bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2019–02–24
fifty papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit
  1. Cancer Metabolism Drives a Stromal Regenerative Response.
  2. NAD+ metabolism governs the proinflammatory senescence-associated secretome.
  3. PINK1 Inhibits Local Protein Synthesis to Limit Transmission of Deleterious Mitochondrial DNA Mutations.
  4. mTORC1-driven accumulation of the oncometabolite fumarate as a potential critical step in renal cancer progression.
  5. Regulation of the Elongation Phase of Protein Synthesis Enhances Translation Accuracy and Modulates Lifespan.
  6. Systems biology identifies preserved integrity but impaired metabolism of mitochondria due to a glycolytic defect in Alzheimer's disease neurons.
  7. The OXPHOS supercomplex assembly factor HIG2A responds to changes in energetic metabolism and cell cycle.
  8. Multi-omics identify xanthine as a pro-survival metabolite for nematodes with mitochondrial dysfunction.
  9. Metabolic rewiring beyond Warburg in chronic lymphocytic leukemia: How much do we actually know?
  10. Inducing cancer indolence by targeting mitochondrial Complex I is potentiated by blocking macrophage-mediated adaptive responses.
  11. Cardiac-specific deletion of GCN5L1 restricts recovery from ischemia-reperfusion injury.
  12. MiR-135 suppresses glycolysis and promotes pancreatic cancer cell adaptation to metabolic stress by targeting phosphofructokinase-1.
  13. Systematic Dissection of the Metabolic-Apoptotic Interface in AML Reveals Heme Biosynthesis to Be a Regulator of Drug Sensitivity.
  14. Regulation of leukocyte function by citric acid cycle intermediates.
  15. Succinylation-dependent mitochondrial translocation of PKM2 promotes cell survival in response to nutritional stress.
  16. Glycogen Synthase Kinase 3 Beta Controls Presenilin-1-Mediated Endoplasmic Reticulum Ca²⁺ Leak Directed to Mitochondria in Pancreatic Islets and β-Cells.
  17. SMDT1-driven change in mitochondrial dynamics mediate cell apoptosis in PDAC.
  18. The HGF-MET axis coordinates liver cancer metabolism and autophagy for chemotherapeutic resistance.
  19. Consequences of a Metabolic Glucose-Depletion on the Survival and the Metabolism of Cultured Rat Astrocytes.
  20. Kindlin-2 links mechano-environment to proline synthesis and tumor growth.
  21. Calcium Signaling Controls Pathogenic Th17 Cell-Mediated Inflammation by Regulating Mitochondrial Function.
  22. Redox Imbalance in Idiopathic Pulmonary Fibrosis: A Role for Oxidant Cross-Talk Between NOX Enzymes and Mitochondria.
  23. Pharmacological inhibition of the IKKε/TBK-1 axis potentiates the anti-tumour and anti-metastatic effects of Docetaxel in mouse models of breast cancer.
  24. Differential Regulation of Human Treg and Th17 Cells by Fatty Acid Synthesis and Glycolysis.
  25. Loss of Hepatic Oscillatory Fed microRNAs Abrogates Refed Transition and Causes Liver Dysfunctions.
  26. Mitochondrial localization, import and mitochondrial function of the androgen receptor.
  27. A comparative map of macroautophagy and mitophagy in the vertebrate eye.
  28. LINC00116 codes for a mitochondrial peptide linking respiration and lipid metabolism.
  29. Evolutionary rate correlation between mitochondrial-encoded and mitochondria-associated nuclear-encoded proteins in insects.
  30. Bacterial cGAS-like enzymes synthesize diverse nucleotide signals.
  31. Mammalian Respiratory Complex I Through the Lens of Cryo-EM.
  32. Mitochondrial Haplogroup and the Risk of Acute Kidney Injury Following Cardiac Bypass Surgery.
  33. Carbon-dot-supported atomically dispersed gold as a mitochondrial oxidative stress amplifier for cancer treatment.
  34. Mitophagy Is Essential for Maintaining Cardiac Function During High Fat Diet-Induced Diabetic Cardiomyopathy.
  35. Loss of ALDH1L1 folate enzyme confers a selective metabolic advantage for tumor progression.
  36. Tumours use a metabolic twist to make lipids.
  37. Mitochondrion-processed TERC regulates senescence without affecting telomerase activities.
  38. Nuclear genetic regulation of the human mitochondrial transcriptome.
  39. Vive ut Numquam Moriturus: Tweaking Translational Control to Regulate Longevity.
  40. Ambra1 inhibits paclitaxel-induced apoptosis in breast cancer cells by modulating the Bim/mitochondrial pathway.
  41. NAD+ metabolism as a target for metabolic health: have we found the silver bullet?
  42. 13C-Fingerprinting and Metabolic Flux Analysis of Bacterial Metabolisms.
  43. Arp2/3-branched actin regulates microtubule acetylation level and affects mitochondrial distribution.
  44. Mitochondrial hypoxic stress induces widespread RNA editing by APOBEC3G in natural killer cells.
  45. Serine Metabolism Supports Macrophage IL-1β Production.
  46. A Platform of Synthetic Lethal Gene Interaction Networks Reveals that the GNAQ Uveal Melanoma Oncogene Controls the Hippo Pathway through FAK.
  47. A Noninvasive Comparison Study between Human Gliomas with IDH1 and IDH2 Mutations by MR Spectroscopy.
  48. The ER chaperones BiP and Grp94 selectively associate when BiP is in the ADP conformation.
  49. Epigenetic signature: implications for mitochondrial quality control in human aging.
  50. Cell-Free Mitochondrial DNA in the CSF: A Potential Prognostic Biomarker of Anti-NMDAR Encephalitis.
  1. Cell Metab. 2019 Feb 11. pii: S1550-4131(19)30015-4. [Epub ahead of print]
    Cancer Metabolism Drives a Stromal Regenerative Response.
    Simon Schwörer, Santosha A Vardhana, Craig B Thompson.
      The metabolic reprogramming associated with malignant transformation has led to a growing appreciation of the nutrients required to support anabolic cell growth. Less well studied is how cancer cells satisfy those demands in vivo, where they are dispersed within a complex microenvironment. Tumor-associated stromal components can support tumor growth by providing nutrients that supplement those provided by the local vasculature. These non-malignant stromal cells are phenotypically similar to those that accumulate during wound healing. Owing to their immediate proximity, stromal cells are inevitably affected by the metabolic activity of their cancerous neighbors. Until recently, a role for tumor cell metabolism in influencing the cell fate decisions of neighboring stromal cells has been underappreciated. Here, we propose that metabolites consumed and released by tumor cells act as paracrine factors that regulate the non-malignant cellular composition of a developing tumor by driving stromal cells toward a regenerative response that supports tumor growth.
    Keywords:  cancer metabolism; cancer-associated fibroblasts; effector T cells; metabolism; regeneration; regulatory T cells; tumor microenvironment; tumor-associated macrophages; wound healing
    DOI:  https://doi.org/10.1016/j.cmet.2019.01.015
  2. Nat Cell Biol. 2019 Feb 18.
    NAD+ metabolism governs the proinflammatory senescence-associated secretome.
    Timothy Nacarelli, Lena Lau, Takeshi Fukumoto, Joseph Zundell, Nail Fatkhutdinov, Shuai Wu, Katherine M Aird, Osamu Iwasaki, Andrew V Kossenkov, David Schultz, Ken-Ichi Noma, Joseph A Baur, Zachary Schug, Hsin-Yao Tang, David W Speicher, Gregory David, Rugang Zhang.
      Cellular senescence is a stable growth arrest that is implicated in tissue ageing and cancer. Senescent cells are characterized by an upregulation of proinflammatory cytokines, which is termed the senescence-associated secretory phenotype (SASP). NAD+ metabolism influences both tissue ageing and cancer. However, the role of NAD+ metabolism in regulating the SASP is poorly understood. Here, we show that nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme of the NAD+ salvage pathway, governs the proinflammatory SASP independent of senescence-associated growth arrest. NAMPT expression is regulated by high mobility group A (HMGA) proteins during senescence. The HMGA-NAMPT-NAD+ signalling axis promotes the proinflammatory SASP by enhancing glycolysis and mitochondrial respiration. HMGA proteins and NAMPT promote the proinflammatory SASP through NAD+-mediated suppression of AMPK kinase, which suppresses the p53-mediated inhibition of p38 MAPK to enhance NF-κB activity. We conclude that NAD+ metabolism governs the proinflammatory SASP. Given the tumour-promoting effects of the proinflammatory SASP, our results suggest that anti-ageing dietary NAD+ augmentation should be administered with precision.
    DOI:  https://doi.org/10.1038/s41556-019-0287-4
  3. Mol Cell. 2019 Feb 01. pii: S1097-2765(19)30013-9. [Epub ahead of print]
    PINK1 Inhibits Local Protein Synthesis to Limit Transmission of Deleterious Mitochondrial DNA Mutations.
    Yi Zhang, Zong-Heng Wang, Yi Liu, Yong Chen, Nuo Sun, Marjan Gucek, Fan Zhang, Hong Xu.
      We have previously proposed that selective inheritance, the limited transmission of damaging mtDNA mutations from mother to offspring, is based on replication competition in Drosophila melanogaster. This model, which stems from our observation that wild-type mitochondria propagate much more vigorously in the fly ovary than mitochondria carrying fitness-impairing mutations, implies that germ cells recognize the fitness of individual mitochondria and selectively boost the propagation of healthy ones. Here, we demonstrate that the protein kinase PINK1 preferentially accumulates on mitochondria enriched for a deleterious mtDNA mutation. PINK1 phosphorylates Larp to inhibit protein synthesis on the mitochondrial outer membrane. Impaired local translation on defective mitochondria in turn limits the replication of their mtDNA and hence the transmission of deleterious mutations to the offspring. Our work confirms that selective inheritance occurs at the organelle level during Drosophila oogenesis and provides molecular entry points to test this model in other systems.
    Keywords:  AKAP1; DNA replication; Larp1; PINK1; local protein synthesis; mitochondria; mitochondrial quality control; mtDNA; oogenesis; selective inheritance
    DOI:  https://doi.org/10.1016/j.molcel.2019.01.013
  4. Mol Cell Oncol. 2019 ;6(1): 1537709
    mTORC1-driven accumulation of the oncometabolite fumarate as a potential critical step in renal cancer progression.
    Luca Drusian, Alessandra Boletta.
      Modeling renal cancer in the mouse has been challenging. We recently showed that upregulation of mechanistic target of rapamycin complex 1 (mTORC1) in a restricted segment of the renal tubule leads to downregulation of the tricarboxylic acid (TCA) cycle enzyme fumarate hydratase, to accumulation of the oncometabolite fumarate, and gradual transformation from benign cysts into cystadenomas and papillary carcinomas.
    Keywords:  Renal carcinoma; fumarate; fumarate hydratase; mTOR; oncometabolite
    DOI:  https://doi.org/10.1080/23723556.2018.1537709
  5. Curr Biol. 2019 Feb 04. pii: S0960-9822(19)30031-4. [Epub ahead of print]
    Regulation of the Elongation Phase of Protein Synthesis Enhances Translation Accuracy and Modulates Lifespan.
