bims-camemi 2020-09-20 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2020‒09‒20
thirty-six papers selected by
Christian Frezza,

Plasticity of ether lipids promotes ferroptosis susceptibility and evasion.
Teleological Role of L-2-Hydroxyglutarate Dehydrogenase in the Kidney.
Compartmental reorganization suppresses tumours.
Fgr kinase is required for proinflammatory macrophage activation during diet-induced obesity.
SAM50, a side door to the mitochondria: The case of cytotoxic proteases.
mTOR-mediated cancer drug resistance suppresses autophagy and generates a druggable metabolic vulnerability.
Altered mitochondrial fusion drives defensive glutathione synthesis in cells able to switch to glycolytic ATP production.
De novo polyamine synthesis supports metabolic and functional responses in activated murine Natural Killer cells.
Exercise and immunometabolic regulation in cancer.
Neuronal metabolic rewiring promotes resilience to neurodegeneration caused by mitochondrial dysfunction.
Re-equilibration of imbalanced NAD metabolism ameliorates the impact of telomere dysfunction.
Targeting Metabolic Pathways in Kidney Cancer: Rationale and Therapeutic Opportunities.
Nuclear-mitochondrial crosstalk: On the role of the nuclear receptor liver receptor homolog-1 (NR5A2) in the regulation of mitochondrial metabolism, cell survival, and cancer.
Eukaryotic cell biology is temporally coordinated to support the energetic demands of protein homeostasis.
LDHB inhibition induces mitophagy and facilitates the progression of CSFV infection.
A Network of Macrophages Supports Mitochondrial Homeostasis in the Heart.
NuRD mediates mitochondrial stress-induced longevity via chromatin remodeling in response to acetyl-CoA level.
pH-Gated Succinate Secretion Regulates Muscle Remodeling in Response to Exercise.
Decoding mitochondrial heterogeneity in single muscle fibres by imaging mass cytometry.
Reprogrammed mRNA translation drives resistance to therapeutic targeting of ribosome biogenesis.
Increased lysosomal biomass is responsible for the resistance of triple-negative breast cancers to CDK4/6 inhibition.
NCLX pumps up the heat.
Histone Deacetylase 3 Couples Mitochondria to Drive IL-1β-Dependent Inflammation by Configuring Fatty Acid Oxidation.
Mitochondrial control of innate immune signaling by irradiated cancer cells.
TET2 promotes anti-tumor immunity by governing G-MDSCs and CD8+ T-cell numbers.
UQCRH downregulation promotes Warburg effect in renal cell carcinoma cells.
BAK core dimers bind lipids and can be bridged by them.
Androgen receptor modulates metastatic routes of VHL wild-type clear cell renal cell carcinoma in an oxygen-dependent manner.
Quantitative genetic screening reveals a Ragulator-FLCN feedback loop that regulates the mTORC1 pathway.
Cryo-EM structure of the entire mammalian F-type ATP synthase.
IRF1-mediated downregulation of PGC1α contributes to cardiorenal syndrome type 4.
Time-restricted feeding alters lipid and amino acid metabolite rhythmicity without perturbing clock gene expression.
PD-L1-mediated gasdermin C expression switches apoptosis to pyroptosis in cancer cells and facilitates tumour necrosis.
TET2 directs mammary luminal cell differentiation and endocrine response.
A Cellular Mechanism to Detect and Alleviate Reductive Stress.
Mitochondrial cristae modeled as an out-of-equilibrium membrane driven by a proton field.

Nature. 2020 Sep 16.

Plasticity of ether lipids promotes ferroptosis susceptibility and evasion.

Yilong Zou, Whitney S Henry, Emily L Ricq, Emily T Graham, Vaishnavi V Phadnis, Pema Maretich, Sateja Paradkar, Natalie Boehnke, Amy A Deik, Ferenc Reinhardt, John K Eaton, Bryan Ferguson, Wenyu Wang, Joshua Fairman, Heather R Keys, Vlado Dančík, Clary B Clish, Paul A Clemons, Paula T Hammond, Laurie A Boyer, Robert A Weinberg, Stuart L Schreiber.

Ferroptosis-an iron-dependent, non-apoptotic cell death process-is involved in various degenerative diseases and represents a targetable susceptibility in certain cancers1. The ferroptosis-susceptible cell state can either pre-exist in cells that arise from certain lineages or be acquired during cell-state transitions2-5. However, precisely how susceptibility to ferroptosis is dynamically regulated remains poorly understood. Here we use genome-wide CRISPR-Cas9 suppressor screens to identify the oxidative organelles peroxisomes as critical contributors to ferroptosis sensitivity in human renal and ovarian carcinoma cells. Using lipidomic profiling we show that peroxisomes contribute to ferroptosis by synthesizing polyunsaturated ether phospholipids (PUFA-ePLs), which act as substrates for lipid peroxidation that, in turn, results in the induction of ferroptosis. Carcinoma cells that are initially sensitive to ferroptosis can switch to a ferroptosis-resistant state in vivo in mice, which is associated with extensive downregulation of PUFA-ePLs. We further find that the pro-ferroptotic role of PUFA-ePLs can be extended beyond neoplastic cells to other cell types, including neurons and cardiomyocytes. Together, our work reveals roles for the peroxisome-ether-phospholipid axis in driving susceptibility to and evasion from ferroptosis, highlights PUFA-ePL as a distinct functional lipid class that is dynamically regulated during cell-state transitions, and suggests multiple regulatory nodes for therapeutic interventions in diseases that involve ferroptosis.

DOI: https://doi.org/10.1038/s41586-020-2732-8
Dis Model Mech. 2020 Sep 14. pii: dmm.045898. [Epub ahead of print]

Teleological Role of L-2-Hydroxyglutarate Dehydrogenase in the Kidney.

Garrett Brinkley, Hyeyoung Nam, Eunhee Shim, Richard Kirkman, Anirban Kundu, Suman Karki, Yasaman Heidarian, Jason M Tennessen, Juan Liu, Jason W Locasale, Tao Guo, Shi Wei, Jennifer Gordetsky, Teresa L Johnson-Pais, Devin Absher, Dinesh Rakheja, Anil K Challa, Sunil Sudarshan.

  L-2-hydroxyglutarate (L-2HG) is an oncometabolite found elevated in renal tumors. However, this molecule may have physiologic roles that extend beyond its association with cancer as L-2HG levels are elevated in response to hypoxia and during Drosophila larval development. L-2HG is known to be metabolized by L-2HG dehydrogenase (L2HGDH), and loss of L2HGDH leads to elevated L-2HG levels. Despite being highly expressed in the kidney, L2HGDH's role in renal metabolism has not been explored. Here, we report our findings utilizing a novel CRISPR/Cas9 murine knockout model with a specific focus on the role of L2HGDH in the kidney. Histologically, L2hgdh KO kidneys have no demonstrable histologic abnormalities. However, GC/MS metabolomics demonstrates significantly reduced levels of the TCA cycle intermediate succinate in multiple tissues. Isotope labeling studies with [U-13C] glucose demonstrate that restoration of L2HGDH in renal cancer cells (which lowers L-2HG) leads to enhanced incorporation of label into TCA cycle intermediates. Subsequent biochemical studies demonstrate that L-2HG can inhibit the TCA cycle enzyme α-ketoglutarate dehydrogenase. Bioinformatic analysis of mRNA expression data from renal tumors demonstrates that L2HGDH is co-expressed with genes encoding TCA cycle enzymes as well as the gene encoding the transcription factor PGC-1α, which is known to regulate mitochondrial metabolism. Restoration of PGC-1α in renal tumor cells results in increased L2HGDH expression with a concomitant reduction if L-2HG levels. Collectively, our studies provide new insight into the physiologic role for L2HGDH as well as mechanisms that promote L-2HG accumulation in disease states.

