bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2022–10–23
sixty-one papers selected by
Christian Frezza, Universität zu Köln
  1. Lipids reroute mitochondria.
  2. HIRA loss transforms FH-deficient cells.
  3. The metabolite-controlled ubiquitin conjugase Ubc8 promotes mitochondrial protein import.
  4. Principles and functions of metabolic compartmentalization.
  5. Assessment of Mitochondrial Dysfunctions After Sirtuin Inhibition.
  6. The gut drives fat cravings.
  7. Oxidation state-specific fluorescent copper sensors reveal oncogene-driven redox changes that regulate labile copper(II) pools.
  8. MTCH2 is a mitochondrial outer membrane protein insertase.
  9. BCAT1 redox function maintains mitotic fidelity.
  10. SZT2 maintains hematopoietic stem cell homeostasis via nutrient-mediated mTORC1 regulation.
  11. Tissue-specific mitochondrial HIGD1C promotes oxygen sensitivity in carotid body chemoreceptors.
  12. Understanding emerging bioactive metabolites with putative roles in cancer biology.
  13. Glutamine synthetase limits b-catenin-mutated liver cancer growth by maintaining nitrogen homeostasis and suppressing mTORC1.
  14. Nitrosylation rewires metabolism.
  15. Nitric oxide-driven modifications of lipoic arm inhibit α-ketoacid dehydrogenases.
  16. Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH.
  17. Beyond ATP, new roles of mitochondria.
  18. Relief of CoA sequestration and restoration of mitochondrial function in a mouse model of propionic acidemia.
  19. Inhibiting glutamine utilization creates a synthetic lethality for suppression of ATP citrate lyase in KRas-driven cancer cells.
  20. Circadian lncRNA ADIRF-AS1 binds PBAF and regulates renal clear cell tumorigenesis.
  21. ATF4-dependent fructolysis fuels growth of glioblastoma multiforme.
  22. Purine nucleoside phosphorylase controls nicotinamide riboside metabolism in mammalian cells.
  23. Single protonation of the reduced quinone in respiratory complex I drives four-proton pumping.
  24. Deregulated transcription factors in cancer cell metabolisms and reprogramming.
  25. Gut reaction: it's not all about enzymes.
  26. The role of lipids in cancer progression and metastasis.
  27. Rerouting the drug response: Overcoming metabolic adaptation in KRAS-mutant cancers.
  28. p53 mutation in normal esophagus promotes multiple stages of carcinogenesis but is constrained by clonal competition.
  29. An evolutionary trade-off between host immunity and metabolism drives fatty liver in male mice.
  30. A path to translation: How 3D patient tumor avatars enable next generation precision oncology.
  31. A common framework for mouse hypothalamic cell atlases.
  32. Landscape of epithelial mesenchymal plasticity as an emergent property of coordinated teams in regulatory networks.
  33. N-myc mediated translation control is a therapeutic vulnerability in medulloblastoma.
  34. A local tumor microenvironment acquired super-enhancer induces an oncogenic driver in colorectal carcinoma.
  35. Time-restricted feeding mitigates obesity through adipocyte thermogenesis.
  36. Methionine uptake via the SLC43A2 transporter is essential for regulatory T-cell survival.
  37. Ferroptosis heterogeneity in triple-negative breast cancer reveals an innovative immunotherapy combination strategy.
  38. Metabolic Recruitment in Brain Tissue.
  39. Glucose-6-phosphate dehydrogenase exerts anti-stress effects independently of its enzymatic activity.
  40. Advances in energy metabolism in renal fibrosis.
  41. Caveolae couple mechanical stress to integrin recycling and activation.
  42. Comprehensive single-cell transcriptional profiling defines shared and unique epithelial injury responses during kidney fibrosis.
  43. Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements.
  44. Gene therapy for primary mitochondrial diseases: experimental advances and clinical challenges.
  45. Endocytosis triggers V-ATPase-SYK-mediated priming of cGAS activation and innate immune response.
  46. Parkin drives pS65-Ub turnover independently of canonical autophagy in Drosophila.
  47. Vitamin K: A new guardian against ferroptosis.
  48. Proximal tubular Bmal1 protects against chronic kidney injury and renal fibrosis by maintaining of cellular metabolic homeostasis.
  49. Variable metabolic scaling breaks the law: from 'Newtonian' to 'Darwinian' approaches.
  50. Fructose-1,6-bisphosphatase 1 functions as a protein phosphatase to dephosphorylate histone H3 and suppresses PPARα-regulated gene transcription and tumour growth.
  51. Human ZBP1 induces cell death-independent inflammatory signaling via RIPK3 and RIPK1.
  52. COX7A2L genetic variants determine cardiorespiratory fitness in mice and human.
  53. Prohibitin 1 regulates mtDNA release and downstream inflammatory responses.
  54. The Cancermuts software package for the prioritization of missense cancer variants: a case study of AMBRA1 in melanoma.
  55. The proneural transcription factor ASCL1 regulates cell proliferation and primes for differentiation in neuroblastoma.
  56. Clathrin-associated AP-1 controls termination of STING signalling.
  57. The hypoxia response pathway promotes PEP carboxykinase and gluconeogenesis in C. elegans.
  58. Mammalian oocytes store mRNAs in a mitochondria-associated membraneless compartment.
  59. Borgs are giant genetic elements with potential to expand metabolic capacity.
  60. PTEN in Immunity.
  61. HRG-9 homologues regulate haem trafficking from haem-enriched compartments.
  1. Nat Metab. 2022 Oct;4(10): 1218
    Lipids reroute mitochondria.
    Michael Attwaters.
      
    DOI:  https://doi.org/10.1038/s42255-022-00662-1
  2. Sci Adv. 2022 Oct 21. 8(42): eabq8297
    HIRA loss transforms FH-deficient cells.
    Lorea Valcarcel-Jimenez, Connor Rogerson, Cissy Yong, Christina Schmidt, Ming Yang, Monica Cremades-Rodelgo, Victoria Harle, Victoria Offord, Kim Wong, Ariane Mora, Alyson Speed, Veronica Caraffini, Maxine Gia Binh Tran, Eamonn R Maher, Grant D Stewart, Sakari Vanharanta, David J Adams, Christian Frezza.
      Fumarate hydratase (FH) is a mitochondrial enzyme that catalyzes the reversible hydration of fumarate to malate in the tricarboxylic acid (TCA) cycle. Germline mutations of FH lead to hereditary leiomyomatosis and renal cell carcinoma (HLRCC), a cancer syndrome characterized by a highly aggressive form of renal cancer. Although HLRCC tumors metastasize rapidly, FH-deficient mice develop premalignant cysts in the kidneys, rather than carcinomas. How Fh1-deficient cells overcome these tumor-suppressive events during transformation is unknown. Here, we perform a genome-wide CRISPR-Cas9 screen to identify genes that, when ablated, enhance the proliferation of Fh1-deficient cells. We found that the depletion of the histone cell cycle regulator (HIRA) enhances proliferation and invasion of Fh1-deficient cells in vitro and in vivo. Mechanistically, Hira loss activates MYC and its target genes, increasing nucleotide metabolism specifically in Fh1-deficient cells, independent of its histone chaperone activity. These results are instrumental for understanding mechanisms of tumorigenesis in HLRCC and the development of targeted treatments for patients.
    DOI:  https://doi.org/10.1126/sciadv.abq8297
  3. Life Sci Alliance. 2023 Jan;pii: e202201526. [Epub ahead of print]6(1):
    The metabolite-controlled ubiquitin conjugase Ubc8 promotes mitochondrial protein import.
