports that GDAP1-LAMP-1 is a new tethering pair of mitochondria and lysosome membrane contacts. We observed mitochondria-lysosome MCSs in soma and axons of cultured mouse embryonic motor neurons and human neuroblastoma cells. GDAP1 deficiency reduces the MCSs between these organelles, causes mitochondrial network abnormalities, and decreases levels of cellular glutathione (GSH). The supply of GSH-MEE suffices to rescue the lysosome membranes and the defects of the mitochondrial network, but not the interorganelle MCSs nor early autophagic events. Overall, we show that GDAP1 enables the proper function of mitochondrial MCSs in both degradative and nondegradative pathways, which could explain primary insults in GDAP1-related CMT pathophysiology, and highlights new redox-sensitive targets in axonopathies where mitochondria and lysosomes are involved.

DOI: https://doi.org/10.1093/hmg/ddaa243
Biochim Biophys Acta Mol Cell Res. 2020 Dec 23. pii: S0167-4889(20)30300-1. [Epub ahead of print] 118942

TMEM70 forms oligomeric scaffolds within mitochondrial cristae promoting in situ assembly of mammalian ATP synthase proton channel.

Hela Bahri, Jeremie Buratto, Manuel Rojo, Jim Paul Dompierre, Bénédicte Salin, Corinne Blancard, Sylvain Cuvellier, Marie Rose, Amel Ben Ammar Elgaaied, Emmanuel Tetaud, Jean-Paul di Rago, Anne Devin, Stéphane Duvezin-Caubet.

  Mitochondrial ATP-synthesis is catalyzed by a F1Fo-ATP synthase, an enzyme of dual genetic origin enriched at the edge of cristae where it plays a key role in their structure/stability. The enzyme's biogenesis remains poorly understood, both from a mechanistic and a compartmentalization point of view. The present study provides novel molecular insights into this process through investigations on a human protein called TMEM70 with an unclear role in the assembly of ATP synthase. A recent study has revealed the existence of physical interactions between TMEM70 and the subunit c (Su.c), a protein present in 8 identical copies forming a transmembrane oligomeric ring (c-ring) within the ATP synthase proton translocating domain (Fo). Herein we analyzed the ATP-synthase assembly in cells lacking TMEM70, mitochondrial DNA or F1 subunits and observe a direct correlation between TMEM70 and Su.c levels, regardless of the status of other ATP synthase subunits or of mitochondrial bioenergetics. Immunoprecipitation, two-dimensional blue-native/SDS-PAGE, and pulse-chase experiments reveal that TMEM70 forms large oligomers that interact with Su.c not yet incorporated into ATP synthase complexes. Moreover, discrete TMEM70-Su.c complexes with increasing Su.c contents can be detected, suggesting a role for TMEM70 oligomers in the gradual assembly of the c-ring. Furthermore, we demonstrate using expansion super-resolution microscopy the specific localization of TMEM70 at the inner cristae membrane, distinct from the MICOS component MIC60. Taken together, our results show that TMEM70 oligomers provide a scaffold for c-ring assembly and that mammalian ATP synthase is assembled within inner cristae membranes.

Keywords:  ATP synthase; cristae; human mitochondria; membrane protein; organelle biogenesis; protein complex

DOI:  https://doi.org/10.1016/j.bbamcr.2020.118942
Cancer Discov. 2020 Dec 23. pii: CD-20-0219. [Epub ahead of print]

Phenotypic mapping of pathological crosstalk between glioblastoma and innate immune cells by synthetic genetic tracing.

Matthias Jürgen Schmitt, Carlos Company, Yuliia Dramaretska, Iros Barozzi, Andreas Göhrig, Sonia Kertalli, Melanie Großmann, Heike Naumann, Maria Pilar Sanchez-Bailon, Danielle Hulsman, Rainer Glass, Massimo Squatrito, Michela Serresi, Gaetano Gargiulo.

