bims-camemi 2021-09-05 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2021–09–05
33 papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit

Autophagy in major human diseases.
Vps13D functions in a Pink1-dependent and Parkin-independent mitophagy pathway.
Cell reprogramming shapes the mitochondrial DNA landscape.
Patient-Derived Xenografts to Study Cancer Metabolism: When Does X Mark the Spot?
STING-driven interferon signaling triggers metabolic alterations in pancreas cancer cells visualized by [18F]FLT PET imaging.
Metabolic flexibility maintains proliferation and migration of FGFR signaling-deficient lymphatic endothelial cells.
c-MYC Triggers Lipid Remodelling During Early Somatic Cell Reprogramming to Pluripotency.
High levels of TFAM repress mammalian mitochondrial DNA transcription in vivo.
Metabolic regulation of T cells in the tumor microenvironment by nutrient availability and diet.
Oncogenic HSP90 facilitates metabolic alterations in aggressive B-cell lymphomas.
Y705 and S727 are required for mitochondrial import and transcriptional activities of STAT3 and regulate proliferation of embryonic and tissue stem cells.
The mitochondrial permeability transition pore activates the mitochondrial unfolded protein response and promotes aging.
Loss of SNORA73 reprograms cellular metabolism and protects against steatohepatitis.
The mechanism of MICU-dependent gating of the mitochondrial Ca2+ uniporter.
CARS senses cysteine deprivation to activate AMPK for cell survival.
The context-specific roles of urea cycle enzymes in tumorigenesis.
Potassium and Sodium Channels and the Warburg Effect: Biophysical Regulation of Cancer Metabolism.
A nutrient-responsive hormonal circuit mediates an inter-tissue program regulating metabolic homeostasis in adult Drosophila.
Astrocyte metabolism of the medium-chain fatty acids octanoic acid and decanoic acid promotes GABA synthesis in neurons via elevated glutamine supply.
Autophagy promotes growth of tumors with high mutational burden by inhibiting a T-cell immune response.
Aurora kinase A inhibition reverses the Warburg effect and elicits unique metabolic vulnerabilities in glioblastoma.
Nectar-feeding bats and birds show parallel molecular adaptations in sugar metabolism enzymes.
Cyclic AMP-binding protein Epac1 acts as a metabolic sensor to promote cardiomyocyte lipotoxicity.
Protocol for assessing real-time changes in mitochondrial morphology, fission and fusion events in live cells using confocal microscopy.
Therapeutic targeting of both dihydroorotate dehydrogenase and nucleoside transport in MYCN-amplified neuroblastoma.
The polar oxy-metabolome reveals the 4-hydroxymandelate CoQ10 synthesis pathway.
Organelle-specific regulation of ferroptosis.
Cancer evolution: Darwin and beyond.
Human genetic analyses of organelles highlight the nucleus in age-related trait heritability.
Mass spectrometric characterization of cyclic dinucleotides (CDNs) in vivo.
Cysteine Boosts Fitness Under Hypoxia-Mimicked Conditions in Ovarian Cancer by Metabolic Reprogramming.
Naked mole-rat brain mitochondria tolerate in vitro ischemia.
From OCR and ECAR to energy: perspectives on the design and interpretation of bioenergetics studies.

EMBO J. 2021 Aug 30. e108863

Autophagy in major human diseases.

Daniel J Klionsky, Giulia Petroni, Ravi K Amaravadi, Eric H Baehrecke, Andrea Ballabio, Patricia Boya, José Manuel Bravo-San Pedro, Ken Cadwell, Francesco Cecconi, Augustine M K Choi, Mary E Choi, Charleen T Chu, Patrice Codogno, Maria Isabel Colombo, Ana Maria Cuervo, Vojo Deretic, Ivan Dikic, Zvulun Elazar, Eeva-Liisa Eskelinen, Gian Maria Fimia, David A Gewirtz, Douglas R Green, Malene Hansen, Marja Jäättelä, Terje Johansen, Gábor Juhász, Vassiliki Karantza, Claudine Kraft, Guido Kroemer, Nicholas T Ktistakis, Sharad Kumar, Carlos Lopez-Otin, Kay F Macleod, Frank Madeo, Jennifer Martinez, Alicia Meléndez, Noboru Mizushima, Christian Münz, Josef M Penninger, Rushika M Perera, Mauro Piacentini, Fulvio Reggiori, David C Rubinsztein, Kevin M Ryan, Junichi Sadoshima, Laura Santambrogio, Luca Scorrano, Hans-Uwe Simon, Anna Katharina Simon, Anne Simonsen, Alexandra Stolz, Nektarios Tavernarakis, Sharon A Tooze, Tamotsu Yoshimori, Junying Yuan, Zhenyu Yue, Qing Zhong, Lorenzo Galluzzi, Federico Pietrocola.

  Autophagy is a core molecular pathway for the preservation of cellular and organismal homeostasis. Pharmacological and genetic interventions impairing autophagy responses promote or aggravate disease in a plethora of experimental models. Consistently, mutations in autophagy-related processes cause severe human pathologies. Here, we review and discuss preclinical data linking autophagy dysfunction to the pathogenesis of major human disorders including cancer as well as cardiovascular, neurodegenerative, metabolic, pulmonary, renal, infectious, musculoskeletal, and ocular disorders.

Keywords:  aging; cancer; inflammation; metabolic syndromes; neurodegeneration

DOI:  https://doi.org/10.15252/embj.2021108863
J Cell Biol. 2021 Nov 01. pii: e202104073. [Epub ahead of print]220(11):

Vps13D functions in a Pink1-dependent and Parkin-independent mitophagy pathway.

James L Shen, Tina M Fortier, Ruoxi Wang, Eric H Baehrecke.

Defects in autophagy cause problems in metabolism, development, and disease. The autophagic clearance of mitochondria, mitophagy, is impaired by the loss of Vps13D. Here, we discover that Vps13D regulates mitophagy in a pathway that depends on the core autophagy machinery by regulating Atg8a and ubiquitin localization. This process is Pink1 dependent, with loss of pink1 having similar autophagy and mitochondrial defects as loss of vps13d. The role of Pink1 has largely been studied in tandem with Park/Parkin, an E3 ubiquitin ligase that is widely considered to be crucial in Pink1-dependent mitophagy. Surprisingly, we find that loss of park does not exhibit the same autophagy and mitochondrial deficiencies as vps13d and pink1 mutant cells and contributes to mitochondrial clearance through a pathway that is parallel to vps13d. These findings provide a Park-independent pathway for Pink1-regulated mitophagy and help to explain how Vps13D regulates autophagy and mitochondrial morphology and contributes to neurodegenerative diseases.

DOI: https://doi.org/10.1083/jcb.202104073
Nat Commun. 2021 Sep 02. 12(1): 5241

Cell reprogramming shapes the mitochondrial DNA landscape.

Wei Wei, Daniel J Gaffney, Patrick F Chinnery.

