bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2020–08–02
fifty-one papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit
  1. Na+ controls hypoxic signalling by the mitochondrial respiratory chain.
  2. Dihydroxyacetone phosphate signals glucose availability to mTORC1.
  3. The induction of AMPK-dependent autophagy leads to P53 degradation and affects cell growth and migration in kidney cancer cells.
  4. Purine metabolism regulates DNA repair and therapy resistance in glioblastoma.
  5. Role of O-Linked N-acetylglucosamine (O-GlcNAc) Protein Modification in Cellular (Patho)Physiology.
  6. SGLT2 Inhibition Mediates Protection from Diabetic Kidney Disease by Promoting Ketone Body-Induced mTORC1 Inhibition.
  7. Long-chain fatty acyl-CoA esters regulate metabolism via allosteric control of AMPK β1 isoforms.
  8. Mitofusin 2 Dysfunction and Disease in Mice and Men.
  9. The mitophagy effector FUNDC1 controls mitochondrial reprogramming and cellular plasticity in cancer cells.
  10. STAT3 serine phosphorylation is required for TLR4 metabolic reprogramming and IL-1β expression.
  11. The Mitochondrial Proteomic Signatures of Human Skeletal Muscle Linked to Insulin Resistance.
  12. Characterizing the ecological and evolutionary dynamics of cancer.
  13. Lysosomal activity regulates Caenorhabditis elegans mitochondrial dynamics through vitamin B12 metabolism.
  14. Clingy genes: Why were genes for ribosomal proteins retained in many mitochondrial genomes?
  15. Itaconic acid impairs the mitochondrial function by the inhibition of complexes II and IV and induction of the permeability transition pore opening in rat liver mitochondria.
  16. An acidic residue buried in the dimer interface of isocitrate dehydrogenase 1 (IDH1) helps regulate catalysis and pH sensitivity.
  17. MTOR-initiated metabolic switch and degeneration in the retinal pigment epithelium.
  18. DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance.
  19. VDAC oligomer pores: a mechanism in disease triggered by mtDNA release.
  20. Regulation of cancer cell glucose metabolism is determinant for cancer cell fate after melatonin administration.
  21. Dimethyl-2-oxoglutarate improves redox balance and mitochondrial function in muscle pericytes of individuals with diabetes mellitus.
  22. Biophysical properties of AKAP95 protein condensates regulate splicing and tumorigenesis.
  23. A spoonful of DHAP keeps mTORC1 running on sugars.
  24. BAX-dependent mitochondrial pathway mediates the crosstalk between ferroptosis and apoptosis.
  25. A Mitochondrial Stress-Specific Form of HSF1 Protects against Age-Related Proteostasis Collapse.
  26. Lipoic acid and autophagy: new insights into stem cell aging.
  27. Combined Proteomic and Genetic Interaction Mapping Reveals New RAS Effector Pathways and Susceptibilities.
  28. NADP modulates RNA m6A methylation and adipogenesis via enhancing FTO activity.
  29. Complex I mutations synergize to worsen the phenotypic expression of Leber's hereditary optic neuropathy.
  30. Glutamine deprivation alters the origin and function of cancer cell exosomes.
  31. Wiskott-Aldrich syndrome protein restricts cGAS-STING activation by dsDNA immune complexes.
  32. Regenerative Reprogramming of the Intestinal Stem Cell State via Hippo Signaling Suppresses Metastatic Colorectal Cancer.
  33. Imaging Mass Spectrometry Reveals Tumor Metabolic Heterogeneity.
  34. Peroxisomal Membrane Contact Sites in Mammalian Cells.
  35. Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation.
  36. MtDNA sequence features associated with 'selfish genomes' predict tissue-specific segregation and reversion.
  37. Organelle Cooperation in Stem Cell Fate: Lysosomes as Emerging Regulators of Cell Identity.
  38. HIF-1α regulates cellular metabolism, and Imatinib resistance by targeting phosphogluconate dehydrogenase in gastrointestinal stromal tumors.
  39. The mitochondrial ADP/ATP carrier exists and functions as a monomer.
  40. Spatiotemporal DNA methylome dynamics of the developing mouse fetus.
  41. The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic.
  42. APOBEC3-dependent kataegis and TREX1-driven chromothripsis during telomere crisis.
  43. Determinants of Endoplasmic Reticulum-to-Lipid Droplet Protein Targeting.
  44. MiT/TFE factors control ER-phagy via transcriptional regulation of FAM134B.
  45. Cysteine as a Carbon Source, a Hot Spot in Cancer Cells Survival.
  46. Mitochondrial calcium signalling and neurodegenerative diseases.
  47. AMPK as a direct sensor of long-chain fatty acyl-CoA esters.
  48. Microbiota-derived metabolite promotes HDAC3 activity in the gut.
  49. CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning.
  50. Oncogenic splicing regulated by phase separation.
  51. Alpha-ketoglutarate utilization in Saccharomyces cerevisiae: transport, compartmentation and catabolism.
  1. Nature. 2020 Jul 29.
    Na+ controls hypoxic signalling by the mitochondrial respiratory chain.
    Pablo Hernansanz-Agustín, Carmen Choya-Foces, Susana Carregal-Romero, Elena Ramos, Tamara Oliva, Tamara Villa-Piña, Laura Moreno, Alicia Izquierdo-Álvarez, J Daniel Cabrera-García, Ana Cortés, Ana Victoria Lechuga-Vieco, Pooja Jadiya, Elisa Navarro, Esther Parada, Alejandra Palomino-Antolín, Daniel Tello, Rebeca Acín-Pérez, Juan Carlos Rodríguez-Aguilera, Plácido Navas, Ángel Cogolludo, Iván López-Montero, Álvaro Martínez-Del-Pozo, Javier Egea, Manuela G López, John W Elrod, Jesús Ruíz-Cabello, Anna Bogdanova, José Antonio Enríquez, Antonio Martínez-Ruiz.
      All metazoans depend on the consumption of O2 by the mitochondrial oxidative phosphorylation system (OXPHOS) to produce energy. In addition, the OXPHOS uses O2 to produce reactive oxygen species that can drive cell adaptations1-4, a phenomenon that occurs in hypoxia4-8 and whose precise mechanism remains unknown. Ca2+ is the best known ion that acts as a second messenger9, yet the role ascribed to Na+ is to serve as a mere mediator of membrane potential10. Here we show that Na+ acts as a second messenger that regulates OXPHOS function and the production of reactive oxygen species by modulating the fluidity of the inner mitochondrial membrane. A conformational shift in mitochondrial complex I during acute hypoxia11 drives acidification of the matrix and the release of free Ca2+ from calcium phosphate (CaP) precipitates. The concomitant activation of the mitochondrial Na+/Ca2+ exchanger promotes the import of Na+ into the matrix. Na+ interacts with phospholipids, reducing inner mitochondrial membrane fluidity and the mobility of free ubiquinone between complex II and complex III, but not inside supercomplexes. As a consequence, superoxide is produced at complex III. The inhibition of Na+ import through the Na+/Ca2+ exchanger is sufficient to block this pathway, preventing adaptation to hypoxia. These results reveal that Na+ controls OXPHOS function and redox signalling through an unexpected interaction with phospholipids, with profound consequences for cellular metabolism.
    DOI:  https://doi.org/10.1038/s41586-020-2551-y
  2. Nat Metab. 2020 Jul 27.
    Dihydroxyacetone phosphate signals glucose availability to mTORC1.
    Jose M Orozco, Patrycja A Krawczyk, Sonia M Scaria, Andrew L Cangelosi, Sze Ham Chan, Tenzin Kunchok, Caroline A Lewis, David M Sabatini.
      The mechanistic target of rapamycin complex 1 (mTORC1) kinase regulates cell growth by setting the balance between anabolic and catabolic processes. To be active, mTORC1 requires the environmental presence of amino acids and glucose. While a mechanistic understanding of amino acid sensing by mTORC1 is emerging, how glucose activates mTORC1 remains mysterious. Here, we used metabolically engineered human cells lacking the canonical energy sensor AMP-activated protein kinase to identify glucose-derived metabolites required to activate mTORC1 independent of energetic stress. We show that mTORC1 senses a metabolite downstream of the aldolase and upstream of the GAPDH-catalysed steps of glycolysis and pinpoint dihydroxyacetone phosphate (DHAP) as the key molecule. In cells expressing a triose kinase, the synthesis of DHAP from DHA is sufficient to activate mTORC1 even in the absence of glucose. DHAP is a precursor for lipid synthesis, a process under the control of mTORC1, which provides a potential rationale for the sensing of DHAP by mTORC1.
    DOI:  https://doi.org/10.1038/s42255-020-0250-5
  3. Exp Cell Res. 2020 Jul 24. pii: S0014-4827(20)30439-0. [Epub ahead of print] 112190
    The induction of AMPK-dependent autophagy leads to P53 degradation and affects cell growth and migration in kidney cancer cells.
    Simone Patergnani, Sonia Guzzo, Alessandra Mangolini, Lucio dell'Atti, Paolo Pinton, Gianluca Aguiari.
      The most common subtype of renal cell carcinoma (RCC) is the clear cell RCC (ccRCC) that accounts for 70-80% of cases. The fate of ccRCC is linked to alterations of genes that regulate TP53. The dysfunction of p53 affects several processes including autophagy, which is increased in different advanced carcinomas and could be associated with cancer progression. We report that different kidney cancer cell lines show higher levels of autophagy than control cells. The increased autophagy is associated with the upregulation of miR501-5p, which stimulates mTOR-independent autophagy by the activation of AMP kinase. AMPK activation occurs through the decrease of ATP generation caused by the downregulation of the mitochondrial calcium uniporter (MCU) that leads to the reduction of mitochondrial calcium uptake. Autophagy induction promotes the degradation of p53 through the autophagolysosomal machinery. Consistently, the inhibition of autophagy reduces both cell proliferation and migration enhancing the expression of p53, p21 and E-Cadherin as well as decreasing Vimentin synthesis. Taken together, these findings indicate that autophagy is involved in the progression of kidney cancer. Therefore, the pharmacological targeting of this process could be considered an interesting option for the treatment of advanced renal carcinoma.
    Keywords:  AMPK; Autophagy; Cell growth; Kidney cancer; MicroRNAs; p53
    DOI:  https://doi.org/10.1016/j.yexcr.2020.112190
  4. Nat Commun. 2020 Jul 30. 11(1): 3811
    Purine metabolism regulates DNA repair and therapy resistance in glioblastoma.
    Weihua Zhou, Yangyang Yao, Andrew J Scott, Kari Wilder-Romans, Joseph J Dresser, Christian K Werner, Hanshi Sun, Drew Pratt, Peter Sajjakulnukit, Shuang G Zhao, Mary Davis, Barbara S Nelson, Christopher J Halbrook, Li Zhang, Francesco Gatto, Yoshie Umemura, Angela K Walker, Maureen Kachman, Jann N Sarkaria, Jianping Xiong, Meredith A Morgan, Alnawaz Rehemtualla, Maria G Castro, Pedro Lowenstein, Sriram Chandrasekaran, Theodore S Lawrence, Costas A Lyssiotis, Daniel R Wahl.