Glioblastoma is a lethal brain tumor which exhibits heterogeneity and resistance to therapy. Our understanding of tumor homeostasis is limited by a lack of genetic tools to selectively identify tumor states and fate transitions. Here, we use glioblastoma subtype signatures to construct synthetic genetic tracing cassettes and investigate tumor heterogeneity at cellular and molecular level, in vitro and in vivo. Through synthetic locus control regions, we demonstrated that proneural glioblastoma is a hardwired identity, whereas the mesenchymal glioblastoma is an adaptive and metastable cell state driven by pro-inflammatory and differentiation cues and DNA damage, but not hypoxia. Importantly, we discovered that innate immune cells divert glioblastoma cells to a proneural-to-mesenchymal transition which confers therapeutic resistance. Our synthetic genetic tracing methodology is simple, scalable and widely applicable to study homeostasis in development and diseases. In glioblastoma, the method causally links distinct (micro)environmental, genetic and pharmacological perturbations and mesenchymal commitment.

DOI: https://doi.org/10.1158/2159-8290.CD-20-0219
Cell Rep. 2020 Dec 22. pii: S2211-1247(20)31533-3. [Epub ahead of print]33(12): 108544

Ribosome 18S m6A Methyltransferase METTL5 Promotes Translation Initiation and Breast Cancer Cell Growth.

Bowen Rong, Qian Zhang, Jinkai Wan, Shenghui Xing, Ruofei Dai, Yuan Li, Jiabin Cai, Jiaying Xie, Yang Song, Jiawei Chen, Lei Zhang, Guoquan Yan, Wen Zhang, Hai Gao, Jing-Dong J Han, Qianhui Qu, Honghui Ma, Ye Tian, Fei Lan.

  N6 methylation at adenosine 1832 (m6A1832) of mammalian 18S rRNA, occupying a critical position within the decoding center, is modified by a conserved methyltransferase, METTL5. Here, we find that METTL5 shows strong substrate preference toward the 18S A1832 motif but not the other reported m6A motifs. Comparison with a yeast ribosome structural model unmodified at this site indicates that the modification may facilitate mRNA binding by inducing conformation changes in the mammalian ribosomal decoding center. METTL5 promotes p70-S6K activation and proper translation initiation, and the loss of METTL5 significantly reduces the abundance of polysome. METTL5 expression is elevated in breast cancer patient samples and is required for growth of several breast cancer cell lines. We further find that Caenorhabditis elegans lacking the homolog metl-5 develop phenotypes known to be associated with impaired translation. Altogether, our findings uncover critical and conserved roles of METTL5 in the regulation of translation.

Keywords:  18S; ER-UPR; METTL5; S6K; decoding center; lifespan; m6A1832; rRNA modification; ribosome; translation initiation

DOI:  https://doi.org/10.1016/j.celrep.2020.108544
Mol Cell. 2020 Dec 22. pii: S1097-2765(20)30904-7. [Epub ahead of print]

Increased demand for NAD+ relative to ATP drives aerobic glycolysis.

Alba Luengo, Zhaoqi Li, Dan Y Gui, Lucas B Sullivan, Maria Zagorulya, Brian T Do, Raphael Ferreira, Adi Naamati, Ahmed Ali, Caroline A Lewis, Craig J Thomas, Stefani Spranger, Nicholas J Matheson, Matthew G Vander Heiden.

  Aerobic glycolysis, or preferential fermentation of glucose-derived pyruvate to lactate despite available oxygen, is associated with proliferation across many organisms and conditions. To better understand that association, we examined the metabolic consequence of activating the pyruvate dehydrogenase complex (PDH) to increase pyruvate oxidation at the expense of fermentation. We find that increasing PDH activity impairs cell proliferation by reducing the NAD+/NADH ratio. This change in NAD+/NADH is caused by increased mitochondrial membrane potential that impairs mitochondrial electron transport and NAD+ regeneration. Uncoupling respiration from ATP synthesis or increasing ATP hydrolysis restores NAD+/NADH homeostasis and proliferation even when glucose oxidation is increased. These data suggest that when demand for NAD+ to support oxidation reactions exceeds the rate of ATP turnover in cells, NAD+ regeneration by mitochondrial respiration becomes constrained, promoting fermentation, despite available oxygen. This argues that cells engage in aerobic glycolysis when the demand for NAD+ is in excess of the demand for ATP.