Keywords:  L-2-Hydroxyglutarate Dehydrogenase; L-2-hydroxyglutarate; PPARG coactivator 1-α; TCA cycle

DOI:  https://doi.org/10.1242/dmm.045898
Nat Rev Cancer. 2020 Sep 15.

Compartmental reorganization suppresses tumours.

Sarah Seton-Rogers.

DOI: https://doi.org/10.1038/s41568-020-00305-1
Nat Metab. 2020 Sep;2(9): 974-988

Fgr kinase is required for proinflammatory macrophage activation during diet-induced obesity.

Rebeca Acín-Pérez, Salvador Iborra, Yolanda Martí-Mateos, Emma C L Cook, Ruth Conde-Garrosa, Anton Petcherski, Mª Del Mar Muñoz, Raquel Martínez de Mena, Karthickeyan Chella Krishnan, Concepción Jiménez, Juan Pedro Bolaños, Markku Laakso, Aldon J Lusis, Orian S Shirihai, David Sancho, José Antonio Enríquez.

Proinflammatory macrophages are key in the development of obesity. In addition, reactive oxygen species (ROS), which activate the Fgr tyrosine kinase, also contribute to obesity. Here we show that ablation of Fgr impairs proinflammatory macrophage polarization while preventing high-fat diet (HFD)-induced obesity in mice. Systemic ablation of Fgr increases lipolysis and liver fatty acid oxidation, thereby avoiding steatosis. Knockout of Fgr in bone marrow (BM)-derived cells is sufficient to protect against insulin resistance and liver steatosis following HFD feeding, while the transfer of Fgr-expressing BM-derived cells reverts protection from HFD feeding in Fgr-deficient hosts. Scavenging of mitochondrial peroxides is sufficient to prevent Fgr activation in BM-derived cells and HFD-induced obesity. Moreover, Fgr expression is higher in proinflammatory macrophages and correlates with obesity traits in both mice and humans. Thus, our findings reveal the mitochondrial ROS-Fgr kinase as a key regulatory axis in proinflammatory adipose tissue macrophage activation, diet-induced obesity, insulin resistance and liver steatosis.

DOI: https://doi.org/10.1038/s42255-020-00273-8
Pharmacol Res. 2020 Sep 09. pii: S1043-6618(20)31504-8. [Epub ahead of print] 105196

SAM50, a side door to the mitochondria: The case of cytotoxic proteases.

Stefania Lionello, Giovanni Marzaro, Denis Martinvalet.

  SAM50, a 7-8 nm diameter β-barrel channel of the mitochondrial outer membrane, is the central channel of the sorting and assembly machinery (SAM) complex involved in the biogenesis of β-barrel proteins. Interestingly, SAM50 is not known to have channel translocase activity; however, we have recently found that this channel is necessary and sufficient for mitochondrial entry of cytotoxic proteases. Cytotoxic lymphocytes eliminate cells that pose potential hazards, such as virus- and bacteria-infected cells as well as cancer cells. They induce cell death following the delivery of granzyme cytotoxic proteases into the cytosol of the target cell. Although granzyme A and granzyme B (GA and GB), the best characterized of the five human granzymes, trigger very distinct apoptotic cascades, they share the ability to directly target the mitochondria. GA and GB do not have a mitochondrial targeting signal, yet they enter the target cell mitochondria to disrupt respiratory chain complex I and induce mitochondrial reactive oxygen species (ROS)-dependent cell death. We found that granzyme mitochondrial entry requires SAM50 and the translocase of the inner membrane 22 (TIM22). Preventing granzymes' mitochondrial entry compromises their cytotoxicity, indicating that this event is unexpectedly an important step for cell death. Although mitochondria are best known for their roles in cell metabolism and energy conversion, these double-membrane organelles are also involved in Ca2+ homeostasis, metabolite transport, cell cycle regulation, cell signaling, differentiation, stress response, redox homeostasis, aging, and cell death. This multiplicity of functions is matched with the complexity and plasticity of the mitochondrial proteome as well as the organelle's morphological and structural versatility. Indeed, mitochondria are extremely dynamic and undergo fusion and fission events in response to diverse cellular cues. In humans, there are 1,500 different mitochondrial proteins, the vast majority of which are encoded in the nuclear genome and translated by cytosolic ribosomes, after which they must be imported and properly addressed to the right mitochondrial compartment. To this end, mitochondria are equipped with a very sophisticated and highly specific protein import machinery. The latter is centered on translocase complexes embedded in the outer and inner mitochondrial membranes working along five different import pathways. We will briefly describe these import pathways to put into perspective our finding regarding the ability of granzymes to enter the mitochondria.

Keywords:  SAM50; cytotoxic lymphocytes; granzyme; mitochondria; mitochondrial protein import

DOI:  https://doi.org/10.1016/j.phrs.2020.105196
Nat Commun. 2020 Sep 17. 11(1): 4684

mTOR-mediated cancer drug resistance suppresses autophagy and generates a druggable metabolic vulnerability.

Niklas Gremke, Pierfrancesco Polo, Aaron Dort, Jean Schneikert, Sabrina Elmshäuser, Corinna Brehm, Ursula Klingmüller, Anna Schmitt, Hans Christian Reinhardt, Oleg Timofeev, Michael Wanzel, Thorsten Stiewe.

Cancer cells have a characteristic metabolism, mostly caused by alterations in signal transduction networks rather than mutations in metabolic enzymes. For metabolic drugs to be cancer-selective, signaling alterations need to be identified that confer a druggable vulnerability. Here, we demonstrate that many tumor cells with an acquired cancer drug resistance exhibit increased sensitivity to mechanistically distinct inhibitors of cancer metabolism. We demonstrate that this metabolic vulnerability is driven by mTORC1, which promotes resistance to chemotherapy and targeted cancer drugs, but simultaneously suppresses autophagy. We show that autophagy is essential for tumor cells to cope with therapeutic perturbation of metabolism and that mTORC1-mediated suppression of autophagy is required and sufficient for generating a metabolic vulnerability leading to energy crisis and apoptosis. Our study links mTOR-induced cancer drug resistance to autophagy defects as a cause of a metabolic liability and opens a therapeutic window for the treatment of otherwise therapy-refractory tumor patients.

DOI: https://doi.org/10.1038/s41467-020-18504-7
Biochim Biophys Acta Mol Cell Res. 2020 Sep 11. pii: S0167-4889(20)30212-3. [Epub ahead of print] 118854

Altered mitochondrial fusion drives defensive glutathione synthesis in cells able to switch to glycolytic ATP production.

David A Patten, Shawn McGuirk, Ujval Anilkumar, Ghadi Antoun, Karan Gandhi, Gaganvir Parmar, Mohamed Ariff Iqbal, Jacob Wong, Richard B Richardson, Julie St-Pierre, Ruth S Slack, Mary-Ellen Harper.