      Intratumoral genomic heterogeneity in glioblastoma (GBM) is a barrier to overcoming therapy resistance. Treatments that are effective independent of genotype are urgently needed. By correlating intracellular metabolite levels with radiation resistance across dozens of genomically-distinct models of GBM, we find that purine metabolites, especially guanylates, strongly correlate with radiation resistance. Inhibiting GTP synthesis radiosensitizes GBM cells and patient-derived neurospheres by impairing DNA repair. Likewise, administration of exogenous purine nucleosides protects sensitive GBM models from radiation by promoting DNA repair. Neither modulating pyrimidine metabolism nor purine salvage has similar effects. An FDA-approved inhibitor of GTP synthesis potentiates the effects of radiation in flank and orthotopic patient-derived xenograft models of GBM. High expression of the rate-limiting enzyme of de novo GTP synthesis is associated with shorter survival in GBM patients. These findings indicate that inhibiting purine synthesis may be a promising strategy to overcome therapy resistance in this genomically heterogeneous disease.
    DOI:  https://doi.org/10.1038/s41467-020-17512-x
  5. Physiol Rev. 2020 Jul 30.
    Role of O-Linked N-acetylglucosamine (O-GlcNAc) Protein Modification in Cellular (Patho)Physiology.
    John C Chatham, Jianhua Zhang, Adam Raymond Wende.
      In the mid 1980s, the identification of serine and threonine residues on nuclear and cytoplasmic proteins modified by an O-linkage by a N-acetylglucosamine moiety (O-GlcNAc) overturned the widely held assumption that glycosylation only occurred in the endoplasmic reticulum, Golgi apparatus, and secretory pathways. In contrast to traditional glycosylation, the O-GlcNAc modification does not lead to complex branched glycan structures and is rapidly cycled on and off proteins by O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), respectively. Since its discovery O-GlcNAcylation has been shown to contribute to numerous cellular functions including signaling, protein localization and stability, transcription, chromatin remodeling, mitochondrial function, and cell survival. Dysregulation in O-GlcNAc cycling has been implicated in the progression of a wide range of diseases such as diabetes, diabetic complications, cancer, cardiovascular, and neurodegenerative diseases. This review will outline our current understanding of the processes involved in regulating O-GlcNAc turnover, the role of O-GlcNAcylation in regulating cellular physiology, and how dysregulation in O-GlcNAc cycling contributes to pathophysiological processes.
    Keywords:  Calcium; Glucose; Insulin; O-GlcNAc; metabolism
    DOI:  https://doi.org/10.1152/physrev.00043.2019
  6. Cell Metab. 2020 Jul 19. pii: S1550-4131(20)30358-2. [Epub ahead of print]
    SGLT2 Inhibition Mediates Protection from Diabetic Kidney Disease by Promoting Ketone Body-Induced mTORC1 Inhibition.
    Issei Tomita, Shinji Kume, Sho Sugahara, Norihisa Osawa, Kosuke Yamahara, Mako Yasuda-Yamahara, Naoko Takeda, Masami Chin-Kanasaki, Tatsuroh Kaneko, Eric Mayoux, Michael Mark, Motoko Yanagita, Hisakazu Ogita, Shin-Ichi Araki, Hiroshi Maegawa.
      SGLT2 inhibitors offer strong renoprotection in subjects with diabetic kidney disease (DKD). But the mechanism for such protection is not clear. Here, we report that in damaged proximal tubules of high-fat diet-fed ApoE-knockout mice, a model of non-proteinuric DKD, ATP production shifted from lipolysis to ketolysis dependent due to hyperactivation of the mechanistic target of rapamycin complex 1 (mTORC1). We further found that empagliflozin raised endogenous ketone body (KB) levels, and thus its use or treatment with 1,3-butanediol, a KB precursor, prevented decreases in renal ATP levels and organ damage in the mice. The renoprotective effect of empagliflozin was abolished by gene deletion of Hmgcs2, a rate-limiting enzyme of ketogenesis. Furthermore, KBs attenuated mTORC1-associated podocyte damage and proteinuria in diabetic db/db mice. Our findings show that SGLT2 inhibition-associated renoprotection is mediated by an elevation of KBs that in turn corrects mTORC1 hyperactivation that occurs in non-proteinuric and proteinuric DKD.
    Keywords:  SGLT2 inhibitor; atherosclerosis; diabetic kidney disease; ketolysis; ketone body; lipolysis; mTORC1; nutrient-sensing signal; renal energy metabolism
    DOI:  https://doi.org/10.1016/j.cmet.2020.06.020
  7. Nat Metab. 2020 Jul 27.
    Long-chain fatty acyl-CoA esters regulate metabolism via allosteric control of AMPK β1 isoforms.
    Stephen L Pinkosky, John W Scott, Eric M Desjardins, Brennan K Smith, Emily A Day, Rebecca J Ford, Christopher G Langendorf, Naomi X Y Ling, Tracy L Nero, Kim Loh, Sandra Galic, Ashfaqul Hoque, William J Smiles, Kevin R W Ngoei, Michael W Parker, Yan Yan, Karsten Melcher, Bruce E Kemp, Jonathan S Oakhill, Gregory R Steinberg.
      Long-chain fatty acids (LCFAs) play important roles in cellular energy metabolism, acting as both an important energy source and signalling molecules1. LCFA-CoA esters promote their own oxidation by acting as allosteric inhibitors of acetyl-CoA carboxylase, which reduces the production of malonyl-CoA and relieves inhibition of carnitine palmitoyl-transferase 1, thereby promoting LCFA-CoA transport into the mitochondria for β-oxidation2-6. Here we report a new level of regulation wherein LCFA-CoA esters per se allosterically activate AMP-activated protein kinase (AMPK) β1-containing isoforms to increase fatty acid oxidation through phosphorylation of acetyl-CoA carboxylase. Activation of AMPK by LCFA-CoA esters requires the allosteric drug and metabolite site formed between the α-subunit kinase domain and the β-subunit. β1 subunit mutations that inhibit AMPK activation by the small-molecule activator A769662, which binds to the allosteric drug and metabolite site, also inhibit activation by LCFA-CoAs. Thus, LCFA-CoA metabolites act as direct endogenous AMPK β1-selective activators and promote LCFA oxidation.
    DOI:  https://doi.org/10.1038/s42255-020-0245-2
  8. Front Physiol. 2020 ;11 782
    Mitofusin 2 Dysfunction and Disease in Mice and Men.
    Gerald W Dorn.
      A causal relationship between Mitofusin (MFN) 2 gene mutations and the hereditary axonal neuropathy Charcot-Marie-Tooth disease type 2A (CMT2A) was described over 15 years ago. During the intervening period much has been learned about MFN2 functioning in mitochondrial fusion, calcium signaling, and quality control, and the consequences of these MFN2 activities on cell metabolism, fitness, and development. Nevertheless, the challenge of defining the central underlying mechanism(s) linking mitochondrial abnormalities to progressive dying-back of peripheral arm and leg nerves in CMT2A is largely unmet. Here, a different perspective of why, in humans, MFN2 dysfunction preferentially impacts peripheral nerves is provided based on recent insights into its role in determining whether individual mitochondria will be fusion-competent and retained within the cell, or are fusion-impaired, sequestered, and eliminated by mitophagy. Evidence for and against a regulatory role of mitofusins in mitochondrial transport is reviewed, nagging questions defined, and implications on mitochondrial fusion, quality control, and neuronal degeneration discussed. Finally, in the context of recently described mitofusin activating peptides and small molecules, an overview is provided of potential therapeutic applications for pharmacological enhancement of mitochondrial fusion and motility in CMT2A and other neurodegenerative conditions.
    Keywords:  Charcot-Marie-Tooth disease; mitochondrial fusion; mitochondrial transport; mitophagy; neurodegeneration
    DOI:  https://doi.org/10.3389/fphys.2020.00782
  9. Sci Signal. 2020 Jul 28. pii: eaaz8240. [Epub ahead of print]13(642):
    The mitophagy effector FUNDC1 controls mitochondrial reprogramming and cellular plasticity in cancer cells.
    Jie Li, Ekta Agarwal, Irene Bertolini, Jae Ho Seo, M Cecilia Caino, Jagadish C Ghosh, Andrew V Kossenkov, Qin Liu, Hsin-Yao Tang, Aaron R Goldman, Lucia R Languino, David W Speicher, Dario C Altieri.
      Mitochondria are signaling hubs in eukaryotic cells. Here, we showed that the mitochondrial FUN14 domain-containing protein-1 (FUNDC1), an effector of Parkin-independent mitophagy, also participates in cellular plasticity by sustaining oxidative bioenergetics, buffering ROS production, and supporting cell proliferation. Targeting this pathway in cancer cells suppressed tumor growth but rendered transformed cells more motile and invasive in a manner dependent on ROS-mediated mitochondrial dynamics and mitochondrial repositioning to the cortical cytoskeleton. Global metabolomics and proteomics profiling identified a FUNDC1 interactome at the mitochondrial inner membrane, comprising the AAA+ protease, LonP1, and subunits of oxidative phosphorylation, complex V (ATP synthase). Independently of its previously identified role in mitophagy, FUNDC1 enabled LonP1 proteostasis, which in turn preserved complex V function and decreased ROS generation. Therefore, mitochondrial reprogramming by a FUNDC1-LonP1 axis controls tumor cell plasticity by switching between proliferative and invasive states in cancer.
    DOI:  https://doi.org/10.1126/scisignal.aaz8240
  10. Nat Commun. 2020 Jul 30. 11(1): 3816
    STAT3 serine phosphorylation is required for TLR4 metabolic reprogramming and IL-1β expression.
    Jesse J Balic, Hassan Albargy, Kevin Luu, Francis J Kirby, W Samantha N Jayasekara, Finbar Mansell, Daniel J Garama, Dominic De Nardo, Nikola Baschuk, Cynthia Louis, Fiachra Humphries, Katherine Fitzgerald, Eicke Latz, Daniel J Gough, Ashley Mansell.
      Detection of microbial components such as lipopolysaccharide (LPS) by Toll-like receptor 4 (TLR4) on macrophages induces a robust pro-inflammatory response that is dependent on metabolic reprogramming. These innate metabolic changes have been compared to aerobic glycolysis in tumour cells. However, the mechanisms by which TLR4 activation leads to mitochondrial and glycolytic reprogramming are unknown. Here we show that TLR4 activation induces a signalling cascade recruiting TRAF6 and TBK-1, while TBK-1 phosphorylates STAT3 on S727. Using a genetically engineered mouse model incapable of undergoing STAT3 Ser727 phosphorylation, we show ex vivo and in vivo that STAT3 Ser727 phosphorylation is critical for LPS-induced glycolytic reprogramming, production of the central immune response metabolite succinate and inflammatory cytokine production in a model of LPS-induced inflammation. Our study identifies non-canonical STAT3 activation as the crucial signalling intermediary for TLR4-induced glycolysis, macrophage metabolic reprogramming and inflammation.