    Saskia Rödl, Fabian den Brave, Markus Räschle, Büsra Kizmaz, Svenja Lenhard, Carina Groh, Hanna Becker, Jannik Zimmermann, Bruce Morgan, Elke Richling, Thomas Becker, Johannes M Herrmann.
      Mitochondria play a key role in cellular energy metabolism. Transitions between glycolytic and respiratory conditions induce considerable adaptations of the cellular proteome. These metabolism-dependent changes are particularly pronounced for the protein composition of mitochondria. Here, we show that the yeast cytosolic ubiquitin conjugase Ubc8 plays a crucial role in the remodeling process when cells transition from respiratory to fermentative conditions. Ubc8 is a conserved and well-studied component of the catabolite control system that is known to regulate the stability of gluconeogenic enzymes. Unexpectedly, we found that Ubc8 also promotes the assembly of the translocase of the outer membrane of mitochondria (TOM) and increases the levels of its cytosol-exposed receptor subunit Tom22. Ubc8 deficiency results in compromised protein import into mitochondria and reduced steady-state levels of mitochondrial proteins. Our observations show that Ubc8, which is controlled by the prevailing metabolic conditions, promotes the switch from glucose synthesis to glucose usage in the cytosol and induces the biogenesis of the mitochondrial TOM machinery to improve mitochondrial protein import during phases of metabolic transition.
    DOI:  https://doi.org/10.26508/lsa.202201526
  4. Nat Metab. 2022 Oct;4(10): 1232-1244
    Principles and functions of metabolic compartmentalization.
    Liron Bar-Peled, Nora Kory.
      Metabolism has historically been studied at the levels of whole cells, whole tissues and whole organisms. As a result, our understanding of how compartmentalization-the spatial and temporal separation of pathways and components-shapes organismal metabolism remains limited. At its essence, metabolic compartmentalization fulfils three important functions or 'pillars': establishing unique chemical environments, providing protection from reactive metabolites and enabling the regulation of metabolic pathways. However, how these pillars are established, regulated and maintained at both the cellular and systemic levels remains unclear. Here we discuss how the three pillars are established, maintained and regulated within the cell and discuss the consequences of dysregulation of metabolic compartmentalization in human disease. Organelles are increasingly emerging as 'command-and-control centres' and the increased understanding of metabolic compartmentalization is revealing new aspects of metabolic homeostasis, with this knowledge being translated into therapies for the treatment of cancer and certain neurodegenerative diseases.
    DOI:  https://doi.org/10.1038/s42255-022-00645-2
  5. Methods Mol Biol. 2023 ;2589 269-291
    Assessment of Mitochondrial Dysfunctions After Sirtuin Inhibition.
    Christian Marx, Lisa Marx-Blümel, Jürgen Sonnemann, Zhao-Qi Wang.
      Posttranslational modifications are important for protein functions and cellular signaling pathways. The acetylation of lysine residues is catalyzed by histone acetyltransferases (HATs) and removed by histone deacetylases (HDACs), with the latter being grouped into four phylogenetic classes. The class III of the HDAC family, the sirtuins (SIRTs), contributes to gene expression, genomic stability, cell metabolism, and tumorigenesis. Thus, several specific SIRT inhibitors (SIRTi) have been developed to target cancer cell proliferation. Here we provide an overview of methods to study SIRT-dependent cell metabolism and mitochondrial functionality. The chapter describes metabolic flux analysis using Seahorse analyzers, methods for normalization of Seahorse data, flow cytometry and fluorescence microscopy to determine the mitochondrial membrane potential, mitochondrial content per cell and mitochondrial network structures, and Western blot analysis to measure mitochondrial proteins.
    Keywords:  Flow cytometry; Metabolism; Mitochondria; SIRT; Seahorse analysis; Sirtuin inhibition; Western blot
    DOI:  https://doi.org/10.1007/978-1-0716-2788-4_18
  6. Nat Metab. 2022 Oct;4(10): 1217
    The gut drives fat cravings.
    Joseph Willson.
      
    DOI:  https://doi.org/10.1038/s42255-022-00661-2
  7. Proc Natl Acad Sci U S A. 2022 Oct 25. 119(43): e2202736119
    Oxidation state-specific fluorescent copper sensors reveal oncogene-driven redox changes that regulate labile copper(II) pools.
    Aidan T Pezacki, Carson D Matier, Xingxing Gu, Eric Kummelstedt, Sarah E Bond, Laura Torrente, Kelly L Jordan-Sciutto, Gina M DeNicola, Timothy A Su, Donita C Brady, Christopher J Chang.
      Copper is an essential metal nutrient for life that often relies on redox cycling between Cu(I) and Cu(II) oxidation states to fulfill its physiological roles, but alterations in cellular redox status can lead to imbalances in copper homeostasis that contribute to cancer and other metalloplasias with metal-dependent disease vulnerabilities. Copper-responsive fluorescent probes offer powerful tools to study labile copper pools, but most of these reagents target Cu(I), with limited methods for monitoring Cu(II) owing to its potent fluorescence quenching properties. Here, we report an activity-based sensing strategy for turn-on, oxidation state-specific detection of Cu(II) through metal-directed acyl imidazole chemistry. Cu(II) binding to a metal and oxidation state-specific receptor that accommodates the harder Lewis acidity of Cu(II) relative to Cu(I) activates the pendant dye for reaction with proximal biological nucleophiles and concomitant metal ion release, thus avoiding fluorescence quenching. Copper-directed acyl imidazole 649 for Cu(II) (CD649.2) provides foundational information on the existence and regulation of labile Cu(II) pools, including identifying divalent metal transporter 1 (DMT1) as a Cu(II) importer, labile Cu(II) increases in response to oxidative stress induced by depleting total glutathione levels, and reciprocal increases in labile Cu(II) accompanied by decreases in labile Cu(I) induced by oncogenic mutations that promote oxidative stress.
    Keywords:  activity-based sensing; cancer metabolism; fluorescent copper probe; oxidative stress; transition metal signaling
    DOI:  https://doi.org/10.1073/pnas.2202736119
  8. Science. 2022 Oct 21. 378(6617): 317-322
    MTCH2 is a mitochondrial outer membrane protein insertase.
    Alina Guna, Taylor A Stevens, Alison J Inglis, Joseph M Replogle, Theodore K Esantsi, Gayathri Muthukumar, Kelly C L Shaffer, Maxine L Wang, Angela N Pogson, Jeff J Jones, Brett Lomenick, Tsui-Fen Chou, Jonathan S Weissman, Rebecca M Voorhees.
      In the mitochondrial outer membrane, α-helical transmembrane proteins play critical roles in cytoplasmic-mitochondrial communication. Using genome-wide CRISPR screens, we identified mitochondrial carrier homolog 2 (MTCH2), and its paralog MTCH1, and showed that it is required for insertion of biophysically diverse tail-anchored (TA), signal-anchored, and multipass proteins, but not outer membrane β-barrel proteins. Purified MTCH2 was sufficient to mediate insertion into reconstituted proteoliposomes. Functional and mutational studies suggested that MTCH2 has evolved from a solute carrier transporter. MTCH2 uses membrane-embedded hydrophilic residues to function as a gatekeeper for the outer membrane, controlling mislocalization of TAs into the endoplasmic reticulum and modulating the sensitivity of leukemia cells to apoptosis. Our identification of MTCH2 as an insertase provides a mechanistic explanation for the diverse phenotypes and disease states associated with MTCH2 dysfunction.