  Mitochondria are highly dynamic organelles. Alterations in mitochondrial dynamics are causal or are linked to numerous neurodegenerative, neuromuscular, and metabolic diseases. It is generally thought that cells with altered mitochondrial structure are prone to mitochondrial dysfunction, increased reactive oxygen species generation and widespread oxidative damage. The objective of the current study was to investigate the relationship between mitochondrial dynamics and the master cellular antioxidant, glutathione (GSH). We reveal that mouse embryonic fibroblasts (MEFs) lacking the mitochondrial fusion machinery display elevated levels of GSH, which limits oxidative damage. Moreover, targeted metabolomics and 13C isotopic labeling experiments demonstrate that cells lacking the inner membrane fusion GTPase OPA1 undergo widespread metabolic remodeling altering the balance of citric acid cycle intermediates and ultimately favoring GSH synthesis. Interestingly, the GSH precursor and antioxidant n-acetylcysteine did not increase GSH levels in OPA1 KO cells, suggesting that cysteine is not limiting for GSH production in this context. Post-mitotic neurons were unable to increase GSH production in the absence of OPA1. Finally, the ability to use glycolysis for ATP production was a requirement for GSH accumulation following OPA1 deletion. Thus, our results demonstrate a novel role for mitochondrial fusion in the regulation of GSH synthesis, and suggest that cysteine availability is not limiting for GSH synthesis in conditions of mitochondrial fragmentation. These findings provide a possible explanation for the heightened sensitivity of certain cell types to alterations in mitochondrial dynamics.

Keywords:  Mitofusin 1 & 2; Optic Atrophy 1; glutathione; metabolism; mitochondrial dynamics; mitochondrial fusion

DOI:  https://doi.org/10.1016/j.bbamcr.2020.118854
Eur J Immunol. 2020 Sep 18.

De novo polyamine synthesis supports metabolic and functional responses in activated murine Natural Killer cells.

Katie L O'Brien, Nadine Assmann, Eimear O'Connor, Cathal Keane, Jessica Walls, Chloe Choi, Peter J Oefner, Clair M Gardiner, Katja Dettmer, David K Finlay.

  Cellular metabolism is dynamically regulated in Natural Killer (NK) cells and strongly influences their responses. Metabolic dysfunction is linked to defective NK cell responses in diseases such as obesity and cancer. The transcription factors, sterol regulatory element binding protein (SREBP) and cMyc are crucial for controlling NK cell metabolic and functional responses, though the mechanisms involved are not fully understood. This study reveals a new role for SREBP in NK cells in supporting de novo polyamine synthesis through facilitating elevated cMyc expression. Polyamines have diverse roles and their de novo synthesis is required for NK cell glycolytic and oxidative metabolism and to support optimal NK cell effector functions. When NK cells with impaired SREBP activity were supplemented with exogenous polyamines, NK cell metabolic defects were not rescued but these NK cells displayed significant improvement in some effector functions. One role for polyamines is in the control of protein translation where spermidine supports the posttranslational hypusination of translation factor eIF5a. Pharmacological inhibition of hypusination also impacts upon NK cell metabolism and effector function. Considering recent evidence that cholesterol-rich tumour microenvironments inhibit SREBP activation and drive lymphocyte dysfunction, this study provides key mechanistic insight into this tumour-evasion strategy. This article is protected by copyright. All rights reserved.

Keywords:  SREBP; cMyc; metabolism; natural killer cell; polyamines

DOI:  https://doi.org/10.1002/eji.202048784
Nat Metab. 2020 Sep;2(9): 849-857

Exercise and immunometabolic regulation in cancer.

Graeme J Koelwyn, Xueqian Zhuang, Tuomas Tammela, Andrea Schietinger, Lee W Jones.

Unhealthful lifestyle factors, such as obesity, disrupt organismal homeostasis and accelerate cancer pathogenesis, partly through metabolic and immunological dysregulation. Exercise is a prototypical strategy that maintains and restores homeostasis at the organismal, tissue, cellular and molecular levels and can prevent or inhibit numerous disease conditions, including cancer. Here, we review unhealthful lifestyle factors that contribute to metabolic and immunological dysregulation and drive tumourigenesis, focusing on patient physiology (host)-tissue-tumour microenvironment interactions. We also discuss how exercise may influence distant tissue microenvironments, thereby improving tissue function through both metabolic and immunospecific pathways. Finally, we consider future directions that merit consideration in basic and clinical translational exercise studies.

DOI: https://doi.org/10.1038/s42255-020-00277-4
Sci Adv. 2020 Aug;6(35): eaba8271

Neuronal metabolic rewiring promotes resilience to neurodegeneration caused by mitochondrial dysfunction.

E Motori, I Atanassov, S M V Kochan, K Folz-Donahue, V Sakthivelu, P Giavalisco, N Toni, J Puyal, N-G Larsson.

Neurodegeneration in mitochondrial disorders is considered irreversible because of limited metabolic plasticity in neurons, yet the cell-autonomous implications of mitochondrial dysfunction for neuronal metabolism in vivo are poorly understood. Here, we profiled the cell-specific proteome of Purkinje neurons undergoing progressive OXPHOS deficiency caused by disrupted mitochondrial fusion dynamics. We found that mitochondrial dysfunction triggers a profound rewiring of the proteomic landscape, culminating in the sequential activation of precise metabolic programs preceding cell death. Unexpectedly, we identified a marked induction of pyruvate carboxylase (PCx) and other anaplerotic enzymes involved in replenishing tricarboxylic acid cycle intermediates. Suppression of PCx aggravated oxidative stress and neurodegeneration, showing that anaplerosis is protective in OXPHOS-deficient neurons. Restoration of mitochondrial fusion in end-stage degenerating neurons fully reversed these metabolic hallmarks, thereby preventing cell death. Our findings identify a previously unappreciated pathway conferring resilience to mitochondrial dysfunction and show that neurodegeneration can be reversed even at advanced disease stages.

DOI: https://doi.org/10.1126/sciadv.aba8271
EMBO J. 2020 Sep 16. e103420

Re-equilibration of imbalanced NAD metabolism ameliorates the impact of telomere dysfunction.

Chongkui Sun, Kun Wang, Amanda J Stock, Yi Gong, Tyler G Demarest, Beimeng Yang, Neelam Giri, Lea Harrington, Blanche P Alter, Sharon A Savage, Vilhelm A Bohr, Yie Liu.

  Short telomeres are a principal defining feature of telomere biology disorders, such as dyskeratosis congenita (DC), for which there are no effective treatments. Here, we report that primary fibroblasts from DC patients and late generation telomerase knockout mice display lower nicotinamide adenine dinucleotide (NAD) levels, and an imbalance in the NAD metabolome that includes elevated CD38 NADase and reduced poly(ADP-ribose) polymerase and SIRT1 activities, respectively, affecting many associated biological pathways. Supplementation with the NAD precursor, nicotinamide riboside, and CD38 inhibition improved NAD homeostasis, thereby alleviating telomere damage, defective mitochondrial biosynthesis and clearance, cell growth retardation, and cellular senescence of DC fibroblasts. These findings reveal a direct, underlying role of NAD dysregulation when telomeres are short and underscore its relevance to the pathophysiology and interventions of human telomere-driven diseases.

Keywords:  CD38 NADase; NAD metabolism; mitochondrial impairment; replicative senescence; telomere biology disorders

DOI:  https://doi.org/10.15252/embj.2019103420
Cancer J. 2020 Sep/Oct;26(5):26(5): 407-418

Targeting Metabolic Pathways in Kidney Cancer: Rationale and Therapeutic Opportunities.

Christian R Hoerner, Susanna Y Miao, James J Hsieh, Alice C Fan.