    Jianling Xie, Viviane de Souza Alves, Tobias von der Haar, Louise O'Keefe, Roman V Lenchine, Kirk B Jensen, Rui Liu, Mark J Coldwell, Xuemin Wang, Christopher G Proud.
      Maintaining accuracy during protein synthesis is crucial to avoid producing misfolded and/or non-functional proteins. The target of rapamycin complex 1 (TORC1) pathway and the activity of the protein synthesis machinery are known to negatively regulate lifespan in many organisms, although the precise mechanisms involved remain unclear. Mammalian TORC1 signaling accelerates the elongation stage of protein synthesis by inactivating eukaryotic elongation factor 2 kinase (eEF2K), which, when active, phosphorylates and inhibits eEF2, which mediates the movement of ribosomes along mRNAs, thereby slowing down the rate of elongation. We show that eEF2K enhances the accuracy of protein synthesis under a range of conditions and in several cell types. For example, our data reveal it links mammalian (m)TORC1 signaling to the accuracy of translation. Activation of eEF2K decreases misreading or termination readthrough errors during elongation, whereas knocking down or knocking out eEF2K increases their frequency. eEF2K also promotes the correct recognition of start codons in mRNAs. Reduced translational fidelity is known to correlate with shorter lifespan. Consistent with this, deletion of the eEF2K ortholog or other factors implicated in translation fidelity in Caenorhabditis elegans decreases lifespan, and eEF2K is required for lifespan extension induced by nutrient restriction. Our data uncover a novel mechanism linking nutrient supply, mTORC1 signaling, and the elongation stage of protein synthesis, which enhances the accuracy of protein synthesis. Our data also indicate that modulating translation elongation and its fidelity affects lifespan.
    Keywords:  Caenorhabditis elegans; caloric restriction; eEF2; eEF2K; elongation; lifespan; mTOR; tRNA; translation fidelity
    DOI:  https://doi.org/10.1016/j.cub.2019.01.029
  6. Aging Cell. 2019 Feb 21. e12924
    Systems biology identifies preserved integrity but impaired metabolism of mitochondria due to a glycolytic defect in Alzheimer's disease neurons.
    Pierre Theurey, Niamh M C Connolly, Ilaria Fortunati, Emy Basso, Susette Lauwen, Camilla Ferrante, Catarina Moreira Pinho, Alvin Joselin, Anna Gioran, Daniele Bano, David S Park, Maria Ankarcrona, Paola Pizzo, Jochen H M Prehn.
      Mitochondrial dysfunction is implicated in most neurodegenerative diseases, including Alzheimer's disease (AD). We here combined experimental and computational approaches to investigate mitochondrial health and bioenergetic function in neurons from a double transgenic animal model of AD (PS2APP/B6.152H). Experiments in primary cortical neurons demonstrated that AD neurons had reduced mitochondrial respiratory capacity. Interestingly, the computational model predicted that this mitochondrial bioenergetic phenotype could not be explained by any defect in the mitochondrial respiratory chain (RC), but could be closely resembled by a simulated impairment in the mitochondrial NADH flux. Further computational analysis predicted that such an impairment would reduce levels of mitochondrial NADH, both in the resting state and following pharmacological manipulation of the RC. To validate these predictions, we utilized fluorescence lifetime imaging microscopy (FLIM) and autofluorescence imaging and confirmed that transgenic AD neurons had reduced mitochondrial NAD(P)H levels at rest, and impaired power of mitochondrial NAD(P)H production. Of note, FLIM measurements also highlighted reduced cytosolic NAD(P)H in these cells, and extracellular acidification experiments showed an impaired glycolytic flux. The impaired glycolytic flux was identified to be responsible for the observed mitochondrial hypometabolism, since bypassing glycolysis with pyruvate restored mitochondrial health. This study highlights the benefits of a systems biology approach when investigating complex, nonintuitive molecular processes such as mitochondrial bioenergetics, and indicates that primary cortical neurons from a transgenic AD model have reduced glycolytic flux, leading to reduced cytosolic and mitochondrial NAD(P)H and reduced mitochondrial respiratory capacity.
    Keywords:  Alzheimer's disease; glycolysis; mitochondria; neurons; systems biology
    DOI:  https://doi.org/10.1111/acel.12924
  7. J Cell Physiol. 2019 Feb 18.
    The OXPHOS supercomplex assembly factor HIG2A responds to changes in energetic metabolism and cell cycle.
    Celia Salazar, Alvaro A Elorza, Glenda Cofre, Paula Ruiz-Hincapie, Orian Shirihai, Lina María Ruiz.
      HIG2A promotes cell survival under hypoxia and mediates the assembly of complex III and complex IV into respiratory chain supercomplexes. In the present study, we show that human HIGD2A and mouse Higd2a gene expressions are regulated by hypoxia, glucose, and the cell cycle-related transcription factor E2F1. The latter was found to bind the promoter region of HIGD2A. Differential expression of the HIGD2A gene was found in C57BL/6 mice in relation to tissue and age. Besides, the silencing of HIGD2A evidenced the modulation of mitochondrial dynamics proteins namely, OPA1 as a fusion protein increases, while FIS1, a fission protein, decreases. Besides, the mitochondrial membrane potential (ΔΨm) increased. The protein HIG2A is localized in the mitochondria and nucleus. Moreover, we observed that the HIG2A protein interacts with OPA1. Changes in oxygen concentration, glucose availability, and cell cycle regulate HIGD2A expression. Alterations in HIGD2A expression are associated with changes in mitochondrial physiology.
    Keywords:  E2F1; HIG2A; OPA1; OXPHOS supercomplexes; cell cycle; hypoxia; mitochondrial dynamics
    DOI:  https://doi.org/10.1002/jcp.28362
  8. EMBO J. 2019 Feb 22. pii: e99558. [Epub ahead of print]
    Multi-omics identify xanthine as a pro-survival metabolite for nematodes with mitochondrial dysfunction.
    Anna Gioran, Antonia Piazzesi, Fabio Bertan, Jonas Schroer, Lena Wischhof, Pierluigi Nicotera, Daniele Bano.
      Aberrant mitochondrial function contributes to the pathogenesis of various metabolic and chronic disorders. Inhibition of insulin/IGF-1 signaling (IIS) represents a promising avenue for the treatment of mitochondrial diseases, although many of the molecular mechanisms underlying this beneficial effect remain elusive. Using an unbiased multi-omics approach, we report here that IIS inhibition reduces protein synthesis and favors catabolism in mitochondrial deficient Caenorhabditis elegans We unveil that the lifespan extension does not occur through the restoration of mitochondrial respiration, but as a consequence of an ATP-saving metabolic rewiring that is associated with an evolutionarily conserved phosphoproteome landscape. Furthermore, we identify xanthine accumulation as a prominent downstream metabolic output of IIS inhibition. We provide evidence that supplementation of FDA-approved xanthine derivatives is sufficient to promote fitness and survival of nematodes carrying mitochondrial lesions. Together, our data describe previously unknown molecular components of a metabolic network that can extend the lifespan of short-lived mitochondrial mutant animals.
    Keywords:  insulin/IGF‐1 signaling (IIS); metabolism; mitochondrial diseases; xanthine
    DOI:  https://doi.org/10.15252/embj.201899558
  9. Crit Rev Oncol Hematol. 2019 Feb;pii: S1040-8428(18)30376-7. [Epub ahead of print]134 65-70
    Metabolic rewiring beyond Warburg in chronic lymphocytic leukemia: How much do we actually know?
    Gabriela Galicia-Vázquez, Raquel Aloyz.
      Chronic Lymphocytic Leukemia (CLL) is the most common adult leukemia in the western world. CLL consists of the accumulation of malignant B-cells in the blood stream and homing tissues. Although treatable, this disease is not curable, and resistance or relapse is often present. In many cancers, the study of metabolic reprograming has uncovered novel targets that are already being exploited in the clinic. However, CLL metabolism is still poorly understood. The ability of CLL lymphocytes to adapt to diverse microenvironments is accompanied by modifications in cell metabolism, revealing the challenge of targeting the CLL lymphocytes present in all different compartments. Despite this, the study of CLL metabolism led to an ongoing clinical trial using glucose uptake and mitochondrial respiration inhibitors. In contrast, glutamine and fatty acid metabolism remain to be further exploited in CLL. Here, we summarize the present knowledge of CLL metabolism, as well as the metabolic influence of Myc, ATM and p53 on CLL lymphocytes.
    Keywords:  ATM; BTK; Central carbon metabolism rewiring; Primary CLL lymphocytes; TP53; ibrutinib
    DOI:  https://doi.org/10.1016/j.critrevonc.2018.12.003
  10. Nat Commun. 2019 Feb 22. 10(1): 903
    Inducing cancer indolence by targeting mitochondrial Complex I is potentiated by blocking macrophage-mediated adaptive responses.
    Ivana Kurelac, Luisa Iommarini, Renaud Vatrinet, Laura Benedetta Amato, Monica De Luise, Giulia Leone, Giulia Girolimetti, Nikkitha Umesh Ganesh, Victoria Louise Bridgeman, Luigi Ombrato, Marta Columbaro, Moira Ragazzi, Lara Gibellini, Manuela Sollazzo, Rene Gunther Feichtinger, Silvia Vidali, Maurizio Baldassarre, Sarah Foriel, Michele Vidone, Andrea Cossarizza, Daniela Grifoni, Barbara Kofler, Ilaria Malanchi, Anna Maria Porcelli, Giuseppe Gasparre.
      Converting carcinomas in benign oncocytomas has been suggested as a potential anti-cancer strategy. One of the oncocytoma hallmarks is the lack of respiratory complex I (CI). Here we use genetic ablation of this enzyme to induce indolence in two cancer types, and show this is reversed by allowing the stabilization of Hypoxia Inducible Factor-1 alpha (HIF-1α). We further show that on the long run CI-deficient tumors re-adapt to their inability to respond to hypoxia, concordantly with the persistence of human oncocytomas. We demonstrate that CI-deficient tumors survive and carry out angiogenesis, despite their inability to stabilize HIF-1α. Such adaptive response is mediated by tumor associated macrophages, whose blockage improves the effect of CI ablation. Additionally, the simultaneous pharmacological inhibition of CI function through metformin and macrophage infiltration through PLX-3397 impairs tumor growth in vivo in a synergistic manner, setting the basis for an efficient combinatorial adjuvant therapy in clinical trials.
    DOI:  https://doi.org/10.1038/s41467-019-08839-1
  11. J Mol Cell Cardiol. 2019 Feb 15. pii: S0022-2828(19)30039-2. [Epub ahead of print]129 69-78
    Cardiac-specific deletion of GCN5L1 restricts recovery from ischemia-reperfusion injury.
    Janet R Manning, Dharendra Thapa, Manling Zhang, Michael W Stoner, Javier Traba, Charles F McTiernan, Catherine Corey, Sruti Shiva, Michael N Sack, Iain Scott.