    DOI:  https://doi.org/10.1038/s41467-020-17669-5
  11. Int J Mol Sci. 2020 Jul 28. pii: E5374. [Epub ahead of print]21(15):
    The Mitochondrial Proteomic Signatures of Human Skeletal Muscle Linked to Insulin Resistance.
    Rikke Kruse, Navid Sahebekhtiari, Kurt Højlund.
       INTRODUCTION: Mitochondria are essential in energy metabolism and cellular survival, and there is growing evidence that insulin resistance in chronic metabolic disorders, such as obesity, type 2 diabetes (T2D), and aging, is linked to mitochondrial dysfunction in skeletal muscle. Protein profiling by proteomics is a powerful tool to investigate mechanisms underlying complex disorders. However, despite significant advances in proteomics within the past two decades, the technologies have not yet been fully exploited in the field of skeletal muscle proteome. Area covered: Here, we review the currently available studies characterizing the mitochondrial proteome in human skeletal muscle in insulin-resistant conditions, such as obesity, T2D, and aging, as well as exercise-mediated changes in the mitochondrial proteome. Furthermore, we outline technical challenges and limitations and methodological aspects that should be considered when planning future large-scale proteomics studies of mitochondria from human skeletal muscle. Authors' view: At present, most proteomic studies of skeletal muscle or isolated muscle mitochondria have demonstrated a reduced abundance of proteins in several mitochondrial biological processes in obesity, T2D, and aging, whereas the beneficial effects of exercise involve an increased content of muscle proteins involved in mitochondrial metabolism. Powerful mass-spectrometry-based proteomics now provides unprecedented opportunities to perform in-depth proteomics of muscle mitochondria, which in the near future is expected to increase our understanding of the complex molecular mechanisms underlying the link between mitochondrial dysfunction and insulin resistance in chronic metabolic disorders.
    Keywords:  Type 2 diabetes; insulin resistance; mitochondria; mitochondrial proteomics; skeletal muscle
    DOI:  https://doi.org/10.3390/ijms21155374
  12. Nat Genet. 2020 Jul 27.
    Characterizing the ecological and evolutionary dynamics of cancer.
    Nastaran Zahir, Ruping Sun, Daniel Gallahan, Robert A Gatenby, Christina Curtis.
      Tumor initiation and progression are somatic evolutionary processes driven by the accumulation of genetic alterations, some of which confer selective fitness advantages to the host cell. This gene-centric model has shaped the field of cancer biology and advanced understanding of cancer pathophysiology. Importantly, however, each genotype encodes diverse phenotypic traits that permit acclimation to varied microenvironmental conditions. Epigenetic and transcriptional changes also contribute to the heritable phenotypic variation required for evolution. Additionally, interactions between cancer cells and surrounding stromal and immune cells through autonomous and non-autonomous signaling can influence competition for survival. Therefore, a mechanistic understanding of tumor progression must account for evolutionary and ecological dynamics. In this Perspective, we outline technological advances and model systems to characterize tumor progression through space and time. We discuss the importance of unifying experimentation with computational modeling and opportunities to inform cancer control.
    DOI:  https://doi.org/10.1038/s41588-020-0668-4
  13. Proc Natl Acad Sci U S A. 2020 Jul 31. pii: 202008021. [Epub ahead of print]
    Lysosomal activity regulates Caenorhabditis elegans mitochondrial dynamics through vitamin B12 metabolism.
    Wei Wei, Gary Ruvkun.
      Mitochondrial fission and fusion are highly regulated by energy demand and physiological conditions to control the production, activity, and movement of these organelles. Mitochondria are arrayed in a periodic pattern in Caenorhabditis elegans muscle, but this pattern is disrupted by mutations in the mitochondrial fission component dynamin DRP-1. Here we show that the dramatically disorganized mitochondria caused by a mitochondrial fission-defective dynamin mutation is strongly suppressed to a more periodic pattern by a second mutation in lysosomal biogenesis or acidification. Vitamin B12 is normally imported from the bacterial diet via lysosomal degradation of B12-binding proteins and transport of vitamin B12 to the mitochondrion and cytoplasm. We show that the lysosomal dysfunction induced by gene inactivations of lysosomal biogenesis or acidification factors causes vitamin B12 deficiency. Growth of the C. elegans dynamin mutant on an Escherichia coli strain with low vitamin B12 also strongly suppressed the mitochondrial fission defect. Of the two C. elegans enzymes that require B12, gene inactivation of methionine synthase suppressed the mitochondrial fission defect of a dynamin mutation. We show that lysosomal dysfunction induced mitochondrial biogenesis, which is mediated by vitamin B12 deficiency and methionine restriction. S-adenosylmethionine, the methyl donor of many methylation reactions, including histones, is synthesized from methionine by S-adenosylmethionine synthase; inactivation of the sams-1 S-adenosylmethionine synthase also suppresses the drp-1 fission defect, suggesting that vitamin B12 regulates mitochondrial biogenesis and then affects mitochondrial fission via chromatin pathways.
    Keywords:  interorganelle communication; methionine restriction; mitochondrial dynamics; vacuolar V-ATPase; vitamin B12
    DOI:  https://doi.org/10.1073/pnas.2008021117
  14. Biochim Biophys Acta Bioenerg. 2020 Jul 23. pii: S0005-2728(20)30125-0. [Epub ahead of print]1861(11): 148275
    Clingy genes: Why were genes for ribosomal proteins retained in many mitochondrial genomes?
    Lea Bertgen, Timo Mühlhaus, Johannes M Herrmann.
      Why mitochondria still retain their own genome is a puzzle given the enormous effort to maintain a mitochondrial translation machinery. Most mitochondrially encoded proteins are membrane-embedded subunits of the respiratory chain. Their hydrophobicity presumably impedes their import into mitochondria. However, many mitochondrial genomes also encode protein subunits of the mitochondrial ribosome. These proteins lack transmembrane domains and hydrophobicity cannot explain why their genes remained in mitochondria. In this review, we provide an overview about mitochondrially encoded subunits of mitochondrial ribosomes of fungi, plants and protists. Moreover, we discuss and evaluate different hypotheses which were put forward to explain why (ribosomal) proteins remained mitochondrially encoded. It seems likely that the synthesis of ribosomal proteins in the mitochondrial matrix is used to regulate the assembly of the mitochondrial ribosome within mitochondria and to avoid problems that mitochondrial proteins might pose for cytosolic proteostasis and for the assembly of cytosolic ribosomes.
    Keywords:  Eukaryotes; Evolution; Gene transfer; Mitochondria; Respiratory chain; Ribosomes
    DOI:  https://doi.org/10.1016/j.bbabio.2020.148275
  15. Biochimie. 2020 Jul 25. pii: S0300-9084(20)30165-6. [Epub ahead of print]
    Itaconic acid impairs the mitochondrial function by the inhibition of complexes II and IV and induction of the permeability transition pore opening in rat liver mitochondria.
    Konstantin N Belosludtsev, Natalia V Belosludtseva, Ekaterina A Kosareva, Eugeny Yu Talanov, Sergey V Gudkov, Mikhail V Dubinin.
      Itaconic acid (methylene-succinic acid, ItA) is an unsaturated dicarboxylic acid that is secreted by mammalian macrophages in response to a pro-inflammatory stimulus and shows an anti-inflammatory/antibacterial effect. Being a mitochondrial metabolite, it exhibits an inhibitory activity on succinate dehydrogenase and subsequently induces mitochondrial dysfunction. The present study has shown that ItA dose-dependently inhibited ADP- and DNP-stimulated (uncoupled) respiration of rat liver mitochondria energized with succinate. This effect of ItA could be related to the suppression of the activity of complex II and the combined activity of complexes II + III of the respiratory chain. At the same time, ItA had no effect on the activity of the dicarboxylate carrier, which catalyzes the transport of succinate across the inner mitochondrial membrane. It was found that 4 mM ItA diminished the rates of ADP- and DNP-stimulated mitochondrial respiration supported by the substrates of complex I glutamate and malate. A study of the effect of ItA on the activity of complexes of the respiratory chain showed that it significantly decreases the activity of complex IV. It was observed that 4 mM ItA inhibited the rate of H2O2 production by mitochondria. At the same time, ItA promoted the opening of the cyclosporin A-sensitive Ca2+-dependent permeability transition pore. The latter was revealed as the decrease in the calcium retention capacity of mitochondria and the stimulation of release of cytochrome c from the organelles. ItA by itself promotes the cytochrome c release from mitochondria. Possible mechanisms of the effect of ItA on mitochondrial function are discussed.
    Keywords:  Dicarboxylate carrier; Itaconic acid; MPT pore; Mitochondria; Mitochondrial respiration; Oxidative phosphorylation; ROS production; Respiration chain complexes
    DOI:  https://doi.org/10.1016/j.biochi.2020.07.011
  16. Biochem J. 2020 Jul 30. pii: BCJ20200311. [Epub ahead of print]
    An acidic residue buried in the dimer interface of isocitrate dehydrogenase 1 (IDH1) helps regulate catalysis and pH sensitivity.
    Lucas A Luna, Zachary Lesecq, Katharine A White, An Hoang, David A Scott, Olga Zagnitko, Andrey A Bobkov, Diane L Barber, Jamie M Schiffer, Daniel G Isom, Christal D Sohl.
      Isocitrate dehydrogenase 1 (IDH1) catalyzes the reversible NADP+-dependent conversion of isocitrate to α-ketoglutarate (αKG) to provide critical cytosolic substrates and drive NADPH-dependent reactions like lipid biosynthesis and glutathione regeneration. In biochemical studies, the forward reaction is studied at neutral pH, while the reverse reaction is typically characterized in more acidic buffers. This led us to question whether IDH1 catalysis is pH-regulated, which would have functional implications under conditions that alter cellular pH, like apoptosis, hypoxia, cancer, and neurodegenerative diseases. Here, we show evidence of catalytic regulation of IDH1 by pH, identifying a trend of increasing kcat values for αKG production upon increasing pH in the buffers we tested. To understand the molecular determinants of IDH1 pH sensitivity, we used the pHinder algorithm to identify buried ionizable residues predicted to have shifted pKa values. Such residues can serve as pH sensors, with changes in protonation states leading to conformational changes that regulate catalysis. We identified an acidic residue buried at the IDH1 dimer interface, D273, with a predicted pKa value upshifted into the physiological range. D273 point mutations had decreased catalytic efficiency and, importantly, loss of pH-regulated catalysis. Based on these findings, we conclude that IDH1 activity is regulated, at least in part, by pH. We show this regulation is mediated by at least one buried acidic residue ~12 Å from the IDH1 active site. By establishing mechanisms of regulation of this well-conserved enzyme, we highlight catalytic features that may be susceptible to pH changes caused by cell stress and disease.