Alterations in cellular sugar, amino acid and nucleic acid, and lipid metabolism, as well as in mitochondrial function, are a hallmark of renal cell carcinoma (RCC). The activation of oncogenes such as hypoxia-inducible factor and loss of the von Hippel-Lindau function and other tumor suppressors frequently occur early on during tumorigenesis and are the drivers for these changes, collectively known as "metabolic reprogramming," which promotes cellular growth, proliferation, and stress resilience. However, tumor cells can become addicted to reprogrammed metabolism. Here, we review the current knowledge of metabolic addictions in clear cell RCC, the most common form of RCC, and to what extent this has created therapeutic opportunities to interfere with such altered metabolic pathways to selectively target tumor cells. We highlight preclinical and emerging clinical data on novel therapeutics targeting metabolic traits in clear cell RCC to provide a comprehensive overview on current strategies to exploit metabolic reprogramming clinically.

DOI: https://doi.org/10.1097/PPO.0000000000000472
IUBMB Life. 2020 Sep 15.

Nuclear-mitochondrial crosstalk: On the role of the nuclear receptor liver receptor homolog-1 (NR5A2) in the regulation of mitochondrial metabolism, cell survival, and cancer.

Svenja Michalek, Thomas Brunner.

  Liver receptor homolog-1 (LRH-1, NR5A2) is an orphan nuclear receptor with widespread activities in the regulation of development, stemness, metabolism, steroidogenesis, and proliferation. Many of the LRH-1-regulated processes target the mitochondria and associated activities. While under physiological conditions, a balanced LRH-1 expression and regulation contribute to the maintenance of a physiological equilibrium, deregulation of LRH-1 has been associated with inflammation and cancer. In this review, we discuss the role and mechanism(s) of how LRH-1 regulates metabolic processes, cell survival, and cancer in a nuclear-mitochondrial crosstalk, and evaluate its potential as a pharmacological target.

Keywords:  apoptosis; cancer; metabolism; mitochondria; nuclear receptors

DOI:  https://doi.org/10.1002/iub.2386
Nat Commun. 2020 Sep 17. 11(1): 4706

Eukaryotic cell biology is temporally coordinated to support the energetic demands of protein homeostasis.

John S O' Neill, Nathaniel P Hoyle, J Brian Robertson, Rachel S Edgar, Andrew D Beale, Sew Y Peak-Chew, Jason Day, Ana S H Costa, Christian Frezza, Helen C Causton.

Yeast physiology is temporally regulated, this becomes apparent under nutrient-limited conditions and results in respiratory oscillations (YROs). YROs share features with circadian rhythms and interact with, but are independent of, the cell division cycle. Here, we show that YROs minimise energy expenditure by restricting protein synthesis until sufficient resources are stored, while maintaining osmotic homeostasis and protein quality control. Although nutrient supply is constant, cells sequester and store metabolic resources via increased transport, autophagy and biomolecular condensation. Replete stores trigger increased H+ export which stimulates TORC1 and liberates proteasomes, ribosomes, chaperones and metabolic enzymes from non-membrane bound compartments. This facilitates translational bursting, liquidation of storage carbohydrates, increased ATP turnover, and the export of osmolytes. We propose that dynamic regulation of ion transport and metabolic plasticity are required to maintain osmotic and protein homeostasis during remodelling of eukaryotic proteomes, and that bioenergetic constraints selected for temporal organisation that promotes oscillatory behaviour.

DOI: https://doi.org/10.1038/s41467-020-18330-x
Autophagy. 2020 Sep 14.

LDHB inhibition induces mitophagy and facilitates the progression of CSFV infection.

Shuangqi Fan, Keke Wu, Mingqiu Zhao, Jin Yuan, Shengming Ma, Ereng Zhu, Yuming Chen, Hongxing Ding, Lin Yi, Jinding Chen.

  Cellular metabolism caters to the energy and metabolite needs of cells. Although the role of the terminal metabolic enzyme LDHB (lactate dehydrogenase B) in the glycolysis pathway has been widely studied in cancer cells, its role in viral infection is relatively unknown. In this study, we found that CSFV (classical swine fever virus) infection reduces pyruvate levels while promotes lactate release in pigs and in PK-15 cells. Moreover, using a yeast two-hybrid screening system, we identified LDHB as a novel interacting partner of CSFV non-structural protein NS3. These results were confirmed via co-immunoprecipitation, glutathione S-transferase and confocal assays. Furthermore, knockdown of LDHB via interfering RNA induced mitochondrial fission and mitophagy, as detected reduced mitochondrial mass. Upon inhibition of LDHB, expression of the mitophagy proteins TOMM20 and VDAC1 decreased and the ubiquitination of MFN2, a mitochondrial fusion mediator, was promoted. In addition, a sensitive dual ﬂuorescence reporter (mito-mRFP-EGFP) was utilized to analyze the delivery of autophagosomes to lysosomes in LDHB inhibition cells. Furthermore, LDHB inhibition promoted NFKB signaling, which was regulated by mitophagy; meanwhile, infection with CSFV negated these NFKB anti-viral responses. Inhibition of LDHB also inhibited apoptosis, providing an environment conducive to persistent viral infection. Finally, we demonstrated that LDHB inhibition promoted CSFV growth via mitophagy, whereas its overexpression decreased CSFV replication. Our data revealed a novel mechanism through which LDHB, a metabolic enzyme, mediates CSFV infection, and provides new avenues for the development of anti-viral strategies.

Keywords:  cellular metabolism; classical swine fever virus; lactate dehydrogenase B; mitochondrial fission; mitophagy; viral infection

DOI:  https://doi.org/10.1080/15548627.2020.1823123
Cell. 2020 Sep 09. pii: S0092-8674(20)31073-4. [Epub ahead of print]

A Network of Macrophages Supports Mitochondrial Homeostasis in the Heart.

José A Nicolás-Ávila, Ana V Lechuga-Vieco, Lorena Esteban-Martínez, María Sánchez-Díaz, Elena Díaz-García, Demetrio J Santiago, Andrea Rubio-Ponce, Jackson LiangYao Li, Akhila Balachander, Juan A Quintana, Raquel Martínez-de-Mena, Beatriz Castejón-Vega, Andrés Pun-García, Paqui G Través, Elena Bonzón-Kulichenko, Fernando García-Marqués, Lorena Cussó, Noelia A-González, Andrés González-Guerra, Marta Roche-Molina, Sandra Martin-Salamanca, Georgiana Crainiciuc, Gabriela Guzmán, Jagoba Larrazabal, Elías Herrero-Galán, Jorge Alegre-Cebollada, Greg Lemke, Carla V Rothlin, Luis Jesús Jimenez-Borreguero, Guillermo Reyes, Antonio Castrillo, Manuel Desco, Pura Muñoz-Cánoves, Borja Ibáñez, Miguel Torres, Lai Guan Ng, Silvia G Priori, Héctor Bueno, Jesús Vázquez, Mario D Cordero, Juan A Bernal, José A Enríquez, Andrés Hidalgo.

  Cardiomyocytes are subjected to the intense mechanical stress and metabolic demands of the beating heart. It is unclear whether these cells, which are long-lived and rarely renew, manage to preserve homeostasis on their own. While analyzing macrophages lodged within the healthy myocardium, we discovered that they actively took up material, including mitochondria, derived from cardiomyocytes. Cardiomyocytes ejected dysfunctional mitochondria and other cargo in dedicated membranous particles reminiscent of neural exophers, through a process driven by the cardiomyocyte's autophagy machinery that was enhanced during cardiac stress. Depletion of cardiac macrophages or deficiency in the phagocytic receptor Mertk resulted in defective elimination of mitochondria from the myocardial tissue, activation of the inflammasome, impaired autophagy, accumulation of anomalous mitochondria in cardiomyocytes, metabolic alterations, and ventricular dysfunction. Thus, we identify an immune-parenchymal pair in the murine heart that enables transfer of unfit material to preserve metabolic stability and organ function.