      GCN5L1 regulates mitochondrial protein acetylation, cellular bioenergetics, reactive oxygen species (ROS) generation, and organelle positioning in a number of diverse cell types. However, the functional role of GCN5L1 in the heart is currently unknown. As many of the factors regulated by GCN5L1 play a major role in ischemia-reperfusion (I/R) injury, we sought to determine if GCN5L1 is an important nexus in the response to cardiac ischemic stress. Deletion of GCN5L1 in cardiomyocytes resulted in impaired myocardial post-ischemic function and increased infarct development in isolated work-performing hearts. GCN5L1 knockout hearts displayed hallmarks of ROS damage, and scavenging of ROS restored cardiac function and reduced infarct volume in vivo. GCN5L1 knockdown in cardiac-derived AC16 cells was associated with reduced activation of the pro-survival MAP kinase ERK1/2, which was also reversed by ROS scavenging, leading to restored cell viability. We therefore conclude that GCN5L1 activity provides an important protection against I/R induced, ROS-mediated damage in the ischemic heart.
    Keywords:  ERK1/2; Ex vivo working heart; GCN5L1; Ischemia reperfusion; Reactive oxygen species
    DOI:  https://doi.org/10.1016/j.yjmcc.2019.02.009
  12. Nat Commun. 2019 Feb 18. 10(1): 809
    MiR-135 suppresses glycolysis and promotes pancreatic cancer cell adaptation to metabolic stress by targeting phosphofructokinase-1.
    Ying Yang, Mari B Ishak Gabra, Eric A Hanse, Xazmin H Lowman, Thai Q Tran, Haiqing Li, Neta Milman, Juan Liu, Michael A Reid, Jason W Locasale, Ziv Gil, Mei Kong.
      Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal human cancers. It thrives in a nutrient-poor environment; however, the mechanisms by which PDAC cells undergo metabolic reprogramming to adapt to metabolic stress are still poorly understood. Here, we show that microRNA-135 is significantly increased in PDAC patient samples compared to adjacent normal tissue. Mechanistically, miR-135 accumulates specifically in response to glutamine deprivation and requires ROS-dependent activation of mutant p53, which directly promotes miR-135 expression. Functionally, we found miR-135 targets phosphofructokinase-1 (PFK1) and inhibits aerobic glycolysis, thereby promoting the utilization of glucose to support the tricarboxylic acid (TCA) cycle. Consistently, miR-135 silencing sensitizes PDAC cells to glutamine deprivation and represses tumor growth in vivo. Together, these results identify a mechanism used by PDAC cells to survive the nutrient-poor tumor microenvironment, and also provide insight regarding the role of mutant p53 and miRNA in pancreatic cancer cell adaptation to metabolic stresses.
    DOI:  https://doi.org/10.1038/s41467-019-08759-0
  13. Cell Metab. 2019 Feb 05. pii: S1550-4131(19)30011-7. [Epub ahead of print]
    Systematic Dissection of the Metabolic-Apoptotic Interface in AML Reveals Heme Biosynthesis to Be a Regulator of Drug Sensitivity.
    Kevin H Lin, Abigail Xie, Justine C Rutter, Yeong-Ran Ahn, Julia M Lloyd-Cowden, Amanda G Nichols, Ryan S Soderquist, Timothy R Koves, Deborah M Muoio, Nancie J MacIver, Jatinder K Lamba, Timothy S Pardee, Chad M McCall, David A Rizzieri, Kris C Wood.
      Crosstalk between metabolic and survival pathways is critical for cellular homeostasis, but the connectivity between these processes remains poorly defined. We used loss-of-function CRISPR/Cas9 knockout screening to identify metabolic genes capable of influencing cellular commitment to apoptosis, using sensitization to the BCL-2 inhibitor ABT-199 in BCL-2-dependent acute myeloid leukemia (AML) cell lines as a proxy for apoptotic disposition. This analysis revealed metabolic pathways that specifically cooperate with BCL-2 to sustain survival. In particular, our analysis singled out heme biosynthesis as an unappreciated apoptosis-modifying pathway. Although heme is broadly incorporated into the proteome, reduction of heme biosynthesis potentiates apoptosis through the loss of ETC activity, resulting in baseline depolarization of the mitochondrial membrane and an increased propensity to undergo apoptosis. Collectively, our findings chart the first apoptotic map of metabolism, motivating the design of metabolically engaged combination chemotherapies and nominating heme biosynthesis as an apoptotic modulator in AML.
    Keywords:  CRISPR; acute myeloid leukemia; apoptosis; cancer metabolism; genetic screens; heme biosynthesis; mitochondria
    DOI:  https://doi.org/10.1016/j.cmet.2019.01.011
  14. J Leukoc Biol. 2019 Feb 21.
    Regulation of leukocyte function by citric acid cycle intermediates.
    Naeem K Patil, Julia K Bohannon, Antonio Hernandez, Tazeen K Patil, Edward R Sherwood.
      Cellular metabolism is a means of generating ATP to provide energy for key cellular functions. However, recent research shows that citric acid cycle intermediates target vital cellular functions of the innate immune system. Succinate, itaconate, citrate, and fumarate have been shown to mediate or regulate important myeloid cell functions during infection and inflammation. This review covers the regulatory functions of citric acid cycle intermediates in myeloid cells and discusses potential translational applications, key mechanistic questions, and future research directions.
    Keywords:  citrate; fumarate; itaconate; metabolic reprogramming; succinate
    DOI:  https://doi.org/10.1002/JLB.3MIR1118-415R
  15. Cell Death Dis. 2019 Feb 20. 10(3): 170
    Succinylation-dependent mitochondrial translocation of PKM2 promotes cell survival in response to nutritional stress.
    Hailong Qi, Xianling Ning, Chang Yu, Xin Ji, Yan Jin, Michael A McNutt, Yuxin Yin.
      Tumor growth and progression is characteristically associated with the synergistic effects of uncontrolled cellular proliferation and cell survival under stress. Pyruvate kinase M2 (PKM2) contributes to both of these effects. However, the specific mechanism by which PKM2 promotes uncontrolled proliferation or cell survival under stress in different nutritional environments is unclear. We show that succinylation mediated mitochondrial translocation of PKM2 under glucose starvation plays a role in switching the cellular machinery from proliferation to cell survival mode and vice versa. Mitochondrial PKM2 inhibits ubiquitination-mediated degradation of voltage-dependent anion channel 3 (VDAC3) and increases mitochondrial permeability to generate more ATP for cell survival under nutritional depletion. We found there is a positive correlation of upregulation of mitochondrial PKM2 and upregulation of VDAC3 in human colon cancer. This shows the mechanisms identified in this study in fact play a role in neoplastic biology. We therefore developed a small molecule designated compound 8 that blocks mitochondrial translocation of PKM2 and inhibits tumor development. Our data suggest that blocking PKM2 mitochondrial function with a small molecule inhibitor has potential for cancer treatment.
    DOI:  https://doi.org/10.1038/s41419-018-1271-9
  16. Cell Physiol Biochem. 2019 ;52(1): 57-75
    Glycogen Synthase Kinase 3 Beta Controls Presenilin-1-Mediated Endoplasmic Reticulum Ca²⁺ Leak Directed to Mitochondria in Pancreatic Islets and β-Cells.
    Christiane Klec, Corina T Madreiter-Sokolowski, Sarah Stryeck, Vinay Sachdev, Madalina Duta-Mare, Benjamin Gottschalk, Maria R Depaoli, Rene Rost, Jesse Hay, Markus Waldeck-Weiermair, Dagmar Kratky, Tobias Madl, Roland Malli, Wolfgang F Graier.
       BACKGROUND/AIMS: In pancreatic β-cells, the intracellular Ca²⁺ homeostasis is an essential regulator of the cells major functions. The endoplasmic reticulum (ER) as interactive intracellular Ca²⁺ store balances cellular Ca²⁺. In this study basal ER Ca²⁺ homeostasis was evaluated in order to reveal potential β-cell-specificity of ER Ca²⁺ handling and its consequences for mitochondrial Ca²⁺, ATP and respiration.
    METHODS: The two pancreatic cell lines INS-1 and MIN-6, freshly isolated pancreatic islets, and the two non-pancreatic cell lines HeLA and EA.hy926 were used. Cytosolic, ER and mitochondrial Ca²⁺ and ATP measurements were performed using single cell fluorescence microscopy and respective (genetically-encoded) sensors/dyes. Mitochondrial respiration was monitored by respirometry. GSK3β activity was measured with ELISA.
    RESULTS: An atypical ER Ca²⁺ leak was observed exclusively in pancreatic islets and β-cells. This continuous ER Ca²⁺ efflux is directed to mitochondria and increases basal respiration and organellar ATP levels, is established by GSK3β-mediated phosphorylation of presenilin-1, and is prevented by either knockdown of presenilin-1 or an inhibition/knockdown of GSK3β. Expression of a presenlin-1 mutant that mimics GSK3β-mediated phosphorylation established a β-cell-like ER Ca²⁺ leak in HeLa and EA.hy926 cells. The ER Ca²⁺ loss in β-cells was compensated at steady state by Ca²⁺ entry that is linked to the activity of TRPC3.
    CONCLUSION: Pancreatic β-cells establish a cell-specific ER Ca²⁺ leak that is under the control of GSK3β and directed to mitochondria, thus, reflecting a cell-specific intracellular Ca²⁺ handling for basal mitochondrial activity.
    Keywords:  Ca²⁺ leak; Endoplasmic reticulum Ca²⁺; Insulin release; Mitochondria; Presenilin-1; Respiration
    DOI:  https://doi.org/10.33594/000000005
  17. Biochem Biophys Res Commun. 2019 Feb 16. pii: S0006-291X(19)30230-X. [Epub ahead of print]
    SMDT1-driven change in mitochondrial dynamics mediate cell apoptosis in PDAC.
    Kun-Feng Xie, Dong-Dong Guo, Xing-Jing Luo.
      Mitochondrial Ca2+ uptake, an important governing for Ca2+ homeostasis, is catalyzed by the mitochondrial calcium uniporter (MCU) complex. SMDT1, as a subunit of MCU complex, was essential for bridging the calcium-sensing role of MICU1 and MICU2 with the calcium-conducting role of MCU. However, the molecular mechanism and regulatory purpose of SMDT1 remain largely unexplored, especially no study was reported in cancer. Here, we firstly reported that how SMDT1 exerted its role through mediating mitochondrial dynamic in PDAC malignancy. In this study, by screening online of subunit of MCU complex, we confirmed that SMDT1 expression was significantly positive correlated with PDAC prognosis. The GEO datasets showed decreased SMDT1 expression in PDAC tumor compared with non-tumor tissues. SMDT1 overexpression could notably inhibit cell proliferation and induce cell apoptosis. Further analysis demonstrated that up-regulated SMDT1 in ASPC1 and Canpan1 cells led to increased accumulation of pro apoptotic protein BAX and decrease in anti-apoptotic proteins Bcl-2 and Bclx. And more releasing of cytochrome c located in cytosolic. Mechanistically, in the morphological analysis of mitochondria, more fragmented mitochondria were presented in SMDT1 overexpression cells by promting the phosphorylation of Drp1, increasing Fis and decreasing MFN1. Meanwhile, more Drp1 was translocated on the mitochondrial from the cytoplasm in up-regulated SMDT1 cells. On the basis of the evidence above we deduce that SMDT1-driven change in mitochondrial dynamics mediated cells apoptosis in PDAC. And, SMDT1 could serve as an important therapeutic target to normalize mitochondrial dynamic responsible for poor prognosis in PDAC.
