bims-camemi 2019-10-27 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2019–10–27
38 papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit

Mitochondria as multifaceted regulators of cell death.
Oncometabolites in renal cancer.
The CoQ oxidoreductase FSP1 acts parallel to GPX4 to inhibit ferroptosis.
MiT/TFE Family of Transcription Factors, Lysosomes, and Cancer.
Tricarboxylic acid cycle enzyme activities in a mouse model of methylmalonic aciduria.
Fantastic beasts and how to find them-Molecular identification of the mitochondrial ATP-sensitive potassium channel.
The mitochondrial deoxyguanosine kinase is required for cancer cell stemness in lung adenocarcinoma.
TMEM70 facilitates biogenesis of mammalian ATP synthase by promoting subunit c incorporation into the rotor structure of the enzyme.
Metabolic regulation of gene expression by histone lactylation.
Mitophagy dependent macrophage reprogramming protects against kidney fibrosis.
Low-Intensity Running and High-Intensity Swimming Exercises Differentially Improve Energy Metabolism in Mice With Mild Spinal Muscular Atrophy.
A small molecule protects mitochondrial integrity by inhibiting mTOR activity.
Mitochondrial fragmentation limits NK cell-based tumor immunosurveillance.
KDM3A Senses Oxygen Availability to Regulate PGC-1α-Mediated Mitochondrial Biogenesis.
Fumarate metabolic signature for the detection of Reed Syndrome in humans.
PTEN inhibition attenuates endothelial cell apoptosis in coronary heart disease via modulating the AMPK-CREB-Mfn2-mitophagy signaling pathway.
Dietary tryptophan links encephalogenicity of autoreactive T cells with gut microbial ecology.
FSP1 is a glutathione-independent ferroptosis suppressor.
The Charcot-Marie Tooth Disease Mutation R94Q in MFN2 Decreases ATP Production but Increases Mitochondrial Respiration under Conditions of Mild Oxidative Stress.
An Early mtUPR: Redistribution of the Nuclear Transcription Factor Rox1 to Mitochondria Protects against Intramitochondrial Proteotoxic Aggregates.
Mitochondrial stress causes neuronal dysfunction via an ATF4-dependent increase in L-2-hydroxyglutarate.
Protein lysine acetylation: grease or sand in the gears of β-cell mitochondria?
ER-Mitochondria Calcium Transfer, Organelle Contacts and Neurodegenerative Diseases.
Resolving complexity in mitochondrial disease: Towards precision medicine.
Regulation of the ER stress response by a mitochondrial microprotein.
Fibroblastic reticular cells enhance T cell metabolism and survival via epigenetic remodeling.
The cytosolic form of aspartate aminotransferase is required for full activation of TOR complex 1 in fission yeast.
Autophagy in Kidney Disease.
Structural basis of species-selective antagonist binding to the succinate receptor.
Senescent human melanocytes drive skin ageing via paracrine telomere dysfunction.
DNA damage and transcription stress cause ATP-mediated redesign of metabolism and potentiation of anti-oxidant buffering.
Ketosis Ameliorates Renal Cyst Growth in Polycystic Kidney Disease.
Inborn Errors of Metabolism in the Era of Untargeted Metabolomics and Lipidomics.
Induction of metabolic quiescence defines the transitional to follicular B cell switch.
Impairment of Macroautophagy in Dopamine Neurons Has Opposing Effects on Parkinsonian Pathology and Behavior.
Enhanced hexosamine metabolism drives metabolic and signaling networks involving hyaluronan production and O-GlcNAcylation to exacerbate breast cancer.
Mass spectrometry-based methods for analyzing the mitochondrial interactome in mammalian cells.
Histone lactylation links metabolism and gene regulation.

Nat Rev Mol Cell Biol. 2019 Oct 21.

Mitochondria as multifaceted regulators of cell death.

Florian J Bock, Stephen W G Tait.

Through their many and varied metabolic functions, mitochondria power life. Paradoxically, mitochondria also have a central role in apoptotic cell death. Upon induction of mitochondrial apoptosis, mitochondrial outer membrane permeabilization (MOMP) usually commits a cell to die. Apoptotic signalling downstream of MOMP involves cytochrome c release from mitochondria and subsequent caspase activation. As such, targeting MOMP in order to manipulate cell death holds tremendous therapeutic potential across different diseases, including neurodegenerative diseases, autoimmune disorders and cancer. In this Review, we discuss new insights into how mitochondria regulate apoptotic cell death. Surprisingly, recent data demonstrate that besides eliciting caspase activation, MOMP engages various pro-inflammatory signalling functions. As we highlight, together with new findings demonstrating cell survival following MOMP, this pro-inflammatory role suggests that mitochondria-derived signalling downstream of pro-apoptotic cues may also have non-lethal functions. Finally, we discuss the importance and roles of mitochondria in other forms of regulated cell death, including necroptosis, ferroptosis and pyroptosis. Collectively, these new findings offer exciting, unexplored opportunities to target mitochondrial regulation of cell death for clinical benefit.

DOI: https://doi.org/10.1038/s41580-019-0173-8
Nat Rev Nephrol. 2019 Oct 21.

Oncometabolites in renal cancer.

Cissy Yong, Grant D Stewart, Christian Frezza.

The study of cancer metabolism has evolved vastly beyond the remit of tumour proliferation and survival with the identification of the role of 'oncometabolites' in tumorigenesis. Simply defined, oncometabolites are conventional metabolites that, when aberrantly accumulated, have pro-oncogenic functions. Their discovery has led researchers to revisit the Warburg hypothesis, first postulated in the 1950s, of aberrant metabolism as an aetiological determinant of cancer. As such, the identification of oncometabolites and their utilization in diagnostics and prognostics, as novel therapeutic targets and as biomarkers of disease, are areas of considerable interest in oncology. To date, fumarate, succinate, L-2-hydroxyglutarate (L-2-HG) and D-2-hydroxyglutarate (D-2-HG) have been characterized as bona fide oncometabolites. Extensive metabolic reprogramming occurs during tumour initiation and progression in renal cell carcinoma (RCC) and three oncometabolites - fumarate, succinate and L-2-HG - have been implicated in this disease process. All of these oncometabolites inhibit a superfamily of enzymes known as α-ketoglutarate-dependent dioxygenases, leading to epigenetic dysregulation and induction of pseudohypoxic phenotypes, and also have specific pro-oncogenic capabilities. Oncometabolites could potentially be exploited for the development of novel targeted therapies and as biomarkers of disease.

DOI: https://doi.org/10.1038/s41581-019-0210-z
Nature. 2019 Oct 21.

The CoQ oxidoreductase FSP1 acts parallel to GPX4 to inhibit ferroptosis.

Kirill Bersuker, Joseph Hendricks, Zhipeng Li, Leslie Magtanong, Breanna Ford, Peter H Tang, Melissa A Roberts, Bingqi Tong, Thomas J Maimone, Roberto Zoncu, Michael C Bassik, Daniel K Nomura, Scott J Dixon, James A Olzmann.

Ferroptosis is a form of regulated cell death that is caused by the iron-dependent peroxidation of lipids1,2. The glutathione-dependent lipid hydroperoxidase glutathione peroxidase 4 (GPX4) prevents ferroptosis by converting lipid hydroperoxides into non-toxic lipid alcohols3,4. Ferroptosis has been implicated in the cell death that underlies several degenerative conditions2, and induction of ferroptosis by inhibition of GPX4 has emerged as a therapeutic strategy to trigger cancer cell death5. However, sensitivity to GPX4 inhibitors varies greatly across cancer cell lines6, suggesting that additional factors govern resistance to ferroptosis. Here, using a synthetic lethal CRISPR-Cas9 screen, we identify ferroptosis suppressor protein 1 (FSP1) (previously known as apoptosis-inducing factor mitochondrial 2 (AIFM2)) as a potent ferroptosis resistance factor. Our data indicate that myristoylation recruits FSP1 to the plasma membrane where it functions as an oxidoreductase that reduces coenzyme Q10 (CoQ), generating a lipophilic radical-trapping antioxidant (RTA) that halts the propagation of lipid peroxides. We further find that FSP1 expression positively correlates with ferroptosis resistance across hundreds of cancer cell lines, and that FSP1 mediates resistance to ferroptosis in lung cancer cells in culture and in mouse tumor xenografts. Thus, our data identify FSP1 as a key component of a non-mitochondrial CoQ antioxidant system that acts in parallel to the canonical glutathione-based GPX4 pathway. These findings define a new ferroptosis suppression pathway and indicate that pharmacological inhibition of FSP1 may provide an effective strategy to sensitize cancer cells to ferroptosis-inducing chemotherapeutics.

DOI: https://doi.org/10.1038/s41586-019-1705-2
Annu Rev Cancer Biol. 2019 Mar;3 203-222

MiT/TFE Family of Transcription Factors, Lysosomes, and Cancer.