Keywords:  autophagy; heart; macrophage; mitochondria; phagocytosis; proteostasis

DOI:  https://doi.org/10.1016/j.cell.2020.08.031
Sci Adv. 2020 Jul;pii: eabb2529. [Epub ahead of print]6(31):

NuRD mediates mitochondrial stress-induced longevity via chromatin remodeling in response to acetyl-CoA level.

Di Zhu, Xueying Wu, Jun Zhou, Xinyu Li, Xiahe Huang, Jiasheng Li, Junbo Wu, Qian Bian, Yingchun Wang, Ye Tian.

Mild mitochondrial stress experienced early in life can have beneficial effects on the life span of organisms through epigenetic regulations. Here, we report that acetyl-coenzyme A (CoA) represents a critical mitochondrial signal to regulate aging through the chromatin remodeling and histone deacetylase complex (NuRD) in Caenorhabditis elegans Upon mitochondrial stress, the impaired tricarboxylic acid cycle results in a decreased level of citrate, which accounts for reduced production of acetyl-CoA and consequently induces nuclear accumulation of the NuRD and a homeodomain-containing transcription factor DVE-1, thereby enabling decreased histone acetylation and chromatin reorganization. The metabolic stress response is thus established during early life and propagated into adulthood to allow transcriptional regulation for life-span extension. Furthermore, adding nutrients to restore acetyl-CoA production is sufficient to counteract the chromatin changes and diminish the longevity upon mitochondrial stress. Our findings uncover the molecular mechanism of the metabolite-mediated epigenome for the regulation of organismal aging.

DOI: https://doi.org/10.1126/sciadv.abb2529
Cell. 2020 Sep 15. pii: S0092-8674(20)31081-3. [Epub ahead of print]

pH-Gated Succinate Secretion Regulates Muscle Remodeling in Response to Exercise.

Anita Reddy, Luiz H M Bozi, Omar K Yaghi, Evanna L Mills, Haopeng Xiao, Hilary E Nicholson, Margherita Paschini, Joao A Paulo, Ryan Garrity, Dina Laznik-Bogoslavski, Julio C B Ferreira, Christian S Carl, Kim A Sjøberg, Jørgen F P Wojtaszewski, Jacob F Jeppesen, Bente Kiens, Steven P Gygi, Erik A Richter, Diane Mathis, Edward T Chouchani.

  In response to skeletal muscle contraction during exercise, paracrine factors coordinate tissue remodeling, which underlies this healthy adaptation. Here we describe a pH-sensing metabolite signal that initiates muscle remodeling upon exercise. In mice and humans, exercising skeletal muscle releases the mitochondrial metabolite succinate into the local interstitium and circulation. Selective secretion of succinate is facilitated by its transient protonation, which occurs upon muscle cell acidification. In the protonated monocarboxylic form, succinate is rendered a transport substrate for monocarboxylate transporter 1, which facilitates pH-gated release. Upon secretion, succinate signals via its cognate receptor SUCNR1 in non-myofibrillar cells in muscle tissue to control muscle-remodeling transcriptional programs. This succinate-SUCNR1 signaling is required for paracrine regulation of muscle innervation, muscle matrix remodeling, and muscle strength in response to exercise training. In sum, we define a bioenergetic sensor in muscle that utilizes intracellular pH and succinate to coordinate tissue adaptation to exercise.

Keywords:  SUCNR1; exercise; innervation; muscle; succinate

DOI:  https://doi.org/10.1016/j.cell.2020.08.039
Sci Rep. 2020 Sep 18. 10(1): 15336

Decoding mitochondrial heterogeneity in single muscle fibres by imaging mass cytometry.

Charlotte Warren, David McDonald, Roderick Capaldi, David Deehan, Robert W Taylor, Andrew Filby, Doug M Turnbull, Conor Lawless, Amy E Vincent.

The study of skeletal muscle continues to support the accurate diagnosis of mitochondrial disease and remains important in delineating molecular disease mechanisms. The heterogeneous expression of oxidative phosphorylation proteins and resulting respiratory deficiency are both characteristic findings in mitochondrial disease, hence the rigorous assessment of these at a single cell level is incredibly powerful. Currently, the number of proteins that can be assessed in individual fibres from a single section by immunohistochemistry is limited but imaging mass cytometry (IMC) enables the quantification of further, discrete proteins in individual cells. We have developed a novel workflow and bespoke analysis for applying IMC in skeletal muscle biopsies from patients with genetically-characterised mitochondrial disease, investigating the distribution of nine mitochondrial proteins in thousands of single muscle fibres. Using a semi-automated analysis pipeline, we demonstrate the accurate quantification of protein levels using IMC, providing an accurate measure of oxidative phosphorylation deficiency for complexes I-V at the single cell level. We demonstrate signatures of oxidative phosphorylation deficiency for common mtDNA variants and nuclear-encoded complex I variants and a compensatory upregulation of unaffected oxidative phosphorylation components. This technique can now be universally applied to evaluate a wide range of skeletal muscle disorders and protein targets.

DOI: https://doi.org/10.1038/s41598-020-70885-3
EMBO J. 2020 Sep 18. e105111

Reprogrammed mRNA translation drives resistance to therapeutic targeting of ribosome biogenesis.

Eric P Kusnadi, Anna S Trigos, Carleen Cullinane, David L Goode, Ola Larsson, Jennifer R Devlin, Keefe T Chan, David P De Souza, Malcolm J McConville, Grant A McArthur, George Thomas, Elaine Sanij, Gretchen Poortinga, Ross D Hannan, Katherine M Hannan, Jian Kang, Richard B Pearson.

  Elevated ribosome biogenesis in oncogene-driven cancers is commonly targeted by DNA-damaging cytotoxic drugs. Our previous first-in-human trial of CX-5461, a novel, less genotoxic agent that specifically inhibits ribosome biogenesis via suppression of RNA polymerase I (Pol I) transcription, revealed single-agent efficacy in refractory blood cancers. Despite this clinical response, patients were not cured. In parallel, we demonstrated a marked improvement in the in vivo efficacy of CX-5461 in combination with PI3K/AKT/mTORC1 pathway inhibitors. Here, we reveal the molecular basis for this improved efficacy observed in vivo, which is associated with specific suppression of translation of mRNAs encoding regulators of cellular metabolism. Importantly, acquired resistance to this cotreatment is driven by translational rewiring that results in dysregulated cellular metabolism and induction of a cAMP-dependent pathway critical for the survival of blood cancers including lymphoma and acute myeloid leukemia. Our studies thus identify key molecular mechanisms underpinning the response of blood cancers to selective inhibition of ribosome biogenesis and define metabolic vulnerabilities that will facilitate the rational design of more effective regimens for Pol I-directed therapies.

Keywords:  RNA Polymerase I inhibitor; cAMP-EPAC1/2 pathway; hematological cancers; metformin; ribosome biogenesis and function

DOI:  https://doi.org/10.15252/embj.2020105111
Sci Adv. 2020 Jun;pii: eabb2210. [Epub ahead of print]6(25):

Increased lysosomal biomass is responsible for the resistance of triple-negative breast cancers to CDK4/6 inhibition.