    Keywords:  buried ionizable residues; cancer; enzyme kinetics; pH regulation; post translational modification; tumor metabolism
    DOI:  https://doi.org/10.1042/BCJ20200311
  17. FASEB J. 2020 Jul 28.
    MTOR-initiated metabolic switch and degeneration in the retinal pigment epithelium.
    Young-Mi Go, Jing Zhang, Jolyn Fernandes, Christopher Litwin, Rui Chen, Theodore G Wensel, Dean P Jones, Jiyang Cai, Yan Chen.
      The retinal pigment epithelium (RPE) is a particularly vulnerable tissue to age-dependent degeneration. Over the life span, the RPE develops an expanded endo-lysosomal compartment to maintain the high efficiency of phagocytosis and degradation of photoreceptor outer segments (POS) necessary for photoreceptor survival. As the assembly and activation of the mechanistic target of rapamycin complex 1 (mTORC1) occur on the lysosome surface, increased lysosome mass with aging leads to higher mTORC1 activity. The functional consequences of hyperactive mTORC1 in the RPE are unclear. In the current study, we used integrated high-resolution metabolomic and genomic approaches to examine mice with RPE-specific deletion of the tuberous sclerosis 1 (Tsc1) gene which encodes an upstream suppressor of mTORC1. Our data show that RPE cells with constitutively high mTORC1 activity were reprogramed to be hyperactive in glucose and lipid metabolism. Lipolysis was suppressed, mitochondrial carnitine shuttle was inhibited, while genes involved in fatty acid (FA) biosynthesis were upregulated. The metabolic changes occurred prior to structural changes of RPE and retinal degeneration. These findings have revealed cellular events and intrinsic mechanisms that contribute to lipid accumulation in the RPE cells during aging and age-related degeneration.
    Keywords:  AMD; Mtor; aging; lipid; metabolism
    DOI:  https://doi.org/10.1096/fj.202000612R
  18. Genome Biol. 2020 Jul 27. 21(1): 182
    DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance.
    Flora D'Anna, Laurien Van Dyck, Jieyi Xiong, Hui Zhao, Rebecca V Berrens, Junbin Qian, Pawel Bieniasz-Krzywiec, Vikas Chandra, Luc Schoonjans, Jason Matthews, Julie De Smedt, Liesbeth Minnoye, Ricardo Amorim, Sepideh Khorasanizadeh, Qian Yu, Liyun Zhao, Marie De Borre, Savvas N Savvides, M Celeste Simon, Peter Carmeliet, Wolf Reik, Fraydoon Rastinejad, Massimiliano Mazzone, Bernard Thienpont, Diether Lambrechts.
       BACKGROUND: Hypoxia is pervasive in cancer and other diseases. Cells sense and adapt to hypoxia by activating hypoxia-inducible transcription factors (HIFs), but it is still an outstanding question why cell types differ in their transcriptional response to hypoxia.
    RESULTS: We report that HIFs fail to bind CpG dinucleotides that are methylated in their consensus binding sequence, both in in vitro biochemical binding assays and in vivo studies of differentially methylated isogenic cell lines. Based on in silico structural modeling, we show that 5-methylcytosine indeed causes steric hindrance in the HIF binding pocket. A model wherein cell-type-specific methylation landscapes, as laid down by the differential expression and binding of other transcription factors under normoxia, control cell-type-specific hypoxia responses is observed. We also discover ectopic HIF binding sites in repeat regions which are normally methylated. Genetic and pharmacological DNA demethylation, but also cancer-associated DNA hypomethylation, expose these binding sites, inducing HIF-dependent expression of cryptic transcripts. In line with such cryptic transcripts being more prone to cause double-stranded RNA and viral mimicry, we observe low DNA methylation and high cryptic transcript expression in tumors with high immune checkpoint expression, but not in tumors with low immune checkpoint expression, where they would compromise tumor immunotolerance. In a low-immunogenic tumor model, DNA demethylation upregulates cryptic transcript expression in a HIF-dependent manner, causing immune activation and reducing tumor growth.
    CONCLUSIONS: Our data elucidate the mechanism underlying cell-type-specific responses to hypoxia and suggest DNA methylation and hypoxia to underlie tumor immunotolerance.
    Keywords:  Cancer; Cryptic transcripts; DNA methylation; HIF; Hypoxia; Immunotherapy; Transcription factor binding
    DOI:  https://doi.org/10.1186/s13059-020-02087-z
  19. Cell Biol Int. 2020 Jul 27.
    VDAC oligomer pores: a mechanism in disease triggered by mtDNA release.
    Jialong Yan, Wei Liu, Fen Feng, Linxi Chen.
      A recent study suggests that voltage-dependent anion channel (VDAC) oligomer pores promote mitochondrial outer membrane permeabilization (MOMP) and allow mtDNA to be released into the cytosol in live cells. It challenges the notion that only occurs in apoptotic cells via BAX/BAK macropores. Cytosolic mtDNA activates cyclic GMP-AMP synthase (cGAS) / Stimulator of IFN Gene (STING) pathway and triggers type I interferon (IFN) response thereafter, which ultimately causes systemic lupus erythematosus (SLE). Mechanistically, mtDNA can interact with three positively charged residues (Lys12, Arg15, and Lys20) at the N-terminus of VDAC1, thereby strengthening VDAC1 oligomerization and facilitating mtDNA release. Additionally, there are other pathways that can mediate mtDNA release, such as BAX/BAK macropores and virus-derived pores. The mtDNA released into the cytosol also triggers type I IFN response via the generally accepted cGAS-STING-TANK-binding kinase 1(TBK1)-IFN regulatory factor 3 (IRF-3) axis. Collectively, VDAC oligomer pores provide us an attractive direction for us to understand mtDNA release-related diseases. This article is protected by copyright. All rights reserved.
    Keywords:  Biochemistry; Diseases; Intercellular communication; Mitochondria
    DOI:  https://doi.org/10.1002/cbin.11427
  20. J Cell Physiol. 2020 Jul 29.
    Regulation of cancer cell glucose metabolism is determinant for cancer cell fate after melatonin administration.
    Carmen Rodríguez, Noelia Puente-Moncada, Russel J Reiter, Ana M Sánchez-Sánchez, Federico Herrera, Jezabel Rodríguez-Blanco, Cristina Duarte-Olivenza, María Turos-Cabal, Isaac Antolín, Vanesa Martín.
      Several oncogenic pathways plus local microenvironmental conditions, such as hypoxia, converge on the regulation of cancer cells metabolism. The major metabolic alteration consists of a shift from oxidative phosphorylation as the major glucose consumer to aerobic glycolysis, although most of cancer cells utilize both pathways to a greater or lesser extent. Aerobic glycolysis, together with the directly related metabolic pathways such as the tricarboxylic acid cycle, the pentose phosphate pathway, or gluconeogenesis are currently considered as therapeutic targets in cancer research. Melatonin has been reported to present numerous antitumor effects, which result in a reduced cell growth. This is achieved with both low and high concentrations with no relevant side effects. Indeed, high concentrations of this indolamine reduce proliferation of cancer types resistant to low concentrations and induce cell death in some types of tumors. Previous work suggest that regulation of glucose metabolism and other related pathways play an important role in the antitumoral effects of high concentration of melatonin. In the present review, we analyze recent work on the regulation by such concentrations of this indolamine on aerobic glycolysis, gluconeogenesis, the tricarboxylic acid cycle and the pentose phosphate pathways of cancer cells.
    Keywords:  TCA cycle; aerobic glycolysis; gluconeogenesis; melatonin cytotoxicity; pentose phosphate pathway; tumor metabolism
    DOI:  https://doi.org/10.1002/jcp.29886
  21. Diabetologia. 2020 Jul 30.
    Dimethyl-2-oxoglutarate improves redox balance and mitochondrial function in muscle pericytes of individuals with diabetes mellitus.
    Ashton Faulkner, Anita Tamiato, William Cathery, Andrea Rampin, Carlo Maria Caravaggi, Eva Jover, Steve Allen, Harry Mellor, David Hauton, Lisa C Heather, Gaia Spinetti, Paolo Madeddu.
       AIMS/HYPOTHESIS: Treatment of vascular complications of diabetes remains inadequate. We reported that muscle pericytes (MPs) from limb muscles of vascular patients with diabetes mellitus display elevated levels of oxidative stress causing a dysfunctional phenotype. Here, we investigated whether treatment with dimethyl-2-oxoglutarate (DM-2OG), a tricarboxylic acid cycle metabolite with antioxidant properties, can restore a healthy metabolic and functional phenotype.
    METHODS: MPs were isolated from limb muscles of diabetes patients with vascular disease (D-MPs) and from non-diabetic control participants (ND-MPs). Metabolic status was assessed in untreated and DM-2OG-treated (1 mmol/l) cells using an extracellular flux analyser and anion-exchange chromatography-mass spectrometry (IC-MS/MS). Redox status was measured using commercial kits and IC-MS/MS, with antioxidant and metabolic enzyme expression assessed by quantitative RT-PCR and western blotting. Myogenic differentiation and proliferation and pericyte-endothelial interaction were assessed as functional readouts.
    RESULTS: D-MPs showed mitochondrial dysfunction, suppressed glycolytic activity and reduced reactive oxygen species-buffering capacity, but no suppression of antioxidant systems when compared with ND-MP controls. DM-2OG supplementation improved redox balance and mitochondrial function, without affecting glycolysis or antioxidant systems. Nonetheless, this was not enough for treated D-MPs to regain the level of proliferation and myogenic differentiation of ND-MPs. Interestingly, DM-2OG exerted a positive effect on pericyte-endothelial cell interaction in the co-culture angiogenesis assay, independent of the diabetic status.
    CONCLUSIONS/INTERPRETATION: These novel findings support the concept of using DM-2OG supplementation to improve pericyte redox balance and mitochondrial function, while concurrently allowing for enhanced pericyte-endothelial crosstalk. Such effects may help to prevent or slow down vasculopathy in skeletal muscles of people with diabetes. Graphical abstract.
    Keywords:  2-Oxoglutarate; Diabetes mellitus; Mitochondria; Pericytes; Redox; Vascular protection
    DOI:  https://doi.org/10.1007/s00125-020-05230-4
  22. Nat Cell Biol. 2020 Jul 27.
    Biophysical properties of AKAP95 protein condensates regulate splicing and tumorigenesis.
    Wei Li, Jing Hu, Bi Shi, Francesco Palomba, Michelle A Digman, Enrico Gratton, Hao Jiang.