Rushika M Perera, Chiara Di Malta, Andrea Ballabio.

  Cancer cells have an increased demand for energy sources to support accelerated rates of growth. When nutrients become limiting, cancer cells may switch to nonconventional energy sources that are mobilized through nutrient scavenging pathways involving autophagy and the lysosome. Thus, several cancers are highly reliant on constitutive activation of these pathways to degrade and recycle cellular materials. Here, we focus on the MiT/TFE family of transcription factors, which control transcriptional programs for autophagy and lysosome biogenesis and have emerged as regulators of energy metabolism in cancer. These new findings complement earlier reports that chromosomal translocations and amplifications involving the MiT/TFE genes contribute to the etiology and pathophysiology of renal cell carcinoma, melanoma, and sarcoma, suggesting pleiotropic roles for these factors in a wider array of cancers. Understanding the interplay between the oncogenic and stress-adaptive roles of MiT/TFE factors could shed light on fundamental mechanisms of cellular homeostasis and point to new strategies for cancer treatment.

Keywords:  MITF; TFE3; TFEB; autophagy; lysosome; mTORCl

DOI:  https://doi.org/10.1146/annurev-cancerbio-030518-055835
Mol Genet Metab. 2019 Oct 17. pii: S1096-7192(19)30462-7. [Epub ahead of print]

Tricarboxylic acid cycle enzyme activities in a mouse model of methylmalonic aciduria.

Parith Wongkittichote, Gary Cunningham, Marshall L Summar, Elena Pumbo, Patrick Forny, Matthias R Baumgartner, Kimberly A Chapman.

  Methylmalonic acidemia (MMA) is a propionate pathway disorder caused by dysfunction of the mitochondrial enzyme methylmalonyl-CoA mutase (MMUT). MMUT catalyzes the conversion of methylmalonyl-CoA to succinyl-CoA, an anaplerotic reaction which feeds into the tricarboxylic acid (TCA) cycle. As part of the pathological mechanisms of MMA, previous studies have suggested there is decreased TCA activity due to a "toxic inhibition" of TCA cycle enzymes by MMA related metabolites, in addition to reduced anaplerosis. Here, we have utilized mitochondria isolated from livers of a mouse model of MMA (Mut-ko/ki) and their littermate controls (Ki/wt) to examine the amounts and enzyme functions of most of the TCA cycle enzymes. We have performed mRNA quantification, protein semi-quantitation, and enzyme activity quantification for TCA cycle enzymes in these samples. Expression profiling showed increased mRNA levels of fumarate hydratase in the Mut-ko/ki samples, which by contrast had reduced protein levels as detected by immunoblot, while all other mRNA levels were unaltered. Immunoblotting also revealed decreased protein levels of 2-oxoglutarate dehydrogenase and malate dehydrogenase 2. Interesting, the decreased protein amount of 2-oxoglutarate dehydrogenase was reflected in decreased activity for this enzyme while there is a trend towards decreased activity of fumarate hydratase and malate dehydrogenase 2. Citrate synthase, isocitrate dehydrogenase 2/3, succinyl-CoA synthase, and succinate dehydrogenase are not statistically different in terms of quantity of enzyme or activity. Finally, we found decreased activity when examining the function of methylmalonyl-CoA mutase in series with succinate synthase and succinate dehydrogenase in the Mut-ko/ki mice compared to their littermate controls, as expected. This study demonstrates decreased activity of certain TCA cycle enzymes and by corollary decreased TCA cycle function, but it supports decreased protein quantity rather than "toxic inhibition" as the underlying mechanism of action. SUMMARY: Methylmalonic acidemia (MMA) is an inborn metabolic disorder of propionate catabolism. In this disorder, toxic metabolites are considered to be the major pathogenic mechanism for acute and long-term complications. However, despite optimized therapies aimed at reducing metabolite levels, patients continue to suffer from late complications, including metabolic stroke and renal insufficiency. Since the propionate pathway feeds into the tricarboxylic acid (TCA) cycle, we investigated TCA cycle function in a constitutive MMA mouse model. We demonstrated decreased amounts of the TCA enzymes, Mdh2 and Ogdh as semi-quantified by immunoblot. Enzymatic activity of Ogdh is also decreased in the MMA mouse model compared to controls. Thus, when the enzyme amounts are decreased, we see the enzymatic activity also decreased to a similar extent for Ogdh. Further studies to elucidate the structural and/or functional links between the TCA cycle and propionate pathways might lead to new treatment approaches for MMA patients.

Keywords:  Anaplerosis; Citric acid cycle; Energy metabolism; Methylmalonic aciduria; Mitochondria; TCA cycle; Tricarboxylic acid cycle

DOI:  https://doi.org/10.1016/j.ymgme.2019.10.007
Cell Calcium. 2019 Oct 15. pii: S0143-4160(19)30167-8. [Epub ahead of print]84 102100

Fantastic beasts and how to find them-Molecular identification of the mitochondrial ATP-sensitive potassium channel.

Sean M Davidson, Gyorgy Szabadkai, Michael R Duchen.

  Despite reported sightings over many years, certain mitochondrial-specific channels have proven to be elusive beasts, evading molecular identification. However, combining modern genetics with a wave of their ion-sensing wand, researchers have managed to capture first the mitochondrial calcium uniporter, and now that semi-mythological beast, the mitochondrial ATP-sensitive potassium (mitoKATP) channel.

Keywords:  Ischaemia and reperfusion; Katp channel; Mitochondria

DOI:  https://doi.org/10.1016/j.ceca.2019.102100
EMBO Mol Med. 2019 Oct 21. e10849

The mitochondrial deoxyguanosine kinase is required for cancer cell stemness in lung adenocarcinoma.

Shengchen Lin, Chongbiao Huang, Jianwei Sun, Oana Bollt, Xiuchao Wang, Eric Martine, Jiaxin Kang, Matthew D Taylor, Bin Fang, Pankaj K Singh, John Koomen, Jihui Hao, Shengyu Yang.

  The mitochondrial deoxynucleotide triphosphate (dNTP) is maintained by the mitochondrial deoxynucleoside salvage pathway and dedicated for the mtDNA homeostasis, and the mitochondrial deoxyguanosine kinase (DGUOK) is a rate-limiting enzyme in this pathway. Here, we investigated the role of the DGUOK in the self-renewal of lung cancer stem-like cells (CSC). Our data support that DGUOK overexpression strongly correlates with cancer progression and patient survival. The depletion of DGUOK robustly inhibited lung adenocarcinoma tumor growth, metastasis, and CSC self-renewal. Mechanistically, DGUOK is required for the biogenesis of respiratory complex I and mitochondrial OXPHOS, which in turn regulates CSC self-renewal through AMPK-YAP1 signaling. The restoration of mitochondrial OXPHOS in DGUOK KO lung cancer cells using NDI1 was able to prevent AMPK-mediated phosphorylation of YAP and to rescue CSC stemness. Genetic targeting of DGUOK using doxycycline-inducible CRISPR/Cas9 was able to markedly induce tumor regression. Our findings reveal a novel role for mitochondrial dNTP metabolism in lung cancer tumor growth and progression, and implicate that the mitochondrial deoxynucleotide salvage pathway could be potentially targeted to prevent CSC-mediated therapy resistance and metastatic recurrence.

Keywords:  DGUOK; cancer stem cell; lung cancer; metastasis; mitochondria

DOI:  https://doi.org/10.15252/emmm.201910849
FASEB J. 2019 Oct 25. fj201900685RR

TMEM70 facilitates biogenesis of mammalian ATP synthase by promoting subunit c incorporation into the rotor structure of the enzyme.

Jana Kovalčíková, Marek Vrbacký, Petr Pecina, Kateřina Tauchmannová, Hana Nůsková, Vilma Kaplanová, Andrea Brázdová, Lukáš Alán, Jan Eliáš, Kristýna Čunátová, Vladimír Kořínek, Radislav Sedlacek, Tomáš Mráček, Josef Houštěk.