Anne Fassl, Christopher Brain, Monther Abu-Remaileh, Iga Stukan, Deborah Butter, Piotr Stepien, Avery S Feit, Johann Bergholz, Wojciech Michowski, Tobias Otto, Qing Sheng, Alice Loo, Walter Michael, Ralph Tiedt, Carmine DeAngelis, Rachel Schiff, Baishan Jiang, Bojana Jovanovic, Karolina Nowak, Maria Ericsson, Michael Cameron, Nathanael Gray, Deborah Dillon, Jean J Zhao, David M Sabatini, Rinath Jeselsohn, Myles Brown, Kornelia Polyak, Piotr Sicinski.

Inhibitors of cyclin-dependent kinases CDK4 and CDK6 have been approved for treatment of hormone receptor-positive breast cancers. In contrast, triple-negative breast cancers (TNBCs) are resistant to CDK4/6 inhibition. Here, we demonstrate that a subset of TNBC critically requires CDK4/6 for proliferation, and yet, these TNBC are resistant to CDK4/6 inhibition due to sequestration of CDK4/6 inhibitors into tumor cell lysosomes. This sequestration is caused by enhanced lysosomal biogenesis and increased lysosomal numbers in TNBC cells. We developed new CDK4/6 inhibitor compounds that evade the lysosomal sequestration and are efficacious against resistant TNBC. We also show that coadministration of lysosomotropic or lysosome-destabilizing compounds (an antibiotic azithromycin, an antidepressant siramesine, an antimalaria compound chloroquine) renders resistant tumor cells sensitive to currently used CDK4/6 inhibitors. Lastly, coinhibition of CDK2 arrested proliferation of CDK4/6 inhibitor-resistant cells. These observations may extend the use of CDK4/6 inhibitors to TNBCs that are refractory to current anti-CDK4/6 therapies.

DOI: https://doi.org/10.1126/sciadv.abb2210
Cell Calcium. 2020 Aug 28. pii: S0143-4160(20)30122-6. [Epub ahead of print]92 102280

NCLX pumps up the heat.

Trayambak Pathak, Mohamed Trebak.

  Mitochondrial Ca2+ signaling is a well-appreciated regulator of cell metabolism and energy production. A major function of mitochondria in brown adipose tissue (BAT) is thermogenesis. Assali et al. offer new insights into how the mitochondrial Ca2+ extrusion mediator NCLX is crucial for BAT survival and thermogenesis.

Keywords:  Brown adipose tissue; Mitochondrial Ca(2+) signaling; Mitochondrial Na(+)/Ca(2+) exchanger NCLX; Non-shivering thermogenesis

DOI:  https://doi.org/10.1016/j.ceca.2020.102280
Mol Cell. 2020 Sep 04. pii: S1097-2765(20)30578-5. [Epub ahead of print]

Histone Deacetylase 3 Couples Mitochondria to Drive IL-1β-Dependent Inflammation by Configuring Fatty Acid Oxidation.

Zhexu Chi, Sheng Chen, Ting Xu, Wenxuan Zhen, Weiwei Yu, Danlu Jiang, Xingchen Guo, Zhen Wang, Kailian Zhang, Mobai Li, Jian Zhang, Hui Fang, Dehang Yang, Qizhen Ye, Xuyan Yang, Hui Lin, Fan Yang, Xue Zhang, Di Wang.

Immune cell function depends on specific metabolic programs dictated by mitochondria, including nutrient oxidation, macromolecule synthesis, and post-translational modifications. Mitochondrial adaptations have been linked to acute and chronic inflammation, but the metabolic cues and precise mechanisms remain unclear. Here we reveal that histone deacetylase 3 (HDAC3) is essential for shaping mitochondrial adaptations for IL-1β production in macrophages through non-histone deacetylation. In vivo, HDAC3 promoted lipopolysaccharide-induced acute inflammation and high-fat diet-induced chronic inflammation by enhancing NLRP3-dependent caspase-1 activation. HDAC3 configured the lipid profile in stimulated macrophages and restricted fatty acid oxidation (FAO) supported by exogenous fatty acids for mitochondria to acquire their adaptations and depolarization. Rather than affecting nuclear gene expression, HDAC3 translocated to mitochondria to deacetylate and inactivate an FAO enzyme, mitochondrial trifunctional enzyme subunit α. HDAC3 may serve as a controlling node that balances between acquiring mitochondrial adaptations and sustaining their fitness for IL-1β-dependent inflammation.

DOI: https://doi.org/10.1016/j.molcel.2020.08.015
Oncoimmunology. 2020 Jul 22. 9(1): 1797292

Mitochondrial control of innate immune signaling by irradiated cancer cells.

Takahiro Yamazaki, Lorenzo Galluzzi.

  Type I interferon (IFN) release by irradiated cancer cells is paramount for radiation therapy to elicit anticancer immunity. Our findings demonstrate that mitochondrial outer membrane permeabilization (MOMP) triggered by RT enables exposure of mitochondrial DNA to the cytosol, hence setting off CGAS-driven type I IFN synthesis. These data point to the existence of a therapeutically actionable mitochondrial checkpoint that restricts innate immune signaling in irradiated cancer cells.

Keywords:  Abscopal responses; STING; autophagy; caspases; immunogenic cell death; micronuclei; venetoclax

DOI:  https://doi.org/10.1080/2162402X.2020.1797292
EMBO Rep. 2020 Sep 14. e49425

TET2 promotes anti-tumor immunity by governing G-MDSCs and CD8+ T-cell numbers.

Shuangqi Li, Jiuxing Feng, Feizhen Wu, Jiabin Cai, Xinyu Zhang, Haikun Wang, Irfete S Fetahu, Isabella Iwanicki, Dingailu Ma, Tao Hu, Hang Liu, Bingjie Wang, Guoming Shi, Li Tan, Yujiang Geno Shi.

  The host immune response is a fundamental mechanism for attenuating cancer progression. Here we report a role for the DNA demethylase and tumor suppressor TET2 in host anti-tumor immunity. Deletion of Tet2 in mice elevates IL-6 levels upon tumor challenge. Elevated IL-6 stimulates immunosuppressive granulocytic myeloid-derived suppressor cells (G-MDSCs), which in turn reduce CD8+ T cells upon tumor challenge. Consequently, systematic knockout of Tet2 in mice leads to accelerated syngeneic tumor growth, which is constrained by anti-PD-1 blockade. Removal of G-MDSCs by the anti-mouse Ly6g antibodies restores CD8+ T-cell numbers in Tet2-/- mice and reboots their anti-tumor activity. Importantly, anti-IL-6 antibody treatment blocks the expansion of G-MDSCs and inhibits syngeneic tumor growth. Collectively, these findings reveal a TET2-mediated IL-6/G-MDSCs/CD8+ T-cell immune response cascade that safeguards host adaptive anti-tumor immunity, offering a cell non-autonomous mechanism of TET2 for tumor suppression.

Keywords:  IL-6; Tet2; anti-tumor immune response; granulocytic myeloid-derived suppressor cells; syngeneic tumor

DOI:  https://doi.org/10.15252/embr.201949425
Sci Rep. 2020 Sep 14. 10(1): 15021

UQCRH downregulation promotes Warburg effect in renal cell carcinoma cells.

Yanting Luo, Louise Medina Bengtsson, Xuechun Wang, Tianhe Huang, Guoqiang Liu, Sean Murphy, Caiqin Wang, John Koren, Zachary Schafer, Xin Lu.