Individual induced pluripotent stem cells (iPSCs) show considerable phenotypic heterogeneity, but the reasons for this are not fully understood. Comprehensively analysing the mitochondrial genome (mtDNA) in 146 iPSC and fibroblast lines from 151 donors, we show that most age-related fibroblast mtDNA mutations are lost during reprogramming. However, iPSC-specific mutations are seen in 76.6% (108/141) of iPSC lines at a mutation rate of 8.62 × 10-5/base pair. The mutations observed in iPSC lines affect a higher proportion of mtDNA molecules, favouring non-synonymous protein-coding and tRNA variants, including known disease-causing mutations. Analysing 11,538 single cells shows stable heteroplasmy in sub-clones derived from the original donor during differentiation, with mtDNA variants influencing the expression of key genes involved in mitochondrial metabolism and epidermal cell differentiation. Thus, the dynamic mtDNA landscape contributes to the heterogeneity of human iPSCs and should be considered when using reprogrammed cells experimentally or as a therapy.

DOI: https://doi.org/10.1038/s41467-021-25482-x
Cancer Res. 2021 Sep 01. 81(17): 4399-4401

Patient-Derived Xenografts to Study Cancer Metabolism: When Does X Mark the Spot?

Christopher S Nabel, Matthew G Vander Heiden.

A major goal of cancer research is to understand the requirements for cancer growth and progression that can be exploited to treat patients. Model systems reduce the complexity and heterogeneity of human cancers to explore therapeutic hypotheses, however, some relevant aspects of human biology are not well represented by certain models, complicating the translation of preclinical findings to help patients. Here we discuss the advantages and limitations of patient-derived xenografts as a model system to study cancer metabolism, offering a framework to best use these models to address different types of metabolism-specific research questions.

DOI: https://doi.org/10.1158/0008-5472.CAN-21-0770
Proc Natl Acad Sci U S A. 2021 Sep 07. pii: e2105390118. [Epub ahead of print]118(36):

STING-driven interferon signaling triggers metabolic alterations in pancreas cancer cells visualized by [18F]FLT PET imaging.

Keke Liang, Evan R Abt, Thuc M Le, Arthur Cho, Amanda M Dann, Jing Cui, Luyi Li, Khalid Rashid, Amanda L Creech, Liu Wei, Razmik Ghukasyan, Ethan W Rosser, Nanping Wu, Giuseppe Carlucci, Johannes Czernin, Timothy R Donahue, Caius G Radu.

  Type I interferons (IFNs) are critical effectors of emerging cancer immunotherapies designed to activate pattern recognition receptors (PRRs). A challenge in the clinical translation of these agents is the lack of noninvasive pharmacodynamic biomarkers that indicate increased intratumoral IFN signaling following PRR activation. Positron emission tomography (PET) imaging enables the visualization of tissue metabolic activity, but whether IFN signaling-induced alterations in tumor cell metabolism can be detected using PET has not been investigated. We found that IFN signaling augments pancreatic ductal adenocarcinoma (PDAC) cell nucleotide metabolism via transcriptional induction of metabolism-associated genes including thymidine phosphorylase (TYMP). TYMP catalyzes the first step in the catabolism of thymidine, which competitively inhibits intratumoral accumulation of the nucleoside analog PET probe 3'-deoxy-3'-[18F]fluorothymidine ([18F]FLT). Accordingly, IFN treatment up-regulates cancer cell [18F]FLT uptake in the presence of thymidine, and this effect is dependent upon TYMP expression. In vivo, genetic activation of stimulator of interferon genes (STING), a PRR highly expressed in PDAC, enhances the [18F]FLT avidity of xenograft tumors. Additionally, small molecule STING agonists trigger IFN signaling-dependent TYMP expression in PDAC cells and increase tumor [18F]FLT uptake in vivo following systemic treatment. These findings indicate that [18F]FLT accumulation in tumors is sensitive to IFN signaling and that [18F]FLT PET may serve as a pharmacodynamic biomarker for STING agonist-based therapies in PDAC and possibly other malignancies characterized by elevated STING expression.

Keywords:  PET imaging; STING; interferon; nucleotide metabolism; pancreatic cancer

DOI:  https://doi.org/10.1073/pnas.2105390118
J Biol Chem. 2021 Aug 30. pii: S0021-9258(21)00950-9. [Epub ahead of print] 101149

Metabolic flexibility maintains proliferation and migration of FGFR signaling-deficient lymphatic endothelial cells.

Hongyuan Song, Jie Zhu, Ping Li, Fei Han, Longhou Fang, Pengchun Yu.

  Metabolic flexibility is the capacity of cells to alter fuel metabolism in response to changes in metabolic demand or nutrient availability. It is critical for maintaining cellular bioenergetics and is involved in the pathogenesis of cardiovascular disease and metabolic disorders. However, the regulation and function of metabolic flexibility in lymphatic endothelial cells (LECs) remain unclear. We have previously shown that glycolysis is the predominant metabolic pathway to generate ATP in LECs and that fibroblast growth factor receptor (FGFR) signaling controls lymphatic vessel formation by promoting glycolysis. Here we found that chemical inhibition of FGFR activity or knockdown of FGFR1 induces substantial upregulation of fatty acid β-oxidation (FAO) while reducing glycolysis and cellular ATP generation in LECs. Interestingly, such compensatory elevation was not observed in glucose oxidation and glutamine oxidation. Mechanistic studies show that FGFR blockade promotes the expression of CPT1A, a rate-limiting enzyme of FAO; this is achieved by dampened ERK activation, which in turn upregulates the expression of the peroxisome proliferator activated receptor α (PPARα). Metabolic analysis further demonstrates that CPT1A depletion decreases total cellular ATP levels in FGFR1-deficient rather than wild-type LECs. This result suggests that FAO, which makes a negligible contribution to cellular energy under normal conditions, can partially compensate for energy deficiency caused by FGFR inhibition. Consequently, CPT1A silencing potentiates the effect of FGFR1 knockdown on impeding LEC proliferation and migration. Collectively, our study identified a key role of metabolic flexibility in modulating the effect of FGFR signaling on LEC growth.

Keywords:  CPT1A; ERK; cell metabolism; cell migration; cell proliferation; fatty acid oxidation; fibroblast growth factor receptor; glycolysis; lymphatic endothelial cell

DOI:  https://doi.org/10.1016/j.jbc.2021.101149
Stem Cell Rev Rep. 2021 Sep 02.

c-MYC Triggers Lipid Remodelling During Early Somatic Cell Reprogramming to Pluripotency.

Javier Prieto, Juan Carlos García-Cañaveras, Marian León, Ramón Sendra, Xavier Ponsoda, Juan Carlos Izpisúa Belmonte, Agustín Lahoz, Josema Torres.