      It remains unknown if biophysical or material properties of biomolecular condensates regulate cancer. Here we show that AKAP95, a nuclear protein that regulates transcription and RNA splicing, plays an important role in tumorigenesis by supporting cancer cell growth and suppressing oncogene-induced senescence. AKAP95 forms phase-separated and liquid-like condensates in vitro and in nucleus. Mutations of key residues to different amino acids perturb AKAP95 condensation in opposite directions. Importantly, the activity of AKAP95 in splice regulation is abolished by disruption of condensation, significantly impaired by hardening of condensates, and regained by substituting its condensation-mediating region with other condensation-mediating regions from irrelevant proteins. Moreover, the abilities of AKAP95 in regulating gene expression and supporting tumorigenesis require AKAP95 to form condensates with proper liquidity and dynamicity. These results link phase separation to tumorigenesis and uncover an important role of appropriate biophysical properties of protein condensates in gene regulation and cancer.
    DOI:  https://doi.org/10.1038/s41556-020-0550-8
  23. Nat Metab. 2020 Jul 27.
    A spoonful of DHAP keeps mTORC1 running on sugars.
    Gerta Hoxhaj, Jason W Locasale, Issam Ben-Sahra.
      
    DOI:  https://doi.org/10.1038/s42255-020-0246-1
  24. Apoptosis. 2020 Jul 31.
    BAX-dependent mitochondrial pathway mediates the crosstalk between ferroptosis and apoptosis.
    Young-Sun Lee, Kalishwaralal Kalimuthu, Yong Seok Park, Xu Luo, M Haroon A Choudry, David L Bartlett, Yong J Lee.
      Ferroptosis is considered a distinctive form of cell death compared to other types of death such as apoptosis. It is known to result from iron-dependent accumulation of lipid peroxides rather than caspase activation. However, we reported recently that ferroptosis interplays with apoptosis. In this study, we investigated a possible mechanism of this interplay between ferroptosis and apoptosis. Results from our studies reveal that combined treatment of the ferroptotic agent erastin and the apoptotic agent TRAIL effectively disrupted mitochondrial membrane potential (ΔΨm) and subsequently promoted caspase activation. The alterations of mitochondrial membrane potential are probably due to an increase in oligomerization of BAX and its accumulation at the mitochondria during treatment with erastin and TRAIL. Interestingly, the combined treatment-promoted apoptosis was effectively inhibited in BAX-deficient HCT116 cells, but not BAK-deficient cells. These results indicate that the BAX-associated mitochondria-dependent pathway plays a pivotal role in erastin-enhanced TRAIL-induced apoptosis.
    Keywords:  Apoptosis; BAX; Crosstalk; Ferroptosis; Mitochondria-dependent pathway
    DOI:  https://doi.org/10.1007/s10495-020-01627-z
  25. Dev Cell. 2020 Jul 15. pii: S1534-5807(20)30546-3. [Epub ahead of print]
    A Mitochondrial Stress-Specific Form of HSF1 Protects against Age-Related Proteostasis Collapse.
    Rhianna Williams, Mihails Laskovs, Rebecca I Williams, Ananya Mahadevan, John Labbadia.
      The loss of protein homeostasis (proteostasis) is a primary driver of age-related tissue dysfunction. Recent studies have revealed that the failure of proteostasis with age is triggered by developmental and reproductive cues that repress the activity of proteostasis-related pathways in early adulthood. In Caenorhabditis elegans, reduced mitochondrial electron transport chain (ETC) function during development can override signals that promote proteostasis collapse in aged tissues. However, it is unclear precisely how these beneficial effects are mediated. Here, we reveal that in response to ETC impairment, the PP2A complex generates a dephosphorylated, mitochondrial stress-specific variant of the transcription factor HSF-1. This results in the selective induction of small heat shock proteins in adulthood, thereby protecting against age-related proteostasis collapse. We propose that mitochondrial signals early in life can protect the aging cytosolic proteome by tailoring HSF-1 activity to preferentially drive the expression of non-ATP-dependent chaperones.
    Keywords:  HSF1; PP2A; aging; mitochondria; molecular chaperones; protein aggregation; proteostasis; stress responses
    DOI:  https://doi.org/10.1016/j.devcel.2020.06.038
  26. EMBO Rep. 2020 Jul 27. e202051175
    Lipoic acid and autophagy: new insights into stem cell aging.
    Peng Zhang, Bruce A Edgar.
      The gastrointestinal tract undergoes homeostatic self-renewal to replace aged and damaged epithelial cells. This process, sustained by intestinal stem cells (ISCs), can operate accurately for many years but gradually declines with age. Although stem cell aging has been intensively explored, the mechanisms remain poorly understood. In this issue of EMBO Reports, Du et al report that alpha-lipoic acid (ALA) sustains an active endocytosis-autophagy network that effectively reverses age-dependent ISC hyperplasia in Drosophila (Du et al, 2020). This work suggests a new strategy for treating aging-associated gastrointestinal diseases.
    DOI:  https://doi.org/10.15252/embr.202051175
  27. Cancer Discov. 2020 Jul 29. pii: CD-19-1274. [Epub ahead of print]
    Combined Proteomic and Genetic Interaction Mapping Reveals New RAS Effector Pathways and Susceptibilities.
    Marcus Robert Kelly, Kaja Kostyrko, Kyuho Han, Nancie Ann Mooney, Edwin E Jeng, Kaitlyn Spees, Phuong T Dinh, Keene L Abbott, Dana Marie Gwinn, E Alejandro Sweet-Cordero, Michael Cory Bassik, Peter K Jackson.
      Activating mutations in RAS GTPases drive many cancers, but limited understanding of less-studied RAS interactors, and of the specific roles of different RAS interactor paralogs, continues to limit target discovery. We developed a multistage discovery and screening process to systematically identify genes conferring RAS-related susceptibilities in lung adenocarcinoma. Using affinity purification mass spectrometry, we generated a protein-protein interaction map of RAS interactors and pathway components containing hundreds of interactions. From this network, we constructed a CRISPR dual knockout library targeting 119 RAS-related genes that we screened for KRAS-dependent genetic interactions (GIs). This approach identified new RAS effectors, including the adhesion controller RADIL and the endocytosis regulator RIN1, and >250 synthetic lethal GIs, including a potent KRAS-dependent interaction between RAP1GDS1 and RHOA. Many GIs link specific paralogs within and between gene families. These findings illustrate the power of multiomic approaches to uncover synthetic lethal combinations specific for hitherto untreatable cancer genotypes.
    DOI:  https://doi.org/10.1158/2159-8290.CD-19-1274
  28. Nat Chem Biol. 2020 Jul 27.
    NADP modulates RNA m6A methylation and adipogenesis via enhancing FTO activity.
    Lina Wang, Chengli Song, Na Wang, Songyu Li, Qiaoling Liu, Zhen Sun, Kai Wang, Shi-Cang Yu, Qingkai Yang.
      Metabolism is often regulated by the transcription and translation of RNA. In turn, it is likely that some metabolites regulate enzymes controlling reversible RNA modification, such as N6-methyladenosine (m6A), to modulate RNA. This hypothesis is at least partially supported by the findings that multiple metabolic diseases are highly associated with fat mass and obesity-associated protein (FTO), an m6A demethylase. However, knowledge about whether and which metabolites directly regulate m6A remains elusive. Here, we show that NADP directly binds FTO, independently increases FTO activity, and promotes RNA m6A demethylation and adipogenesis. We screened a set of metabolites using a fluorescence quenching assay and NADP was identified to remarkably bind FTO. In vitro demethylation assays indicated that NADP enhances FTO activity. Furthermore, NADP regulated mRNA m6A via FTO in vivo, and deletion of FTO blocked NADP-enhanced adipogenesis in 3T3-L1 preadipocytes. These results build a direct link between metabolism and RNA m6A demethylation.
    DOI:  https://doi.org/10.1038/s41589-020-0601-2
  29. J Biol Chem. 2020 Jul 28. pii: jbc.RA120.014603. [Epub ahead of print]
    Complex I mutations synergize to worsen the phenotypic expression of Leber's hereditary optic neuropathy.
    Yanchun Ji, Juanjuan Zhang, Yuanyuan Lu, Qiuzi Yi, Mengquan Chen, Shipeng Xie, Xiaoting Mao, Yun Xiao, Feilong Meng, Minlian Zhang, Rulai Yang, Min-Xin Guan.
      Leber's hereditary optic neuropathy (LHON) is a maternal inheritance of eye disease due to the mitochondrial DNA mtDNA) mutations. We previously discovered a 3866T>C mutation within the gene for the ND1 subunit of complex I as possibly amplifying disease progression for patients bearing the disease-causing 11778G>A mutation, within the gene for the ND4 subunit of Complex I. However, whether and how the ND1 mutation exacerbates the ND4 mutation were unknown. In this report, we showed that four Chinese families bearing both m.3866T>C and m.11778G>A mutations exhibited higher penetrances of LHON than 6 Chinese pedigrees carrying only the m.3866T>C mutation or families harboring only the m.11778G>A mutation. The protein structure analysis revealed that the m.3866T>C (I187T) and m.11778G>A (R340H) mutations destabilized the specific interactions with other residues of ND1 and ND4, thereby altering the structure and function of complex I, respectively. Cellular data obtained using cybrids constructed by transferring mitochondria from the Chinese families into mtDNA-less (ro) cells demonstrated that the mutations perturbed the stability, assembly and activity of complex I, leading to changes in mitochondrial ATP levels and membrane potential, and increasing the production of reactive oxygen species. These mitochondrial dysfunctions promoted the apoptotic sensitivity of cells and decreased mitophagy. Cybrids bearing only m.3866T>C mutation displayed mild mitochondrial dysfunctions while those harboring both m.3866T>C and m.11778G>A mutations exhibited greater mitochondrial dysfunctions. These suggested that the m.3866T>C mutation acted as the synergy with m.11778G>A mutation, aggravating mitochondrial dysfunctions contributing to higher penetrance of LHON in these families carrying both mtDNA mutations.
    Keywords:  Leber’s hereditary optic neuropathy; Modifier; NADH: ubiquinone oxidoreductase; apoptosis; human genetics; mitochondrial DNA; mitochondrial disease; mitochondrial respiratory chain complex; mitophagy; molecular modeling; organelle; oxygen radicals; pathogenesis; penetrance; vision
    DOI:  https://doi.org/10.1074/jbc.RA120.014603
  30. EMBO J. 2020 Jul 28. e103009
    Glutamine deprivation alters the origin and function of cancer cell exosomes.
    Shih-Jung Fan, Benjamin Kroeger, Pauline P Marie, Esther M Bridges, John D Mason, Kristie McCormick, Christos E Zois, Helen Sheldon, Nasullah Khalid Alham, Errin Johnson, Matthew Ellis, Maria Irina Stefana, Cláudia C Mendes, Stephen Mark Wainwright, Christopher Cunningham, Freddie C Hamdy, John F Morris, Adrian L Harris, Clive Wilson, Deborah Ci Goberdhan.