Ubiquinol-cytochrome c reductase hinge protein (UQCRH) is the hinge protein for the multi-subunit complex III of the mitochondrial electron transport chain and is involved in the electron transfer reaction between cytochrome c1 and c. Recent genome-wide transcriptomic and epigenomic profiling of clear cell renal cell carcinoma (ccRCC) by The Cancer Genome Atlas (TCGA) identified UQCRH as the top-ranked gene showing inverse correlation between DNA hypermethylation and mRNA downregulation. The function and underlying mechanism of UQCRH in the Warburg effect metabolism of ccRCC have not been characterized. Here, we verified the clinical association of low UQCRH expression and shorter survival of ccRCC patients through in silico analysis and identified KMRC2 as a highly relevant ccRCC cell line that displays hypermethylation-induced UQCRH extinction. Ectopic overexpression of UQCRH in KMRC2 restored mitochondrial membrane potential, increased oxygen consumption, and attenuated the Warburg effect at the cellular level. UQCRH overexpression in KMRC2 induced higher apoptosis and slowed down in vitro and in vivo tumor growth. UQCRH knockout by CRISPR/Cas9 had little impact on the metabolism and proliferation of 786O ccRCC cell line, suggesting the dispensable role of UQCRH in cells that have entered a Warburg-like state through other mechanisms. Together, our study suggests that loss of UQCRH expression by hypermethylation may promote kidney carcinogenesis through exacerbating the functional decline of mitochondria thus reinforcing the Warburg effect.

DOI: https://doi.org/10.1038/s41598-020-72107-2
Nat Struct Mol Biol. 2020 Sep 14.

BAK core dimers bind lipids and can be bridged by them.

Angus D Cowan, Nicholas A Smith, Jarrod J Sandow, Eugene A Kapp, Yepy H Rustam, James M Murphy, Jason M Brouwer, Jonathan P Bernardini, Michael J Roy, Ahmad Z Wardak, Iris K Tan, Andrew I Webb, Jacqueline M Gulbis, Brian J Smith, Gavin E Reid, Grant Dewson, Peter M Colman, Peter E Czabotar.

BAK and BAX are essential mediators of apoptosis that oligomerize in response to death cues, thereby causing permeabilization of the mitochondrial outer membrane. Their transition from quiescent monomers to pore-forming oligomers involves a well-characterized symmetric dimer intermediate. However, no essential secondary interface that can be disrupted by mutagenesis has been identified. Here we describe crystal structures of human BAK core domain (α2-α5) dimers that reveal preferred binding sites for membrane lipids and detergents. The phospholipid headgroup and one acyl chain (sn2) associate with one core dimer while the other acyl chain (sn1) associates with a neighboring core dimer, suggesting a mechanism by which lipids contribute to the oligomerization of BAK. Our data support a model in which, unlike for other pore-forming proteins whose monomers assemble into oligomers primarily through protein-protein interfaces, the membrane itself plays a role in BAK and BAX oligomerization.

DOI: https://doi.org/10.1038/s41594-020-0494-5
Oncogene. 2020 Sep 17.

Androgen receptor modulates metastatic routes of VHL wild-type clear cell renal cell carcinoma in an oxygen-dependent manner.

Qingbo Huang, Yin Sun, Wei Zhai, Xin Ma, Donglai Shen, Songliang Du, Bosen You, Yuanjie Niu, Chi-Ping Huang, Xu Zhang, Chawnshang Chang.

Recent studies indicated that the androgen receptor (AR) plays important roles in modulating metastasis of VHL-mutant clear cell renal cell carcinoma (ccRCC). However, the precise mechanisms of AR roles in VHL wild-type (VHL-wt) ccRCC, remain unclear. Here we found that AR interacted with VHL to modulate the metastasis of VHL-wt ccRCC via an oxygen-dependent manner. Mechanism dissection revealed that AR could transcriptionally suppress the miR-185-5p expression in the presence of functional VHL-wt protein under a normoxic condition, which might then result in increasing the expression of VEGF-A and VEGF-C via targeting the 3'UTR of mRNAs at a post-transcriptional level. In contrast, under a hypoxic condition, AR could increase miR-185-5p expression to suppress VEGF-C expression, yet this miR-185-5p effect on VEGF-A was reversed via AR's positive regulation on the HIF2α-increased VEGF-A expression that resulted in increasing VEGF-A in the VHL-wt RCC cells. These distinct AR functions under different oxygen conditions may involve the VHL-impacted ubiquitination and nuclear localization of AR. The differential regulation of VEGF-A vs VEGF-C by AR may then result in differential impacts on the ccRCC metastatic destinations of VHL-wt ccRCC cells under different oxygen conditions. These finer mechanisms may help in the development of a novel therapy to better suppress the ccRCC progression under different oxygenization conditions.

DOI: https://doi.org/10.1038/s41388-020-01455-0
Sci Signal. 2020 Sep 15. pii: eaba5665. [Epub ahead of print]13(649):

Quantitative genetic screening reveals a Ragulator-FLCN feedback loop that regulates the mTORC1 pathway.

Erica De Zan, Ruud van Stiphout, Bianca V Gapp, Vincent A Blomen, Thijn R Brummelkamp, Sebastian M B Nijman.

Forward genetic screens in mammalian cell lines, such as RNAi and CRISPR-Cas9 screens, have made major contributions to the elucidation of diverse signaling pathways. Here, we exploited human haploid cells as a robust comparative screening platform and report a set of quantitative forward genetic screens for identifying regulatory mechanisms of mTORC1 signaling, a key growth control pathway that senses diverse metabolic states. Selected chemical and genetic perturbations in this screening platform, including rapamycin treatment and genetic ablation of the Ragulator subunit LAMTOR4, revealed the known core mTORC1 regulatory signaling complexes and the intimate interplay of the mTORC1 pathway with lysosomal function, validating the approach. In addition, we identified a differential requirement for LAMTOR4 and LAMTOR5 in regulating the mTORC1 pathway under fed and starved conditions. Furthermore, we uncovered a previously unknown "synthetic-sick" interaction between the tumor suppressor folliculin and LAMTOR4, which may have therapeutic implications in cancer treatment. Together, our study demonstrates the use of iterative "perturb and observe" genetic screens to uncover regulatory mechanisms driving complex mammalian signaling networks.

DOI: https://doi.org/10.1126/scisignal.aba5665
Nat Struct Mol Biol. 2020 Sep 14.

Cryo-EM structure of the entire mammalian F-type ATP synthase.

Gergely Pinke, Long Zhou, Leonid A Sazanov.

The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the 'proton translocation cluster' attached to the c-ring and a more distant 'hook apparatus' holding subunit e. Unexpectedly, this subunit is anchored to a lipid 'plug' capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine.

DOI: https://doi.org/10.1038/s41594-020-0503-8
Nat Commun. 2020 09 16. 11(1): 4664

IRF1-mediated downregulation of PGC1α contributes to cardiorenal syndrome type 4.

Yinghui Huang, Shaobo Wang, Jie Zhou, Yong Liu, Changhong Du, Ke Yang, Xianjin Bi, Mingying Liu, Wenhao Han, Kailong Wang, Jiachuan Xiong, Song Wang, Yue Wang, Ling Nie, Chi Liu, Daohai Zhang, Jun Gu, Chunyu Zeng, Jinghong Zhao.

Cardiorenal syndrome type 4 (CRS4) is a common complication of chronic kidney disease (CKD), but the pathogenic mechanisms remain elusive. Here we report that morphological and functional changes in myocardial mitochondria are observed in CKD mice, especially decreases in oxidative phosphorylation and fatty acid metabolism. High phosphate (HP), a hallmark of CKD, contributes to myocardial energy metabolism dysfunction by downregulating peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC1α). Furthermore, the transcriptional factor interferon regulatory factor 1 (IRF1) is revealed as the key molecule upregulated by HP through histone H3K9 acetylation, and responsible for the HP-mediated transcriptional inhibition of PGC1α by directly binding to its promoter region. Conversely, restoration of PGC1α expression or genetic knockdown of IRF1 significantly attenuates HP-induced alterations in vitro and in vivo. These findings demonstrate that IRF1-PGC1α axis-mediated myocardial energy metabolism remodeling plays a crucial role in the pathogenesis of CRS4.