Metabolic rewiring and mitochondrial dynamics remodelling are hallmarks of cell reprogramming, but the roles of the reprogramming factors in these changes are not fully understood. Here we show that c-MYC induces biosynthesis of fatty acids and increases the rate of pentose phosphate pathway. Time-course profiling of fatty acids and complex lipids during cell reprogramming using lipidomics revealed a profound remodelling of the lipid content, as well as the saturation and length of their acyl chains, in a c-MYC-dependent manner. Pluripotent cells displayed abundant cardiolipins and scarce phosphatidylcholines, with a prevalence of monounsaturated acyl chains. Cells undergoing cell reprogramming showed an increase in mitochondrial membrane potential that paralleled that of mitochondrial-specific cardiolipins. We conclude that c-MYC controls the rewiring of somatic cell metabolism early in cell reprogramming by orchestrating cell proliferation, synthesis of macromolecular components and lipid remodelling, all necessary processes for a successful phenotypic transition to pluripotency. c-MYC promotes anabolic metabolism, mitochondrial fitness and lipid remodelling early in cell reprogramming. A high rate of aerobic glycolysis is crucial to provide intermediaries for biosynthetic pathways. To ensure the availability of nucleotides, amino acids and lipids for cell proliferation, cells must provide with a constant flux of the elemental building blocks for macromolecule assembly and fulfil the anabolic demands to reach the critical cellular mass levels to satisfactorily undergo cell division. A high rate of aerobic glycolysis is induced by c-MYC, increasing the amounts of intracellular Glucose-6-phosphate (G6P), fructose-6-phosphate (F6P), and glyceraldehyde-3-phosphate (GA3P), which can all enter pentose phosphate pathway (PPP) to produce Ribose-5-Phosphate (R5P) and NADPH, which are necessary for the biosynthesis of biomolecules such as proteins, nucleic acids, or lipids. C-MYC-dependent activation of glucose-6-phosphate dehydrogenase (G6PD) may play a critical role in the shunting of G6P to PPP and generation of NADPH. High glycolytic flux increases the amounts of dihydroxyacetone phosphate (DHAP), which is crucial for biosynthesis of phospholipids and triacylglycerols, and pyruvate (Pyr), which can be converted to citrate (Cit) in the mitochondria and enter the biosynthesis of fatty acids (FA). During cell reprogramming, c-MYC-dependent lipid remodelling leads to Polyunsaturated Fatty Acid (PUFA) downregulation and Monounsaturated Fatty Acid (MUFA) upregulation, which may play critical roles in cytoarchitectural remodelling of cell membrane or non-canonical autophagy, respectively. Cardiolipin (pink dots) rise early in cell reprogramming correlates with an increase in mitochondrial fitness, suggesting that c-MYC may restore proper levels of cardiolipins and antioxidant proteins, such as UCP2, to guarantee an optimal mitochondrial function while upholding ROS levels, reinforcing the idea of cell rejuvenation early in cell reprogramming.

DOI: https://doi.org/10.1007/s12015-021-10239-2
Life Sci Alliance. 2021 Nov;pii: e202101034. [Epub ahead of print]4(11):

High levels of TFAM repress mammalian mitochondrial DNA transcription in vivo.

Nina A Bonekamp, Min Jiang, Elisa Motori, Rodolfo Garcia Villegas, Camilla Koolmeister, Ilian Atanassov, Andrea Mesaros, Chan Bae Park, Nils-Göran Larsson.

Mitochondrial transcription factor A (TFAM) is compacting mitochondrial DNA (dmtDNA) into nucleoids and directly controls mtDNA copy number. Here, we show that the TFAM-to-mtDNA ratio is critical for maintaining normal mtDNA expression in different mouse tissues. Moderately increased TFAM protein levels increase mtDNA copy number but a normal TFAM-to-mtDNA ratio is maintained resulting in unaltered mtDNA expression and normal whole animal metabolism. Mice ubiquitously expressing very high TFAM levels develop pathology leading to deficient oxidative phosphorylation (OXPHOS) and early postnatal lethality. The TFAM-to-mtDNA ratio varies widely between tissues in these mice and is very high in skeletal muscle leading to strong repression of mtDNA expression and OXPHOS deficiency. In the heart, increased mtDNA copy number results in a near normal TFAM-to-mtDNA ratio and maintained OXPHOS capacity. In liver, induction of LONP1 protease and mitochondrial RNA polymerase expression counteracts the silencing effect of high TFAM levels. TFAM thus acts as a general repressor of mtDNA expression and this effect can be counterbalanced by tissue-specific expression of regulatory factors.

DOI: https://doi.org/10.26508/lsa.202101034
Semin Immunol. 2021 Aug 27. pii: S1044-5323(21)00016-6. [Epub ahead of print] 101485

Metabolic regulation of T cells in the tumor microenvironment by nutrient availability and diet.

Steven Zhao, Ronal M Peralta, Natalia Avina-Ochoa, Greg M Delgoffe, Susan M Kaech.

  Recent advances in immunotherapies such as immune checkpoint blockade (ICB) and chimeric antigen receptor T cells (CAR-T) for the treatment of cancer have generated excitement over their ability to yield durable, and potentially curative, responses in a multitude of cancers. These findings have established that the immune system is capable of eliminating tumors and led us to a better, albeit still incomplete, understanding of the mechanisms by which tumors interact with and evade destruction by the immune system. Given the central role of T cells in immunotherapy, elucidating the cell intrinsic and extrinsic factors that govern T cell function in tumors will facilitate the development of immunotherapies that establish durable responses in a greater number of patients. One such factor is metabolism, a set of fundamental cellular processes that not only sustains cell survival and proliferation, but also serves as a means for cells to interpret their local environment. Nutrient sensing is critical for T cells that must infiltrate into a metabolically challenging tumor microenvironment and expand under these harsh conditions to eliminate cancerous cells. Here we introduce T cell exhaustion with respect to cellular metabolism, followed by a discussion of nutrient availability at the tumor and organismal level in relation to T cell metabolism and function to provide rationale for the study and targeting of metabolism in anti-tumor immune responses.

Keywords:  Cancer metabolism; Immuno-oncology; Immunometabolism; Immunotherapy; T cells; Tumor microenvironment

DOI:  https://doi.org/10.1016/j.smim.2021.101485
Cancer Res. 2021 Sep 03. pii: canres.CAN-21-2734-E.2021. [Epub ahead of print]

Oncogenic HSP90 facilitates metabolic alterations in aggressive B-cell lymphomas.

M Nieves Calvo-Vidal, Nahuel Zamponi, Jan Krumsiek, Max A Stockslager, Maria V Revuelta, Jude M Phillip, Rossella Marullo, Ekaterina Tikhonova, Nikita Kotlov, Jayeshkumar Patel, Shao Ning Yang, Lucy Yang, Tony Taldone, Catherine Thieblemont, John P Leonard, Peter Martin, Giorgio Inghirami, Gabriela Chiosis, Scott R Manalis, Leandro Cerchietti.

HSP90 is critical for the maintenance of cellular proteostasis. In cancer cells, HSP90 also becomes a nucleating site for the stabilization of multiprotein complexes including signaling pathways and transcription complexes. Here we describe the role of this HSP90 form, referred to as oncogenic HSP90, in the regulation of cytosolic metabolic pathways in proliferating B-cell lymphoma cells. Oncogenic HSP90 assisted in the organization of metabolic enzymes into non-membrane-bound functional compartments. Under experimental conditions that conserved cellular proteostasis, oncogenic HSP90 coordinated and sustained multiple metabolic pathways required for energy production and maintenance of cellular biomass as well as for secretion of extracellular metabolites. Conversely, inhibition of oncogenic HSP90, in the absence of apparent client protein degradation, decreased the efficiency of MYC-driven metabolic reprogramming. This study reveals that oncogenic HSP90 supports metabolism in B-cell lymphoma cells and patients with diffuse large B-cell lymphoma, providing a novel mechanism of activity for HSP90 inhibitors.

DOI: https://doi.org/10.1158/0008-5472.CAN-21-2734
Development. 2021 Sep 02. pii: dev.199477. [Epub ahead of print]

Y705 and S727 are required for mitochondrial import and transcriptional activities of STAT3 and regulate proliferation of embryonic and tissue stem cells.

Margherita Peron, Alberto Dinarello, Giacomo Meneghetti, Laura Martorano, Riccardo M Betto, Nicola Facchinello, Annachiara Tesoriere, Natascia Tiso, Graziano Martello, Francesco Argenton.