  Biogenesis of F1Fo ATP synthase, the key enzyme of mitochondrial energy provision, depends on transmembrane protein 70 (TMEM70), localized in the inner mitochondrial membrane of higher eukaryotes. TMEM70 absence causes severe ATP-synthase deficiency and leads to a neonatal mitochondrial encephalocardiomyopathy in humans. However, the exact biochemical function of TMEM70 remains unknown. Using TMEM70 conditional knockout in mice, we show that absence of TMEM70 impairs the early stage of enzyme biogenesis by preventing incorporation of hydrophobic subunit c into rotor structure of the enzyme. This results in the formation of an incomplete, pathologic enzyme complex consisting of F1 domain and peripheral stalk but lacking Fo proton channel composed of subunits c and a. We demonstrated direct interaction between TMEM70 and subunit c and showed that overexpression of subunit c in TMEM70-/- cells partially rescued TMEM70 defect. Accordingly, TMEM70 knockdown prevented subunit c accumulation otherwise observed in F1-deficient cells. Altogether, we identified TMEM70 as specific ancillary factor for subunit c. The biologic role of TMEM70 is to increase the low efficacy of spontaneous assembly of subunit c oligomer, the key and rate-limiting step of ATP-synthase biogenesis, and thus to reach an adequately high physiologic level of ATP synthase in mammalian tissues.-Kovalčíková, J., Vrbacký, M., Pecina, P., Tauchmannová, K., Nůsková, H., Kaplanová, V., Brázdová, A., Alán, L., Eliáš, J., Čunátová, K., Kořínek, V., Sedlacek, R., Mráček, T., Houštěk, J. TMEM70 facilitates biogenesis of mammalian ATP synthase by promoting subunit c incorporation into the rotor structure of the enzyme.

Keywords:  ATP5G assembly; ancillary factor; mitochondria; mouse knockout

DOI:  https://doi.org/10.1096/fj.201900685RR
Nature. 2019 Oct;574(7779): 575-580

Metabolic regulation of gene expression by histone lactylation.

Di Zhang, Zhanyun Tang, He Huang, Guolin Zhou, Chang Cui, Yejing Weng, Wenchao Liu, Sunjoo Kim, Sangkyu Lee, Mathew Perez-Neut, Jun Ding, Daniel Czyz, Rong Hu, Zhen Ye, Maomao He, Y George Zheng, Howard A Shuman, Lunzhi Dai, Bing Ren, Robert G Roeder, Lev Becker, Yingming Zhao.

The Warburg effect, which originally described increased production of lactate in cancer, is associated with diverse cellular processes such as angiogenesis, hypoxia, polarization of macrophages and activation of T cells. This phenomenon is intimately linked to several diseases including neoplasia, sepsis and autoimmune diseases1,2. Lactate, which is converted from pyruvate in tumour cells, is widely known as an energy source and metabolic by-product. However, its non-metabolic functions in physiology and disease remain unknown. Here we show that lactate-derived lactylation of histone lysine residues serves as an epigenetic modification that directly stimulates gene transcription from chromatin. We identify 28 lactylation sites on core histones in human and mouse cells. Hypoxia and bacterial challenges induce the production of lactate by glycolysis, and this acts as a precursor that stimulates histone lactylation. Using M1 macrophages that have been exposed to bacteria as a model system, we show that histone lactylation has different temporal dynamics from acetylation. In the late phase of M1 macrophage polarization, increased histone lactylation induces homeostatic genes that are involved in wound healing, including Arg1. Collectively, our results suggest that an endogenous 'lactate clock' in bacterially challenged M1 macrophages turns on gene expression to promote homeostasis. Histone lactylation thus represents an opportunity to improve our understanding of the functions of lactate and its role in diverse pathophysiological conditions, including infection and cancer.

DOI: https://doi.org/10.1038/s41586-019-1678-1
JCI Insight. 2019 Oct 22. pii: 132826. [Epub ahead of print]

Mitophagy dependent macrophage reprogramming protects against kidney fibrosis.

Divya Bhatia, Kuei-Pin Chung, Kiichi Nakahira, Edwin Patino, Michelle C Rice, Lisa K Torres, Thangamani Muthukumar, Augustine Mk Choi, Oleh M Akchurin, Mary E Choi.

  Mitophagy, by maintaining mitochondrial quality control, plays a key role in maintaining kidney function and is impaired in pathologic states. Macrophages are well-known for their pathogenic role in kidney fibrosis. Here, we report that PINK1/Parkin-mediated mitophagy in macrophages is compromised in experimental and human kidney fibrosis. We demonstrate downregulation of mitophagy regulators, mitofusin-2 (MFN2) and Parkin, downstream of PINK1 in kidney fibrosis. Loss of either Pink1 or Prkn promoted renal extracellular matrix accumulation and frequency of profibrotic/M2 macrophages. Pink1-/- or Prkn-/- bone-marrow-derived macrophages (BMDMs) showed enhanced expression of rictor. Mitochondria from TGF-β1-treated Pink1-/- BMDMs exhibited increased superoxide levels, and reduced respiration and ATP production. In addition, mitophagy in macrophages involves PINK1-mediated phosphorylation of downstream MFN2 and MFN2-facilitated recruitment of Parkin to damaged mitochondria, and macrophage-specific deletion of Mfn2 aggravates kidney fibrosis. Moreover, mitophagy regulators were downregulated in human CKD kidney and TGF-β1-treated human renal macrophages, whereas Mdivi1 treatment suppressed mitophagy mediators and promoted fibrotic response. Taken together, our study is the first to demonstrate that macrophage mitophagy plays a protective role against kidney fibrosis via regulating PINK1/MFN2/Parkin-mediated pathway.

Keywords:  Fibrosis; Macrophages; Mitochondria; Nephrology

DOI:  https://doi.org/10.1172/jci.insight.132826
Front Physiol. 2019 ;10 1258

Low-Intensity Running and High-Intensity Swimming Exercises Differentially Improve Energy Metabolism in Mice With Mild Spinal Muscular Atrophy.

Léo Houdebine, Domenico D'Amico, Jean Bastin, Farah Chali, Céline Desseille, Valentin Rumeau, Judy Soukkari, Carole Oudot, Thaïs Rouquet, Bruno Bariohay, Julien Roux, Delphine Sapaly, Laure Weill, Philippe Lopes, Fatima Djouadi, Cynthia Bezier, Frédéric Charbonnier, Olivier Biondi.

  Spinal Muscular Atrophy (SMA), an autosomal recessive neurodegenerative disease characterized by the loss of spinal-cord motor-neurons, is caused by mutations on Survival-of-Motor Neuron (SMN)-1 gene. The expression of SMN2, a SMN1 gene copy, partially compensates for SMN1 disruption due to exon-7 excision in 90% of transcripts subsequently explaining the strong clinical heterogeneity. Several alterations in energy metabolism, like glucose intolerance and hyperlipidemia, have been reported in SMA at both systemic and cellular level, prompting questions about the potential role of energy homeostasis and/or production involvement in disease progression. In this context, we have recently reported the tolerance of mild SMA-like mice (SmnΔ7/Δ7; huSMN2 +/+) to 10 months of low-intensity running or high-intensity swimming exercise programs, respectively involving aerobic and a mix aerobic/anaerobic muscular metabolic pathways. Here, we investigated whether those exercise-induced benefits were associated with an improvement in metabolic status in mild SMA-like mice. We showed that untrained SMA-like mice exhibited a dysregulation of lipid metabolism with an enhancement of lipogenesis and adipocyte deposits when compared to control mice. Moreover, they displayed a high oxygen consumption and energy expenditure through β-oxidation increase yet for the same levels of spontaneous activity. Interestingly, both exercises significantly improved lipid metabolism and glucose homeostasis in SMA-like mice, and enhanced oxygen consumption efficiency with the maintenance of a high oxygen consumption for higher levels of spontaneous activity. Surprisingly, more significant effects were obtained with the high-intensity swimming protocol with the maintenance of high lipid oxidation. Finally, when combining electron microscopy, respiratory chain complexes expression and enzymatic activity measurements in muscle mitochondria, we found that (1) a muscle-specific decreased in enzymatic activity of respiratory chain I, II, and IV complexes for equal amount of mitochondria and complexes expression and (2) a significant decline in mitochondrial maximal oxygen consumption, were reduced by both exercise programs. Most of the beneficial effects were obtained with the high-intensity swimming protocol. Taking together, our data support the hypothesis that active physical exercise, including high-intensity protocols, induces metabolic adaptations at both systemic and cellular levels, providing further evidence for its use in association with SMN-overexpressing therapies, in the long-term care of SMA patients.

Keywords:  Spinal Muscular Atrophy; energy metabolism; fat oxidation; muscle mitochondria; oxygen consumption; physical exercise; respiratory chain

DOI:  https://doi.org/10.3389/fphys.2019.01258
Proc Natl Acad Sci U S A. 2019 Oct 25. pii: 201911246. [Epub ahead of print]

A small molecule protects mitochondrial integrity by inhibiting mTOR activity.

Ran Cao, Li Li, Zhengxin Ying, Zichen Cao, Yongfen Ma, Xiaoxu Mao, Jiaojiao Li, Xiangbing Qi, Zhiyuan Zhang, Xiaodong Wang.