      Exosomes are secreted extracellular vesicles carrying diverse molecular cargos, which can modulate recipient cell behaviour. They are thought to derive from intraluminal vesicles formed in late endosomal multivesicular bodies (MVBs). An alternate exosome formation mechanism, which is conserved from fly to human, is described here, with exosomes carrying unique cargos, including the GTPase Rab11, generated in Rab11-positive recycling endosomal MVBs. Release of Rab11-positive exosomes from cancer cells is increased relative to late endosomal exosomes by reducing growth regulatory Akt/mechanistic Target of Rapamycin Complex 1 (mTORC1) signalling or depleting the key metabolic substrate glutamine, which diverts membrane flux through recycling endosomes. Vesicles produced under these conditions promote tumour cell proliferation and turnover and modulate blood vessel networks in xenograft mouse models in vivo. Their growth-promoting activity, which is also observed in vitro, is Rab11a-dependent, involves ERK-MAPK-signalling and is inhibited by antibodies against amphiregulin, an EGFR ligand concentrated on these vesicles. Therefore, glutamine depletion or mTORC1 inhibition stimulates release from Rab11a compartments of exosomes with pro-tumorigenic functions, which we propose promote stress-induced tumour adaptation.
    Keywords:  Rab11(a); exosome; extracellular vesicle; mechanistic Target of Rapamycin; multivesicular body
    DOI:  https://doi.org/10.15252/embj.2019103009
  31. JCI Insight. 2020 Jul 28. pii: 132857. [Epub ahead of print]
    Wiskott-Aldrich syndrome protein restricts cGAS-STING activation by dsDNA immune complexes.
    Giulia Maria Piperno, Asma Naseem, Giulia Silvestrelli, Roberto Amadio, Nicoletta Caronni, Karla Evelia Cervantes Luevano, Nalan Liv, Judith Klumperman, Andrea Colliva, Hashim Ali, Francesca Graziano, Philippe Benaroch, Hans Haecker, Richard N Hanna, Federica Benvenuti.
      Dysregulated sensing of self nucleic acid is a leading cause of autoimmunity in multifactorial and monogenic diseases. Mutations in Wiskott-Aldrich syndrome protein (WASp), a key regulator of cytoskeletal dynamics in immune cells, cause autoimmune manifestations and increased production of type-I interferons by innate cells. Here we show that complexes of self-DNA and autoantibodies (DNA-IC) contribute to elevated interferon levels via activation of the cGAS-STING pathway of cytosolic sensing. Mechanistically, lack of endosomal F-actin nucleation by WASp causes a delay in endolysosomal maturation and prolongs the transit time of ingested DNA-IC. Stalling in maturation-defective organelles facilitates leakage of DNA-IC into the cytosol, promoting activation of the TBK1-STING pathway. Genetic deletion of STING, STING and cGAS chemical inhibitors abolish interferon production and rescue systemic activation of interferon stimulated genes in vivo. These data unveil the contribution of cytosolic self-nucleic acid sensing in WAS and underscore the importance of WASp-mediated endosomal actin remodelling to prevent innate activation.
    Keywords:  Cell Biology; Dendritic cells; Immunology; Innate immunity
    DOI:  https://doi.org/10.1172/jci.insight.132857
  32. Cell Stem Cell. 2020 Jul 24. pii: S1934-5909(20)30341-6. [Epub ahead of print]
    Regenerative Reprogramming of the Intestinal Stem Cell State via Hippo Signaling Suppresses Metastatic Colorectal Cancer.
    Priscilla Cheung, Jordi Xiol, Michael T Dill, Wei-Chien Yuan, Riccardo Panero, Jatin Roper, Fernando G Osorio, Dejan Maglic, Qi Li, Basanta Gurung, Raffaele A Calogero, Ömer H Yilmaz, Junhao Mao, Fernando D Camargo.
      Although the Hippo transcriptional coactivator YAP is considered oncogenic in many tissues, its roles in intestinal homeostasis and colorectal cancer (CRC) remain controversial. Here, we demonstrate that the Hippo kinases LATS1/2 and MST1/2, which inhibit YAP activity, are required for maintaining Wnt signaling and canonical stem cell function. Hippo inhibition induces a distinct epithelial cell state marked by low Wnt signaling, a wound-healing response, and transcription factor Klf6 expression. Notably, loss of LATS1/2 or overexpression of YAP is sufficient to reprogram Lgr5+ cancer stem cells to this state and thereby suppress tumor growth in organoids, patient-derived xenografts, and mouse models of primary and metastatic CRC. Finally, we demonstrate that genetic deletion of YAP and its paralog TAZ promotes the growth of these tumors. Collectively, our results establish the role of YAP as a tumor suppressor in the adult colon and implicate Hippo kinases as therapeutic vulnerabilities in colorectal malignancies.
    Keywords:  Hippo signaling; Wnt signaling; colorectal cancer; intestinal stem cells; metastasis; regeneration
    DOI:  https://doi.org/10.1016/j.stem.2020.07.003
  33. iScience. 2020 Jul 10. pii: S2589-0042(20)30542-3. [Epub ahead of print]23(8): 101355
    Imaging Mass Spectrometry Reveals Tumor Metabolic Heterogeneity.
    Yang Zhang, Christelle Guillermier, Thomas De Raedt, Andrew G Cox, Ophelia Maertens, Dean Yimlamai, Mingyue Lun, Adam Whitney, Richard L Maas, Wolfram Goessling, Karen Cichowski, Matthew L Steinhauser.
      Malignant tumors exhibit high degrees of genomic heterogeneity at the cellular level, leading to the view that subpopulations of tumor cells drive growth and treatment resistance. To examine the degree to which tumors also exhibit metabolic heterogeneity at the level of individual cells, we employed multi-isotope imaging mass spectrometry (MIMS) to quantify utilization of stable isotopes of glucose and glutamine along with a label for cell division. Mouse models of melanoma and malignant peripheral nerve sheath tumors (MPNSTs) exhibited striking heterogeneity of substrate utilization, evident in both proliferating and non-proliferating cells. We identified a correlation between metabolic heterogeneity, proliferation, and therapeutic resistance. Heterogeneity in metabolic substrate usage as revealed by incorporation of glucose and glutamine tracers is thus a marker for tumor proliferation. Collectively, our data demonstrate that MIMS provides a powerful tool with which to dissect metabolic functions of individual cells within the native tumor environment.
    Keywords:  Biological Sciences; Cancer Systems Biology
    DOI:  https://doi.org/10.1016/j.isci.2020.101355
  34. Front Cell Dev Biol. 2020 ;8 512
    Peroxisomal Membrane Contact Sites in Mammalian Cells.
    Chao Chen, Jing Li, Xuhui Qin, Wei Wang.
      Peroxisomes participate in essential cellular metabolic processes, such as oxidation of fatty acids (FAs) and maintenance of reactive oxygen species (ROS) homeostasis. Peroxisomes must communicate with surrounding organelles to exchange information and metabolites. The formation of membrane contact sites (MCSs), where protein-protein or protein-lipid complexes tether the opposing membranes of two organelles, represents an essential means of organelle crosstalk. Peroxisomal MCS (PO-MCS) studies are emerging but are still in the early stages. In this review, we summarize the identified PO-MCSs with the ER, mitochondria, lipid droplets, and lysosomes in mammalian cells and discuss their tethering mechanisms and physiological roles. We also highlight several features of PO-MCSs that may help future studies.
    Keywords:  membrane contact sites; metabolism; organelle crosstalk; peroxisomes; tethering complexes
    DOI:  https://doi.org/10.3389/fcell.2020.00512
  35. Nat Commun. 2020 Jul 31. 11(1): 3830
    Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation.
    Ravi Kiran Koripella, Manjuli R Sharma, Kalpana Bhargava, Partha P Datta, Prem S Kaushal, Pooja Keshavan, Linda L Spremulli, Nilesh K Banavali, Rajendra K Agrawal.
      The mammalian mitochondrial ribosome (mitoribosome) and its associated translational factors have evolved to accommodate greater participation of proteins in mitochondrial translation. Here we present the 2.68-3.96 Å cryo-EM structures of the human 55S mitoribosome in complex with the human mitochondrial elongation factor G1 (EF-G1mt) in three distinct conformational states, including an intermediate state and a post-translocational state. These structures reveal the role of several mitochondria-specific (mito-specific) mitoribosomal proteins (MRPs) and a mito-specific segment of EF-G1mt in mitochondrial tRNA (tRNAmt) translocation. In particular, the mito-specific C-terminal extension in EF-G1mt is directly involved in translocation of the acceptor arm of the A-site tRNAmt. In addition to the ratchet-like and independent head-swiveling motions exhibited by the small mitoribosomal subunit, we discover significant conformational changes in MRP mL45 at the nascent polypeptide-exit site within the large mitoribosomal subunit that could be critical for tethering of the elongating mitoribosome onto the inner-mitochondrial membrane.
    DOI:  https://doi.org/10.1038/s41467-020-17715-2
  36. Nucleic Acids Res. 2020 Jul 27. pii: gkaa622. [Epub ahead of print]
    MtDNA sequence features associated with 'selfish genomes' predict tissue-specific segregation and reversion.
    Ellen C Røyrvik, Iain G Johnston.
      Mitochondrial DNA (mtDNA) encodes cellular machinery vital for cell and organism survival. Mutations, genetic manipulation, and gene therapies may produce cells where different types of mtDNA coexist in admixed populations. In these admixtures, one mtDNA type is often observed to proliferate over another, with different types dominating in different tissues. This 'segregation bias' is a long-standing biological mystery that may pose challenges to modern mtDNA disease therapies, leading to substantial recent attention in biological and medical circles. Here, we show how an mtDNA sequence's balance between replication and transcription, corresponding to molecular 'selfishness', in conjunction with cellular selection, can potentially modulate segregation bias. We combine a new replication-transcription-selection (RTS) model with a meta-analysis of existing data to show that this simple theory predicts complex tissue-specific patterns of segregation in mouse experiments, and reversion in human stem cells. We propose the stability of G-quadruplexes in the mtDNA control region, influencing the balance between transcription and replication primer formation, as a potential molecular mechanism governing this balance. Linking mtDNA sequence features, through this molecular mechanism, to cellular population dynamics, we use sequence data to obtain and verify the sequence-specific predictions from this hypothesis on segregation behaviour in mouse and human mtDNA.
    DOI:  https://doi.org/10.1093/nar/gkaa622
  37. Front Cell Dev Biol. 2020 ;8 591
    Organelle Cooperation in Stem Cell Fate: Lysosomes as Emerging Regulators of Cell Identity.
    Lisa M Julian, William L Stanford.