  The STAT3 transcription factor, acting both in the nucleus and mitochondria, maintains embryonic stem cell pluripotency and promotes their proliferation. In this work, using zebrafish, we determined in vivo that mitochondrial STAT3 regulates mtDNA transcription in embryonic and larval stem cell niches and that this activity affects their proliferation rates. As a result, we demonstrated that STAT3 import inside mitochondria requires Y705 phosphorylation by Jak, while its mitochondrial transcriptional activity, as well as its effect on proliferation, depends on the MAPK target S727. These data were confirmed using mouse embryonic stem cells: while the Y705 mutated STAT3 cannot enter mitochondria, the S727 mutation does not affect the import in the organelle and is responsible for STAT3-dependent mitochondrial transcription. Surprisingly, STAT3-dependent increase of mitochondrial transcription seems independent from STAT3 binding to STAT3 responsive elements. Finally, loss of function experiments, with chemical inhibition of the JAK/STAT3 pathway or genetic ablation of stat3 gene, demonstrated that STAT3 is also required for cell proliferation in the intestine of zebrafish.

Keywords:  ESC; STAT3; mitochondria; transcription; zebrafish

DOI:  https://doi.org/10.1242/dev.199477
Elife. 2021 09 01. pii: e63453. [Epub ahead of print]10

The mitochondrial permeability transition pore activates the mitochondrial unfolded protein response and promotes aging.

Suzanne Angeli, Anna Foulger, Manish Chamoli, Tanuja Harshani Peiris, Akos Gerencser, Azar Asadi Shahmirzadi, Julie Andersen, Gordon Lithgow.

  Mitochondrial activity determines aging rate and the onset of chronic diseases. The mitochondrial permeability transition pore (mPTP) is a pathological pore in the inner mitochondrial membrane thought to be composed of the F-ATP synthase (complex V). OSCP, a subunit of F-ATP synthase, helps protect against mPTP formation. How the destabilization of OSCP may contribute to aging, however, is unclear. We have found that loss OSCP in the nematode Caenorhabditis elegans initiates the mPTP and shortens lifespan specifically during adulthood, in part via initiation of the mitochondrial unfolded protein response (UPRmt). Pharmacological or genetic inhibition of the mPTP inhibits the UPRmt and restores normal lifespan. Loss of the putative pore-forming component of F-ATP synthase extends adult lifespan, suggesting that the mPTP normally promotes aging. Our findings reveal how an mPTP/UPRmt nexus may contribute to aging and age-related diseases and how inhibition of the UPRmt may be protective under certain conditions.

Keywords:  C. elegans; F-ATP synthase; aging; c-subunit; cell biology; mitochondrial permeability transition pore; mitochondrial unfolded protein response; oscp/atp-3

DOI:  https://doi.org/10.7554/eLife.63453
Nat Commun. 2021 Sep 01. 12(1): 5214

Loss of SNORA73 reprograms cellular metabolism and protects against steatohepatitis.

Arthur C Sletten, Jessica W Davidson, Busra Yagabasan, Samantha Moores, Michaela Schwaiger-Haber, Hideji Fujiwara, Sarah Gale, Xuntian Jiang, Rohini Sidhu, Susan Gelman, Shuang Zhao, Gary Patti, Daniel S Ory, Jean E Schaffer.

Dyslipidemia and resulting lipotoxicity are pathologic signatures of metabolic syndrome and type 2 diabetes. Excess lipid causes cell dysfunction and induces cell death through pleiotropic mechanisms that link to oxidative stress. However, pathways that regulate the response to metabolic stress are not well understood. Herein, we show that disruption of the box H/ACA SNORA73 small nucleolar RNAs encoded within the small nucleolar RNA hosting gene 3 (Snhg3) causes resistance to lipid-induced cell death and general oxidative stress in cultured cells. This protection from metabolic stress is associated with broad reprogramming of oxidative metabolism that is dependent on the mammalian target of rapamycin signaling axis. Furthermore, we show that knockdown of SNORA73 in vivo protects against hepatic steatosis and lipid-induced oxidative stress and inflammation. Our findings demonstrate a role for SNORA73 in the regulation of metabolism and lipotoxicity.

DOI: https://doi.org/10.1038/s41467-021-25457-y
Elife. 2021 Aug 31. pii: e69312. [Epub ahead of print]10

The mechanism of MICU-dependent gating of the mitochondrial Ca2+ uniporter.

Vivek Garg, Junji Suzuki, Ishan Paranjpe, Tiffany Unsulangi, Liron Boyman, Lorin S Milescu, W Jonathan Lederer, Yuriy Kirichok.

  Ca2+ entry into mitochondria is through the mitochondrial calcium uniporter complex (MCUcx), a Ca2+-selective channel composed of five subunit types. Two MCUcx subunits (MCU and EMRE) span the inner mitochondrial membrane, while three Ca2+-regulatory subunits (MICU1, MICU2 and MICU3) reside in the intermembrane space. Here we provide rigorous analysis of Ca2+ and Na+ fluxes via MCUcx in intact isolated mitochondria to understand the function of MICU subunits. We also perform direct patch clamp recordings of macroscopic and single MCUcx currents to gain further mechanistic insight. This comprehensive analysis shows that the MCUcx pore, composed of the EMRE and MCU subunits, is not occluded nor plugged by MICUs during the absence or presence of extramitochondrial Ca2+ as has been widely reported. Instead, MICUs potentiate activity of MCUcx as extramitochondrial Ca2+ is elevated. MICUs achieve this by modifying the gating properties of MCUcx allowing it to spend more time in the open state.

Keywords:  molecular biophysics; mouse; structural biology

DOI:  https://doi.org/10.7554/eLife.69312
EMBO J. 2021 Sep 02. e108028

CARS senses cysteine deprivation to activate AMPK for cell survival.

Mengqiu Yuan, Ronghui Yan, Yi Zhang, Yue Qiu, Zetan Jiang, Haiying Liu, Ying Wang, Linchong Sun, Huafeng Zhang, Ping Gao.

  Adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK) is an important cellular metabolite-sensing enzyme that can directly sense changes not only in ATP but also in metabolites associated with carbohydrates and fatty acids. However, less is known about whether and how AMPK senses variations in cellular amino acids. Here, we show that cysteine deficiency significantly triggers calcium/calmodulin-dependent protein kinase kinase 2 (CaMKK2)-mediated activation of AMPK. In addition, we found that CaMKK2 directly associates with cysteinyl-tRNA synthetase (CARS), which then binds to AMPKγ2 under cysteine deficiency to activate AMPK. Interestingly, we discovered that cysteine inhibits the binding of CARS to AMPKγ2, and thus, under cysteine deficiency conditions wherein the inhibitory effect of cysteine is abrogated, CARS mediates the binding of AMPK to CaMKK2, resulting in the phosphorylation and activation of AMPK by CaMKK2. Importantly, we demonstrate that blocking AMPK activation leads to cell death under cysteine-deficient conditions. In summary, our study is the first to show that CARS senses the absence of cysteine and activates AMPK through the cysteine-CARS-CaMKK2-AMPKγ2 axis, a novel adaptation strategy for cell survival under nutrient deprivation conditions.

Keywords:  AMPK; CARS; cell survival; cyst(e)ine

DOI:  https://doi.org/10.15252/embj.2021108028
Mol Cell. 2021 Aug 27. pii: S1097-2765(21)00645-6. [Epub ahead of print]

The context-specific roles of urea cycle enzymes in tumorigenesis.