    DOI:  https://doi.org/10.1126/science.add1856
  9. Cell Rep. 2022 Oct 18. pii: S2211-1247(22)01379-1. [Epub ahead of print]41(3): 111524
    BCAT1 redox function maintains mitotic fidelity.
    Liliana Francois, Pavle Boskovic, Julian Knerr, Wei He, Gianluca Sigismondo, Carsten Schwan, Tushar H More, Magdalena Schlotter, Jeroen Krijgsveld, Karsten Hiller, Robert Grosse, Peter Lichter, Bernhard Radlwimmer.
      The metabolic enzyme branched-chain amino acid transaminase 1 (BCAT1) drives cell proliferation in aggressive cancers such as glioblastoma. Here, we show that BCAT1 localizes to mitotic structures and has a non-metabolic function as a mitotic regulator. Furthermore, BCAT1 is required for chromosome segregation in cancer and induced pluripotent stem cells and tumor growth in human cerebral organoid and mouse syngraft models. Applying gene knockout and rescue strategies, we show that the BCAT1 CXXC redox motif is crucial for controlling cysteine sulfenylation specifically in mitotic cells, promoting Aurora kinase B localization to centromeres, and securing accurate chromosome segregation. These findings offer an explanation for the well-established role of BCAT1 in promoting cancer cell proliferation. In summary, our data establish BCAT1 as a component of the mitotic apparatus that safeguards mitotic fidelity through a moonlighting redox functionality.
    Keywords:  BCAT1; CP: Cell biology; cancer; chromosome segregation; metabolism; mitosis; moonlighting function; redox; stem cells
    DOI:  https://doi.org/10.1016/j.celrep.2022.111524
  10. J Clin Invest. 2022 Oct 17. pii: e146272. [Epub ahead of print]132(20):
    SZT2 maintains hematopoietic stem cell homeostasis via nutrient-mediated mTORC1 regulation.
    Na Yin, Gang Jin, Yuying Ma, Hanfei Zhao, Guangyue Zhang, Ming O Li, Min Peng.
      The mTORC1 pathway coordinates nutrient and growth factor signals to maintain organismal homeostasis. Whether nutrient signaling to mTORC1 regulates stem cell function remains unknown. Here, we show that SZT2 - a protein required for mTORC1 downregulation upon nutrient deprivation - is critical for hematopoietic stem cell (HSC) homeostasis. Ablation of SZT2 in HSCs decreased the reserve and impaired the repopulating capacity of HSCs. Furthermore, ablation of both SZT2 and TSC1 - 2 repressors of mTORC1 on the nutrient and growth factor arms, respectively - led to rapid HSC depletion, pancytopenia, and premature death of the mice. Mechanistically, loss of either SZT2 or TSC1 in HSCs led to only mild elevation of mTORC1 activity and reactive oxygen species (ROS) production. Loss of both SZT2 and TSC1, on the other hand, simultaneously produced a dramatic synergistic effect, with an approximately 10-fold increase of mTORC1 activity and approximately 100-fold increase of ROS production, which rapidly depleted HSCs. These data demonstrate a critical role of nutrient mTORC1 signaling in HSC homeostasis and uncover a strong synergistic effect between nutrient- and growth factor-mediated mTORC1 regulation in stem cells.
    Keywords:  Amino acid metabolism; Bone marrow transplantation; Hematology; Hematopoietic stem cells; Metabolism
    DOI:  https://doi.org/10.1172/JCI146272
  11. Elife. 2022 Oct 18. pii: e78915. [Epub ahead of print]11
    Tissue-specific mitochondrial HIGD1C promotes oxygen sensitivity in carotid body chemoreceptors.
    Alba Timón-Gómez, Alexandra L Scharr, Nicholas Y Wong, Erwin Ni, Arijit Roy, Min Liu, Julisia Chau, Jack L Lampert, Homza Hireed, Noah S Kim, Masood Jan, Alexander R Gupta, Ryan W Day, James M Gardner, Richard J A Wilson, Antoni Barrientos, Andy J Chang.
      Mammalian carotid body arterial chemoreceptors function as an early warning system for hypoxia, triggering acute life-saving arousal and cardiorespiratory reflexes. To serve this role, carotid body glomus cells are highly sensitive to decreases in oxygen availability. While the mitochondria and plasma membrane signaling proteins have been implicated in oxygen sensing by glomus cells, the mechanism underlying their mitochondrial sensitivity to hypoxia compared to other cells is unknown. Here, we identify HIGD1C, a novel hypoxia-inducible gene domain factor isoform, as an electron transport chain Complex IV-interacting protein that is almost exclusively expressed in the carotid body and is therefore not generally necessary for mitochondrial function. Importantly, HIGD1C is required for carotid body oxygen sensing and enhances Complex IV sensitivity to hypoxia. Thus, we propose that HIGD1C promotes exquisite oxygen sensing by the carotid body, illustrating how specialized mitochondria can be used as sentinels of metabolic stress to elicit essential adaptive behaviors.
    Keywords:  biochemistry; chemical biology; human; mouse; neuroscience; rat
    DOI:  https://doi.org/10.7554/eLife.78915
  12. Front Oncol. 2022 ;12 1014748
    Understanding emerging bioactive metabolites with putative roles in cancer biology.
    Olivier Philips, Mukhayyo Sultonova, Beau Blackmore, J Patrick Murphy.
      Dysregulated metabolism in cancers is, by now, well established. Although metabolic adaptations provide cancers with the ability to synthesize the precursors required for rapid biosynthesis, some metabolites have direct functional, or bioactive, effects in human cells. Here we summarize recently identified metabolites that have bioactive roles either as post-translational modifications (PTMs) on proteins or in, yet unknown ways. We propose that these metabolites could play a bioactive role in promoting or inhibiting cancer cell phenotypes in a manner that is mostly unexplored. To study these potentially important bioactive roles, we discuss several novel metabolomic and proteomic approaches aimed at defining novel PTMs and metabolite-protein interactions. Understanding metabolite PTMs and protein interactors of bioactive metabolites may provide entirely new therapeutic targets for cancer.
    Keywords:  bioactive metabolite; cancer metabolism; cancer therapeutics; metabolite-protein interaction profiling; post-translational modification
    DOI:  https://doi.org/10.3389/fonc.2022.1014748
  13. J Clin Invest. 2022 Oct 18. pii: e161408. [Epub ahead of print]
    Glutamine synthetase limits b-catenin-mutated liver cancer growth by maintaining nitrogen homeostasis and suppressing mTORC1.
    Weiwei Dai, Jianliang Shen, Junrong Yan, Alex J Bott, Sara Maimouni, Heineken Q Daguplo, Yujue Wang, Khoosheh Khayati, Jessie Yanxiang Guo, Lanjing Zhang, Yongbo Wang, Alexander Valvezan, Wen-Xing Ding, Xin Chen, Xiaoyang Su, Shenglan Gao, Wei-Xing Zong.