    Keywords:  Apoptosis; Mitochondrial dynamics; PDAC; Poor outcome; SMDT1
    DOI:  https://doi.org/10.1016/j.bbrc.2019.02.043
  18. Autophagy. 2019 Feb 20. 1-22
    The HGF-MET axis coordinates liver cancer metabolism and autophagy for chemotherapeutic resistance.
    Xing Huang, Guangming Gan, Xiaoxiao Wang, Ting Xu, Wei Xie.
      Notwithstanding the numerous drugs available for liver cancer, emerging evidence suggests that chemotherapeutic resistance is a significant issue. HGF and its receptor MET play critical roles in liver carcinogenesis and metastasis, mainly dependent on the activity of receptor tyrosine kinase. However, for unknown reasons, all HGF-MET kinase activity-targeted drugs have failed or have been suspended in clinical trials thus far. Macroautophagy/autophagy is a protective 'self-eating' process for resisting metabolic stress by recycling obsolete components, whereas the impact of autophagy-mediated reprogrammed metabolism on therapeutic resistance is largely unclear, especially in liver cancer. In the present study, we first observed that HGF stimulus facilitated the Warburg effect and glutaminolysis to promote biogenesis in multiple liver cancer cells. We then identified the pyruvate dehydrogenase complex (PDHC) and GLS/GLS1 as crucial substrates of HGF-activated MET kinase; MET-mediated phosphorylation inhibits PDHC activity but activates GLS to promote cancer cell metabolism and biogenesis. We further found that the key residues of kinase activity in MET (Y1234/1235) also constitute a conserved LC3-interacting region motif (Y1234-Y1235-x-V1237). Therefore, on inhibiting HGF-mediated MET kinase activation, Y1234/1235-dephosphorylated MET induced autophagy to maintain biogenesis for cancer cell survival. Moreover, we verified that Y1234/1235-dephosphorylated MET correlated with autophagy in clinical liver cancer. Finally, a combination of MET inhibitor and autophagy suppressor significantly improved the therapeutic efficiency of liver cancer in vitro and in mice. Together, our findings reveal an HGF-MET axis-coordinated functional interaction between tyrosine kinase signaling and autophagy, and establish a MET-autophagy double-targeted strategy to overcome chemotherapeutic resistance in liver cancer. Abbreviations: ALDO: aldolase, fructose-bisphosphate; CQ: chloroquine; DLAT/PDCE2: dihydrolipoamide S-acetyltransferase; EMT: epithelial-mesenchymal transition; ENO: enolase; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GLS/GLS1: glutaminase; GLUL/GS: glutamine-ammonia ligase; GPI/PGI: glucose-6-phosphate isomerase; HCC: hepatocellular carcinoma; HGF: hepatocyte growth factor; HK: hexokinase; LDH: lactate dehydrogenase; LIHC: liver hepatocellular carcinoma; LIR: LC3-interacting region; PDH: pyruvate dehydrogenase; PDHA1: pyruvate dehydrogenase E1 alpha 1 subunit; PDHX: pyruvate dehydrogenase complex component X; PFK: phosphofructokinase; PK: pyruvate kinase; RTK: receptor tyrosine kinase; TCGA: The Cancer Genome Atlas.
    Keywords:  Biogenesis; Warburg effect; combined treatment; glutaminolysis; targeted therapy
    DOI:  https://doi.org/10.1080/15548627.2019.1580105
  19. Neurochem Res. 2019 Feb 20.
    Consequences of a Metabolic Glucose-Depletion on the Survival and the Metabolism of Cultured Rat Astrocytes.
    Christian Arend, Eric Ehrke, Ralf Dringen.
      Brain astrocytes are considered to be highly glycolytic, but these cells also produce ATP via mitochondrial oxidative phosphorylation. To investigate how a metabolic depletion of glucose will affect the metabolism of astrocytes, we applied glucose at an initial concentration of 2 mM to cultured primary astrocytes and monitored the cell viability and various metabolic parameters during an incubation for up to 2 weeks. Already within 2 days of incubation the cells had completely consumed the applied glucose and lactate had accumulated in the medium to a concentration of around 3 mM. During the subsequent 10 days of incubation, the cell viability was not compromised while the extracellular lactate concentration declined to values of around 0.2 mM, before the cell viability was compromised. Application of known inhibitors of mitochondrial metabolism strongly accelerated glucose consumption and initial lactate production, while the lactate consumption was completely (antimycin A or 8-hydroxy efavirenz) and partially (efavirenz, metformin or tyrphostin 23) inhibited which caused rapid and delayed cell toxicity, respectively. The switch from glycolytic glucose metabolism to mitochondrial metabolism during the incubation was neither accompanied by alterations in the specific cytosolic lactate dehydrogenase activity or in the WST1 reduction capacity nor in the mitochondrial citrate synthase activity, but a cellular redistribution of mitochondria from a perinuclear to a more spread cytoplasmic localization was observed during the lactate consumption phase. These results demonstrate that cultured astrocytes survive a metabolism-induced glucose depletion very well by consuming lactate as fuel for mitochondrial ATP generation.
    Keywords:  Glucose; Glycolysis; Lactate; Metabolism; Mitochondria
    DOI:  https://doi.org/10.1007/s11064-019-02752-1
  20. Nat Commun. 2019 Feb 19. 10(1): 845
    Kindlin-2 links mechano-environment to proline synthesis and tumor growth.
    Ling Guo, Chunhong Cui, Kuo Zhang, Jiaxin Wang, Yilin Wang, Yixuan Lu, Ka Chen, Jifan Yuan, Guozhi Xiao, Bin Tang, Ying Sun, Chuanyue Wu.
      Cell metabolism is strongly influenced by mechano-environment. We show here that a fraction of kindlin-2 localizes to mitochondria and interacts with pyrroline-5-carboxylate reductase 1 (PYCR1), a key enzyme for proline synthesis. Extracellular matrix (ECM) stiffening promotes kindlin-2 translocation into mitochondria and its interaction with PYCR1, resulting in elevation of PYCR1 level and consequent increase of proline synthesis and cell proliferation. Depletion of kindlin-2 reduces PYCR1 level, increases reactive oxygen species (ROS) production and apoptosis, and abolishes ECM stiffening-induced increase of proline synthesis and cell proliferation. In vivo, both kindlin-2 and PYCR1 levels are markedly increased in lung adenocarcinoma. Ablation of kindlin-2 in lung adenocarcinoma substantially reduces PYCR1 and proline levels, and diminishes fibrosis in vivo, resulting in marked inhibition of tumor growth and reduction of mortality rate. Our findings reveal a mechanoresponsive kindlin-2-PYCR1 complex that links mechano-environment to proline metabolism and signaling, and suggest a strategy to inhibit tumor growth.
    DOI:  https://doi.org/10.1038/s41467-019-08772-3
  21. Cell Metab. 2019 Feb 12. pii: S1550-4131(19)30019-1. [Epub ahead of print]
    Calcium Signaling Controls Pathogenic Th17 Cell-Mediated Inflammation by Regulating Mitochondrial Function.
    Ulrike Kaufmann, Sascha Kahlfuss, Jun Yang, Elitza Ivanova, Sergei B Koralov, Stefan Feske.
      Pathogenic Th17 cells play important roles in many autoimmune and inflammatory diseases. Their function depends on T cell receptor (TCR) signaling and cytokines that activate signal transducer and activator of transcription 3 (STAT3). TCR engagement activates stromal interaction molecule 1 (STIM1) and calcium (Ca2+) influx through Ca2+-release-activated Ca2+ (CRAC) channels. Here, we show that abolishing STIM1 and Ca2+ influx in T cells expressing a hyperactive form of STAT3 (STAT3C) attenuates pathogenic Th17 cell function and inflammation associated with STAT3C expression. Deletion of STIM1 in pathogenic Th17 cells reduces the expression of genes required for mitochondrial function and oxidative phosphorylation (OXPHOS) but enhances reactive oxygen species (ROS) production. STIM1 deletion or inhibition of OXPHOS is associated with a non-pathogenic Th17 gene expression signature and impaired pathogenic Th17 cell function. Our findings establish Ca2+ influx as a critical regulator of mitochondrial function and oxidative stress in pathogenic Th17 cell-mediated multiorgan inflammation.
    Keywords:  Ca2+; ETC; IL-17; OXPHOS; ROS; SOCE; STAT3; STIM1; Th17; airway inflammation; antioxidant; calcium; colitis; electron transport chain; metabolism; mitochondria; oxidative phosphorylation; pathogenic T helper 17 cells; reactive oxygen species; store-operated calcium entry
    DOI:  https://doi.org/10.1016/j.cmet.2019.01.019
  22. Antioxid Redox Signal. 2019 Feb 22.
    Redox Imbalance in Idiopathic Pulmonary Fibrosis: A Role for Oxidant Cross-Talk Between NOX Enzymes and Mitochondria.
    Carmen Veith, Agnes Boots, Musa Idris, Frederik Jan van Schooten, Albert van der Vliet.
       SIGNIFICANCE: Idiopathic pulmonary fibrosis (IPF) is a progressive age-related lung disease with a median survival of only 3 years after diagnosis. The pathogenic mechanisms behind IPF are not clearly understood and current therapeutic approaches have not been successful in improving disease outcomes. Recent advances: IPF is characterized by increased production of reactive oxygen species (ROS), primarily by NADPH oxidases (NOXes) and mitochondria, as well as altered antioxidant defenses. Recent studies have identified the NOX isoform NOX4 as a key player in various important aspects of IPF pathology. In addition, mitochondrial dysfunction is thought to enhance pathological features of IPF, in part by increasing mitochondrial ROS production and altering cellular metabolism. Recent findings indicate reciprocal interactions between NOX enzymes and mitochondria, which affect regulation of NOX activity as well as mitochondrial function and mtROS production, and collectively promote epithelial injury and profibrotic signaling. Critical Issues and Future Directions: The precise molecular mechanisms by which ROS from NOX or mitochondria contribute to IPF pathology are not known. This review will summarize current knowledge with respect to the various aspects of ROS imbalance in the context of IPF and its proposed roles in disease development, with specific emphasis on the importance of inappropriate NOX activation, mitochondrial dysfunction, and the emerging evidence of NOX-mitochondria crosstalk as important drivers in IPF pathobiology.
    DOI:  https://doi.org/10.1089/ars.2019.7742
  23. Cancer Lett. 2019 Feb 18. pii: S0304-3835(19)30110-7. [Epub ahead of print]
    Pharmacological inhibition of the IKKε/TBK-1 axis potentiates the anti-tumour and anti-metastatic effects of Docetaxel in mouse models of breast cancer.
    Ryan T Bishop, Silvia Marino, Daniëlle de Ridder, Richard J Allen, Diane V Lefley, Andrew H Sims, Ning Wang, Penelope D Ottewell, Aymen I Idris.