      Regulation of stem cell fate is best understood at the level of gene and protein regulatory networks, though it is now clear that multiple cellular organelles also have critical impacts. A growing appreciation for the functional interconnectedness of organelles suggests that an orchestration of integrated biological networks functions to drive stem cell fate decisions and regulate metabolism. Metabolic signaling itself has emerged as an integral regulator of cell fate including the determination of identity, activation state, survival, and differentiation potential of many developmental, adult, disease, and cancer-associated stem cell populations and their progeny. As the primary adenosine triphosphate-generating organelles, mitochondria are well-known regulators of stem cell fate decisions, yet it is now becoming apparent that additional organelles such as the lysosome are important players in mediating these dynamic decisions. In this review, we will focus on the emerging role of organelles, in particular lysosomes, in the reprogramming of both metabolic networks and stem cell fate decisions, especially those that impact the determination of cell identity. We will discuss the inter-organelle interactions, cell signaling pathways, and transcriptional regulatory mechanisms with which lysosomes engage and how these activities impact metabolic signaling. We will further review recent data that position lysosomes as critical regulators of cell identity determination programs and discuss the known or putative biological mechanisms. Finally, we will briefly highlight the potential impact of elucidating mechanisms by which lysosomes regulate stem cell identity on our understanding of disease pathogenesis, as well as the development of refined regenerative medicine, biomarker, and therapeutic strategies.
    Keywords:  cancer stem cell (CSC); lysosomes; metabolism; neural crest (NC); neural stem cell (NSC); pluripotent stem cell (PSC); stem cell identity and fate
    DOI:  https://doi.org/10.3389/fcell.2020.00591
  38. Cell Death Dis. 2020 Jul 27. 11(7): 586
    HIF-1α regulates cellular metabolism, and Imatinib resistance by targeting phosphogluconate dehydrogenase in gastrointestinal stromal tumors.
    Kangjing Xu, Zhongyuan He, Ming Chen, Nuofan Wang, Diancai Zhang, Li Yang, Zekuan Xu, Hao Xu.
      The pentose phosphate pathway (PPP) plays a critical role in maintaining cellular redox homeostasis in tumor cells and macromolecule biosynthesis. Upregulation of the PPP has been shown in several types of tumor. However, how the PPP is regulated to confer selective growth advantages on drug resistant tumor cells is not well understood. Here we show a metabolic shift from tricarboxylic acid cycle (TCA) to PPP after a long period induction of Imatinib (IM). One of the rate-limiting enzymes of the PPP-phosphogluconate dehydrogenase (PGD), is dramatically upregulated in gastrointestinal stromal tumors (GISTs) and GIST cell lines resistant to Imatinib (IM) compared with sensitive controls. Functional studies revealed that the overexpression of PGD in resistant GIST cell lines promoted cell proliferation and suppressed cell apoptosis. Mechanistic analyses suggested that the protein level of hypoxia inducible factor-1α (HIF-1α) increased during long time stimulation of reactive oxygen species (ROS) produced by IM. Importantly, we further demonstrated that HIF-1α also had positive correlation with PGD, resulting in the change of metabolic pathway, and ultimately causing drug resistance in GIST. Our findings show that long term use of IM alters the metabolic phenotype of GIST through ROS and HIF-1α, and this may contribute to IM resistance. Our work offers preclinical proof of metabolic target as an effective strategy for the treatment of drug resistance in GIST.
    DOI:  https://doi.org/10.1038/s41419-020-02768-4
  39. Biochem Soc Trans. 2020 Jul 29. pii: BST20190933. [Epub ahead of print]
    The mitochondrial ADP/ATP carrier exists and functions as a monomer.
    Edmund R S Kunji, Jonathan J Ruprecht.
      For more than 40 years, the oligomeric state of members of the mitochondrial carrier family (SLC25) has been the subject of debate. Initially, the consensus was that they were dimeric, based on the application of a large number of different techniques. However, the structures of the mitochondrial ADP/ATP carrier, a member of the family, clearly demonstrated that its structural fold is monomeric, lacking a conserved dimerisation interface. A re-evaluation of previously published data, with the advantage of hindsight, concluded that technical errors were at the basis of the earlier dimer claims. Here, we revisit this topic, as new claims for the existence of dimers of the bovine ADP/ATP carrier have emerged using native mass spectrometry of mitochondrial membrane vesicles. However, the measured mass does not agree with previously published values, and a large number of post-translational modifications are proposed to account for the difference. Contrarily, these modifications are not observed in electron density maps of the bovine carrier. If they were present, they would interfere with the structure and function of the carrier, including inhibitor and substrate binding. Furthermore, the reported mass does not account for three tightly bound cardiolipin molecules, which are consistently observed in other studies and are important stabilising factors for the transport mechanism. The monomeric carrier has all of the required properties for a functional transporter and undergoes large conformational changes that are incompatible with a stable dimerisation interface. Thus, our view that the native mitochondrial ADP/ATP carrier exists and functions as a monomer remains unaltered.
    Keywords:  adenine nucleotide translocase; biophysical techniques; molecular mass determination; native mass spectrometry; oligomeric state; structure
    DOI:  https://doi.org/10.1042/BST20190933
  40. Nature. 2020 Jul;583(7818): 752-759
    Spatiotemporal DNA methylome dynamics of the developing mouse fetus.
    Yupeng He, Manoj Hariharan, David U Gorkin, Diane E Dickel, Chongyuan Luo, Rosa G Castanon, Joseph R Nery, Ah Young Lee, Yuan Zhao, Hui Huang, Brian A Williams, Diane Trout, Henry Amrhein, Rongxin Fang, Huaming Chen, Bin Li, Axel Visel, Len A Pennacchio, Bing Ren, Joseph R Ecker.
      Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited1,2. Here, as part of the mouse Encyclopedia of DNA Elements (ENCODE) project, we profiled 168 methylomes from 12 mouse tissues or organs at 9 developmental stages from embryogenesis to adulthood. We identified 1,808,810 genomic regions that showed variations in CG methylation by comparing the methylomes of different tissues or organs from different developmental stages. These DNA elements predominantly lose CG methylation during fetal development, whereas the trend is reversed after birth. During late stages of fetal development, non-CG methylation accumulated within the bodies of key developmental transcription factor genes, coinciding with their transcriptional repression. Integration of genome-wide DNA methylation, histone modification and chromatin accessibility data enabled us to predict 461,141 putative developmental tissue-specific enhancers, the human orthologues of which were enriched for disease-associated genetic variants. These spatiotemporal epigenome maps provide a resource for studies of gene regulation during tissue or organ progression, and a starting point for investigating regulatory elements that are involved in human developmental disorders.
    DOI:  https://doi.org/10.1038/s41586-020-2119-x
  41. Nature. 2020 Jul 29.
    The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic.
    Eliran Kadosh, Irit Snir-Alkalay, Avanthika Venkatachalam, Shahaf May, Audrey Lasry, Ela Elyada, Adar Zinger, Maya Shaham, Gitit Vaalani, Marco Mernberger, Thorsten Stiewe, Eli Pikarsky, Moshe Oren, Yinon Ben-Neriah.
      Somatic mutations in p53, which inactivate the tumour-suppressor function of p53 and often confer oncogenic gain-of-function properties, are very common in cancer1,2. Here we studied the effects of hotspot gain-of-function mutations in Trp53 (the gene that encodes p53 in mice) in mouse models of WNT-driven intestinal cancer caused by Csnk1a1 deletion3,4 or ApcMin mutation5. Cancer in these models is known to be facilitated by loss of p533,6. We found that mutant versions of p53 had contrasting effects in different segments of the gut: in the distal gut, mutant p53 had the expected oncogenic effect; however, in the proximal gut and in tumour organoids it had a pronounced tumour-suppressive effect. In the tumour-suppressive mode, mutant p53 eliminated dysplasia and tumorigenesis in Csnk1a1-deficient and ApcMin/+ mice, and promoted normal growth and differentiation of tumour organoids derived from these mice. In these settings, mutant p53 was more effective than wild-type p53 at inhibiting tumour formation. Mechanistically, the tumour-suppressive effects of mutant p53 were driven by disruption of the WNT pathway, through preventing the binding of TCF4 to chromatin. Notably, this tumour-suppressive effect was completely abolished by the gut microbiome. Moreover, a single metabolite derived from the gut microbiota-gallic acid-could reproduce the entire effect of the microbiome. Supplementing gut-sterilized p53-mutant mice and p53-mutant organoids with gallic acid reinstated the TCF4-chromatin interaction and the hyperactivation of WNT, thus conferring a malignant phenotype to the organoids and throughout the gut. Our study demonstrates the substantial plasticity of a cancer mutation and highlights the role of the microenvironment in determining its functional outcome.
    DOI:  https://doi.org/10.1038/s41586-020-2541-0
  42. Nat Genet. 2020 Jul 27.
    APOBEC3-dependent kataegis and TREX1-driven chromothripsis during telomere crisis.
    John Maciejowski, Aikaterini Chatzipli, Alexandra Dananberg, Kevan Chu, Eleonore Toufektchan, Leszek J Klimczak, Dmitry A Gordenin, Peter J Campbell, Titia de Lange.
      Chromothripsis and kataegis are frequently observed in cancer and may arise from telomere crisis, a period of genome instability during tumorigenesis when depletion of the telomere reserve generates unstable dicentric chromosomes1-5. Here we examine the mechanism underlying chromothripsis and kataegis by using an in vitro telomere crisis model. We show that the cytoplasmic exonuclease TREX1, which promotes the resolution of dicentric chromosomes4, plays a prominent role in chromothriptic fragmentation. In the absence of TREX1, the genome alterations induced by telomere crisis primarily involve breakage-fusion-bridge cycles and simple genome rearrangements rather than chromothripsis. Furthermore, we show that the kataegis observed at chromothriptic breakpoints is the consequence of cytosine deamination by APOBEC3B. These data reveal that chromothripsis and kataegis arise from a combination of nucleolytic processing by TREX1 and cytosine editing by APOBEC3B.
    DOI:  https://doi.org/10.1038/s41588-020-0667-5
  43. Dev Cell. 2020 Jul 27. pii: S1534-5807(20)30549-9. [Epub ahead of print]
    Determinants of Endoplasmic Reticulum-to-Lipid Droplet Protein Targeting.
    Maria-Jesus Olarte, Siyoung Kim, Morris E Sharp, Jessica M J Swanson, Robert V Farese, Tobias C Walther.
      Lipid droplet (LD) formation from the endoplasmic reticulum (ER) is accompanied by the targeting and accumulation of specific hydrophobic, membrane-embedded proteins on LDs. The determinants of this process are unknown. Here, we study the hydrophobic membrane motifs of two Drosophila melanogaster proteins, GPAT4 and ALG14, that utilize this pathway, and we identify crucial sequence features that mediate LD accumulation. Molecular dynamics simulations and studies in cells reveal that LD targeting of these motifs requires deeply inserted tryptophans that have lower free energy in the LD oil phase and positively charged residues near predicted hairpin hinges that become less constrained in the LD environment. Analyzing hydrophobic motifs from similar LD-targeting proteins, it appears that the distribution of tryptophan and positively charged residues distinguishes them from non-LD-targeting membrane motifs. Our studies identify specific sequence features and principles of hydrophobic membrane motifs that mediate their accumulation on LDs.