DOI: https://doi.org/10.1038/s41467-020-18519-0
Nat Commun. 2020 09 16. 11(1): 4643

Time-restricted feeding alters lipid and amino acid metabolite rhythmicity without perturbing clock gene expression.

Leonidas S Lundell, Evelyn B Parr, Brooke L Devlin, Lars R Ingerslev, Ali Altıntaş, Shogo Sato, Paolo Sassone-Corsi, Romain Barrès, Juleen R Zierath, John A Hawley.

Time-restricted feeding (TRF) improves metabolism independent of dietary macronutrient composition or energy restriction. To elucidate mechanisms underpinning the effects of short-term TRF, we investigated skeletal muscle and serum metabolic and transcriptomic profiles from 11 men with overweight/obesity after TRF (8 h day-1) and extended feeding (EXF, 15 h day-1) in a randomised cross-over design (trial registration: ACTRN12617000165381). Here we show that muscle core clock gene expression was similar after both interventions. TRF increases the amplitude of oscillating muscle transcripts, but not muscle or serum metabolites. In muscle, TRF induces rhythmicity of several amino acid transporter genes and metabolites. In serum, lipids are the largest class of periodic metabolites, while the majority of phase-shifted metabolites are amino acid related. In conclusion, short-term TRF in overweight men affects the rhythmicity of serum and muscle metabolites and regulates the rhythmicity of genes controlling amino acid transport, without perturbing core clock gene expression.

DOI: https://doi.org/10.1038/s41467-020-18412-w
Nat Cell Biol. 2020 Sep 14.

PD-L1-mediated gasdermin C expression switches apoptosis to pyroptosis in cancer cells and facilitates tumour necrosis.

Junwei Hou, Rongce Zhao, Weiya Xia, Chiung-Wen Chang, Yun You, Jung-Mao Hsu, Lei Nie, Yeh Chen, Yu-Chuan Wang, Chunxiao Liu, Wei-Jan Wang, Yun Wu, Baozhen Ke, Jennifer L Hsu, Kebin Huang, Zu Ye, Yi Yang, Xianghou Xia, Yintao Li, Chia-Wei Li, Bin Shao, John A Tainer, Mien-Chie Hung.

Although pyroptosis is critical for macrophages against pathogen infection, its role and mechanism in cancer cells remains unclear. PD-L1 has been detected in the nucleus, with unknown function. Here we show that PD-L1 switches TNFα-induced apoptosis to pyroptosis in cancer cells, resulting in tumour necrosis. Under hypoxia, p-Stat3 physically interacts with PD-L1 and facilitates its nuclear translocation, enhancing the transcription of the gasdermin C (GSDMC) gene. GSDMC is specifically cleaved by caspase-8 with TNFα treatment, generating a GSDMC N-terminal domain that forms pores on the cell membrane and induces pyroptosis. Nuclear PD-L1, caspase-8 and GSDMC are required for macrophage-derived TNFα-induced tumour necrosis in vivo. Moreover, high expression of GSDMC correlates with poor survival. Antibiotic chemotherapy drugs induce pyroptosis in breast cancer. These findings identify a non-immune checkpoint function of PD-L1 and provide an unexpected concept that GSDMC/caspase-8 mediates a non-canonical pyroptosis pathway in cancer cells, causing tumour necrosis.

DOI: https://doi.org/10.1038/s41556-020-0575-z
Nat Commun. 2020 09 15. 11(1): 4642

TET2 directs mammary luminal cell differentiation and endocrine response.

Mi Ran Kim, Meng-Ju Wu, Yingsheng Zhang, Jer-Yen Yang, Chun Ju Chang.

Epigenetic regulation plays an important role in governing stem cell fate and tumorigenesis. Lost expression of a key DNA demethylation enzyme TET2 is associated with human cancers and has been linked to stem cell traits in vitro; however, whether and how TET2 regulates mammary stem cell fate and mammary tumorigenesis in vivo remains to be determined. Here, using our recently established mammary specific Tet2 deletion mouse model, the data reveals that TET2 plays a pivotal role in mammary gland development and luminal lineage commitment. We show that TET2 and FOXP1 form a chromatin complex that mediates demethylation of ESR1, GATA3, and FOXA1, three key genes that are known to coordinately orchestrate mammary luminal lineage specification and endocrine response, and also are often silenced by DNA methylation in aggressive breast cancers. Furthermore, Tet2 deletion-PyMT breast cancer mouse model exhibits enhanced mammary tumor development with deficient ERα expression that confers tamoxifen resistance in vivo. As a result, this study elucidates a role for TET2 in governing luminal cell differentiation and endocrine response that underlies breast cancer resistance to anti-estrogen treatments.

DOI: https://doi.org/10.1038/s41467-020-18129-w
Cell. 2020 Sep 10. pii: S0092-8674(20)31076-X. [Epub ahead of print]

A Cellular Mechanism to Detect and Alleviate Reductive Stress.

Andrew G Manford, Fernando Rodríguez-Pérez, Karen Y Shih, Zhuo Shi, Charles A Berdan, Mangyu Choe, Denis V Titov, Daniel K Nomura, Michael Rape.

  Metazoan organisms rely on conserved stress response pathways to alleviate adverse conditions and preserve cellular integrity. Stress responses are particularly important in stem cells that provide lifetime support for tissue formation and repair, but how these protective systems are integrated into developmental programs is poorly understood. Here we used myoblast differentiation to identify the E3 ligase CUL2FEM1B and its substrate FNIP1 as core components of the reductive stress response. Reductive stress, as caused by prolonged antioxidant signaling or mitochondrial inactivity, reverts the oxidation of invariant Cys residues in FNIP1 and allows CUL2FEM1B to recognize its target. The ensuing proteasomal degradation of FNIP1 restores mitochondrial activity to preserve redox homeostasis and stem cell integrity. The reductive stress response is therefore built around a ubiquitin-dependent rheostat that tunes mitochondrial activity to redox needs and implicates metabolic control in coordination of stress and developmental signaling.

Keywords:  FEM1B; FNIP1; KEAP1; mitochondria; oxidative stress; proteasome; reactive oxygen; reductive stress; ubiquitin

DOI:  https://doi.org/10.1016/j.cell.2020.08.034
Phys Rev E. 2020 Aug;102(2-1): 022401

Mitochondrial cristae modeled as an out-of-equilibrium membrane driven by a proton field.

Nirbhay Patil, Stéphanie Bonneau, Fréderic Joubert, Anne-Florence Bitbol, Hélène Berthoumieux.

As the places where most of the fuel of the cell, namely, ATP, is synthesized, mitochondria are crucial organelles in eukaryotic cells. The shape of the invaginations of the mitochondria inner membrane, known as a crista, has been identified as a signature of the energetic state of the organelle. However, the interplay between the rate of ATP synthesis and the crista shape remains unclear. In this work, we investigate the crista membrane deformations using a pH-dependent Helfrich model, maintained out of equilibrium by a diffusive flux of protons. This model gives rise to shape changes of a cylindrical invagination, in particular to the formation of necks between wider zones under variable, and especially oscillating, proton flux.

DOI: https://doi.org/10.1103/PhysRevE.102.022401