      IκB kinase subunit epsilon (IKKε), a key component of NFκB and interferon signalling, has been identified as a breast cancer oncogene. Here we report that the IKKε/TBK1 axis plays a role in the initiation and progression of breast cancer osteolytic metastasis. Cancer-specific knockdown of IKKε in the human MDA-MB-231-BT cells and treatment with the verified IKKε/TBK1 inhibitor Amlexanox reduced skeletal tumour growth and osteolysis in mice. In addition, combined administration of Amlexanox with Docetaxel reduced mammary tumour growth of syngeneic 4T1 cells, inhibited metastases and improved survival in mice after removal of the primary tumour. Functional and mechanistic studies in breast cancer cells, osteoclasts and osteoblasts revealed that IKKε inhibition reduces the ability of breast cancer cells to grow, move and enhance osteoclastogenesis by engaging both IRF and NFκB signalling pathways. Thus, therapeutic targeting of the IKKε/TBK1 axis may be of value in the treatment of advanced triple negative breast cancer.
    Keywords:  IKKε; NFκB; bone; bone metastasis; breast cancer; combination treatment; osteoblast; osteoclast; osteolysis
    DOI:  https://doi.org/10.1016/j.canlet.2019.02.032
  24. Front Immunol. 2019 ;10 115
    Differential Regulation of Human Treg and Th17 Cells by Fatty Acid Synthesis and Glycolysis.
    Deborah Cluxton, Andreea Petrasca, Barry Moran, Jean M Fletcher.
      In this study we examined the metabolic requirements of human T helper cells and the effect of manipulating metabolic pathways in Th17 and Treg cells. The Th17:Treg cell axis is dysregulated in a number of autoimmune or inflammatory diseases and therefore it is of key importance to identify novel strategies to modulate this axis in favor of Treg cells. We investigated the role of carbohydrate and fatty acid metabolism in the regulation of human memory T helper cell subsets, in order to understand how T cells are regulated at the site of inflammation where essential nutrients including oxygen may be limiting. We found that Th17 lineage cells primarily utilize glycolysis, as glucose-deprivation and treatment with rapamycin resulted in a reduction in these cells. On the other hand, Treg cells exhibited increased glycolysis, mitochondrial respiration, and fatty acid oxidation, whereas Th17 cells demonstrated a reliance upon fatty acid synthesis. Treg cells were somewhat reliant on glycolysis, but to a lesser extent than Th17 cells. Here we expose a fundamental difference in the metabolic requirements of human Treg and Th17 cells and a possible mechanism for manipulating the Th17:Treg cell axis.
    Keywords:  T cells; Th17 cells; Treg cells; fatty acid synthesis; glycolysis (glycolytic pathway); immune modulation; immunometabolism
    DOI:  https://doi.org/10.3389/fimmu.2019.00115
  25. Cell Rep. 2019 Feb 19. pii: S2211-1247(19)30123-8. [Epub ahead of print]26(8): 2212-2226.e7
    Loss of Hepatic Oscillatory Fed microRNAs Abrogates Refed Transition and Causes Liver Dysfunctions.
    Babukrishna Maniyadath, Tandrika Chattopadhyay, Srikant Verma, Sujata Kumari, Prineeta Kulkarni, Kushal Banerjee, Asmitha Lazarus, Saurabh S Kokane, Trupti Shetty, Krishanpal Anamika, Ullas Kolthur-Seetharam.
      Inability to mediate fed-fast transitions in the liver is known to cause metabolic dysfunctions and diseases. Intuitively, a failure to inhibit futile translation of state-specific transcripts during fed-fast cycles would abrogate dynamic physiological transitions. Here, we have discovered hepatic fed microRNAs that target fasting-induced genes and are essential for a refed transition. Our findings highlight the role of these fed microRNAs in orchestrating system-level control over liver physiology and whole-body energetics. By targeting SIRT1, PGC1α, and their downstream genes, fed microRNAs regulate metabolic and mitochondrial pathways. MicroRNA expression, processing, and RISC loading oscillate during these cycles and possibly constitute an anticipatory mechanism. Fed-microRNA oscillations are deregulated during aging. Scavenging of hepatic fed microRNAs causes uncontrolled gluconeogenesis and failure in the catabolic-to-anabolic switching upon feeding, which are hallmarks of metabolic diseases. Besides identifying mechanisms that enable efficient physiological toggling, our study highlights fed microRNAs as candidate therapeutic targets.
    Keywords:  PGC1α; SIRT1; energetics; fast; fatty acid oxidation; fed; gluconeogenesis; liver; microRNA; mitochondria
    DOI:  https://doi.org/10.1016/j.celrep.2019.01.087
  26. J Biol Chem. 2019 Feb 21. pii: jbc.RA118.006727. [Epub ahead of print]
    Mitochondrial localization, import and mitochondrial function of the androgen receptor.
    Prachi Bajpai, Emine Koc, Guru Sonpavde, Rajender Singh, Keshav K Singh.
      Nuclear localization of androgen receptor (AR) directs transcriptional regulation of a host of genes, referred to as genomic signaling. Additionally, non-nuclear or non-genomic activities of the AR have long been described, but the understanding of these activities remains elusive. Here, we report that AR is imported into and localizes to mitochondria and has a novel role in regulating multiple mitochondrial processes. Employing complementary experimental approaches of AR knockdown in AR-expressing cells and ectopic AR expression in AR-deficient cells, we demonstrate an inverse relationship between AR expression and mtDNA content and transcription factor A, mitochondrial (TFAM), a regulator of mtDNA content. We show that AR localizes to mitochondria in prostate tissues and cell lines and is imported into mitochondria in vitro. We also found that AR contains a 36-amino-acids-long mitochondrial localization sequence (MLS) capable of targeting a passenger protein (GFP) to the mitochondria and that deletion of the MLS abolishes the import of AR into the mitochondria. Ectopic AR expression reduced the expression of oxidative phosphorylation (OXPHOS) subunits. Interestingly, AR also controlled translation of mtDNA-encoded genes by regulating expression of multiple nuclear DNA-encoded mitochondrial ribosomal proteins. Consistent with these observations, OXPHOS supercomplexes were destabilized and OXPHOS enzymatic activities were reduced in AR-expressing cells and restored upon AR knockdown. Moreover, mitochondrial impairment induced AR expression and increased its translocation into mitochondria. We conclude that AR localizes to mitochondria where it controls multiple mitochondrial functions and mitonuclear communication. Our studies also suggest that mitochondria are novel players in non-genomic activities of AR.
    Keywords:  androgen receptor; cell signaling; gene transcription; genomic signaling; mitochondria; mitochondrial localization sequence; non genomic signaling; oxidative phosphorylation; prostate cancer; retrograde signaling
    DOI:  https://doi.org/10.1074/jbc.RA118.006727
  27. Autophagy. 2019 Feb 20. 1-13
    A comparative map of macroautophagy and mitophagy in the vertebrate eye.
    Thomas G McWilliams, Alan R Prescott, Beatriz Villarejo-Zori, Graeme Ball, Patricia Boya, Ian G Ganley.
      Photoreception is pivotal to our experience and perception of the natural world; hence the eye is of prime importance for most vertebrate animals to sense light. Central to visual health is mitochondrial homeostasis, and the selective autophagic turnover of mitochondria (mitophagy) is predicted to play a key role here. Despite studies that link aberrant mitophagy to ocular dysfunction, little is known about the prevalence of basal mitophagy, or its relationship to general autophagy, in the visual system. In this study, we utilize the mito-QC mouse and a closely related general macroautophagy reporter model to profile basal mitophagy and macroautophagy in the adult and developing eye. We report that ocular macroautophagy is widespread, but surprisingly mitophagy does not always follow the same pattern of occurrence. We observe low levels of mitophagy in the lens and ciliary body, in stark contrast to the high levels of general MAP1LC3-dependent macroautophagy in these regions. We uncover a striking reversal of this process in the adult retina, where mitophagy accounts for a larger degree of the macroautophagy taking place, specifically in the photoreceptor neurons of the outer nuclear layer. We also show the developmental regulation of autophagy in a variety of ocular tissues. In particular, mitophagy in the adult mouse retina is reversed in localization during the latter stages of development. Our work thus defines the landscape of mitochondrial homeostasis in the mammalian eye, and in doing so highlights the selective nature of autophagy in vivo and the specificity of the reporters used. Abbreviations: ATG: autophagy related; GFP: green fluorescent protein; LC3: microtubule associated protein 1 light chain 3; ONH: optic nerve head; ONL: outer nuclear layer; RPE: retinal pigment epithelium.
    Keywords:  -QC; Autophagy; ciliary body; cornea; eye; hyaloid; lens; mitochondria; mitophagy; retina
    DOI:  https://doi.org/10.1080/15548627.2019.1580509
  28. Proc Natl Acad Sci U S A. 2019 Feb 22. pii: 201809105. [Epub ahead of print]
    LINC00116 codes for a mitochondrial peptide linking respiration and lipid metabolism.
    Anastasia Chugunova, Elizaveta Loseva, Pavel Mazin, Aleksandra Mitina, Tsimafei Navalayeu, Dmitry Bilan, Polina Vishnyakova, Maria Marey, Anna Golovina, Marina Serebryakova, Philipp Pletnev, Maria Rubtsova, Waltraud Mair, Anna Vanyushkina, Philipp Khaitovich, Vsevolod Belousov, Mikhail Vysokikh, Petr Sergiev, Olga Dontsova.
      Genes coding for small peptides have been frequently misannotated as long noncoding RNA (lncRNA) genes. Here we have demonstrated that one such transcript is translated into a 56-amino-acid-long peptide conserved in chordates, corroborating the work published while this manuscript was under review. The Mtln peptide could be detected in mitochondria of mouse cell lines and tissues. In line with its mitochondrial localization, lack of the Mtln decreases the activity of mitochondrial respiratory chain complex I. Unlike the integral components and assembly factors of NADH:ubiquinone oxidoreductase, Mtln does not alter its enzymatic activity directly. Interaction of Mtln with NADH-dependent cytochrome b5 reductase stimulates complex I functioning most likely by providing a favorable lipid composition of the membrane. Study of Mtln illuminates the importance of small peptides, whose genes might frequently be misannotated as lncRNAs, for the control of vitally important cellular processes.
    Keywords:  lipid metabolism; mitochondria; peptide; respiration; sORF
    DOI:  https://doi.org/10.1073/pnas.1809105116
  29. Mol Biol Evol. 2019 Feb 20. pii: msz036. [Epub ahead of print]
    Evolutionary rate correlation between mitochondrial-encoded and mitochondria-associated nuclear-encoded proteins in insects.
    Zhichao Yan, Gongyin Ye, John H Werren.
      The mitochondrion is a pivotal organelle for energy production, and includes components encoded by both the mitochondrial and nuclear genomes. Functional and evolutionary interactions are expected between the nuclear and mitochondrial encoded components. The topic is of broad interest in biology, with implications to genetics, evolution, and medicine. Here we compare the evolutionary rates of mitochondrial proteins and ribosomal RNAs to rates of mitochondria-associated nuclear-encoded proteins, across the major orders of holometabolous insects. There are significant evolutionary rate correlations (ERCs) between mitochondrial-encoded and mitochondria-associated nuclear-encoded proteins, which is likely driven by different rates of mitochondrial sequence evolution and correlated changes in the interacting nuclear-encoded proteins. The pattern holds after correction for phylogenetic relationships and considering protein conservation levels. Correlations are stronger for both nuclear-encoded OXPHOS proteins that are in contact with mitochondrial OXPHOS proteins and for nuclear-encoded mitochondrial ribosomal amino acids directly contacting the mitochondrial rRNAs. We find that ERC between mitochondrial- and nuclear-encoded proteins is a strong predictor of nuclear-encoded proteins known to interact with mitochondria, and ERC shows promise for identifying new candidate proteins with mitochondrial function. Twenty-three additional candidate nuclear-encoded proteins warrant further study for mitochondrial function based on this approach, including proteins in the minichromosome maintenance helicase (MCM) complex.