  Apoptosis activation by cytochrome c release from mitochondria to cytosol is a normal cellular response to mitochondrial damage. Using cellular apoptosis assay, we have found small-molecule apoptosis inhibitors that protect cells from mitochondrial damage. Previously, we reported the discovery of a small molecule, Compound A, which blocks dopaminergic neuron death in a rat model of Parkinson's disease through targeting succinate dehydrogenase subunit B (SDHB) of complex II to protect the integrity of the mitochondrial respiratory chain. Here, we report a small molecule, Compound R6, which saves cells from apoptosis via mammalian target of rapamycin (mTOR)-mediated induction of autophagy. Additionally, we show that Compound R6 protects mitochondrial integrity and respiration after induction of the intrinsic apoptosis pathway. Encouragingly, and supporting the potential further application of Compound R6 as a tool for basic and medicinal research, a pharmacokinetics (PK) profiling study showed that Compound R6 is metabolically stable and can pass the blood-brain barrier. Moreover, Compound R6 accumulates in the brain of test animals via intravenous and intraperitoneal administration. Finally, we found that Compound R6 confers significant neuroprotective effects on a rat cerebral ischemia/reperfusion model, demonstrating its potential as a promising drug candidate for neurodegenerative diseases.

Keywords:  apoptosis; autophagy; mTOR; mitochondria; stroke

DOI:  https://doi.org/10.1073/pnas.1911246116
Nat Immunol. 2019 Oct 21.

Mitochondrial fragmentation limits NK cell-based tumor immunosurveillance.

Xiaohu Zheng, Yeben Qian, Binqing Fu, Defeng Jiao, Yong Jiang, Peng Chen, Yiqing Shen, Huafeng Zhang, Rui Sun, Zhigang Tian, Haiming Wei.

Natural killer (NK) cells have crucial roles in tumor surveillance. We found that tumor-infiltrating NK cells in human liver cancers had small, fragmented mitochondria in their cytoplasm, whereas liver NK cells outside tumors, as well as peripheral NK cells, had normal large, tubular mitochondria. This fragmentation was correlated with reduced cytotoxicity and NK cell loss, resulting in tumor evasion of NK cell-mediated surveillance, which predicted poor survival in patients with liver cancer. The hypoxic tumor microenvironment drove the sustained activation of mechanistic target of rapamycin-GTPase dynamin-related protein 1 (mTOR-Drp1) in NK cells, resulting in excessive mitochondrial fission into fragments. Inhibition of mitochondrial fragmentation improved mitochondrial metabolism, survival and the antitumor capacity of NK cells. These data reveal a mechanism of immune escape that might be targetable and could invigorate NK cell-based cancer treatments.

DOI: https://doi.org/10.1038/s41590-019-0511-1
Mol Cell. 2019 Oct 04. pii: S1097-2765(19)30724-5. [Epub ahead of print]

KDM3A Senses Oxygen Availability to Regulate PGC-1α-Mediated Mitochondrial Biogenesis.

Xu Qian, Xinjian Li, Zhumei Shi, Xiaoming Bai, Yan Xia, Yanhua Zheng, Daqian Xu, Feng Chen, Yongping You, Jing Fang, Zhibin Hu, Qin Zhou, Zhimin Lu.

  Hypoxia, which occurs during tumor growth, triggers complex adaptive responses in which peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α) plays a critical role in mitochondrial biogenesis and oxidative metabolism. However, how PGC-1α is regulated in response to oxygen availability remains unclear. We demonstrated that lysine demethylase 3A (KDM3A) binds to PGC-1α and demethylates monomethylated lysine (K) 224 of PGC-1α under normoxic conditions. Hypoxic stimulation inhibits KDM3A, which has a high KM of oxygen for its activity, and enhances PGC-1α K224 monomethylation. This modification decreases PGC-1α's activity required for NRF1- and NRF2-dependent transcriptional regulation of TFAM, TFB1M, and TFB2M, resulting in reduced mitochondrial biogenesis. Expression of PGC-1α K224R mutant significantly increases mitochondrial biogenesis, reactive oxygen species (ROS) production, and tumor cell apoptosis under hypoxia and inhibits brain tumor growth in mice. This study revealed that PGC-1α monomethylation, which is dependent on oxygen availability-regulated KDM3A, plays a critical role in the regulation of mitochondrial biogenesis.

Keywords:  KDM3A; PGC-1α; hypoxia; mitochondrial biogenesis; monomethylation; oxygen sensing; tumorigenesis

DOI:  https://doi.org/10.1016/j.molcel.2019.09.019
Clin Cancer Res. 2019 Oct 21. pii: clincanres.1729.2019. [Epub ahead of print]

Fumarate metabolic signature for the detection of Reed Syndrome in humans.

Ruth T Casey, Mary A McLean, Benjamin G Challis, Terri P McVeigh, Anne Y Warren, Lee Mendil, Richard Houghton, Stefano De Sanctis, Vasilis Kosmoliaptsis, Richard N Sandford, Ferdia A Gallagher, Eamonn R Maher.

PURPOSE: Inherited pathogenic variants in genes encoding the metabolic enzymes succinate dehydrogenase (SDH) and fumarate hydratase (FH) predispose to tumour development through accumulation of oncometabolites (succinate and fumarate respectively) (1). Non-invasive in vivo detection of tumour succinate by proton magnetic resonance spectroscopy (1H-MRS) has been reported in SDH-deficient tumours but the potential utility of this approach in the management of patients with hereditary leiomyomatosis and renal cell cancer syndrome or Reed syndrome is unknown.
EXPERIMENTAL DESIGN: Magnetic resonance spectroscopy (1H-MRS) was performed on three cases and correlated with germline genetic results and tumour immunohistochemistry when available.
RESULTS: Here, we have demonstrated a proof-of-principle that 1H-MRS can provide a non-invasive diagnosis of hereditary leiomyomatosis and renal cell cancer syndrome or Reed syndrome through detection of fumarate accumulation in vivo. Conclusion: This study demonstrates that in vivo detection of fumarate could be employed as a functional biomarker.

DOI: https://doi.org/10.1158/1078-0432.CCR-19-1729
J Cell Physiol. 2019 Oct 25.

PTEN inhibition attenuates endothelial cell apoptosis in coronary heart disease via modulating the AMPK-CREB-Mfn2-mitophagy signaling pathway.

Pei Li, Jing Wang, Xia Zhao, Jing Ru, Tian Tian, Yun An, Liying Tang, Yuzhi Bai.

  Atherosclerosis (AS) is a major pathogenic factor in patients with cardiovascular diseases, and endothelial dysfunction (ED) plays a primary role in the occurrence and development of AS. In our study, we attempted to evaluate the role of phosphatase and tensin homolog (PTEN) in endothelial cell apoptosis under oxidized low-density lipoprotein (ox-LDL) stimulation and identify the associated mechanisms. The results of our study demonstrated that ox-LDL induced human umbilical vein endothelial cell (HUVEC) death via mitochondrial apoptosis, as evidenced by reduced mitochondrial potential, increased mitochondria permeability transition pore opening, cellular calcium overload, and caspase-9/-3 activation. In addition, ox-LDL also suppressed cellular energy production via downregulating the mitochondrial respiratory complex. Moreover, ox-LDL impaired HUVECs migration. Western blot analysis showed that PTEN expression was upregulated after exposure to ox-LDL and knockdown of PTEN could attenuate ox-LDL-mediated endothelial cell damage. Furthermore, we found that ox-LDL impaired mitophagy activity, whereas PTEN deletion could improve mitophagic flux and this effect relied on the activity of the AMP-activated protein kinase (AMPK)-cAMP-response element-binding protein (CREB)-Mitofusin-2 (Mfn2) axis. When the AMPK-CREB-Mfn2 pathway was inhibited, PTEN deletion-associated HUVECs protection was significantly reduced, suggesting that the AMPK-CREB-Mfn2-mitophagy axis is required for PTEN deletion-mediated endothelial cell survival under ox-LDL. Taken together, our results indicate that ox-LDL-induced endothelial cell damage is associated with PTEN overexpression, and inhibition of PTEN could promote endothelial survival via activating the AMPK-CREB-Mfn2-mitophagy signaling pathway.

Keywords:  AMPK-CREB-Mfn2 signaling pathway; Mfn2; PTEN; endothelial cell dysfunction; mitophagy; ox-LDL

DOI:  https://doi.org/10.1002/jcp.29366
Nat Commun. 2019 Oct 25. 10(1): 4877

Dietary tryptophan links encephalogenicity of autoreactive T cells with gut microbial ecology.

Jana K Sonner, Melanie Keil, Maren Falk-Paulsen, Neha Mishra, Ateequr Rehman, Magdalena Kramer, Katrin Deumelandt, Julian Röwe, Khwab Sanghvi, Lara Wolf, Anna von Landenberg, Hendrik Wolff, Richa Bharti, Iris Oezen, Tobias V Lanz, Florian Wanke, Yilang Tang, Ines Brandao, Soumya R Mohapatra, Lisa Epping, Alexandra Grill, Ralph Röth, Beate Niesler, Sven G Meuth, Christiane A Opitz, Jürgen G Okun, Christoph Reinhardt, Florian C Kurschus, Wolfgang Wick, Helge B Bode, Philip Rosenstiel, Michael Platten.