    Keywords:  LiveDrop; UDP-N-acetylglucosaminyltransferase subunit; endoplasmic reticulum; glycerol-3-phosphate acyltransferase 4; lipid droplets; protein targeting
    DOI:  https://doi.org/10.1016/j.devcel.2020.07.001
  44. EMBO J. 2020 Jul 27. e105696
    MiT/TFE factors control ER-phagy via transcriptional regulation of FAM134B.
    Laura Cinque, Chiara De Leonibus, Maria Iavazzo, Natalie Krahmer, Daniela Intartaglia, Francesco Giuseppe Salierno, Rossella De Cegli, Chiara Di Malta, Maria Svelto, Carmela Lanzara, Marianna Maddaluno, Luca Giorgio Wanderlingh, Antje K Huebner, Marcella Cesana, Florian Bonn, Elena Polishchuk, Christian A Hübner, Ivan Conte, Ivan Dikic, Matthias Mann, Andrea Ballabio, Francesca Sacco, Paolo Grumati, Carmine Settembre.
      Lysosomal degradation of the endoplasmic reticulum (ER) via autophagy (ER-phagy) is emerging as a critical regulator of cell homeostasis and function. The recent identification of ER-phagy receptors has shed light on the molecular mechanisms underlining this process. However, the signaling pathways regulating ER-phagy in response to cellular needs are still largely unknown. We found that the nutrient responsive transcription factors TFEB and TFE3-master regulators of lysosomal biogenesis and autophagy-control ER-phagy by inducing the expression of the ER-phagy receptor FAM134B. The TFEB/TFE3-FAM134B axis promotes ER-phagy activation upon prolonged starvation. In addition, this pathway is activated in chondrocytes by FGF signaling, a critical regulator of skeletal growth. FGF signaling induces JNK-dependent proteasomal degradation of the insulin receptor substrate 1 (IRS1), which in turn inhibits the PI3K-PKB/Akt-mTORC1 pathway and promotes TFEB/TFE3 nuclear translocation and enhances FAM134B transcription. Notably, FAM134B is required for protein secretion in chondrocytes, and cartilage growth and bone mineralization in medaka fish. This study identifies a new signaling pathway that allows ER-phagy to respond to both metabolic and developmental cues.
    Keywords:   TFEB ; ER-phagy; FGF signaling; Fam134B; IRS1/PI3K signaling
    DOI:  https://doi.org/10.15252/embj.2020105696
  45. Front Oncol. 2020 ;10 947
    Cysteine as a Carbon Source, a Hot Spot in Cancer Cells Survival.
    Jacinta Serpa.
      Cancer cells undergo a metabolic rewiring in order to fulfill the energy and biomass requirements. Cysteine is a pivotal organic compound that contributes for cancer metabolic remodeling at three different levels: (1) in redox control, free or as a component of glutathione; (2) in ATP production, via hydrogen sulfide (H2S) production, serving as a donor to electron transport chain (ETC), and (3) as a carbon source for biomass and energy production. In the present review, emphasis will be given to the role of cysteine as a carbon source, focusing on the metabolic reliance on cysteine, benefiting the metabolic fitness and survival of cancer cells. Therefore, the interplay between cysteine metabolism and other metabolic pathways, as well as the regulation of cysteine metabolism related enzymes and transporters, will be also addressed. Finally, the usefulness of cysteine metabolic route as a target in cancer treatment will be highlighted.
    Keywords:  cancer metabolic remodeling; cysteine; cysteine metabolism; cysteine transport; targeting cysteine route
    DOI:  https://doi.org/10.3389/fonc.2020.00947
  46. Neuronal Signal. 2018 Dec;2(4): NS20180061
    Mitochondrial calcium signalling and neurodegenerative diseases.
    Elena Britti, Fabien Delaspre, Jordi Tamarit, Joaquim Ros.
      Calcium is utilised by cells in signalling and in regulating ATP production; it also contributes to cell survival and, when concentrations are unbalanced, triggers pathways for cell death. Mitochondria contribute to calcium buffering, meaning that mitochondrial calcium uptake and release is intimately related to cytosolic calcium concentrations. This review focuses on the proteins contributing to mitochondrial calcium homoeostasis, the roles of the mitochondrial permeability transition pore (MPTP) and mitochondrial calcium-activated proteins, and their relevance in neurodegenerative pathologies. It also covers alterations to calcium homoeostasis in Friedreich ataxia (FA).
    Keywords:  calcium homoeostasis; mitochondria; mitochondrial permeability transition pore; neurodegeneration
    DOI:  https://doi.org/10.1042/NS20180061
  47. Nat Metab. 2020 Jul 27.
    AMPK as a direct sensor of long-chain fatty acyl-CoA esters.
    D Grahame Hardie.
      
    DOI:  https://doi.org/10.1038/s42255-020-0249-y
  48. Nature. 2020 Jul 30.
    Microbiota-derived metabolite promotes HDAC3 activity in the gut.
    Shu-En Wu, Seika Hashimoto-Hill, Vivienne Woo, Emily M Eshleman, Jordan Whitt, Laura Engleman, Rebekah Karns, Lee A Denson, David B Haslam, Theresa Alenghat.
      The coevolution of mammalian hosts and their beneficial commensal microbes has led to development of a symbiotic host-microbiota relationship1. Epigenetic machinery permits mammalian cells to integrate environmental signals2, however, how these pathways are finely tuned by diverse cues from commensal bacteria is not well understood. Here, we reveal a highly selective pathway through which microbiota-derived inositol phosphate regulates histone deacetylase 3 (HDAC3) activity in the intestine. Despite abundant HDAC inhibitors in the intestine such as butyrate, we unexpectedly found that HDAC3 activity was sharply increased in intestinal epithelial cells (IECs) of microbiota-replete mice compared to germ-free mice. This discordance was reconciled by finding that commensal bacteria, including E. coli, stimulated HDAC activity through metabolism of phytate and inositol trisphosphate production. Intestinal exposure to inositol trisphosphate and phytate ingestion both promoted recovery following intestinal damage. Remarkably, inositol trisphosphate also induced growth of patient-derived intestinal organoids, stimulated HDAC3-dependent proliferation, and countered butyrate inhibition of colonic growth. Collectively, these data reveal inositol trisphosphate as a microbiota-derived metabolite that activates a mammalian histone deacetylase to promote epithelial repair. Thus, HDAC3 represents a converging epigenetic sensor of distinct metabolites that calibrates host responses to diverse microbial signals.
    DOI:  https://doi.org/10.1038/s41586-020-2604-2
  49. Nature. 2020 Jul 27.
    CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning.
    Zhaoqing Ba, Jiangman Lou, Adam Yongxin Ye, Hai-Qiang Dai, Edward W Dring, Sherry G Lin, Suvi Jain, Nia Kyritsis, Kyong-Rim Kieffer-Kwon, Rafael Casellas, Frederick W Alt.
      RAG endonuclease initiates V(D)J recombination in progenitor (pro)-B cells1. Upon binding a recombination center (RC)-based JH, RAG scans upstream chromatin via loop extrusion, potentially mediated by cohesin, to locate Ds and assemble a DJH-based RC2. CTCF looping factor-bound elements (CBEs) within IGCR1 upstream of Ds impede RAG-scanning3-5; but their inactivation allows scanning to proximal VHs where additional CBEs activate rearrangement and impede scanning any further upstream5. Distal VH utilization is thought to involve diffusional RC access following large-scale Igh locus contraction6-8. Here, we test the potential of linear RAG-scanning to mediate distal VH usage in G1-arrested v-Abl-pro-B cell lines9, which undergo robust D-to-JH but little VH-to-DJH rearrangements, presumably due to lack of locus contraction2,5. Through an auxin-inducible approach10, we degrade the cohesin-component Rad2110-12 or CTCF12,13 in these G1-arrested lines. Rad21 degradation eliminated all V(D)J recombination and RAG-scanning-associated interactions, except RC-located DQ52-to-JH joining in which synapsis occurs by diffusion2. Remarkably, while CTCF degradation suppressed most CBE-based chromatin interactions, it promoted robust RC interactions with, and robust VH-to-DJH joining of, distal VHs, with patterns similar to those of "locus-contracted" primary pro-B cells. Thus, down-modulation of CTCF-bound scanning-impediment activity promotes cohesin-driven RAG-scanning across the 2.7Mb Igh locus.
    DOI:  https://doi.org/10.1038/s41586-020-2578-0
  50. Nat Cell Biol. 2020 Jul 27.
    Oncogenic splicing regulated by phase separation.
    Bo Liu, Omar Abdel-Wahab.
      
    DOI:  https://doi.org/10.1038/s41556-020-0553-5
  51. Sci Rep. 2020 Jul 30. 10(1): 12838
    Alpha-ketoglutarate utilization in Saccharomyces cerevisiae: transport, compartmentation and catabolism.
    Jinrui Zhang, Bas Mees van den Herik, Sebastian Aljoscha Wahl.
      α-Ketoglutarate (αKG) is a metabolite of the tricarboxylic acid cycle, important for biomass synthesis and a precursor for biotechnological products like 1,4-butanediol. In the eukaryote Saccharomyces cerevisiae αKG is present in different compartments. Compartmentation and (intra-)cellular transport could interfere with heterologous product pathways, generate futile cycles and reduce product yields. Batch and chemostat cultivations at low pH (≤ 5) showed that αKG can be transported, catabolized and used for biomass synthesis. The uptake mechanism of αKG was further investigated under αKG limited chemostat conditions at different pH (3, 4, 5, and 6). At very low pH (3, 4) there is a fraction of undissociated αKG that could diffuse over the periplasmic membrane. At pH 5 this fraction is very low, and the observed growth and residual concentration requires a permease/facilitated uptake mechanism of the mono-dissociated form of αKG. Consumption of αKG under mixed substrate conditions was only observed for low glucose concentrations in chemostat cultivations, suggesting that the putative αKG transporter is repressed by glucose. Fully 13C-labeled αKG was introduced as a tracer during a glucose/αKG co-feeding chemostat to trace αKG transport and utilization. The measured 13C enrichments suggest the major part of the consumed 13C αKG was used for the synthesis of glutamate, and the remainder was transported into the mitochondria and fully oxidized. There was no enrichment observed in glycolytic intermediates, suggesting that there was no gluconeogenic activity under the co-feeding conditions. 13C based flux analysis suggests that the intracellular transport is bi-directional, i.e. there is a fast exchange between the cytosol and mitochondria. The model further estimates that most intracellular αKG (88%) was present in the cytosol. Using literature reported volume fractions, the mitochondria/cytosol concentration ratio was 1.33. Such ratio will not require energy investment for transport towards the mitochondria (based on thermodynamic driving forces calculated with literature pH values). Growth on αKG as sole carbon source was observed, suggesting that S. cerevisiae is not fully Krebs-negative. Using 13C tracing and modelling the intracellular use of αKG under co-feeding conditions showed a link with biomass synthesis, transport into the mitochondria and catabolism. For the engineering of strains that use cytosolic αKG as precursor, both observed sinks should be minimized to increase the putative yields.
    DOI:  https://doi.org/10.1038/s41598-020-69178-6
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