    Keywords:  coevolution; compensatory evolution; insect; mitochondrion; substitution rates
    DOI:  https://doi.org/10.1093/molbev/msz036
  30. Nature. 2019 Feb 20.
    Bacterial cGAS-like enzymes synthesize diverse nucleotide signals.
    Aaron T Whiteley, James B Eaglesham, Carina C de Oliveira Mann, Benjamin R Morehouse, Brianna Lowey, Eric A Nieminen, Olga Danilchanka, David S King, Amy S Y Lee, John J Mekalanos, Philip J Kranzusch.
      Cyclic dinucleotides (CDNs) have central roles in bacterial homeostasis and virulence by acting as nucleotide second messengers. Bacterial CDNs also elicit immune responses during infection when they are detected by pattern-recognition receptors in animal cells. Here we perform a systematic biochemical screen for bacterial signalling nucleotides and discover a large family of cGAS/DncV-like nucleotidyltransferases (CD-NTases) that use both purine and pyrimidine nucleotides to synthesize a diverse range of CDNs. A series of crystal structures establish CD-NTases as a structurally conserved family and reveal key contacts in the enzyme active-site lid that direct purine or pyrimidine selection. CD-NTase products are not restricted to CDNs and also include an unexpected class of cyclic trinucleotide compounds. Biochemical and cellular analyses of CD-NTase signalling nucleotides demonstrate that these cyclic di- and trinucleotides activate distinct host receptors and thus may modulate the interaction of both pathogens and commensal microbiota with their animal and plant hosts.
    DOI:  https://doi.org/10.1038/s41586-019-0953-5
  31. Annu Rev Biophys. 2019 Feb 20.
    Mammalian Respiratory Complex I Through the Lens of Cryo-EM.
    Ahmed-Noor A Agip, James N Blaza, Justin G Fedor, Judy Hirst.
      Single-particle electron cryomicroscopy (cryo-EM) has led to a revolution in structural work on mammalian respiratory complex I. Complex I (mitochondrial NADH:ubiquinone oxidoreductase), a membrane-bound redox-driven proton pump, is one of the largest and most complicated enzymes in the mammalian cell. Rapid progress, following the first 5-Å resolution data on bovine complex I in 2014, has led to a model for mouse complex I at 3.3-Å resolution that contains 96% of the 8,518 residues and to the identification of different particle classes, some of which are assigned to biochemically defined states. Factors that helped improve resolution, including improvements to biochemistry, cryo-EM grid preparation, data collection strategy, and image processing, are discussed. Together with recent structural data from an ancient relative, membrane-bound hydrogenase, cryo-EM on mammalian complex I has provided new insights into the proton-pumping machinery and a foundation for understanding the enzyme's catalytic mechanism. Expected final online publication date for the Annual Review of Biophysics Volume 48 is May 3, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-biophys-052118-115704
  32. Sci Rep. 2019 Feb 19. 9(1): 2279
    Mitochondrial Haplogroup and the Risk of Acute Kidney Injury Following Cardiac Bypass Surgery.
    Nigel S Kanagasundaram, Simon V Baudouin, Sarah Rowling, Mahesh Prabhu, John H Dark, Timothy H J Goodship, Patrick F Chinnery, Gavin Hudson.
      Although mitochondrial dysfunction plays a key role in the pathophysiology of acute kidney injury (AKI), the influence of mitochondrial genetic variability in this process remains unclear. We explored the association between the risk of post-cardiac bypass AKI and mitochondrial haplotype - inherited mitochondrial genomic variations of potentially functional significance. Our single-centre study recruited consecutive patients prior to surgery. Exclusions included stage 5 CKD, non-Caucasian race and subsequent off-pump surgery. Haplogroup analysis allowed characterisation of the study population using the common mutations and by phylogenetic supergroup (WXI and HV). Chi-square tests for association allowed the identification of potential predictors of AKI for use in logistic regression analysis. AKI occurred in 12.8% of the study population (n = 881; male 69.6%, non-diabetic 78.5%, median (interquartile range) age 68.0 (61.0-75.0) years). The haplogroup profile comprised H (42.7%), J (12.1%), T (10.9%), U (14.4%) and K (7.6%). Although the regression model was statistically significant (χ2 = 95.483, p < 0.0005), neither the phylogenetic supergroups nor any individual haplogroup was a significant contributor. We found no significant association between common European haplogroups and the risk of post-cardiac bypass AKI. However, given the major role of mitochondrial dysfunction in AKI, there is a need to replicate our findings in other cohorts and with other aetiologies of AKI.
    DOI:  https://doi.org/10.1038/s41598-018-37944-2
  33. Nat Nanotechnol. 2019 Feb 18.
    Carbon-dot-supported atomically dispersed gold as a mitochondrial oxidative stress amplifier for cancer treatment.
    Ningqiang Gong, Xiaowei Ma, Xiaoxia Ye, Qunfang Zhou, Xiaoai Chen, Xiaoli Tan, Shengkun Yao, Shuaidong Huo, Tingbin Zhang, Shizhu Chen, Xucong Teng, Xixue Hu, Jie Yu, Yaling Gan, Huaidong Jiang, Jinghong Li, Xing-Jie Liang.
      Mitochondrial redox homeostasis, the balance between reactive oxygen species and antioxidants such as glutathione, plays critical roles in many biological processes, including biosynthesis and apoptosis, and thus is a potential target for cancer treatment. Here, we report a mitochondrial oxidative stress amplifier, MitoCAT-g, which consists of carbon-dot-supported atomically dispersed gold (CAT-g) with further surface modifications of triphenylphosphine and cinnamaldehyde. We find that the MitoCAT-g particles specifically target mitochondria and deplete mitochondrial glutathione with atomic economy, thus amplifying the reactive oxygen species damage caused by cinnamaldehyde and finally leading to apoptosis in cancer cells. We show that imaging-guided interventional injection of these particles potently inhibits tumour growth in subcutaneous and orthotopic patient-derived xenograft hepatocellular carcinoma models without adverse effects. Our study demonstrates that MitoCAT-g amplifies the oxidative stress in mitochondria and suppresses tumour growth in vivo, representing a promising agent for anticancer applications.
    DOI:  https://doi.org/10.1038/s41565-019-0373-6
  34. Circ Res. 2019 Feb 21.
    Mitophagy Is Essential for Maintaining Cardiac Function During High Fat Diet-Induced Diabetic Cardiomyopathy.
    Mingming Tong, Toshiro Saito, Peiyong Zhai, Shin-Ichi Oka, Wataru Mizushima, Michinari Nakamura, Shohei Ikeda, Akihiro Shirakabe, Junichi Sadoshima.
       RATIONALE: Diabetic patients develop cardiomyopathy characterized by hypertrophy, diastolic dysfunction, and intracellular lipid accumulation, termed lipotoxicity. Diabetic hearts utilize fatty acids as a major energy source, which produces high levels of oxidative stress, thereby inducing mitochondrial dysfunction.
    OBJECTIVE: To elucidate how mitochondrial function is regulated in diabetic cardiomyopathy.
    METHODS AND RESULTS: Mice were fed either a normal diet (ND) or high fat diet (HFD, 60 kcal % fat). Although autophagic flux was activated by HFD consumption, peaking at 6 weeks (p<0.05), it was attenuated thereafter. Mitophagy, evaluated with Mito-Keima, was increased after 3 weeks of HFD feeding (mitophagy area: 8.3% per cell with ND and 12.4% with HFD) and continued to increase even after 2 months (p<0.05). By isolating adult cardiomyocytes from GFP-LC3 mice fed HFD, we confirmed that mitochondria were sequestrated by LC3 positive autophagosomes during mitophagy. In wild type (WT) mice, cardiac hypertrophy, diastolic dysfunction (EDPVR = 0.051{plus minus}0.009 in ND and 0.11{plus minus}0.004 in HFD) and lipid accumulation occurred within 2 months of HFD feeding (p<0.05). Deletion of atg7 impaired mitophagy, increased lipid accumulation, exacerbated diastolic dysfunction (EDPVR=0.11{plus minus}0.004 in WT and 0.152{plus minus}0.019 in atg7 cKO, p<0.05) and induced systolic dysfunction (ESPVR=24.86{plus minus}2.46 in WT and 15.93{plus minus}1.76 in atg7 cKO, p<0.05) during HFD feeding. Deletion of Parkin partially inhibited mitophagy, increased lipid accumulation and exacerbated diastolic dysfunction (EDPVR=0.124{plus minus}0.005 in WT and 0.176{plus minus}0.018 in Parkin KO, p<0.05) in response to HFD feeding. Injection of Tat-Beclin1 (TB1) activated mitophagy, attenuated mitochondrial dysfunction, decreased lipid accumulation, and protected against cardiac diastolic dysfunction (EDPVR=0.110{plus minus}0.009 in Control peptide and 0.078{plus minus}0.015 in TB1, p<0.05) during HFD feeding.
    CONCLUSIONS: Mitophagy serves as an essential quality control mechanism for mitochondria in the heart during HFD consumption. Impairment of mitophagy induces mitochondrial dysfunction and lipid accumulation, thereby exacerbating diabetic cardiomyopathy. Conversely, activation of mitophagy protects against HFD-induced diabetic cardiomyopathy.
    Keywords:  cardiac dysfunction; high fat diet; lipid accumulation; mitophagy
    DOI:  https://doi.org/10.1161/CIRCRESAHA.118.314607
  35. Chem Biol Interact. 2019 Feb 19. pii: S0009-2797(18)31487-X. [Epub ahead of print]
    Loss of ALDH1L1 folate enzyme confers a selective metabolic advantage for tumor progression.
    Sergey A Krupenko, Natalia I Krupenko.
      ALDH1L1 (cytosolic 10-formyltetrahydrofolate dehydrogenase) is the enzyme in folate metabolism commonly downregulated in human cancers. One of the mechanisms of the enzyme downregulation is methylation of the promoter of the ALDH1L1 gene. Recent studies underscored ALDH1L1 as a candidate tumor suppressor and potential marker of aggressive cancers. In agreement with the ALDH1L1 loss in cancer, its re-expression leads to inhibition of proliferation and to apoptosis, but also affects migration and invasion of cancer cells through a specific folate-dependent mechanism involved in invasive phenotype. A growing body of literature evaluated the prognostic value of ALDH1L1 expression for cancer disease, the regulatory role of the enzyme in cellular proliferation, and associated metabolic and signaling cellular responses. Overall, there is a strong indication that the ALDH1L1 silencing provides metabolic advantage for tumor progression at a later stage when unlimited proliferation and enhanced motility become critical processes for the tumor expansion. Whether the ALDH1L1 loss is involved in tumor initiation is still an open question.