The interaction between the mammalian host and its resident gut microbiota is known to license adaptive immune responses. Nutritional constituents strongly influence composition and functional properties of the intestinal microbial communities. Here, we report that omission of a single essential amino acid - tryptophan - from the diet abrogates CNS autoimmunity in a mouse model of multiple sclerosis. Dietary tryptophan restriction results in impaired encephalitogenic T cell responses and is accompanied by a mild intestinal inflammatory response and a profound phenotypic shift of gut microbiota. Protective effects of dietary tryptophan restriction are abrogated in germ-free mice, but are independent of canonical host sensors of intracellular tryptophan metabolites. We conclude that dietary tryptophan restriction alters metabolic properties of gut microbiota, which in turn have an impact on encephalitogenic T cell responses. This link between gut microbiota, dietary tryptophan and adaptive immunity may help to develop therapeutic strategies for protection from autoimmune neuroinflammation.

DOI: https://doi.org/10.1038/s41467-019-12776-4
Nature. 2019 Oct 21.

FSP1 is a glutathione-independent ferroptosis suppressor.

Sebastian Doll, Florencio Porto Freitas, Ron Shah, Maceler Aldrovandi, Milene Costa da Silva, Irina Ingold, Andrea Goya Grocin, Thamara Nishida Xavier da Silva, Elena Panzilius, Christina Scheel, André Mourão, Katalin Buday, Mami Sato, Jonas Wanninger, Thibaut Vignane, Vaishnavi Mohana, Markus Rehberg, Andrew Flatley, Aloys Schepers, Andreas Kurz, Daniel White, Markus Sauer, Michael Sattler, Edward William Tate, Werner Schmitz, Almut Schulze, Valerie O'Donnel, Bettina Proneth, Grzegorz M Popowicz, Derek Pratt, José Pedro Friedmann Angeli, Marcus Conrad.

Ferroptosis is an iron-dependent form of necrotic cell death marked by oxidative damage to phospholipids1,2. To date, ferroptosis has been believed to be restrained only by the phospholipid hydroperoxide (PLOOH)-reducing enzyme glutathione peroxidase 4 (GPX4)3,4 and radical-trapping antioxidants (RTAs)5,6. The factors which underlie a given cell type's sensitivity to ferroptosis7 are, however, critical to understand the pathophysiological role of ferroptosis and how it may be exploited for cancer treatment. Although metabolic constraints8 and phospholipid composition9,10 contribute to ferroptosis sensitivity, no cell-autonomous mechanisms have been yet been identified that account for ferroptosis resistance. We undertook an expression cloning approach to identify genes able to complement GPX4 loss. These efforts uncovered the flavoprotein "apoptosis inducing factor mitochondria-associated 2 (AIFM2)" as a previously unrecognized anti-ferroptotic gene. AIFM2, hereafter renamed "ferroptosis-suppressor-protein 1" (FSP1), initially described as a pro-apoptotic gene11, confers an unprecedented protection against ferroptosis elicited by GPX4 deletion. We further demonstrate that ferroptosis suppression by FSP1 is mediated via ubiquinone (CoQ10): its reduced form ubiquinol traps lipid peroxyl radicals that mediate lipid peroxidation, while FSP1 catalyses its regeneration by using NAD(P)H. Pharmacological targeting of FSP1 strongly synergizes with GPX4 inhibitors to trigger ferroptosis in a number of cancer entities. In conclusion, FSP1/CoQ10/NAD(P)H exists as a stand-alone parallel system, which co-operates with GPX4 and glutathione (GSH) to suppress phospholipid peroxidation (pLPO) and ferroptosis.

DOI: https://doi.org/10.1038/s41586-019-1707-0
Cells. 2019 Oct 21. pii: E1289. [Epub ahead of print]8(10):

The Charcot-Marie Tooth Disease Mutation R94Q in MFN2 Decreases ATP Production but Increases Mitochondrial Respiration under Conditions of Mild Oxidative Stress.

Christina Wolf, Rahel Zimmermann, Osamah Thaher, Diones Bueno, Verena Wüllner, Michael K E Schäfer, Philipp Albrecht, Axel Methner.

  Charcot-Marie tooth disease is a hereditary polyneuropathy caused by mutations in Mitofusin-2 (MFN2), a GTPase in the outer mitochondrial membrane involved in the regulation of mitochondrial fusion and bioenergetics. Autosomal-dominant inheritance of a R94Q mutation in MFN2 causes the axonal subtype 2A2A which is characterized by early onset and progressive atrophy of distal muscles caused by motoneuronal degeneration. Here, we studied mitochondrial shape, respiration, cytosolic, and mitochondrial ATP content as well as mitochondrial quality control in MFN2-deficient fibroblasts stably expressing wildtype or R94Q MFN2. Under normal culture conditions, R94Q cells had slightly more fragmented mitochondria but a similar mitochondrial oxygen consumption, membrane potential, and ATP production as wildtype cells. However, when inducing mild oxidative stress 24 h before analysis using 100 µM hydrogen peroxide, R94Q cells exhibited significantly increased respiration but decreased mitochondrial ATP production. This was accompanied by increased glucose uptake and an up-regulation of hexokinase 1 and pyruvate kinase M2, suggesting increased pyruvate shuttling into mitochondria. Interestingly, these changes coincided with decreased levels of PINK1/Parkin-mediated mitophagy in R94Q cells. We conclude that mitochondria harboring the disease-causing R94Q mutation in MFN2 are more susceptible to oxidative stress, which causes uncoupling of respiration and ATP production possibly by a less efficient mitochondrial quality control.

Keywords:  MFN2; fusion/fission; mitochondria; oxidative stress

DOI:  https://doi.org/10.3390/cells8101289
Mol Cell. 2019 Oct 14. pii: S1097-2765(19)30731-2. [Epub ahead of print]

An Early mtUPR: Redistribution of the Nuclear Transcription Factor Rox1 to Mitochondria Protects against Intramitochondrial Proteotoxic Aggregates.

Daniel Poveda-Huertes, Stanka Matic, Adinarayana Marada, Lukas Habernig, Mariya Licheva, Lisa Myketin, Ralf Gilsbach, Sergi Tosal-Castano, Daniel Papinski, Patrycja Mulica, Oliver Kretz, Cansu Kücükköse, Asli Aras Taskin, Lutz Hein, Claudine Kraft, Sabrina Büttner, Chris Meisinger, F-Nora Vögtle.

  The mitochondrial proteome is built mainly by import of nuclear-encoded precursors, which are targeted mostly by cleavable presequences. Presequence processing upon import is essential for proteostasis and survival, but the consequences of dysfunctional protein maturation are unknown. We find that impaired presequence processing causes accumulation of precursors inside mitochondria that form aggregates, which escape degradation and unexpectedly do not cause cell death. Instead, cells survive via activation of a mitochondrial unfolded protein response (mtUPR)-like pathway that is triggered very early after precursor accumulation. In contrast to classical stress pathways, this immediate response maintains mitochondrial protein import, membrane potential, and translation through translocation of the nuclear HMG-box transcription factor Rox1 to mitochondria. Rox1 binds mtDNA and performs a TFAM-like function pivotal for transcription and translation. Induction of early mtUPR provides a reversible stress model to mechanistically dissect the initial steps in mtUPR pathways with the stressTFAM Rox1 as the first line of defense.

Keywords:  mitochondria-nuclear communication; mitochondrial protein import; presequence processing; proteostasis; proteotoxic; stress response; unfolded protein response

DOI:  https://doi.org/10.1016/j.molcel.2019.09.026
J Cell Biol. 2019 Oct 23. pii: jcb.201904148. [Epub ahead of print]

Mitochondrial stress causes neuronal dysfunction via an ATF4-dependent increase in L-2-hydroxyglutarate.

Rachel J Hunt, Lucy Granat, Gregory S McElroy, Ramya Ranganathan, Navdeep S Chandel, Joseph M Bateman.

Mitochondrial stress contributes to a range of neurological diseases. Mitonuclear signaling pathways triggered by mitochondrial stress remodel cellular physiology and metabolism. How these signaling mechanisms contribute to neuronal dysfunction and disease is poorly understood. We find that mitochondrial stress in neurons activates the transcription factor ATF4 as part of the endoplasmic reticulum unfolded protein response (UPR) in Drosophila We show that ATF4 activation reprograms nuclear gene expression and contributes to neuronal dysfunction. Mitochondrial stress causes an ATF4-dependent increase in the level of the metabolite L-2-hydroxyglutarate (L-2-HG) in the Drosophila brain. Reducing L-2-HG levels directly, by overexpressing L-2-HG dehydrogenase, improves neurological function. Modulation of L-2-HG levels by mitochondrial stress signaling therefore regulates neuronal function.