      Glutamine synthetase (GS) catalyzes de novo synthesis of glutamine that facilitates cancer cell growth. In the liver, GS functions next to the urea cycle to remove ammonia waste. As dysregulated urea cycle is implicated in cancer development, the impact of GS' ammonia clearance function has not been explored in cancer. Here we show that, oncogenic activation of beta-catenin led to decreased urea cycle and elevated ammonia waste burden. While beta-catenin induced the expression of GS, which is thought to be cancer-promoting, surprisingly, genetic ablation of hepatic GS accelerated the onset of liver tumors in several mouse models that involved β-catenin activation. Mechanistically, GS ablation exacerbated hyperammonemia and facilitated the production of glutamate-derived non-essential amino acids (NEAAs), which subsequently stimulated mTORC1. Pharmacological and genetic inhibition of mTORC1 and glutamic transaminases suppressed tumorigenesis facilitated by GS ablation. While HCC patients, especially those with CTNNB1 mutations, have an overall defective urea cycle and increased expression of GS, there exists a subset of patients with low GS expression that is associated with mTORC1 hyperactivation. Therefore, GS-mediated ammonia clearance serves as a tumor-suppressing mechanism in livers that harbor β-catenin activation mutations and a compromised urea cycle.
    Keywords:  Hepatology; Liver cancer; Metabolism
    DOI:  https://doi.org/10.1172/JCI161408
  14. Nat Chem Biol. 2022 Oct 20.
    Nitrosylation rewires metabolism.
    James A Nathan.
      
    DOI:  https://doi.org/10.1038/s41589-022-01169-2
  15. Nat Chem Biol. 2022 Oct 20.
    Nitric oxide-driven modifications of lipoic arm inhibit α-ketoacid dehydrogenases.
    Gretchen L Seim, Steven V John, Nicholas L Arp, Zixiang Fang, David J Pagliarini, Jing Fan.
      Pyruvate dehydrogenase complex (PDHC) and oxoglutarate dehydrogenase complex (OGDC), which belong to the mitochondrial α-ketoacid dehydrogenase family, play crucial roles in cellular metabolism. These multi-subunit enzyme complexes use lipoic arms covalently attached to their E2 subunits to transfer an acyl group to coenzyme A (CoA). Here, we report a novel mechanism capable of substantially inhibiting PDHC and OGDC: reactive nitrogen species (RNS) can covalently modify the thiols on their lipoic arms, generating a series of adducts that block catalytic activity. S-Nitroso-CoA, a product between RNS and the E2 subunit's natural substrate, CoA, can efficiently deliver these modifications onto the lipoic arm. We found RNS-mediated inhibition of PDHC and OGDC occurs during classical macrophage activation, driving significant rewiring of cellular metabolism over time. This work provides a new mechanistic link between RNS and mitochondrial metabolism with potential relevance for numerous physiological and pathological conditions in which RNS accumulate.
    DOI:  https://doi.org/10.1038/s41589-022-01153-w
  16. Nat Genet. 2022 Oct 17.
    Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH.
    King L Hung, Jens Luebeck, Siavash R Dehkordi, Caterina I Colón, Rui Li, Ivy Tsz-Lo Wong, Ceyda Coruh, Prashanthi Dharanipragada, Shirley H Lomeli, Natasha E Weiser, Gatien Moriceau, Xiao Zhang, Chris Bailey, Kathleen E Houlahan, Wenting Yang, Rocío Chamorro González, Charles Swanton, Christina Curtis, Mariam Jamal-Hanjani, Anton G Henssen, Julie A Law, William J Greenleaf, Roger S Lo, Paul S Mischel, Vineet Bafna, Howard Y Chang.
      Extrachromosomal DNA (ecDNA) is a common mode of oncogene amplification but is challenging to analyze. Here, we adapt CRISPR-CATCH, in vitro CRISPR-Cas9 treatment and pulsed field gel electrophoresis of agarose-entrapped genomic DNA, previously developed for bacterial chromosome segments, to isolate megabase-sized human ecDNAs. We demonstrate strong enrichment of ecDNA molecules containing EGFR, FGFR2 and MYC from human cancer cells and NRAS ecDNA from human metastatic melanoma with acquired therapeutic resistance. Targeted enrichment of ecDNA versus chromosomal DNA enabled phasing of genetic variants, identified the presence of an EGFRvIII mutation exclusively on ecDNAs and supported an excision model of ecDNA genesis in a glioblastoma model. CRISPR-CATCH followed by nanopore sequencing enabled single-molecule ecDNA methylation profiling and revealed hypomethylation of the EGFR promoter on ecDNAs. We distinguished heterogeneous ecDNA species within the same sample by size and sequence with base-pair resolution and discovered functionally specialized ecDNAs that amplify select enhancers or oncogene-coding sequences.
    DOI:  https://doi.org/10.1038/s41588-022-01190-0
  17. Biochem (Lond). 2022 Aug;44(4): 2-8
    Beyond ATP, new roles of mitochondria.
    Ram Prosad Chakrabarty, Navdeep S Chandel.
      Mitochondria, special double-membraned intracellular compartments or 'organelles', are popularly known as the 'powerhouses of the cell', as they generate the bulk of ATP used to fuel cellular biochemical reactions. Mitochondria are also well known for generating metabolites for the synthesis of macromolecules (e.g., carbohydrates, proteins, lipids and nucleic acids). In the mid-1990s, new evidence suggesting that mitochondria, beyond their canonical roles in bioenergetics and biosynthesis, can act as signalling organelles began to emerge, bringing a dramatic shift in our view of mitochondria's roles in controlling cell function. Over the next two and half decades, works from multiple groups have demonstrated how mitochondrial signalling can dictate diverse physiological and pathophysiological outcomes. In this article, we will briefly discuss different mechanisms by which mitochondria can communicate with cytosol and other organelles to regulate cell fate and function and exert paracrine effects. Our molecular understanding of mitochondrial communication with the rest of the cell, i.e. mitochondrial signalling, could reveal new therapeutic strategies to improve health and ameliorate diseases.
    DOI:  https://doi.org/10.1042/bio_2022_119
  18. J Inherit Metab Dis. 2022 Oct 17.
    Relief of CoA sequestration and restoration of mitochondrial function in a mouse model of propionic acidemia.
    Chitra Subramanian, Matthew W Frank, Rajendra Tangallapally, Mi-Kyung Yun, Stephen W White, Richard E Lee, Charles O Rock, Suzanne Jackowski.
      Propionic acidemia (PA, OMIM 606054) is a devastating inborn error of metabolism arising from mutations that reduce the activity of the mitochondrial enzyme propionyl-CoA carboxylase (PCC). The defects in PCC reduce the concentrations of nonesterified coenzyme A (CoASH), thus compromising mitochondrial function and disrupting intermediary metabolism. Here, we use a hypomorphic PA mouse model to test the effectiveness of BBP-671 in correcting the metabolic imbalances in PA. BBP-671 is a high-affinity allosteric pantothenate kinase activator that counteracts feedback inhibition of the enzyme to increase the intracellular concentration of CoA. Liver CoASH and acetyl-CoA are depressed in PA mice and BBP-671 treatment normalizes the cellular concentrations of these two key cofactors. Hepatic propionyl-CoA is also reduced by BBP-671 leading to an improved intracellular C3:C2-CoA ratio. Elevated plasma C3:C2-carnitine ratio and methylcitrate, hallmark biomarkers of PA, are significantly reduced by BBP-671. The large elevations of malate and α-ketoglutarate in the urine of PA mice are biomarkers for compromised tricarboxylic acid cycle activity and BBP-671 therapy reduces the amounts of both metabolites. Furthermore, the low survival of PA mice is restored to normal by BBP-671. These data show that BBP-671 relieves CoA sequestration, improves mitochondrial function, reduces plasma PA biomarkers and extends the lifespan of PA mice, providing the preclinical foundation for the therapeutic potential of BBP-671. This article is protected by copyright. All rights reserved.