Emma Hajaj, Marco Sciacovelli, Christian Frezza, Ayelet Erez.

The expression of the urea cycle (UC) proteins is dysregulated in multiple cancers, providing metabolic benefits to tumor survival, proliferation, and growth. Here, we review the main changes described in the expression of UC enzymes and metabolites in different cancers at various stages and suggest that these changes are dynamic and should hence be viewed in a context-specific manner. Understanding the evolvability in the activity of the UC pathway in cancer has implications for cancer-immune cell interactions and for cancer diagnosis and therapy.

DOI: https://doi.org/10.1016/j.molcel.2021.08.005
Bioelectricity. 2019 Sep 01. 1(3): 188-200

Potassium and Sodium Channels and the Warburg Effect: Biophysical Regulation of Cancer Metabolism.

Jessica Iorio, Giulia Petroni, Claudia Duranti, Elena Lastraioli.

  Ion channels are progressively emerging as a novel class of membrane proteins expressed in several types of human cancers and regulating the different aspects of cancer cell behavior. The metabolism of cancer cells, usually composed by a variable proportion of respiration, glycolysis, and glutaminolysis, leads to the excessive production of acidic metabolic products. The presence of these acidic metabolites inside the cells results in intracellular acidosis, and hinders survival and proliferation. For this reason, tumor cells activate mechanisms of pH control that produce a constitutive increase in intracellular pH (pHi) that is more acidic than the extracellular pH (pHe). This condition forms a perfect microenvironment for metastatic progression and may be permissive for some of the acquired characteristics of tumors. Recent analyses have revealed complex interconnections between oncogenic activation, ion channels, hypoxia signaling and metabolic pathways that are dysregulated in cancer. Here, we summarize the molecular mechanisms of the Warburg effect and hypoxia and their association. Moreover, we discuss the recent findings concerning the involvement of ion channels in various aspects of the Warburg effect and hypoxia, focusing on the role of Na+ and K+ channels in hypoxic and metabolic reprogramming in cancer.

Keywords:  Warburg effect; cancer; ion channels

DOI:  https://doi.org/10.1089/bioe.2019.0017
Nat Commun. 2021 08 30. 12(1): 5178

A nutrient-responsive hormonal circuit mediates an inter-tissue program regulating metabolic homeostasis in adult Drosophila.

Takashi Koyama, Selim Terhzaz, Muhammad T Naseem, Stanislav Nagy, Kim Rewitz, Julian A T Dow, Shireen A Davies, Kenneth V Halberg.

Animals maintain metabolic homeostasis by modulating the activity of specialized organs that adjust internal metabolism to external conditions. However, the hormonal signals coordinating these functions are incompletely characterized. Here we show that six neurosecretory cells in the Drosophila central nervous system respond to circulating nutrient levels by releasing Capa hormones, homologs of mammalian neuromedin U, which activate the Capa receptor (CapaR) in peripheral tissues to control energy homeostasis. Loss of Capa/CapaR signaling causes intestinal hypomotility and impaired nutrient absorption, which gradually deplete internal nutrient stores and reduce organismal lifespan. Conversely, increased Capa/CapaR activity increases fluid and waste excretion. Furthermore, Capa/CapaR inhibits the release of glucagon-like adipokinetic hormone from the corpora cardiaca, which restricts energy mobilization from adipose tissue to avoid harmful hyperglycemia. Our results suggest that the Capa/CapaR circuit occupies a central node in a homeostatic program that facilitates the digestion and absorption of nutrients and regulates systemic energy balance.

DOI: https://doi.org/10.1038/s41467-021-25445-2
Mol Brain. 2021 Sep 03. 14(1): 132

Astrocyte metabolism of the medium-chain fatty acids octanoic acid and decanoic acid promotes GABA synthesis in neurons via elevated glutamine supply.

Jens V Andersen, Emil W Westi, Emil Jakobsen, Nerea Urruticoechea, Karin Borges, Blanca I Aldana.

  The medium-chain fatty acids octanoic acid (C8) and decanoic acid (C10) are gaining attention as beneficial brain fuels in several neurological disorders. The protective effects of C8 and C10 have been proposed to be driven by hepatic production of ketone bodies. However, plasma ketone levels correlates poorly with the cerebral effects of C8 and C10, suggesting that additional mechanism are in place. Here we investigated cellular C8 and C10 metabolism in the brain and explored how the protective effects of C8 and C10 may be linked to cellular metabolism. Using dynamic isotope labeling, with [U-13C]C8 and [U-13C]C10 as metabolic substrates, we show that both C8 and C10 are oxidatively metabolized in mouse brain slices. The 13C enrichment from metabolism of [U-13C]C8 and [U-13C]C10 was particularly prominent in glutamine, suggesting that C8 and C10 metabolism primarily occurs in astrocytes. This finding was corroborated in cultured astrocytes in which C8 increased the respiration linked to ATP production, whereas C10 elevated the mitochondrial proton leak. When C8 and C10 were provided together as metabolic substrates in brain slices, metabolism of C10 was predominant over that of C8. Furthermore, metabolism of both [U-13C]C8 and [U-13C]C10 was unaffected by etomoxir indicating that it is independent of carnitine palmitoyltransferase I (CPT-1). Finally, we show that inhibition of glutamine synthesis selectively reduced 13C accumulation in GABA from [U-13C]C8 and [U-13C]C10 metabolism in brain slices, demonstrating that the glutamine generated from astrocyte C8 and C10 metabolism is utilized for neuronal GABA synthesis. Collectively, the results show that cerebral C8 and C10 metabolism is linked to the metabolic coupling of neurons and astrocytes, which may serve as a protective metabolic mechanism of C8 and C10 supplementation in neurological disorders.

Keywords:  Capric acid (C10); Caprylic acid (C8); MCFA; MCT; Mitochondria; Neurotransmitter recycling; β-hydroxybutyrate

DOI:  https://doi.org/10.1186/s13041-021-00842-2
Nat Cancer. 2020 Sep;1(9): 923-934

Autophagy promotes growth of tumors with high mutational burden by inhibiting a T-cell immune response.

Laura Poillet-Perez, Daniel W Sharp, Yang Yang, Saurabh V Laddha, Maria Ibrahim, Praveen K Bommareddy, Zhixian Sherrie Hu, Joshua Vieth, Michael Haas, Marcus W Bosenberg, Joshua D Rabinowitz, Jian Cao, Jun-Lin Guan, Shridar Ganesan, Chang S Chan, Janice M Mehnert, Edmund C Lattime, Eileen White.

Macroautophagy (hereafter autophagy) degrades and recycles intracellular components to sustain metabolism and survival during starvation. Host autophagy promotes tumor growth by providing essential tumor nutrients. Autophagy also regulates immune cell homeostasis and function and suppresses inflammation. Although host autophagy does not promote a T-cell anti-tumor immune response in tumors with low tumor mutational burden (TMB), whether this was the case in tumors with high TMB was not known. Here we show that autophagy, especially in the liver, promotes tumor immune tolerance by enabling regulatory T-cell function and limiting stimulator of interferon genes, T-cell response and interferon-γ, which enables growth of high-TMB tumors. We have designated this as hepatic autophagy immune tolerance. Autophagy thereby promotes tumor growth through both metabolic and immune mechanisms depending on mutational load and autophagy inhibition is an effective means to promote an antitumor T-cell response in high-TMB tumors.