    Keywords:  ALDH1L1 promoter methylation; Cofilin; Folate metabolism; JNK; Tumor suppression; p53
    DOI:  https://doi.org/10.1016/j.cbi.2019.02.013
  36. Nature. 2019 Feb;566(7744): 333-334
    Tumours use a metabolic twist to make lipids.
    Marteinn Thor Snaebjornsson, Almut Schulze.
      
    Keywords:  Cancer; Metabolism
    DOI:  https://doi.org/10.1038/d41586-019-00352-1
  37. Protein Cell. 2019 Feb 20.
    Mitochondrion-processed TERC regulates senescence without affecting telomerase activities.
    Qian Zheng, Peipei Liu, Ge Gao, Jiapei Yuan, Pengfeng Wang, Jinliang Huang, Leiming Xie, Xinping Lu, Fan Di, Tanjun Tong, Jun Chen, Zhi Lu, Jisong Guan, Geng Wang.
      Mitochondrial dysfunctions play major roles in ageing. How mitochondrial stresses invoke downstream responses and how specificity of the signaling is achieved, however, remains unclear. We have previously discovered that the RNA component of Telomerase TERC is imported into mitochondria, processed to a shorter form TERC-53, and then exported back to the cytosol. Cytosolic TERC-53 levels respond to mitochondrial functions, but have no direct effect on these functions, suggesting that cytosolic TERC-53 functions downstream of mitochondria as a signal of mitochondrial functions. Here, we show that cytosolic TERC-53 plays a regulatory role on cellular senescence and is involved in cognition decline in 10 months old mice, independent of its telomerase function. Manipulation of cytosolic TERC-53 levels affects cellular senescence and cognition decline in 10 months old mouse hippocampi without affecting telomerase activity, and most importantly, affects cellular senescence in terc-/- cells. These findings uncover a senescence-related regulatory pathway with a non-coding RNA as the signal in mammals.
    Keywords:  mitochondria; non-coding RNA; nucleus; retrograde signal; telomerase; transcription regulation
    DOI:  https://doi.org/10.1007/s13238-019-0612-5
  38. Elife. 2019 Feb 18. pii: e41927. [Epub ahead of print]8
    Nuclear genetic regulation of the human mitochondrial transcriptome.
    Aminah T Ali, Lena Boehme, Guillermo Carbajosa, Vlad C Seitan, Kerrin S Small, Alan Hodgkinson.
      Mitochondria play important roles in cellular processes and disease, yet little is known about how the transcriptional regime of the mitochondrial genome varies across individuals and tissues. By analyzing >11,000 RNA-sequencing libraries across 36 tissue/cell types, we find considerable variation in mitochondrial-encoded gene expression along the mitochondrial transcriptome, across tissues and between individuals, highlighting the importance of cell-type specific and post-transcriptional processes in shaping mitochondrial-encoded RNA levels. Using whole-genome genetic data we identify 64 nuclear loci associated with expression levels of 14 genes encoded in the mitochondrial genome, including missense variants within genes involved in mitochondrial function (TBRG4, MTPAP and LONP1), implicating genetic mechanisms that act in trans across the two genomes. We replicate ~21% of associations with independent tissue-matched datasets and find genetic variants linked to these nuclear loci that are associated with cardio-metabolic phenotypes and Vitiligo, supporting a potential role for variable mitochondrial-encoded gene expression in complex disease.
    Keywords:  chromosomes; gene expression; genetics; genomics; human
    DOI:  https://doi.org/10.7554/eLife.41927
  39. Mol Cell. 2019 Feb 21. pii: S1097-2765(19)30096-6. [Epub ahead of print]73(4): 643-644
    Vive ut Numquam Moriturus: Tweaking Translational Control to Regulate Longevity.
    Raz Bar-Ziv, Ngoc-Tram Nguyen, Andrew Dillin.
      Molecular mechanisms regulating aging at the post-transcriptional level are not clear. In this issue of Molecular Cell,D'Amico et al. (2019) demonstrate that the translational inhibition of mitochondrial fission factor (MFF) regulates cellular homeostasis and aging.
    DOI:  https://doi.org/10.1016/j.molcel.2019.02.006
  40. Neoplasma. 2019 Feb 14. pii: 180710N467. [Epub ahead of print]
    Ambra1 inhibits paclitaxel-induced apoptosis in breast cancer cells by modulating the Bim/mitochondrial pathway.
    W L Sun, L Wang, J Luo, H W Zhu, Z W Cai.
      Cancer cells often evade apoptosis induced by anti-cancer drugs, which reduces the efficacy of the drugs. Autophagy/Beclin 1 regulator 1 (Ambra1) is a crucial proautophagic protein. It also plays an important role in the execution of apoptosis. However, the mechanism by which Ambra1 regulates apoptosis has not been fully clarified. Moreover, whether Ambra1 participates in the regulation of paclitaxel-induced apoptosis in breast cancer cells is not clear. Here, we show that Ambra1 inhibits paclitaxel-induced apoptosis in breast cancer cells. Moreover, Bim and mitochondria are key effectors of Ambra1 in this process. Thus, Ambra1 is a protein that makes breast cancer cells resistant to apoptosis by modulating the Bim/mitochondrial pathway. Therefore, Ambra1 may be a potential target for the treatment of breast cancer.
    DOI:  https://doi.org/10.4149/neo_2018_180710N467
  41. Diabetologia. 2019 Feb 16.
    NAD+ metabolism as a target for metabolic health: have we found the silver bullet?
    Niels J Connell, Riekelt H Houtkooper, Patrick Schrauwen.
      NAD+ has gone in and out of fashion within the scientific community a number of times since its discovery in the early 1900s. Over the last decade, NAD+ has emerged as a potential target for combatting metabolic disturbances and the mitochondrial dysfunction that is mediated through sirtuin (SIRT) enzymes. The beneficial metabolic effects of the NAD+/SIRT axis have triggered an increased interest in NAD+ as an enhancer of energy metabolism. As a result, a myriad of publications have focused on NAD+ metabolism, with the majority of the work having been performed using in vitro models, and in vivo work largely consisting of interventions in Caenorhabditis elegans and rodents. Human intervention trials, on the other hand, are scarce. The aim of this review is to provide an overview of the state-of-the-art on influencing NAD+ metabolism in humans and to set the stage for what the future of this exciting field may hold.
    Keywords:  Diabetes; Energy metabolism; Human; Metabolic disease; NAD+; Review
    DOI:  https://doi.org/10.1007/s00125-019-4831-3
  42. Methods Mol Biol. 2019 ;1927 215-230
    13C-Fingerprinting and Metabolic Flux Analysis of Bacterial Metabolisms.
    Whitney Hollinshead, Lian He, Yinjie J Tang.
      13C-assisted metabolism analysis provides rigorous calculations of the intracellular reaction rates (i.e., fluxes) within the central metabolism of microbial hosts. This mapping of the intracellular network within microbes has proven to be essential for understanding the cell physiology. The approach is also a key to identifying central metabolic nodes, probing the rigidity of a metabolic network, revealing cofactor balances, and delineating hidden pathways. Here we present the methodology of using stable isotopic carbon substrates for both qualitative (13C-fingerprinting of functional pathways) and quantitative (Metabolic Flux Analysis) metabolism studies on bacterial species. In this methodology, we include step-by-step instructions to use the open source WUflux software for the steady-state flux calculations based on labeling information of amino acids or free metabolites.
    Keywords:  13C-MFA; Flux ratio; Metabolism; Metabolites; Proteinogenic amino acids; WUflux
    DOI:  https://doi.org/10.1007/978-1-4939-9142-6_15
  43. J Cell Sci. 2019 Feb 19. pii: jcs.226506. [Epub ahead of print]
    Arp2/3-branched actin regulates microtubule acetylation level and affects mitochondrial distribution.
    Peng Shi, Yuan Wang, Yuxing Huang, Chunlei Zhang, Ying Li, Yaoping Liu, Tingting Li, Wei Wang, Xin Liang, Congying Wu.
      Actin and microtubule cytoskeletons regulate cell morphology, participate in organelle trafficking and function in response to diverse environmental cues. Precise spatial-temporal coordination between these two cytoskeletons is essential for cells to live and move. Here we report a novel cross-talk between actin and microtubules, in which the branched actin maintains microtubule organization, dynamics and stability by affecting tubulin acetylation level. We observe that acetylated tubulin significantly decreases upon perturbation of the Arp2/3-branched actin. We subsequently discover that HDAC6 participates in this process by altering its interaction with tubulin and the Arp2/3-stabilizer cortactin. We further identify that the homeostasis of branched actin controls mitochondrial distribution via this microtubule acetylation dependent mechanism. Our findings shed new light on the integral view of cytoskeletal networks, highlighting post-translational modification as another possible form of cytoskeletal inter-regulation, aside from the established cross-talks through structural connection or upstream signaling pathways.
    Keywords:  Arp2/3-branched actin; Cortactin; HDAC6; Microtubule acetylation; Mitochondria
    DOI:  https://doi.org/10.1242/jcs.226506
  44. Genome Biol. 2019 Feb 21. 20(1): 37
    Mitochondrial hypoxic stress induces widespread RNA editing by APOBEC3G in natural killer cells.
    Shraddha Sharma, Jianmin Wang, Emad Alqassim, Scott Portwood, Eduardo Cortes Gomez, Orla Maguire, Per H Basse, Eunice S Wang, Brahm H Segal, Bora E Baysal.
       BACKGROUND: Protein recoding by RNA editing is required for normal health and evolutionary adaptation. However, de novo induction of RNA editing in response to environmental factors is an uncommon phenomenon. While APOBEC3A edits many mRNAs in monocytes and macrophages in response to hypoxia and interferons, the physiological significance of such editing is unclear.
    RESULTS: Here, we show that the related cytidine deaminase, APOBEC3G, induces site-specific C-to-U RNA editing in natural killer cells, lymphoma cell lines, and, to a lesser extent, CD8-positive T cells upon cellular crowding and hypoxia. In contrast to expectations from its anti-HIV-1 function, the highest expression of APOBEC3G is shown to be in cytotoxic lymphocytes. RNA-seq analysis of natural killer cells subjected to cellular crowding and hypoxia reveals widespread C-to-U mRNA editing that is enriched for genes involved in mRNA translation and ribosome function. APOBEC3G promotes Warburg-like metabolic remodeling in HuT78 T cells under similar conditions. Hypoxia-induced RNA editing by APOBEC3G can be mimicked by the inhibition of mitochondrial respiration and occurs independently of HIF-1α.
    CONCLUSIONS: APOBEC3G is an endogenous RNA editing enzyme in primary natural killer cells and lymphoma cell lines. This RNA editing is induced by cellular crowding and mitochondrial respiratory inhibition to promote adaptation to hypoxic stress.
    Keywords:  APOBEC3; Cell stress; Epitranscriptome; Gene knockdown; Hypoxia; Innate immune cells; Mitochondria; NK cells; RNA editing
    DOI:  https://doi.org/10.1186/s13059-019-1651-1
  45. Cell Metab. 2019 Feb 07. pii: S1550-4131(19)30014-2. [Epub ahead of print]
    Serine Metabolism Supports Macrophage IL-1β Production.
    Arianne E Rodriguez, Gregory S Ducker, Leah K Billingham, Carlos A Martinez, Nello Mainolfi, Vipin Suri, Adam Friedman, Mark G Manfredi, Samuel E Weinberg, Joshua D Rabinowitz, Navdeep S Chandel.