    DOI:  https://doi.org/10.1002/jimd.12570
  19. PLoS One. 2022 ;17(10): e0276579
    Inhibiting glutamine utilization creates a synthetic lethality for suppression of ATP citrate lyase in KRas-driven cancer cells.
    Ahmet Hatipoglu, Deepak Menon, Talia Levy, Maria A Frias, David A Foster.
      Metabolic reprogramming is now considered a hallmark of cancer cells. KRas-driven cancer cells use glutaminolysis to generate the tricarboxylic acid cycle intermediate α-ketoglutarate via a transamination reaction between glutamate and oxaloacetate. We reported previously that exogenously supplied unsaturated fatty acids could be used to synthesize phosphatidic acid-a lipid second messenger that activates both mammalian target of rapamycin (mTOR) complex 1 (mTORC1) and mTOR complex 2 (mTORC2). A key target of mTORC2 is Akt-a kinase that promotes survival and regulates cell metabolism. We report here that mono-unsaturated oleic acid stimulates the phosphorylation of ATP citrate lyase (ACLY) at the Akt phosphorylation site at S455 in an mTORC2 dependent manner. Inhibition of ACLY in KRas-driven cancer cells in the absence of serum resulted in loss of cell viability. We examined the impact of glutamine (Gln) deprivation in combination with inhibition of ACLY on the viability of KRas-driven cancer cells. While Gln deprivation was somewhat toxic to KRas-driven cancer cells by itself, addition of the ACLY inhibitor SB-204990 increased the loss of cell viability. However, the transaminase inhibitor aminooxyacetate was minimally toxic and the combination of SB-204990 and aminooxtacetate led to significant loss of cell viability and strong cleavage of poly-ADP ribose polymerase-indicating apoptotic cell death. This effect was not observed in MCF7 breast cancer cells that do not have a KRas mutation or in BJ-hTERT human fibroblasts which have no oncogenic mutation. These data reveal a synthetic lethality between inhibition of glutamate oxaloacetate transaminase and ACLY inhibition that is specific for KRas-driven cancer cells and the apparent metabolic reprogramming induced by activating mutations to KRas.
    DOI:  https://doi.org/10.1371/journal.pone.0276579
  20. Cell Rep. 2022 Oct 18. pii: S2211-1247(22)01364-X. [Epub ahead of print]41(3): 111514
    Circadian lncRNA ADIRF-AS1 binds PBAF and regulates renal clear cell tumorigenesis.
    Rebekah Brooks, Judith Monzy, Bailey Aaron, Xue Zhang, Andrew Kossenkov, James Hayden, Frederick Keeney, David W Speicher, Lin Zhang, Chi V Dang.
      We identify ADIRF-AS1 circadian long non-coding RNA (lncRNA). Deletion of ADIRF-AS1 in U2OS cells alters rhythmicity of clock-controlled genes and expression of extracellular matrix genes. ADIRF-AS1 interacts with all components of the PBAF (PBRM1/BRG1) complex in U2OS cells. Because PBRM1 is a tumor suppressor mutated in over 40% of clear cell renal carcinoma (ccRCC) cases, we evaluate ADIRF-AS1 in ccRCC cells. Reducing ADIRF-AS1 expression in ccRCC cells decreases expression of some PBAF-suppressed genes. Expression of these genes is partially rescued by PBRM1 loss, consistent with ADIRF-AS1 acting in part to modulate PBAF. ADIRF-AS1 expression correlates with survival in human ccRCC, particularly in PBRM1 wild-type, but not mutant, tumors. Loss of ADIRF-AS1 eliminates in vivo tumorigenesis, partially rescued by concurrent loss of PBRM1 only when co-injected with Matrigel, suggesting a PBRM1-independent function of ADIRF-AS1. Our findings suggest that ADIRF-AS1 functions partly through PBAF to regulate specific genes as a BMAL1-CLOCK-regulated, oncogenic lncRNA.
    Keywords:  ADIRF-AS1; CP: Cancer; PBAF; ccRCC; circadian rhythm; clock; lncRNA
    DOI:  https://doi.org/10.1016/j.celrep.2022.111514
  21. Nat Commun. 2022 Oct 16. 13(1): 6108
    ATF4-dependent fructolysis fuels growth of glioblastoma multiforme.
    Chao Chen, Zhenxing Zhang, Caiyun Liu, Bin Wang, Ping Liu, Shu Fang, Fan Yang, Yongping You, Xinjian Li.
      Excessive consumption of fructose in the Western diet contributes to cancer development. However, it is still unclear how cancer cells coordinate glucose and fructose metabolism during tumor malignant progression. We demonstrate here that glioblastoma multiforme (GBM) cells switch their energy supply from glycolysis to fructolysis in response to glucose deprivation. Mechanistically, glucose deprivation induces expression of two essential fructolytic proteins GLUT5 and ALDOB through selectively activating translation of activating transcription factor 4 (ATF4). Functionally, genetic or pharmacological disruption of ATF4-dependent fructolysis significantly inhibits growth and colony formation of GBM cells in vitro and GBM growth in vivo. In addition, ATF4, GLUT5, and ALDOB levels positively correlate with each other in GBM specimens and are poor prognostic indicators in GBM patients. This work highlights ATF4-dependent fructolysis as a metabolic feature and a potential therapeutic target for GBM.
    DOI:  https://doi.org/10.1038/s41467-022-33859-9
  22. J Biol Chem. 2022 Oct 17. pii: S0021-9258(22)01058-4. [Epub ahead of print] 102615
    Purine nucleoside phosphorylase controls nicotinamide riboside metabolism in mammalian cells.
    Andrey Kropotov, Veronika Kulikova, Ljudmila Solovjeva, Alexander Yakimov, Kirill Nerinovski, Maria Svetlova, Julia Sudnitsyna, Alena Plusnina, Maria Antipova, Mikhail Khodorkovskiy, Marie E Migaud, Stepan Gambaryan, Mathias Ziegler, Andrey Nikiforov.
      Nicotinamide riboside (NR) is an effective precursor of nicotinamide adenine dinucleotide (NAD) in human and animal cells. NR supplementation can increase the level of NAD in various tissues and thereby improve physiological functions that are weakened or lost in experimental models of aging or various human pathologies. However, there are also reports questioning the efficacy of NR supplementation. Indeed, the mechanisms of its utilization by cells are not fully understood. Herein, we investigated the role of purine nucleoside phosphorylase (PNP) in NR metabolism in mammalian cells. Using both PNP overexpression and genetic knockout, we show that after being imported into cells by members of the equilibrative nucleoside transporter family, NR is predominantly metabolized by PNP, resulting in nicotinamide (Nam) accumulation. Intracellular cleavage of NR to Nam is prevented by the potent PNP inhibitor Immucillin H in various types of mammalian cells. In turn, suppression of PNP activity potentiates NAD synthesis from NR. Combining pharmacological inhibition of PNP with NR supplementation in mice, we demonstrate that the cleavage of the riboside to Nam is strongly diminished, maintaining high levels of NR in blood, kidney and liver. Moreover, we show that PNP inhibition stimulates Nam mononucleotide and NAD+ synthesis from NR in vivo, in particular, in the kidney. Thus, we establish PNP as a major regulator of NR metabolism in mammals and provide evidence that the health benefits of NR supplementation could be greatly enhanced by concomitant downregulation of PNP activity.