DOI: https://doi.org/10.1083/jcb.201904148
J Mol Biol. 2019 Oct 16. pii: S0022-2836(19)30566-2. [Epub ahead of print]

Protein lysine acetylation: grease or sand in the gears of β-cell mitochondria?

Jaime Santo-Domingo, Loïc Dayon, Andreas Wiederkehr.

  Mitochondria carry out many essential functions in metabolism. A central task is the oxidation of nutrients and the generation of ATP by oxidative phosphorylation. Mitochondrial metabolism needs to be tightly regulated for the cell to respond to changes in ATP demand and nutrient supply. Here we review how protein lysine acetylation contributes to the regulation of mitochondrial metabolism in insulin target tissues and the insulin secreting pancreatic β-cell. We summarize recent evidence showing that in pancreatic β-cells lysine acetylation occurs on a large number of proteins involved in metabolism. Furthermore, we give a brief overview of the molecular mechanism that control lysine acetylation dynamics. We propose that protein lysine acetylation is an important mechanism for the fine-tuning of mitochondrial activity in β-cells during normal physiology. In contrast, nutrient oversupply, oxidative stress or inhibition of the mitochondrial deacetylase SIRT3 leads to protein lysine hyperacetylation, which impairs mitochondrial function. By perturbing mitochondrial activity in β-cells and insulin target tissues, protein lysine hyperacetylation may contribute to the development of T2D.

Keywords:  NADH; SIRT3; beta-cells; energy metabolism; metabolism-secretion coupling; mitochondria

DOI:  https://doi.org/10.1016/j.jmb.2019.09.011
Adv Exp Med Biol. 2020 ;1131 719-746

ER-Mitochondria Calcium Transfer, Organelle Contacts and Neurodegenerative Diseases.

Francesca Vallese, Lucia Barazzuol, Lorenzo Maso, Marisa Brini, Tito Calì.

  It is generally accepted that interorganellar contacts are central to the control of cellular physiology. Virtually, any intracellular organelle can come into proximity with each other and, by establishing physical protein-mediated contacts within a selected fraction of the membrane surface, novel specific functions are acquired. Endoplasmic reticulum (ER) contacts with mitochondria are among the best studied and have a major role in Ca2+ and lipid transfer, signaling, and membrane dynamics.Their functional (and structural) diversity, their dynamic nature as well as the growing number of new players involved in the tethering concurred to make their monitoring difficult especially in living cells. This review focuses on the most established examples of tethers/modulators of the ER-mitochondria interface and on the roles of these contacts in health and disease by specifically dissecting how Ca2+ transfer occurs and how mishandling eventually leads to disease. Additional functions of the ER-mitochondria interface and an overview of the currently available methods to measure/quantify the ER-mitochondria interface will also be discussed.

Keywords:  Bioenergetics; Calcium; ER-mitochondria contact sites; Endoplasmic reticulum; MAM; Mitochondria; Neurodegenerative diseases; Organelle communication; Protein tethers; Signalling

DOI:  https://doi.org/10.1007/978-3-030-12457-1_29
Mol Genet Metab. 2019 Sep 14. pii: S1096-7192(19)30530-X. [Epub ahead of print]

Resolving complexity in mitochondrial disease: Towards precision medicine.

Róisín M Boggan, Albert Lim, Robert W Taylor, Robert McFarland, Sarah J Pickett.

  Mitochondrial diseases, caused by mutations in either the nuclear or mitochondrial genomes (mtDNA), are the most common form of inherited neurometabolic disorders. They are remarkably heterogeneous, both in their clinical presentation and genetic etiology, presenting challenges for diagnosis, clinical management and elucidation of molecular mechanism. The multifaceted nature of these diseases, compounded by the unique characteristics of mitochondrial genetics, cement their space in the field of complex disease. In this review we examine the m.3243A>G variant, one of the most prevalent mitochondrial DNA mutations, using it as an exemplar to demonstrate the challenges presented by these complex disorders. Disease caused by m.3243A>G is one of the most phenotypically diverse of all mitochondrial diseases; we outline known causes of this heterogeneity including mtDNA heteroplasmy, mtDNA copy number and nuclear genetic factors. We consider the impact that this has in the clinic, discussing the personalized management of common manifestations attributed to this pathogenic mtDNA variant, including hearing impairment, diabetes mellitus, myopathy, cardiac disease, stroke-like episodes and gastrointestinal disturbances. Future research into this complex disorder must account for this heterogeneity, benefitting from the use of large patient cohorts to build upon current clinical expertise. Through multi-disciplinary collaboration, the complexities of this mitochondrial disease can be addressed with the variety of diagnostic, prognostic, and treatment approaches that are moulded to best fit the needs of each individual patient.

Keywords:  Complex disease; Heterogeneity; MELAS; Mitochondrial disease; Precision medicine; m.3243A>G

DOI:  https://doi.org/10.1016/j.ymgme.2019.09.003
Nat Commun. 2019 Oct 25. 10(1): 4883

Regulation of the ER stress response by a mitochondrial microprotein.

Qian Chu, Thomas F Martinez, Sammy Weiser Novak, Cynthia J Donaldson, Dan Tan, Joan M Vaughan, Tina Chang, Jolene K Diedrich, Leo Andrade, Andrew Kim, Tong Zhang, Uri Manor, Alan Saghatelian.

Cellular homeostasis relies on having dedicated and coordinated responses to a variety of stresses. The accumulation of unfolded proteins in the endoplasmic reticulum (ER) is a common stress that triggers a conserved pathway called the unfolded protein response (UPR) that mitigates damage, and dysregulation of UPR underlies several debilitating diseases. Here, we discover that a previously uncharacterized 54-amino acid microprotein PIGBOS regulates UPR. PIGBOS localizes to the mitochondrial outer membrane where it interacts with the ER protein CLCC1 at ER-mitochondria contact sites. Functional studies reveal that the loss of PIGBOS leads to heightened UPR and increased cell death. The characterization of PIGBOS reveals an undiscovered role for a mitochondrial protein, in this case a microprotein, in the regulation of UPR originating in the ER. This study demonstrates microproteins to be an unappreciated class of genes that are critical for inter-organelle communication, homeostasis, and cell survival.

DOI: https://doi.org/10.1038/s41467-019-12816-z
Nat Immunol. 2019 Oct 21.

Fibroblastic reticular cells enhance T cell metabolism and survival via epigenetic remodeling.

Flavian D Brown, Debattama R Sen, Martin W LaFleur, Jernej Godec, Veronika Lukacs-Kornek, Frank A Schildberg, Hye-Jung Kim, Kathleen B Yates, Stéphane J H Ricoult, Kevin Bi, Justin D Trombley, Varun N Kapoor, Illana A Stanley, Viviana Cremasco, Nika N Danial, Brendan D Manning, Arlene H Sharpe, W Nicholas Haining, Shannon J Turley.

Lymph node fibroblastic reticular cells (FRCs) respond to signals from activated T cells by releasing nitric oxide, which inhibits T cell proliferation and restricts the size of the expanding T cell pool. Whether interactions with FRCs also support the function or differentiation of activated CD8+ T cells is not known. Here we report that encounters with FRCs enhanced cytokine production and remodeled chromatin accessibility in newly activated CD8+ T cells via interleukin-6. These epigenetic changes facilitated metabolic reprogramming and amplified the activity of pro-survival pathways through differential transcription factor activity. Accordingly, FRC conditioning significantly enhanced the persistence of virus-specific CD8+ T cells in vivo and augmented their differentiation into tissue-resident memory T cells. Our study demonstrates that FRCs play a role beyond restricting T cell expansion-they can also shape the fate and function of CD8+ T cells.

DOI: https://doi.org/10.1038/s41590-019-0515-x
J Biol Chem. 2019 Oct 22. pii: jbc.RA119.010101. [Epub ahead of print]

The cytosolic form of aspartate aminotransferase is required for full activation of TOR complex 1 in fission yeast.

Sophie Reidman, Adiel Cohen, Martin Kupiec, Ronit Weisman.

  The evolutionarily conserved TOR complex 1 (TORC1) activates cell growth and proliferation in response to nutritional signals. In the fission yeast Schizosaccharomyces pombe, TORC1 is essential for vegetative growth, and its activity is regulated in response to nitrogen quantity and quality. Yet, how TORC1 senses nitrogen is poorly understood. Rapamycin, a specific TOR inhibitor, inhibits growth in S. pombe only under conditions in which the activity of TORC1 is compromised. In a genetic screen for rapamycin-sensitive mutations, we isolated caa1-1, a loss-of-function mutation of the cytosolic form of aspartate aminotransferase (Caa1). We demonstrate that loss of caa1 + partially mimics loss of TORC1 activity and that Caa1 is required for full TORC1 activity. Disruption of caa1 + resulted in aspartate auxotrophy, a finding that prompted us to assess the role of aspartate in TORC1 activation. We found that the amino acids glutamine, asparagine, arginine, aspartate, and serine activate TORC1 most efficiently following nitrogen starvation. The glutamine synthetase inhibitor L-methionine sulfoximine (MSX) abolished the ability of asparagine, arginine, aspartate, or serine, but not that of glutamine, to induce TORC1 activity, consistent with a central role for glutamine in activating TORC1. Neither addition of aspartate nor addition of glutamine restored TORC1 activity in caa1-deleted cells or in cells carrying a Caa1 variant with a catalytic-site substitution, suggesting that the catalytic activity of Caa1 is required for TORC1 activation. Taken together, our results reveal the contribution of the key metabolic enzyme Caa1 to TORC1 activity in S. pombe.