Keywords:  Aerobic Glycolysis; Cell Metabolism; Fermentation; NAD+; PDK; Warburg Effect

DOI:  https://doi.org/10.1016/j.molcel.2020.12.012
Cancer Discov. 2020 Dec 28. pii: CD-20-0387. [Epub ahead of print]

Metastasis and immune evasion from extracellular cGAMP hydrolysis.

Jun Li, Mercedes A Duran, Ninjit Dhanota, Walid K Chatila, Sarah E Bettigole, John Kwon, Roshan K Sriram, Matthew Philip Humphries, Manuel Salto-Tellez, Jacqueline A James, Matthew G Hanna, Johannes C Melms, Sreeram Vallabhaneni, Kevin Litchfield, Ieva Usaite, Dhruva Biswas, Rohan Bareja, Hao Wei Li, Maria Laura Martin, Princesca Dorsaint, Julie-Ann Cavallo, Peng Li, Chantal Pauli, Lee Gottesdiener, Benjamin J DiPardo, Travis J Hollmann, Taha Merghoub, Hannah Y Wen, Jorge S Reis-Filho, Nadeem Riaz, Shin-San Michael Su, Anusha Kalbasi, Neil Vasan, Simon N Powell, Jedd D Wolchok, Olivier Elemento, Charles Swanton, Alexander N Shoushtari, Eileen E Parkes, Benjamin Izar, Samuel F Bakhoum.

Cytosolic DNA is characteristic of chromosomally unstable metastatic cancer cells, resulting in constitutive activation of the cGAS-STING innate immune pathway. How tumors co-opt inflammatory signaling while evading immune surveillance remains unknown. Here we show that the ectonucleotidase ENPP1 promotes metastasis by selectively degrading extracellular cGAMP, an immune stimulatory metabolite whose breakdown products include the immune suppressor, adenosine. ENPP1 loss suppresses metastasis, restores tumor immune infiltration, and potentiates response to immune checkpoint blockade in a manner dependent on tumor cGAS and host STING. Conversely, overexpression of wildtype ENPP1, but not an enzymatically weakened mutant, promotes migration and metastasis, in part, through the generation of extracellular adenosine, and renders otherwise sensitive tumors completely resistant to immunotherapy. In human cancers, ENPP1 expression correlates with reduced immune cell infiltration, increased metastasis, and resistance to anti-PD1/PD-L1 treatment. Thus, cGAMP hydrolysis by ENPP1 enables chromosomally unstable tumors to transmute cGAS activation into an immune suppressive pathway.

DOI: https://doi.org/10.1158/2159-8290.CD-20-0387
Anal Biochem. 2020 Dec 19. pii: S0003-2697(20)30615-1. [Epub ahead of print] 114083

The Metabolic Importance of the Glutaminase II Pathway in Normal and Cancerous Cells.

Thambi Dorai, John T Pinto, Travis T Denton, Boris F Krasnikov, Arthur J L Cooper.

  In rapidly dividing cells, including many cancer cells, l-glutamine is a major energy source. Utilization of glutamine is usually depicted as: l-glutamine → l-glutamate (catalyzed by glutaminase isozymes; GLS1 and GLS2), followed by l-glutamate → α-ketoglutarate [catalyzed by glutamate-linked aminotransferases or by glutamate dehydrogenase (GDH)]. α-Ketoglutarate is a major anaplerotic component of the tricarboxylic acid (TCA) cycle. However, the glutaminase II pathway also converts l-glutamine to α-ketoglutarate. This pathway consists of a glutamine transaminase coupled to ω-amidase [Net reaction: L-Glutamine + α-keto acid + H2O → α-ketoglutarate + L-amino acid + NH4+]. This review focuses on the biological importance of the glutaminase II pathway, especially in relation to metabolism of cancer cells. Our studies suggest a component enzyme of the glutaminase II pathway, ω-amidase, is utilized by tumor cells to provide anaplerotic carbon. Inhibitors of GLS1 are currently in clinical trials as anti-cancer agents. However, this treatment will not prevent the glutaminase II pathway from providing anaplerotic carbon derived from glutamine. Specific inhibitors of ω-amidase, perhaps in combination with a GLS1 inhibitor, may provide greater therapeutic efficacy.