    Keywords:  NAD biosynthesis; human; metabolism; mouse; nicotinamide adenine dinucleotide (NAD); nicotinamide riboside; purine nucleoside phosphorylase
    DOI:  https://doi.org/10.1016/j.jbc.2022.102615
  23. FEBS Lett. 2022 Oct 17.
    Single protonation of the reduced quinone in respiratory complex I drives four-proton pumping.
    Alexei A Stuchebrukhov, Tomoyuki Hayashi.
      Complex I is a key proton-pumping enzyme in bacterial and mitochondrial respiratory electron transport chains. Using quantum chemistry and electrostatic calculations, we have examined the pKa of the reduced quinone QH-/QH2 in the catalytic cavity of complex I. We find that pKa(QH-/QH2) is very high, above 20. This means that the energy of a single protonation reaction of the doubly reduced quinone (i.e. the reduced semiquinone QH-) is sufficient to drive four protons across the membrane with a potential of 180mV. Based on these calculations, we propose a possible scheme of redox-linked proton pumping by complex I. The model explains how the energy of the protonation reaction can be divided equally between four pumping units of the pump, and how a single proton can drive translocation of four additional protons in multiple pumping blocks.
    Keywords:  Mitochondria; NADH dehydrogenase; coupled electron-proton transfer; proton pumping; proton translocation; respiratory complex I
    DOI:  https://doi.org/10.1002/1873-3468.14518
  24. Semin Cancer Biol. 2022 Oct 13. pii: S1044-579X(22)00205-X. [Epub ahead of print]
    Deregulated transcription factors in cancer cell metabolisms and reprogramming.
    Rajni Kant, Rajesh Kumar Manne, Mohammad Anas, Vasudevarao Penugurti, Tingjin Chen, Bo-Syong Pan, Che-Chia Hsu, Hui-Kuan Lin.
      Metabolic reprogramming is an important cancer hallmark that plays a key role in cancer malignancies and therapy resistance. Cancer cells reprogram the metabolic pathways to generate not only energy and building blocks but also produce numerous key signaling metabolites to impact signaling and epigenetic/transcriptional regulation for cancer cell proliferation and survival. A deeper understanding of the mechanisms by which metabolic reprogramming is regulated in cancer may provide potential new strategies for cancer targeting. Recent studies suggest that deregulated transcription factors have been observed in various human cancers and significantly impact metabolism and signaling in cancer. In this review, we highlight the key transcription factors that are involved in metabolic control, dissect the crosstalk between signaling and transcription factors in metabolic reprogramming, and offer therapeutic strategies targeting deregulated transcription factors for cancer treatment.
    Keywords:  Cancer treatment; Cell metabolism; Metabolic Reprogramming; Transcription Factors; signaling metabolites
    DOI:  https://doi.org/10.1016/j.semcancer.2022.10.001
  25. Nat Metab. 2022 Oct;4(10): 1219-1220
    Gut reaction: it's not all about enzymes.
    Stephan Kamrad, Anna E Lindell, Kiran R Patil.
      
    DOI:  https://doi.org/10.1038/s42255-022-00637-2
  26. Cell Metab. 2022 Oct 14. pii: S1550-4131(22)00447-8. [Epub ahead of print]
    The role of lipids in cancer progression and metastasis.
    Miguel Martin-Perez, Uxue Urdiroz-Urricelqui, Claudia Bigas, Salvador Aznar Benitah.
      Lipids have essential biological functions in the body (e.g., providing energy storage, acting as a signaling molecule, and being a structural component of membranes); however, an excess of lipids can promote tumorigenesis, colonization, and metastatic capacity of tumor cells. To metastasize, a tumor cell goes through different stages that require lipid-related metabolic and structural adaptations. These adaptations include altering the lipid membrane composition for invading other niches and overcoming cell death mechanisms and promoting lipid catabolism and anabolism for energy and oxidative stress protective purposes. Cancer cells also harness lipid metabolism to modulate the activity of stromal and immune cells to their advantage and to resist therapy and promote relapse. All this is especially worrying given the high fat intake in Western diets. Thus, metabolic interventions aiming to reduce lipid availability to cancer cells or to exacerbate their metabolic vulnerabilities provide promising therapeutic opportunities to prevent cancer progression and treat metastasis.
    Keywords:  lipid metabolism; metastasis; metastatic-initiating cells; tumor storm
    DOI:  https://doi.org/10.1016/j.cmet.2022.09.023
  27. Sci Signal. 2022 Oct 18. 15(756): eabj3490
    Rerouting the drug response: Overcoming metabolic adaptation in KRAS-mutant cancers.
    Deborah Y Moss, Christopher McCann, Emma M Kerr.
      Mutations in guanosine triphosphatase KRAS are common in lung, colorectal, and pancreatic cancers. The constitutive activity of mutant KRAS and its downstream signaling pathways induces metabolic rewiring in tumor cells that can promote resistance to existing therapeutics. In this review, we discuss the metabolic pathways that are altered in response to treatment and those that can, in turn, alter treatment efficacy, as well as the role of metabolism in the tumor microenvironment (TME) in dictating the therapeutic response in KRAS-driven cancers. We highlight metabolic targets that may provide clinical opportunities to overcome therapeutic resistance and improve survival in patients with these aggressive cancers.
    DOI:  https://doi.org/10.1126/scisignal.abj3490
  28. Nat Commun. 2022 Oct 20. 13(1): 6206
    p53 mutation in normal esophagus promotes multiple stages of carcinogenesis but is constrained by clonal competition.
    Kasumi Murai, Stefan Dentro, Swee Hoe Ong, Roshan Sood, David Fernandez-Antoran, Albert Herms, Vasiliki Kostiou, Irina Abnizova, Benjamin A Hall, Moritz Gerstung, Philip H Jones.
      Aging normal human oesophagus accumulates TP53 mutant clones. These are the origin of most oesophageal squamous carcinomas, in which biallelic TP53 disruption is almost universal. However, how p53 mutant clones expand and contribute to cancer development is unclear. Here we show that inducing the p53R245W mutant in single oesophageal progenitor cells in transgenic mice confers a proliferative advantage and clonal expansion but does not disrupt normal epithelial structure. Loss of the remaining p53 allele in mutant cells results in genomically unstable p53R245W/null epithelium with giant polyaneuploid cells and copy number altered clones. In carcinogenesis, p53 mutation does not initiate tumour formation, but tumours developing from areas with p53 mutation and LOH are larger and show extensive chromosomal instability compared to lesions arising in wild type epithelium. We conclude that p53 has distinct functions at different stages of carcinogenesis and that LOH within p53 mutant clones in normal epithelium is a critical step in malignant transformation.
    DOI:  https://doi.org/10.1038/s41467-022-33945-y
  29. Science. 2022 Oct 21. 378(6617): 290-295
    An evolutionary trade-off between host immunity and metabolism drives fatty liver in male mice.
    Joni Nikkanen, Yew Ann Leong, William C Krause, Denis Dermadi, J Alan Maschek, Tyler Van Ry, James E Cox, Ethan J Weiss, Omer Gokcumen, Ajay Chawla, Holly A Ingraham.