Keywords:  Caa1; Psk1; S6 kinase; Schizosaccharomyces pombe; TOR complex (TORC); aspartate amino acid transferase; glutamine synthase; nitrogen sensing; nutrient signaling; serine/threonine protein kinase; target of rapamycin (TOR)

DOI:  https://doi.org/10.1074/jbc.RA119.010101
Annu Rev Physiol. 2019 Oct 22.

Autophagy in Kidney Disease.

Mary E Choi.

Autophagy is a cellular homeostatic program for the turnover of cellular organelles and proteins, in which double-membraned vesicles (autophagosomes) sequester cytoplasmic cargos, which are subsequently delivered to the lysosome for degradation. Emerging evidence implicates autophagy as an important modulator of human disease. Macroautophagy and selective autophagy (e.g., mitophagy, aggrephagy) can influence cellular processes, including cell death, inflammation, and immune responses, and thereby exert both adaptive and maladaptive roles in disease pathogenesis. Autophagy has been implicated in acute kidney injury, which can arise in response to nephrotoxins, sepsis, and ischemia/reperfusion, and in chronic kidney diseases. The latter includes comorbidities of diabetes and recent evidence for chronic obstructive pulmonary disease-associated kidney injury. Roles of autophagy in polycystic kidney disease and kidney cancer have also been described. Targeting the autophagy pathway may have therapeutic benefit in the treatment of kidney disorders. Expected final online publication date for the Annual Review of Physiology, Volume 82 is February 10, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI: https://doi.org/10.1146/annurev-physiol-021119-034658
Nature. 2019 Oct;574(7779): 581-585

Structural basis of species-selective antagonist binding to the succinate receptor.

Matthias Haffke, Dominique Fehlmann, Gabriele Rummel, Jacques Boivineau, Myriam Duckely, Nina Gommermann, Simona Cotesta, Finton Sirockin, Felix Freuler, Amanda Littlewood-Evans, Klemens Kaupmann, Veli-Pekka Jaakola.

The tricarboxylic acid cycle intermediate succinate is involved in metabolic processes and plays a crucial role in the homeostasis of mitochondrial reactive oxygen species1. The receptor responsible for succinate signalling, SUCNR1 (also known as GPR91), is a member of the G-protein-coupled-receptor family2 and links succinate signalling to renin-induced hypertension, retinal angiogenesis and inflammation3-5. Because SUCNR1 senses succinate as an immunological danger signal6-which has relevance for diseases including ulcerative colitis, liver fibrosis7, diabetes and rheumatoid arthritis3,8-it is of interest as a therapeutic target. Here we report the high-resolution crystal structure of rat SUCNR1 in complex with an intracellular binding nanobody in the inactive conformation. Structure-based mutagenesis and radioligand-binding studies, in conjunction with molecular modelling, identified key residues for species-selective antagonist binding and enabled the determination of the high-resolution crystal structure of a humanized rat SUCNR1 in complex with a high-affinity, human-selective antagonist denoted NF-56-EJ40. We anticipate that these structural insights into the architecture of the succinate receptor and its antagonist selectivity will enable structure-based drug discovery and will further help to elucidate the function of SUCNR1 in vitro and in vivo.

DOI: https://doi.org/10.1038/s41586-019-1663-8
EMBO J. 2019 Oct 21. e101982

Senescent human melanocytes drive skin ageing via paracrine telomere dysfunction.

Stella Victorelli, Anthony Lagnado, Jessica Halim, Will Moore, Duncan Talbot, Karen Barrett, James Chapman, Jodie Birch, Mikolaj Ogrodnik, Alexander Meves, Jeff S Pawlikowski, Diana Jurk, Peter D Adams, Diana van Heemst, Marian Beekman, P Eline Slagboom, David A Gunn, João F Passos.

  Cellular senescence has been shown to contribute to skin ageing. However, the role of melanocytes in the process is understudied. Our data show that melanocytes are the only epidermal cell type to express the senescence marker p16INK4A during human skin ageing. Aged melanocytes also display additional markers of senescence such as reduced HMGB1 and dysfunctional telomeres, without detectable telomere shortening. Additionally, senescent melanocyte SASP induces telomere dysfunction in paracrine manner and limits proliferation of surrounding cells via activation of CXCR3-dependent mitochondrial ROS. Finally, senescent melanocytes impair basal keratinocyte proliferation and contribute to epidermal atrophy in vitro using 3D human epidermal equivalents. Crucially, clearance of senescent melanocytes using the senolytic drug ABT737 or treatment with mitochondria-targeted antioxidant MitoQ suppressed this effect. In conclusion, our study provides proof-of-concept evidence that senescent melanocytes affect keratinocyte function and act as drivers of human skin ageing.

Keywords:   SASP ; melanocytes; senescence; skin ageing; telomeres

DOI:  https://doi.org/10.15252/embj.2019101982
Nat Commun. 2019 Oct 25. 10(1): 4887

DNA damage and transcription stress cause ATP-mediated redesign of metabolism and potentiation of anti-oxidant buffering.

Chiara Milanese, Cíntia R Bombardieri, Sara Sepe, Sander Barnhoorn, César Payán-Goméz, Donatella Caruso, Matteo Audano, Silvia Pedretti, Wilbert P Vermeij, Renata M C Brandt, Akos Gyenis, Mirjam M Wamelink, Annelieke S de Wit, Roel C Janssens, René Leen, André B P van Kuilenburg, Nico Mitro, Jan H J Hoeijmakers, Pier G Mastroberardino.

Accumulation of DNA lesions causing transcription stress is associated with natural and accelerated aging and culminates with profound metabolic alterations. Our understanding of the mechanisms governing metabolic redesign upon genomic instability, however, is highly rudimentary. Using Ercc1-defective mice and Xpg knock-out mice, we demonstrate that combined defects in transcription-coupled DNA repair (TCR) and in nucleotide excision repair (NER) directly affect bioenergetics due to declined transcription, leading to increased ATP levels. This in turn inhibits glycolysis allosterically and favors glucose rerouting through the pentose phosphate shunt, eventually enhancing production of NADPH-reducing equivalents. In NER/TCR-defective mutants, augmented NADPH is not counterbalanced by increased production of pro-oxidants and thus pentose phosphate potentiation culminates in an over-reduced redox state. Skin fibroblasts from the TCR disease Cockayne syndrome confirm results in animal models. Overall, these findings unravel a mechanism connecting DNA damage and transcriptional stress to metabolic redesign and protective antioxidant defenses.

DOI: https://doi.org/10.1038/s41467-019-12640-5
Cell Metab. 2019 Oct 15. pii: S1550-4131(19)30515-7. [Epub ahead of print]

Ketosis Ameliorates Renal Cyst Growth in Polycystic Kidney Disease.

Jacob A Torres, Samantha L Kruger, Caroline Broderick, Tselmeg Amarlkhagva, Shagun Agrawal, John R Dodam, Michal Mrug, Leslie A Lyons, Thomas Weimbs.

  Mild reduction in food intake was recently shown to slow polycystic kidney disease (PKD) progression in mouse models, but whether the effect was due to solely reduced calories or some other aspect of the diet has been unclear. We now show that the benefit is due to the induction of ketosis. Time-restricted feeding, without caloric reduction, strongly inhibits mTOR signaling, proliferation, and fibrosis in the affected kidneys in a PKD rat model. A ketogenic diet had a similar effect and led to regression of renal cystic burden. Acute fasting in rat, mouse, and feline models of PKD results in rapid reduction of cyst volume, while oral administration of the ketone β-hydroxybutyrate (BHB) in rats strongly inhibits PKD progression. These results suggest that cystic cells in PKD are metabolically inflexible, which could be exploited by dietary interventions or supplementation with BHB, representing a new therapeutic avenue to treat PKD.

Keywords:  beta-hydroxybutyrate; ketogenic diet; ketosis; metabolic inflexibility; polycystic kidney disease

DOI:  https://doi.org/10.1016/j.cmet.2019.09.012
Metabolites. 2019 Oct 21. pii: E242. [Epub ahead of print]9(10):

Inborn Errors of Metabolism in the Era of Untargeted Metabolomics and Lipidomics.