DOI: https://doi.org/10.1038/s43018-020-00110-7
Nat Commun. 2021 Sep 01. 12(1): 5203

Aurora kinase A inhibition reverses the Warburg effect and elicits unique metabolic vulnerabilities in glioblastoma.

Trang T T Nguyen, Enyuan Shang, Chang Shu, Sungsoo Kim, Angeliki Mela, Nelson Humala, Aayushi Mahajan, Hee Won Yang, Hasan Orhan Akman, Catarina M Quinzii, Guoan Zhang, Mike-Andrew Westhoff, Georg Karpel-Massler, Jeffrey N Bruce, Peter Canoll, Markus D Siegelin.

Aurora kinase A (AURKA) has emerged as a drug target for glioblastoma (GBM). However, resistance to therapy remains a critical issue. By integration of transcriptome, chromatin immunoprecipitation sequencing (CHIP-seq), Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq), proteomic and metabolite screening followed by carbon tracing and extracellular flux analyses we show that genetic and pharmacological AURKA inhibition elicits metabolic reprogramming mediated by inhibition of MYC targets and concomitant activation of Peroxisome Proliferator Activated Receptor Alpha (PPARA) signaling. While glycolysis is suppressed by AURKA inhibition, we note an increase in the oxygen consumption rate fueled by enhanced fatty acid oxidation (FAO), which was accompanied by an increase of Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1α). Combining AURKA inhibitors with inhibitors of FAO extends overall survival in orthotopic GBM PDX models. Taken together, these data suggest that simultaneous targeting of oxidative metabolism and AURKAi might be a potential novel therapy against recalcitrant malignancies.

DOI: https://doi.org/10.1038/s41467-021-25501-x
Curr Biol. 2021 Aug 27. pii: S0960-9822(21)01122-2. [Epub ahead of print]

Nectar-feeding bats and birds show parallel molecular adaptations in sugar metabolism enzymes.

Joshua H T Potter, Rosie Drinkwater, Kalina T J Davies, Nicolas Nesi, Marisa C W Lim, Laurel R Yohe, Hai Chi, Xiaoqing Zhang, Ilya Levantis, Burton K Lim, Christopher C Witt, Georgia Tsagkogeorga, Mario Dos Reis, Yang Liu, William Furey, Matthew J Whitley, Dunja Aksentijevic, Liliana M Dávalos, Stephen J Rossiter.

  In most vertebrates, the demand for glucose as the primary substrate for cellular respiration is met by the breakdown of complex carbohydrates, or energy is obtained by protein and lipid catabolism. In contrast, a few bat and bird species have convergently evolved to subsist on nectar, a sugar-rich mixture of glucose, fructose, and sucrose.1-4 How these nectar-feeders have adapted to cope with life-long high sugar intake while avoiding the onset of metabolic syndrome and diabetes5-7 is not understood. We analyzed gene sequences obtained from 127 taxa, including 22 nectar-feeding bat and bird genera that collectively encompass four independent origins of nectarivory. We show these divergent taxa have undergone pervasive molecular adaptation in sugar catabolism pathways, including parallel selection in key glycolytic and fructolytic enzymes. We also uncover convergent amino acid substitutions in the otherwise evolutionarily conserved aldolase B (ALDOB), which catalyzes rate-limiting steps in fructolysis and glycolysis, and the mitochondrial gatekeeper pyruvate dehydrogenase (PDH), which links glycolysis and the tricarboxylic acid cycle. Metabolomic profile and enzyme functional assays are consistent with increased respiratory flux in nectar-feeding bats and help explain how these taxa can both sustain hovering flight and efficiently clear simple sugars. Taken together, our results indicate that nectar-feeding bats and birds have undergone metabolic adaptations that have enabled them to exploit a unique energy-rich dietary niche among vertebrates.

Keywords:  aldolase B; convergence; fructose; glucose; glycolysis; hovering flight; nectarivory; pyruvate dehydrogenase; transcriptomes

DOI:  https://doi.org/10.1016/j.cub.2021.08.018
Cell Death Dis. 2021 Sep 01. 12(9): 824

Cyclic AMP-binding protein Epac1 acts as a metabolic sensor to promote cardiomyocyte lipotoxicity.

Marion Laudette, Yannis Sainte-Marie, Grégoire Cousin, Dorian Bergonnier, Ismahane Belhabib, Stéphanie Brun, Karina Formoso, Loubna Laib, Florence Tortosa, Camille Bergoglio, Bertrand Marcheix, Jan Borén, Olivier Lairez, Jérémy Fauconnier, Alexandre Lucas, Jeanne Mialet-Perez, Cédric Moro, Frank Lezoualc'h.

Cyclic adenosine monophosphate (cAMP) is a master regulator of mitochondrial metabolism but its precise mechanism of action yet remains unclear. Here, we found that a dietary saturated fatty acid (FA), palmitate increased intracellular cAMP synthesis through the palmitoylation of soluble adenylyl cyclase in cardiomyocytes. cAMP further induced exchange protein directly activated by cyclic AMP 1 (Epac1) activation, which was upregulated in the myocardium of obese patients. Epac1 enhanced the activity of a key enzyme regulating mitochondrial FA uptake, carnitine palmitoyltransferase 1. Consistently, pharmacological or genetic Epac1 inhibition prevented lipid overload, increased FA oxidation (FAO), and protected against mitochondrial dysfunction in cardiomyocytes. In addition, analysis of Epac1 phosphoproteome led us to identify two key mitochondrial enzymes of the the β-oxidation cycle as targets of Epac1, the long-chain FA acyl-CoA dehydrogenase (ACADL) and the 3-ketoacyl-CoA thiolase (3-KAT). Epac1 formed molecular complexes with the Ca2+/calmodulin-dependent protein kinase II (CaMKII), which phosphorylated ACADL and 3-KAT at specific amino acid residues to decrease lipid oxidation. The Epac1-CaMKII axis also interacted with the α subunit of ATP synthase, thereby further impairing mitochondrial energetics. Altogether, these findings indicate that Epac1 disrupts the balance between mitochondrial FA uptake and oxidation leading to lipid accumulation and mitochondrial dysfunction, and ultimately cardiomyocyte death.

DOI: https://doi.org/10.1038/s41419-021-04113-9
STAR Protoc. 2021 Sep 17. 2(3): 100767

Protocol for assessing real-time changes in mitochondrial morphology, fission and fusion events in live cells using confocal microscopy.

Irene Bertolini, Frederick Keeney, Dario C Altieri.

  Changes in mitochondrial size, shape, and subcellular position, a process collectively known as mitochondrial dynamics, are exploited for various cancer traits. Modulation of subcellular mitochondrial trafficking and accumulation at the cortical cytoskeleton has been linked to the machinery of cell movements, fueling cell invasion and metastatic spreading. Here, we detail a technique to track changes in mitochondrial volume using a commercial CellLight™ Mitochondria-RFP/GFP reporter and live confocal microscopy. This allows a real-time study of mitochondrial dynamics in live cells. For complete details on the use and execution of this protocol, please refer to Bertolini et al. (2020).

Keywords:  Cancer; Microscopy; Molecular/Chemical Probes

DOI:  https://doi.org/10.1016/j.xpro.2021.100767
Cell Death Dis. 2021 Aug 30. 12(9): 821

Therapeutic targeting of both dihydroorotate dehydrogenase and nucleoside transport in MYCN-amplified neuroblastoma.