Keywords:  Glutaminase II pathway; Glutamine addiction in cancer; Glutamine transaminases; α-Ketoglutaramate; ω-Amidase

DOI:  https://doi.org/10.1016/j.ab.2020.114083
Mitochondrion. 2020 Dec 28. pii: S1567-7249(20)30230-0. [Epub ahead of print]

Mitochondrial OPA1 cleavage is reversibly activated by differentiation of H9c2 cardiomyoblasts.

Iraselia Garcia, Fredy Calderon, Patrick De la Torre, Shaynah St Vallier, Cristobal Rodriguez, Divya Agarwala, Megan Keniry, Wendy Innis-Whitehouse, Robert Gilkerson.

  Optic atrophy-1 (OPA1) is a dynamin-like GTPase localized to the mitochondrial inner membrane, playing key roles in inner membrane fusion and cristae maintenance. OPA1 is regulated by the mitochondrial transmembrane potential (Δψm): when Δψm is intact, long OPA1 isoforms (L-OPA1) carry out inner membrane fusion. Upon loss of Δψm, L-OPA1 isoforms are proteolytically cleaved to short (S-OPA1) isoforms by the stress-inducible OMA1 metalloprotease, causing collapse of the mitochondrial network and promoting apoptosis. Here, we show that L-OPA1 isoforms of H9c2 cardiomyoblasts are retained under loss of Δψm, despite the presence of OMA1. However, when H9c2s are differentiated to a more cardiac-like phenotype via treatment with retinoic acid (RA) in low serum media, loss of Δ ψm induces robust, and reversible, cleavage of L-OPA1 and subsequent OMA1 degradation. These findings indicate that a potent developmental switch regulates Δ ψm-sensitive OPA1 cleavage, suggesting novel developmental and regulatory mechanisms for OPA1 homeostasis.

Keywords:  Mitochondria; OMA1; OPA1; cardiac; cultured cell; differentiation

DOI:  https://doi.org/10.1016/j.mito.2020.12.007
Proc Natl Acad Sci U S A. 2021 Jan 12. pii: e2014013118. [Epub ahead of print]118(2):

Gene expression regulates metabolite homeostasis during the Crabtree effect: Implications for the adaptation and evolution of Metabolism.

Douglas L Rothman, Stephen C Stearns, Robert G Shulman.

  A key issue in both molecular and evolutionary biology has been to define the roles of genes and phenotypes in the adaptation of organisms to environmental changes. The dominant view has been that an organism's metabolic adaptations are driven by gene expression and that gene mutations, independent of the starting phenotype, are responsible for the evolution of new metabolic phenotypes. We propose an alternate hypothesis, in which the phenotype and genotype together determine metabolic adaptation both in the lifetime of the organism and in the evolutionary selection of adaptive metabolic traits. We tested this hypothesis by flux-balance and metabolic-control analysis of the relative roles of the starting phenotype and gene expression in regulating the metabolic adaptations during the Crabtree effect in yeast, when they are switched from a low- to high-glucose environment. Critical for successful short-term adaptation was the ability of the glycogen/trehalose shunt to balance the glycolytic pathway. The role of later gene expression of new isoforms of glycolytic enzymes, rather than flux control, was to provide additional homeostatic mechanisms allowing an increase in the amount and efficiency of adenosine triphosphate and product formation while maintaining glycolytic balance. We further showed that homeostatic mechanisms, by allowing increased phenotypic plasticity, could have played an important role in guiding the evolution of the Crabtree effect. Although our findings are specific to Crabtree yeast, they are likely to be broadly found because of the well-recognized similarities in glucose metabolism across kingdoms and phyla from yeast to humans.