      Adaptations to infectious and dietary pressures shape mammalian physiology and disease risk. How such adaptations affect sex-biased diseases remains insufficiently studied. In this study, we show that sex-dependent hepatic gene programs confer a robust (~300%) survival advantage for male mice during lethal bacterial infection. The transcription factor B cell lymphoma 6 (BCL6), which masculinizes hepatic gene expression at puberty, is essential for this advantage. However, protection by BCL6 protein comes at a cost during conditions of dietary excess, which result in overt fatty liver and glucose intolerance in males. Deleting hepatic BCL6 reverses these phenotypes but markedly lowers male survival during infection, thus establishing a sex-dependent trade-off between host defense and metabolic systems. Our findings offer strong evidence that some current sex-biased diseases are rooted in ancient evolutionary trade-offs between immunity and metabolism.
    DOI:  https://doi.org/10.1126/science.abn9886
  30. Cancer Cell. 2022 Oct 18. pii: S1535-6108(22)00475-5. [Epub ahead of print]
    A path to translation: How 3D patient tumor avatars enable next generation precision oncology.
    Shree Bose
      3D patient tumor avatars (3D-PTAs) hold promise for next-generation precision medicine. Here, we describe the benefits and challenges of 3D-PTA technologies and necessary future steps to realize their potential for clinical decision making. 3D-PTAs require standardization criteria and prospective trials to establish clinical benefits. Innovative trial designs that combine omics and 3D-PTA readouts may lead to more accurate clinical predictors, and an integrated platform that combines diagnostic and therapeutic development will accelerate new treatments for patients with refractory disease.
    DOI:  https://doi.org/10.1016/j.ccell.2022.09.017
  31. Nat Metab. 2022 Oct;4(10): 1227-1228
    A common framework for mouse hypothalamic cell atlases.
    Alexander C Jackson.
      
    DOI:  https://doi.org/10.1038/s42255-022-00660-3
  32. Elife. 2022 Oct 21. pii: e76535. [Epub ahead of print]11
    Landscape of epithelial mesenchymal plasticity as an emergent property of coordinated teams in regulatory networks.
    Kishore Hari, Varun Ullanat, Archana Balasubramanian, Aditi Gopalan, Mohit Kumar Jolly.
      Elucidating the design principles of regulatory networks driving cellular decision-making has fundamental implications in mapping and eventually controlling cell-fate decisions. Despite being complex, these regulatory networks often only give rise to a few phenotypes. Previously, we identified two 'teams' of nodes in a small cell lung cancer regulatory network that constrained the phenotypic repertoire and aligned strongly with the dominant phenotypes obtained from network simulations (Chauhan et al., 2021). However, it remained elusive whether these 'teams' exist in other networks, and how do they shape the phenotypic landscape. Here, we demonstrate that five different networks of varying sizes governing epithelial-mesenchymal plasticity comprised of two 'teams' of players - one comprised of canonical drivers of epithelial phenotype and the other containing the mesenchymal inducers. These 'teams' are specific to the topology of these regulatory networks and orchestrate a bimodal phenotypic landscape with the epithelial and mesenchymal phenotypes being more frequent and dynamically robust to perturbations, relative to the intermediary/hybrid epithelial/ mesenchymal ones. Our analysis reveals that network topology alone can contain information about corresponding phenotypic distributions, thus obviating the need to simulate them. We propose 'teams' of nodes as a network design principle that can drive cell-fate canalization in diverse decision-making processes.
    Keywords:  computational biology; none; physics of living systems; systems biology
    DOI:  https://doi.org/10.7554/eLife.76535
  33. Cancer Res. 2022 Oct 20. pii: CAN-22-0945. [Epub ahead of print]
    N-myc mediated translation control is a therapeutic vulnerability in medulloblastoma.
    Duygu Kuzuoglu-Ozturk, Ozlem Aksoy, Christin Schmidt, Robin Lea, Jon D Larson, Ryan R L Phelps, Nicole Nasholm, Megan Holt, Adrian Contreras, Miller Huang, Shannon Wong-Michalak, Hao Shao, Robert Wechsler-Reya, Joanna J Phillips, Jason E Gestwicki, Davide Ruggero, William A Weiss.
      Deregulation of N-myc is a leading cause of malignant brain tumors in children. To target N-myc-driven medulloblastoma, most research has focused on identifying genomic alterations or on the analysis of the medulloblastoma transcriptome. Here, we have broadly characterized the translatome of medulloblastoma and shown that N-myc unexpectedly drives selective translation of transcripts that promote protein homeostasis. Cancer cells are constantly exposed to proteotoxic stress associated with alterations in protein production or folding. It remains poorly understood how cancers cope with proteotoxic stress to promote their growth. Here, our data unexpectedly revealed that N-myc regulates the expression of specific components (~5%) of the protein folding machinery at the translational level through the major cap binding protein, eukaryotic initiation factor eIF4E. Reducing eIF4E levels in mouse models of medulloblastoma blocked tumorigenesis. Importantly, targeting Hsp70, a protein folding chaperone translationally regulated by N-myc, suppressed tumor growth in mouse and human medulloblastoma xenograft models. These findings reveal a previously hidden molecular program that promotes medulloblastoma formation and identify new therapies that may have impact in the clinic.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-0945
  34. Nat Commun. 2022 Oct 17. 13(1): 6041
    A local tumor microenvironment acquired super-enhancer induces an oncogenic driver in colorectal carcinoma.
    Royce W Zhou, Jia Xu, Tiphaine C Martin, Alexis L Zachem, John He, Sait Ozturk, Deniz Demircioglu, Ankita Bansal, Andrew P Trotta, Bruno Giotti, Berkley Gryder, Yao Shen, Xuewei Wu, Saul Carcamo, Kaitlyn Bosch, Benjamin Hopkins, Alexander Tsankov, Randolph Steinhagen, Drew R Jones, John Asara, Jerry E Chipuk, Rachel Brody, Steven Itzkowitz, Iok In Christine Chio, Dan Hasson, Emily Bernstein, Ramon E Parsons.
      Tumors exhibit enhancer reprogramming compared to normal tissue. The etiology is largely attributed to cell-intrinsic genomic alterations. Here, using freshly resected primary CRC tumors and patient-matched adjacent normal colon, we find divergent epigenetic landscapes between CRC tumors and cell lines. Intriguingly, this phenomenon extends to highly recurrent aberrant super-enhancers gained in CRC over normal. We find one such super-enhancer activated in epithelial cancer cells due to surrounding inflammation in the tumor microenvironment. We restore this super-enhancer and its expressed gene, PDZK1IP1, following treatment with cytokines or xenotransplantation into nude mice, thus demonstrating cell-extrinsic etiology. We demonstrate mechanistically that PDZK1IP1 enhances the reductive capacity CRC cancer cells via the pentose phosphate pathway. We show this activation enables efficient growth under oxidative conditions, challenging the previous notion that PDZK1IP1 acts as a tumor suppressor in CRC. Collectively, these observations highlight the significance of epigenomic profiling on primary specimens.
    DOI:  https://doi.org/10.1038/s41467-022-33377-8
  35. Science. 2022 Oct 21. 378(6617): 276-284
    Time-restricted feeding mitigates obesity through adipocyte thermogenesis.
    Chelsea Hepler, Benjamin J Weidemann, Nathan J Waldeck, Biliana Marcheva, Jonathan Cedernaes, Anneke K Thorne, Yumiko Kobayashi, Rino Nozawa, Marsha V Newman, Peng Gao, Mengle Shao, Kathryn M Ramsey, Rana K Gupta, Joseph Bass.