Yajie Yu, Jane Ding, Shunqin Zhu, Ahmet Alptekin, Zheng Dong, Chunhong Yan, Yunhong Zha, Han-Fei Ding.

Metabolic reprogramming is an integral part of the growth-promoting program driven by the MYC family of oncogenes. However, this reprogramming also imposes metabolic dependencies that could be exploited therapeutically. Here we report that the pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (DHODH) is an attractive therapeutic target for MYCN-amplified neuroblastoma, a childhood cancer with poor prognosis. Gene expression profiling and metabolomic analysis reveal that MYCN promotes pyrimidine nucleotide production by transcriptional upregulation of DHODH and other enzymes of the pyrimidine-synthesis pathway. Genetic and pharmacological inhibition of DHODH suppresses the proliferation and tumorigenicity of MYCN-amplified neuroblastoma cell lines. Furthermore, we obtain evidence suggesting that serum uridine is a key factor in determining the efficacy of therapeutic agents that target DHODH. In the presence of physiological concentrations of uridine, neuroblastoma cell lines are highly resistant to DHODH inhibition. This uridine-dependent resistance to DHODH inhibitors can be abrogated by dipyridamole, an FDA-approved drug that blocks nucleoside transport. Importantly, dipyridamole synergizes with DHODH inhibition to suppress neuroblastoma growth in animal models. These findings suggest that a combination of targeting DHODH and nucleoside transport is a promising strategy to overcome intrinsic resistance to DHODH-based cancer therapeutics.

DOI: https://doi.org/10.1038/s41419-021-04120-w
Nature. 2021 Sep 01.

The polar oxy-metabolome reveals the 4-hydroxymandelate CoQ10 synthesis pathway.

Robert S Banh, Esther S Kim, Quentin Spillier, Douglas E Biancur, Keisuke Yamamoto, Albert S W Sohn, Guangbin Shi, Drew R Jones, Alec C Kimmelman, Michael E Pacold.

Oxygen is critical for a multitude of metabolic processes that are essential for human life. Biological processes can be identified by treating cells with 18O2 or other isotopically labelled gases and systematically identifying biomolecules incorporating labeled atoms. Here we labelled cell lines of distinct tissue origins with 18O2 to identify the polar oxy-metabolome, defined as polar metabolites labelled with 18O under different physiological O2 tensions. The most highly 18O-labelled feature was 4-hydroxymandelate (4-HMA). We demonstrate that 4-HMA is produced by hydroxyphenylpyruvate dioxygenase-like (HPDL), a protein of previously unknown function in human cells. We identify 4-HMA as an intermediate involved in the biosynthesis of the coenzyme Q10 (CoQ10) headgroup in human cells. The connection of HPDL to CoQ10 biosynthesis provides crucial insights into the mechanisms underlying recently described neurological diseases related to HPDL deficiencies1-4 and cancers with HPDL overexpression5.

DOI: https://doi.org/10.1038/s41586-021-03865-w
Cell Death Differ. 2021 Aug 31.

Organelle-specific regulation of ferroptosis.

Xin Chen, Rui Kang, Guido Kroemer, Daolin Tang.

Ferroptosis, a cell death modality characterized by iron-dependent lipid peroxidation, is involved in the development of multiple pathological conditions, including ischemic tissue damage, infection, neurodegeneration, and cancer. The cellular machinery responsible for the execution of ferroptosis integrates multiple pro-survival or pro-death signals from subcellular organelles and then 'decides' whether to engage the lethal process or not. Here, we outline the evidence implicating different organelles (including mitochondria, lysosomes, endoplasmic reticulum, lipid droplets, peroxisomes, Golgi apparatus, and nucleus) in the ignition or avoidance of ferroptosis, while emphasizing their potential relevance for human disease and their targetability for pharmacological interventions.

DOI: https://doi.org/10.1038/s41418-021-00859-z
EMBO J. 2021 Aug 30. e108389

Cancer evolution: Darwin and beyond.

Roberto Vendramin, Kevin Litchfield, Charles Swanton.

  Clinical and laboratory studies over recent decades have established branched evolution as a feature of cancer. However, while grounded in somatic selection, several lines of evidence suggest a Darwinian model alone is insufficient to fully explain cancer evolution. First, the role of macroevolutionary events in tumour initiation and progression contradicts Darwin's central thesis of gradualism. Whole-genome doubling, chromosomal chromoplexy and chromothripsis represent examples of single catastrophic events which can drive tumour evolution. Second, neutral evolution can play a role in some tumours, indicating that selection is not always driving evolution. Third, increasing appreciation of the role of the ageing soma has led to recent generalised theories of age-dependent carcinogenesis. Here, we review these concepts and others, which collectively argue for a model of cancer evolution which extends beyond Darwin. We also highlight clinical opportunities which can be grasped through targeting cancer vulnerabilities arising from non-Darwinian patterns of evolution.

Keywords:  cancer; cancer evolution; cancer therapy; tumour heterogeneity

DOI:  https://doi.org/10.15252/embj.2021108389
Elife. 2021 Sep 01. pii: e68610. [Epub ahead of print]10

Human genetic analyses of organelles highlight the nucleus in age-related trait heritability.

Rahul Gupta, Konrad Karczewski, Daniel Howrigan, Benjamin Neale, Vamsi Mootha Md.

  Most age-related human diseases are accompanied by a decline in cellular organelle integrity, including impaired lysosomal proteostasis and defective mitochondrial oxidative phosphorylation. An open question, however, is the degree to which inherited variation in or near genes encoding each organelle contributes to age-related disease pathogenesis. Here, we evaluate if genetic loci encoding organelle proteomes confer greater-than-expected age-related disease risk. As mitochondrial dysfunction is a 'hallmark' of aging, we begin by assessing nuclear and mitochondrial DNA loci near genes encoding the mitochondrial proteome and surprisingly observe a lack of enrichment across 24 age-related traits. Within nine other organelles, we find no enrichment with one exception: the nucleus, where enrichment emanates from nuclear transcription factors. In agreement, we find that genes encoding several organelles tend to be 'haplosufficient', while we observe strong purifying selection against heterozygous protein-truncating variants impacting the nucleus. Our work identifies common variation near transcription factors as having outsize influence on age-related trait risk, motivating future efforts to determine if and how this inherited variation then contributes to observed age-related organelle deterioration.

Keywords:  genetics; genomics; human

DOI:  https://doi.org/10.7554/eLife.68610
Anal Bioanal Chem. 2021 Sep 02.

Mass spectrometric characterization of cyclic dinucleotides (CDNs) in vivo.

Andrea Annibal, Roberto Ripa, Eugen Ballhysa, Christian Latza, Nadine Hochhard, Adam Antebi.

  Cyclic dinucleotides (CDNs) are key secondary messenger molecules produced by cyclic dinucleotide synthases that trigger various cellular signaling cascades from bacteria to vertebrates. In mammals, cyclic GMP-AMP synthase (cGAS) has been shown to bind to intracellular DNA and catalyze the production of the dinucleotide 2'3' cGAMP, which signals downstream effectors to regulate immune function, interferon signaling, and the antiviral response. Despite the importance of CDNs, sensitive and accurate methods to measure their levels in vivo are lacking. Here, we report a novel LC-MS/MS method to quantify CDNs in vivo. We characterized the mass spectrometric behavior of four different biologically relevant CDNs (c-di-AMP, c-di-GMP, 3'3' cGAMP, 2'3' cGAMP) and provided a means of visually representing fragmentation resulting from collision-induced dissociation at different energies using collision energy breakdown graphs. We then validated the method and quantified CDNs in two in vivo systems, the bacteria Escherichia coli OP50 and the killifish Nothobranchius furzeri. We found that optimization of LC-MS/MS parameters is crucial to sensitivity and accuracy. These technical advances should help illuminate physiological and pathological roles of these CDNs in in vivo settings. Graphical abstract.