Keywords:  Crabtree effect; adaptation; glucose metabolism; glycogen shunt; homeostasis

DOI:  https://doi.org/10.1073/pnas.2014013118
Mol Cell. 2020 Dec 11. pii: S1097-2765(20)30887-X. [Epub ahead of print]

Functionally distinct roles for TET-oxidized 5-methylcytosine bases in somatic reprogramming to pluripotency.

Blake A Caldwell, Monica Yun Liu, Rexxi D Prasasya, Tong Wang, Jamie E DeNizio, N Adrian Leu, Nana Yaa A Amoh, Christopher Krapp, Yemin Lan, Emily J Shields, Roberto Bonasio, Christopher J Lengner, Rahul M Kohli, Marisa S Bartolomei.

  Active DNA demethylation via ten-eleven translocation (TET) family enzymes is essential for epigenetic reprogramming in cell state transitions. TET enzymes catalyze up to three successive oxidations of 5-methylcytosine (5mC), generating 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), or 5-carboxycytosine (5caC). Although these bases are known to contribute to distinct demethylation pathways, the lack of tools to uncouple these sequential oxidative events has constrained our mechanistic understanding of the role of TETs in chromatin reprogramming. Here, we describe the first application of biochemically engineered TET mutants that unlink 5mC oxidation steps, examining their effects on somatic cell reprogramming. We show that only TET enzymes proficient for oxidation to 5fC/5caC can rescue the reprogramming potential of Tet2-deficient mouse embryonic fibroblasts. This effect correlated with rapid DNA demethylation at reprogramming enhancers and increased chromatin accessibility later in reprogramming. These experiments demonstrate that DNA demethylation through 5fC/5caC has roles distinct from 5hmC in somatic reprogramming to pluripotency.

Keywords:  5-carboxycytosine; 5-formylcytosine; 5-hydroxymethylcytosine; 5caC; 5fC; 5hmC; DNA demethylation; TET; bACE-seq; epigenetics; iPSCs; induced pluripotent stem cells; reprogramming; ten-eleven translocation

DOI:  https://doi.org/10.1016/j.molcel.2020.11.045
PLoS One. 2020 ;15(12): e0243489

The plasticity of the pyruvate dehydrogenase complex confers a labile structure that is associated with its catalytic activity.

Jaehyoun Lee, Seunghee Oh, Saikat Bhattacharya, Ying Zhang, Laurence Florens, Michael P Washburn, Jerry L Workman.

The pyruvate dehydrogenase complex (PDC) is a multienzyme complex that plays a key role in energy metabolism by converting pyruvate to acetyl-CoA. An increase of nuclear PDC has been shown to be correlated with an increase of histone acetylation that requires acetyl-CoA. PDC has been reported to form a ~ 10 MDa macromolecular machine that is proficient in performing sequential catalytic reactions via its three components. In this study, we show that the PDC displays size versatility in an ionic strength-dependent manner using size exclusion chromatography of yeast cell extracts. Biochemical analysis in combination with mass spectrometry indicates that yeast PDC (yPDC) is a salt-labile complex that dissociates into sub-megadalton individual components even under physiological ionic strength. Interestingly, we find that each oligomeric component of yPDC displays a larger size than previously believed. In addition, we show that the mammalian PDC also displays this uncommon characteristic of salt-lability, although it has a somewhat different profile compared to yeast. We show that the activity of yPDC is reduced in higher ionic strength. Our results indicate that the structure of PDC may not always maintain its ~ 10 MDa organization, but is rather variable. We propose that the flexible nature of PDC may allow modulation of its activity.

DOI: https://doi.org/10.1371/journal.pone.0243489
Aging (Albany NY). 2020 12 27.

Sugar-induced dysregulation of purine metabolism impacts lifespan.

Claudia Lennicke, Eliano Dos Santos, Helena M Cochemé.



Keywords:  Drosophila; aging; diabetes; metabolic disease; obesity; purine catabolism; sugar diet; uric acid

DOI:  https://doi.org/10.18632/aging.104223