      Serine is a substrate for nucleotide, NADPH, and glutathione (GSH) synthesis. Previous studies in cancer cells and lymphocytes have shown that serine-dependent one-carbon units are necessary for nucleotide production to support proliferation. Presently, it is unknown whether serine metabolism impacts the function of non-proliferative cells, such as inflammatory macrophages. We find that in macrophages, serine is required for optimal lipopolysaccharide (LPS) induction of IL-1β mRNA expression, but not inflammasome activation. The mechanism involves a requirement for glycine, which is made from serine, to support macrophage GSH synthesis. Cell-permeable GSH, but not the one-carbon donor formate, rescues IL-1β mRNA expression. Pharmacological inhibition of de novo serine synthesis in vivo decreased LPS induction of IL-1β levels and improved survival in an LPS-driven model of sepsis in mice. Our study reveals that serine metabolism is necessary for GSH synthesis to support IL-1β cytokine production.
    Keywords:  IL-1beta; LPS response; glutathione; immunometabolism; inflammation; macrophage; one-carbon metabolism; sepsis; serine metabolism
    DOI:  https://doi.org/10.1016/j.cmet.2019.01.014
  46. Cancer Cell. 2019 Feb 04. pii: S1535-6108(19)30043-1. [Epub ahead of print]
    A Platform of Synthetic Lethal Gene Interaction Networks Reveals that the GNAQ Uveal Melanoma Oncogene Controls the Hippo Pathway through FAK.
    Xiaodong Feng, Nadia Arang, Damiano Cosimo Rigiracciolo, Joo Sang Lee, Huwate Yeerna, Zhiyong Wang, Simone Lubrano, Ayush Kishore, Jonathan A Pachter, Gabriele M König, Marcello Maggiolini, Evi Kostenis, David D Schlaepfer, Pablo Tamayo, Qianming Chen, Eytan Ruppin, J Silvio Gutkind.
      Activating mutations in GNAQ/GNA11, encoding Gαq G proteins, are initiating oncogenic events in uveal melanoma (UM). However, there are no effective therapies for UM. Using an integrated bioinformatics pipeline, we found that PTK2, encoding focal adhesion kinase (FAK), represents a candidate synthetic lethal gene with GNAQ activation. We show that Gαq activates FAK through TRIO-RhoA non-canonical Gαq-signaling, and genetic ablation or pharmacological inhibition of FAK inhibits UM growth. Analysis of the FAK-regulated transcriptome demonstrated that GNAQ stimulates YAP through FAK. Dissection of the underlying mechanism revealed that FAK regulates YAP by tyrosine phosphorylation of MOB1, inhibiting core Hippo signaling. Our findings establish FAK as a potential therapeutic target for UM and other Gαq-driven pathophysiologies that involve unrestrained YAP function.
    Keywords:  FAK; G protein; GNA11; GNAQ; Hippo; MOB1; PTK2; YAP; signal transduction; uveal melanoma
    DOI:  https://doi.org/10.1016/j.ccell.2019.01.009
  47. Metabolites. 2019 Feb 20. pii: E35. [Epub ahead of print]9(2):
    A Noninvasive Comparison Study between Human Gliomas with IDH1 and IDH2 Mutations by MR Spectroscopy.
    Xin Shen, Natalie L Voets, Sarah J Larkin, Nick de Pennington, Puneet Plaha, Richard Stacey, James S O McCullagh, Christopher J Schofield, Stuart Clare, Peter Jezzard, Tom Cadoux-Hudson, Olaf Ansorge, Uzay E Emir.
      The oncogenes that are expressed in gliomas reprogram particular pathways of glucose, amino acids, and fatty acid metabolism. Mutations in isocitrate dehydrogenase genes (IDH1/2) in diffuse gliomas are associated with abnormally high levels of 2-hydroxyglutarate (2-HG) levels. The aim of this study was to determine whether metabolic reprogramming associated with IDH mutant gliomas leads to additional ¹H MRS-detectable differences between IDH1 and IDH2 mutations, and to identify metabolites correlated with 2-HG. A total of 21 glioma patients (age= 37 ± 11, 13 males) were recruited for magnetic resonance spectroscopy (MRS) using semi-localization by adiabatic selective refocusing pulse sequence at an ultra-high-field (7T). For 20 patients, the tumor mutation subtype was confirmed by immunohistochemistry and DNA sequencing. LCModel analysis was applied for metabolite quantification. A two-sample t-test was used for metabolite comparisons between IDH1 (n = 15) and IDH2 (n = 5) mutant gliomas. The Pearson correlation coefficients between 2-HG and associated metabolites were calculated. A Bonferroni correction was applied for multiple comparison. IDH2 mutant gliomas have a higher level of 2-HG/tCho (total choline=phosphocholine+glycerylphosphorylcholine) (2.48 ± 1.01vs.0.72 ± 0.38, Pc < 0.001) and myo-Inositol/tCho (2.70 ± 0.90 vs. 1.46 ± 0.51, Pc = 0.011) compared to IDH1 mutation gliomas. Associated metabolites, myo-Inositol and glucose+taurine were correlated with 2-HG levels. These results show the improved characterization of the metabolic pathways in IDH1 and IDH2 gliomas for precision medicine.
    Keywords:  MR spectroscopy; glioma; isocitrate dehydrogenase; metabolism; neurochemical profile
    DOI:  https://doi.org/10.3390/metabo9020035
  48. J Biol Chem. 2019 Feb 20. pii: jbc.RA118.007050. [Epub ahead of print]
    The ER chaperones BiP and Grp94 selectively associate when BiP is in the ADP conformation.
    Ming Sun, Judy L M Kotler, Shanshan Liu, Timothy O Street.
      Hsp70 and Hsp90 chaperones are critical for protein quality control in the cytosol, while organelle-specific Hsp70/Hsp90 paralogs provide similar protection for mitochondria and the endoplasmic reticulum (ER). Cytosolic Hsp70/Hsp90 can operate sequentially with Hsp90 selectively associating with Hsp70 after Hsp70 is bound to a client protein. This observation has long suggested that Hsp90 could have a preference for interacting with clients at their later stages of folding. However, recent work has shown that cytosolic Hsp70/Hsp90 can directly interact even in the absence of a client, which opens up an alternative possibility that the ordered interactions of Hsp70/Hsp90 with clients could be a consequence of regulated changes in the direct interactions between Hsp70 and Hsp90. However, it is unknown how such regulation could occur mechanistically. Here we find that the ER Hsp70/Hsp90 (BiP/Grp94) can form a direct complex in the absence of a client. Importantly, the direct interaction between BiP/Grp94 is nucleotide-specific, with BiP and Grp94 having higher affinity under ADP conditions and lower affinity under ATP conditions. We show that this nucleotide-specific association between BiP and Grp94 is largely due to the conformation of BiP. When BiP is in the ATP conformation its substrate binding domain blocks Grp94; in contrast, Grp94 can readily associate with the ADP conformation of BiP, which represents the client-bound state of BiP. Our observations provide a mechanism for the sequential involvement of BiP and Grp94 in client folding where the conformation of BiP provides the signal for the subsequent recruitment of Grp94.
    Keywords:  BiP; Grp94; allostery; chaperone; fluorescence anisotropy; fluorescence resonance energy transfer (FRET); heat shock protein 90 (Hsp90); nuclear magnetic resonance (NMR); nucleotide; structural dynamics
    DOI:  https://doi.org/10.1074/jbc.RA118.007050
  49. Aging (Albany NY). 2019 Feb 20.
    Epigenetic signature: implications for mitochondrial quality control in human aging.
    Patrizia D'Aquila, Alberto Montesanto, Francesco De Rango, Francesco Guarasci, Giuseppe Passarino, Dina Bellizzi.
      Maintenance of functional mitochondria is essential to prevent damage leading to aging and diseases. What is more, the research of biomarkers of aging is focusing on better predicting functional capability along the lifetime beyond chronological age. Aim of this study was to identify novel CpG sites the methylation of which might be correlated to the chronological and biological age. We performed methylation analyses of the CpG sites in candidate genes involved in mitochondrial biogenesis, mitophagy, fusion, and fission, all key quality control mechanisms to ensure maintenance of healthy mitochondria and homeostasis during aging, using DNA samples from two independent datasets composed by 381 and 468 differently-aged individuals, respectively. Twelve potential CpG predictors resulted associated with aging in the discovery dataset. Of these, two sites located within RAB32 and RHOT2 genes were replicated in the second dataset. What is more, individuals exhibiting methylation levels of the RAB32 CpG site higher than 10% were observed more prone to disability than people with lower levels.These results seem to provide the first evidence that epigenetic modifications of genes involved in mitochondrial quality control occur over time according to the aging decline, and may then represent potential biomarkers of both chronological and biological age.
    Keywords:  age; aging biomarkers; biological; chronological age; epigenetics biomarkers; geriatric parameters; methylation; mitochondrial quality control
    DOI:  https://doi.org/10.18632/aging.101832
  50. Front Immunol. 2019 ;10 103
    Cell-Free Mitochondrial DNA in the CSF: A Potential Prognostic Biomarker of Anti-NMDAR Encephalitis.
    Yu Peng, Dong Zheng, Xiaomei Zhang, Suyue Pan, Teng Ji, Jun Zhang, Hai-Ying Shen, Hong-Hao Wang.
      Anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis is an autoimmune inflammatory brain disease that can develop a variety of neuropsychiatric presentations. However, the underlying nature of its inflammatory neuronal injury remains unclear. Mitochondrial DNA (mtDNA) is recently regarded as a damage-associated molecular pattern molecule (DAMP) that can initiate an inflammatory response. In the presenting study, we aimed to evaluate the levels of cell-free mtDNA in cerebrospinal fluid (CSF) of patients with anti-NMDAR encephalitis and to determine a potential role of cell-free mtDNA in the prognosis of anti-NMDAR encephalitis. A total of 33 patients with NMDAR encephalitis and 17 patients with other non-inflammatory disorders as controls were included in this study. The CSF levels of cell-free mtDNA were measured by quantitative polymerase chain reaction (qPCR). Cytokines including interleukin (IL)-6, IL-10, and tumor necrosis factor alpha (TNF-α) were measured by ELISA. The modified Rankin scale (mRS) score was evaluated for neurologic disabilities. Our data showed that the CSF levels of cell-free mtDNA and inflammation-associated cytokines were significantly higher in the patients with anti-NMDAR encephalitis compared with those in controls. Positive correlations were detected between the CSF levels of cell-free mtDNA and mRS scores of patients with anti-NMDAR encephalitis at both their admission and 6-month follow up. These findings suggest that the CSF level of cell-free mtDNA reflects the underlying neuroinflammatory process in patients with anti-NMDAR encephalitis and correlates with their clinical mRS scores. Therefore, cell-free mtDNA may be a potential prognostic biomarker for anti-NMDAR encephalitis.
    Keywords:  IL-10; IL-6; TNF-α; anti-NMDAR encephalitis; cell-free mitochondrial DNA; cerebrospinal fluid; cytokines; modified rankin scale
    DOI:  https://doi.org/10.3389/fimmu.2019.00103
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