Keywords:  2′3′ cGAMP; Mass spectrometry; Nothobranchius furzeri; cGAS

DOI:  https://doi.org/10.1007/s00216-021-03628-6
Front Cell Dev Biol. 2021 ;9 722412

Cysteine Boosts Fitness Under Hypoxia-Mimicked Conditions in Ovarian Cancer by Metabolic Reprogramming.

Sofia C Nunes, Cristiano Ramos, Inês Santos, Cindy Mendes, Fernanda Silva, João B Vicente, Sofia A Pereira, Ana Félix, Luís G Gonçalves, Jacinta Serpa.

  Among gynecologic malignancies, ovarian cancer is the third most prevalent and the most common cause of death, especially due to diagnosis at an advanced stage together with resistance to therapy. As a solid tumor grows, cancer cells in the microenvironment are exposed to regions of hypoxia, a selective pressure prompting tumor progression and chemoresistance. We have previously shown that cysteine contributes to the adaptation to this hypoxic microenvironment, but the mechanisms by which cysteine protects ovarian cancer cells from hypoxia-induced death are still to be unveiled. Herein, we hypothesized that cysteine contribution relies on cellular metabolism reprogramming and energy production, being cysteine itself a metabolic source. Our results strongly supported a role of xCT symporter in energy production that requires cysteine metabolism instead of hydrogen sulfide (H2S) per se. Cysteine degradation depends on the action of the H2S-synthesizing enzymes cystathionine β-synthase (CBS), cystathionine γ-lyase (CSE), and/or 3-mercaptopyruvate sulfurtransferase (MpST; together with cysteine aminotransferase, CAT). In normoxia, CBS and CSE inhibition had a mild impact on cysteine-sustained ATP production, pointing out the relevance of CAT + MpST pathway. However, in hypoxia, the concomitant inhibition of CBS and CSE had a stronger impact on ATP synthesis, thus also supporting a role of their hydrogen sulfide and/or cysteine persulfide-synthesizing activity in this stressful condition. However, the relative contributions of each of these enzymes (CBS/CSE/MpST) on cysteine-derived ATP synthesis under hypoxia remains unclear, due to the lack of specific inhibitors. Strikingly, NMR analysis strongly supported a role of cysteine in the whole cellular metabolism rewiring under hypoxia. Additionally, the use of cysteine to supply biosynthesis and bioenergetics was reinforced, bringing cysteine to the plateau of a main carbon sources in cancer. Collectively, this work supports that sulfur and carbon metabolism reprogramming underlies the adaptation to hypoxic microenvironment promoted by cysteine in ovarian cancer.

Keywords:  bioenergetics; carbon source; cysteine; cystine; hydrogen sulfide; hypoxia; microenvironment; ovarian cancer

DOI:  https://doi.org/10.3389/fcell.2021.722412
J Physiol. 2021 Sep 01.

Naked mole-rat brain mitochondria tolerate in vitro ischemia.

Hang Cheng, Matthew E Pamenter.

   KEY POINTS: Ischemia is highly deleterious to mammalian brain and this damage is largely mediated by mitochondrial dysfunction. Naked mole-rats are among the most hypoxia-tolerant mammals and their brain tolerates ischemia ex vivo, but the impact of ischemia on mitochondrial function is unknown. Naked mole-rat but not mouse brain mitochondria retain respiratory capacity and membrane integrity following ischemia or ischemia/reperfusion. Differences in free radical management and respiratory pathway control between species may mediate this tolerance. These results help us understand how natural models of hypoxia-tolerance also tolerate ischemia in brain.
ABSTRACT: Naked mole-rats (NMRs; Heterocephalus glaber) are among the most hypoxia-tolerant mammals. There is evidence that NMR brain tolerates in vitro hypoxia and NMR brain mitochondria exhibit functional plasticity following in vivo hypoxia; however, if and how these organelles tolerate ischemia and how ischemic stress impacts mitochondrial energetics and redox regulation is entirely unknown. We hypothesized that mitochondria fundamentally contribute to in vitro ischemia resistance in NMR brain. To test this, we treated NMR and CD-1 mouse cortical brain sheets with an in vitro ischemic mimic and evaluated mitochondrial respiration capacity and redox regulation following 15- or 30-mins ischemia or ischemia/reperfusion (I/R). We found that, relative to mice, NMR brain largely retains mitochondrial function and redox balance post-ischemia and I/R. Specifically: i) ischemia reduced complex I and II -linked respiration ∼50-70% in mice, versus ∼20-40% in NMR brain, ii) NMR but not mouse brain maintained relatively steady respiration control ratios and robust mitochondrial membrane integrity, iii) electron leakage post-ischemia was lesser in NMR than mouse brain and NMR brain retained higher coupling efficiency, and iv) free radical generation during and following ischemia and I/R was lower from NMR brains than mice. Taken together, our results indicate that NMR brain mitochondria are more tolerant of ischemia and I/R than mice and retain respiratory capacity while avoiding redox derangements. Overall, these findings support the hypothesis that hypoxia-tolerant NMR brain is also ischemia-tolerant and suggest that NMRs may be a natural model of ischemia-tolerance in which to investigate evolutionarily derived solutions to ischemic pathology. This article is protected by copyright. All rights reserved.

Keywords:  electron transport system; free radicals; glutamate dehydrogenase; membrane integrity; mitochondrial permeability transition pore; mitochondrial respiration

DOI:  https://doi.org/10.1113/JP281942
J Biol Chem. 2021 Aug 27. pii: S0021-9258(21)00941-8. [Epub ahead of print] 101140

From OCR and ECAR to energy: perspectives on the design and interpretation of bioenergetics studies.

Cameron A Schmidt, Kelsey H Fisher-Wellman, P Darrell Neufer.

  Biological energy transduction underlies all physiological phenomena in cells. The metabolic systems that support energy transduction have been of great interest due to their association with numerous pathologies including diabetes, cancer, rare genetic diseases, and aberrant cell death. Commercially available bioenergetics technologies (e.g. extracellular flux analysis, high resolution respirometry, fluorescent dye kits, etc.) have made practical assessment of metabolic parameters widely accessible. This has facilitated an explosion in the number of studies exploring, in particular, the biological implications of oxygen consumption rate (OCR) and substrate level phosphorylation via glycolysis (i.e. via extracellular acidification rate (ECAR)). Though these technologies have demonstrated substantial utility and broad applicability to cell biology research, they are also susceptible to historical assumptions, experimental limitations, and other caveats that have led to premature and/or erroneous interpretations. This review enumerates various important considerations for designing and interpreting cellular and mitochondrial bioenergetics experiments, some common challenges and pitfalls in data interpretation, and some potential 'next steps' to be taken that can address these highlighted challenges.

Keywords:  ATP; Anaerobic glycolysis; Bioenergetics; Cell metabolism; Mitochondria

DOI:  https://doi.org/10.1016/j.jbc.2021.101140