Israa T Ismail, Megan R Showalter, Oliver Fiehn.

  Inborn errors of metabolism (IEMs) are a group of inherited diseases with variable incidences. IEMs are caused by disrupting enzyme activities in specific metabolic pathways by genetic mutations, either directly or indirectly by cofactor deficiencies, causing altered levels of compounds associated with these pathways. While IEMs may present with multiple overlapping symptoms and metabolites, early and accurate diagnosis of IEMs is critical for the long-term health of affected subjects. The prevalence of IEMs differs between countries, likely because different IEM classifications and IEM screening methods are used. Currently, newborn screening programs exclusively use targeted metabolic assays that focus on limited panels of compounds for selected IEM diseases. Such targeted approaches face the problem of false negative and false positive diagnoses that could be overcome if metabolic screening adopted analyses of a broader range of analytes. Hence, we here review the prospects of using untargeted metabolomics for IEM screening. Untargeted metabolomics and lipidomics do not rely on predefined target lists and can detect as many metabolites as possible in a sample, allowing to screen for many metabolic pathways simultaneously. Examples are given for nontargeted analyses of IEMs, and prospects and limitations of different metabolomics methods are discussed. We conclude that dedicated studies are needed to compare accuracy and robustness of targeted and untargeted methods with respect to widening the scope of IEM diagnostics.

Keywords:  LC-MS; aminoacidemia.; lysosomal storage disease; mass spectrometry; mitochondrial disorders; organic aciduria; phenylketonuria

DOI:  https://doi.org/10.3390/metabo9100242
Sci Signal. 2019 Oct 22. pii: eaaw5573. [Epub ahead of print]12(604):

Induction of metabolic quiescence defines the transitional to follicular B cell switch.

Jocelyn R Farmer, Hugues Allard-Chamard, Na Sun, Maimuna Ahmad, Alice Bertocchi, Vinay S Mahajan, Toby Aicher, Johan Arnold, Mark D Benson, Jordan Morningstar, Sara Barmettler, Grace Yuen, Samuel J H Murphy, Jolan E Walter, Musie Ghebremichael, Alex K Shalek, Facundo Batista, Robert Gerszten, Shiv Pillai.

Transitional B cells must actively undergo selection for self-tolerance before maturing into their resting follicular B cell successors. We found that metabolic quiescence was acquired at the follicular B cell stage in both humans and mice. In follicular B cells, the expression of genes involved in ribosome biogenesis, aerobic respiration, and mammalian target of rapamycin complex 1 (mTORC1) signaling was reduced when compared to that in transitional B cells. Functional metabolism studies, profiling of whole-cell metabolites, and analysis of cell surface proteins in human B cells suggested that this transition was also associated with increased extracellular adenosine salvage. Follicular B cells increased the abundance of the cell surface ectonucleotidase CD73, which coincided with adenosine 5'-monophosphate-activated protein kinase (AMPK) activation. Differentiation to the follicular B cell stage in vitro correlated with surface acquisition of CD73 on human transitional B cells and was augmented with the AMPK agonist, AICAR. Last, individuals with gain-of-function PIK3CD (PI3Kδ) mutations and increased pS6 activation exhibited a near absence of circulating follicular B cells. Together, our data suggest that mTORC1 attenuation may be necessary for human follicular B cell development. These data identify a distinct metabolic switch during human B cell development at the transitional to follicular stages, which is characterized by an induction of extracellular adenosine salvage, AMPK activation, and the acquisition of metabolic quiescence.

DOI: https://doi.org/10.1126/scisignal.aaw5573
Cell Rep. 2019 Oct 22. pii: S2211-1247(19)31206-9. [Epub ahead of print]29(4): 920-931.e7

Impairment of Macroautophagy in Dopamine Neurons Has Opposing Effects on Parkinsonian Pathology and Behavior.

Benjamin H M Hunn, Siv Vingill, Sarah Threlfell, Javier Alegre-Abarrategui, Morgane Magdelyns, Thierry Deltheil, Nora Bengoa-Vergniory, Peter L Oliver, Milena Cioroch, Natalie M Doig, David M Bannerman, Stephanie J Cragg, Richard Wade-Martins.

  Parkinson's disease (PD) is characterized by the death of dopamine neurons in the substantia nigra pars compacta (SNc) and accumulation of α-synuclein. Impaired autophagy has been implicated and activation of autophagy proposed as a treatment strategy. We generate a human α-synuclein-expressing mouse model of PD with macroautophagic failure in dopamine neurons to understand the interaction between impaired macroautophagy and α-synuclein. We find that impaired macroautophagy generates p62-positive inclusions and progressive neuron loss in the SNc. Despite this parkinsonian pathology, motor phenotypes accompanying human α-synuclein overexpression actually improve with impaired macroautophagy. Real-time fast-scan cyclic voltammetry reveals that macroautophagy impairment in dopamine neurons increases evoked extracellular concentrations of dopamine, reduces dopamine uptake, and relieves paired-stimulus depression. Our findings show that impaired macroautophagy paradoxically enhances dopamine neurotransmission, improving movement while worsening pathology, suggesting that changes to dopamine synapse function compensate for and conceal the underlying PD pathogenesis, with implications for therapies that target autophagy.

Keywords:  Parkinson’s disease; autophagy; behavior; dopamine; mouse models; neurotransmission; pathology

DOI:  https://doi.org/10.1016/j.celrep.2019.09.029
Cell Death Dis. 2019 Oct 23. 10(11): 803

Enhanced hexosamine metabolism drives metabolic and signaling networks involving hyaluronan production and O-GlcNAcylation to exacerbate breast cancer.

Chatchadawalai Chokchaitaweesuk, Takashi Kobayashi, Tomomi Izumikawa, Naoki Itano.

The hexosamine biosynthetic pathway (HBP) metabolically regulates dynamic cellular events by linking nutrient availability to numerous signaling networks. Significant alterations in the HBP are often associated with cancer pathogenesis. In this study, we investigated the molecular events underlying cancer pathogenesis associated with enhanced HBP flux. Multidimensional analysis of microarray datasets demonstrated up-regulation of genes encoding HBP enzymes in clinical breast cancers and revealed that co-expression of hyaluronan synthase 2 (HAS2) and glutamine:fructose-6-phosphate amidotransferase (GFAT), a rate-limiting enzyme of the HBP, was strongly correlated with a poor prognosis in advanced cancer patients. Consistently with the clinical data, comparative analyses of distinct breast cancer mouse models demonstrated enhancement of the HBP gene expression in primary carcinoma cells, with elevation of Has2 expression and hyaluronan production in aggressive breast cancer cells. The silencing of GFAT reduced CD44high/CD24low cancer stem cell (CSC)-like subpopulations, aldehyde dehydrogenase-positive cell populations, and mammosphere size, which were further diminished by gene targeting of Has2. Has2 gene disruption reduced the in vivo growth of aggressive cancer cells and attenuated pro-tumorigenic Akt/GSK3β/β-catenin signaling and cisplatin resistance. Overall protein O-GlcNAcylation was also elevated in association with HBP enhancement in aggressive cancer cells, and the modification exhibited overlapping but distinct roles from the hyaluronan signal in the regulation of CSC-like features. The current data therefore demonstrate that enhanced hexosamine metabolism drives pro-tumorigenic signaling pathways involving hyaluronan and O-GlcNAcylation in aggressive breast cancer.

DOI: https://doi.org/10.1038/s41419-019-2034-y
J Biochem. 2019 Oct 24. pii: mvz090. [Epub ahead of print]

Mass spectrometry-based methods for analyzing the mitochondrial interactome in mammalian cells.

Takumi Koshiba, Hidetaka Kosako.

  Protein-protein interactions are essential biologic processes that occur at inter- and intra-cellular levels. To gain insight into the various complex cellular functions of these interactions, it is necessary to assess them under physiologic conditions. Recent advances in various proteomic technologies allow to investigate protein-protein interaction networks in living cells. The combination of proximity-dependent labeling and chemical cross-linking will greatly enhance our understanding of multi-protein complexes that are difficult to prepare, such as organelle-bound membrane proteins. In this review, we describe our current understanding of mass spectrometry-based proteomics mapping methods for elucidating organelle-bound membrane protein complexes in living cells, with a focus on protein-protein interactions in mitochondrial subcellular compartments.

Keywords:  BioID; XL-MS; interactome; mass spectrometry; mitochondria; protein-protein interactions; proteome

DOI:  https://doi.org/10.1093/jb/mvz090
Nature. 2019 Oct;574(7779): 492-493

Histone lactylation links metabolism and gene regulation.

Luke T Izzo, Kathryn E Wellen.



Keywords:  Epigenetics; Metabolism

DOI:  https://doi.org/10.1038/d41586-019-03122-1