      Misalignment of feeding rhythms with the light-dark cycle leads to disrupted peripheral circadian clocks and obesity. Conversely, restricting feeding to the active period mitigates metabolic syndrome through mechanisms that remain unknown. We found that genetic enhancement of adipocyte thermogenesis through ablation of the zinc finger protein 423 (ZFP423) attenuated obesity caused by consumption of a high-fat diet during the inactive (light) period by increasing futile creatine cycling in mice. Circadian control of adipocyte creatine metabolism underlies the timing of diet-induced thermogenesis, and enhancement of adipocyte circadian rhythms through overexpression of the clock activator brain and muscle Arnt-like protein-1 (BMAL1) ameliorated metabolic complications during diet-induced obesity. These findings uncover rhythmic creatine-mediated thermogenesis as an essential mechanism that drives metabolic benefits during time-restricted feeding.
    DOI:  https://doi.org/10.1126/science.abl8007
  36. Life Sci Alliance. 2022 Dec;pii: e202201663. [Epub ahead of print]5(12):
    Methionine uptake via the SLC43A2 transporter is essential for regulatory T-cell survival.
    Neetu Saini, Afsana Naaz, Shree Padma Metur, Pinki Gahlot, Adhish Walvekar, Anupam Dutta, Umamaheswari Davathamizhan, Apurva Sarin, Sunil Laxman.
      Cell death, survival, or growth decisions in T-cell subsets depend on interplay between cytokine-dependent and metabolic processes. The metabolic requirements of T-regulatory cells (Tregs) for their survival and how these are satisfied remain unclear. Herein, we identified a necessary requirement of methionine uptake and usage for Tregs survival upon IL-2 deprivation. Activated Tregs have high methionine uptake and usage to S-adenosyl methionine, and this uptake is essential for Tregs survival in conditions of IL-2 deprivation. We identify a solute carrier protein SLC43A2 transporter, regulated in a Notch1-dependent manner that is necessary for this methionine uptake and Tregs viability. Collectively, we uncover a specifically regulated mechanism of methionine import in Tregs that is required for cells to adapt to cytokine withdrawal. We highlight the need for methionine availability and metabolism in contextually regulating cell death in this immunosuppressive population of T cells.
    DOI:  https://doi.org/10.26508/lsa.202201663
  37. Cell Metab. 2022 Oct 11. pii: S1550-4131(22)00411-9. [Epub ahead of print]
    Ferroptosis heterogeneity in triple-negative breast cancer reveals an innovative immunotherapy combination strategy.
    Fan Yang, Yi Xiao, Jia-Han Ding, Xi Jin, Ding Ma, Da-Qiang Li, Jin-Xiu Shi, Wei Huang, Yi-Ping Wang, Yi-Zhou Jiang, Zhi-Ming Shao.
      Treatment of triple-negative breast cancer (TNBC) remains challenging. Deciphering the orchestration of metabolic pathways in regulating ferroptosis will provide new insights into TNBC therapeutic strategies. Here, we integrated the multiomics data of our large TNBC cohort (n = 465) to develop the ferroptosis atlas. We discovered that TNBCs had heterogeneous phenotypes in ferroptosis-related metabolites and metabolic pathways. The luminal androgen receptor (LAR) subtype of TNBC was characterized by the upregulation of oxidized phosphatidylethanolamines and glutathione metabolism (especially GPX4), which allowed the utilization of GPX4 inhibitors to induce ferroptosis. Furthermore, we verified that GPX4 inhibition not only induced tumor ferroptosis but also enhanced antitumor immunity. The combination of GPX4 inhibitors and anti-PD1 possessed greater therapeutic efficacy than monotherapy. Clinically, higher GPX4 expression correlated with lower cytolytic scores and worse prognosis in immunotherapy cohorts. Collectively, this study demonstrated the ferroptosis landscape of TNBC and revealed an innovative immunotherapy combination strategy for refractory LAR tumors.
    Keywords:  fatty acid metabolism; ferroptosis; heterogeneity; immunotherapy; treatment; triple-negative breast cancer
    DOI:  https://doi.org/10.1016/j.cmet.2022.09.021
  38. Annu Rev Physiol. 2022 Oct 21.
    Metabolic Recruitment in Brain Tissue.
    L F Barros, I Ruminot, T Sotelo-Hitschfeld, R Lerchundi, I Fernández-Moncada.
      Information processing imposes urgent metabolic demands on neurons, which have negligible energy stores and restricted access to fuel. Here, we discuss metabolic recruitment, the tissue-level phenomenon whereby active neurons harvest resources from their surroundings. The primary event is the neuronal release of K+ that mirrors workload. Astrocytes sense K+ in exquisite fashion thanks to their unique coexpression of NBCe1 and α2β2 Na+[Formula: see text]K+ ATPase, and within seconds switch to Crabtree metabolism, involving GLUT1, aerobic glycolysis, transient suppression of mitochondrial respiration, and lactate export. The lactate surge serves as a secondary recruiter by inhibiting glucose consumption in distant cells. Additional recruiters are glutamate, nitric oxide, and ammonium, which signal over different spatiotemporal domains. The net outcome of these events is that more glucose, lactate, and oxygen are made available. Metabolic recruitment works alongside neurovascular coupling and various averaging strategies to support the inordinate dynamic range of individual neurons. Expected final online publication date for the Annual Review of Physiology, Volume 85 is February 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-physiol-021422-091035
  39. J Biol Chem. 2022 Oct 12. pii: S0021-9258(22)01030-4. [Epub ahead of print] 102587
    Glucose-6-phosphate dehydrogenase exerts anti-stress effects independently of its enzymatic activity.
    Xiaohan Jin, Xuexue Li, Lifang Li, Benfu Zhong, Yang Hong, Jing Niu, Binghui Li.
      G6PD (Glucose-6-phosphate dehydrogenase) is the rate-limiting enzyme in the oxPPP (oxidative pentose phosphate pathway) that can generate cytosolic NADPH for biosynthesis and oxidative defense. Since cytosolic NADPH can be compensatively produced by other sources, the enzymatic activity-deficiency alleles of G6PD are well tolerated in somatic cells, but the effect of null mutations is unclear. Herein, we show that G6PD knockout sensitizes cells to the stresses induced by hydrogen peroxide, superoxide, hypoxia, and the inhibition of the electron transport chain. This effect can be completely reversed by the expressions of natural mutants associated with G6PD deficiency, even without dehydrogenase activity, exactly like the wild type G6PD. Furthermore, we demonstrate that G6PD can physically interact with AMPK (AMPK-activated protein kinase) to facilitate its activity, and directly bind to NAMPT (nicotinamide phosphoribosyltransferase) to promote its activity and maintain the NAD(P)H/NAD(P)+ homeostasis. These functions are necessary to the anti-stress ability of cells but independent of the dehydrogenase activity of G6PD. In addition, the wild type G6PD and naturally inactive mutant also can similarly regulate the metabolism of glucose, glutamine, fatty acid synthesis, and glutathione, and interact with the involved enzymes. Therefore, our findings reveal the previously unidentified functions of G6PD that can act as the important physiological neutralizer of stresses independently of its enzymatic activity.
    Keywords:  G6PD; NADH homeostasis; NAMPT; oxidative stress; pentose phosphate pathway
    DOI:  https://doi.org/10.1016/j.jbc.2022.102587
  40. Life Sci. 2022 Oct 18. pii: S0024-3205(22)00733-0. [Epub ahead of print] 121033
    Advances in energy metabolism in renal fibrosis.
    Xuejiao Wei, Yue Hou, Mengtuan Long, Lili Jiang, Yujun Du.
      Renal fibrosis is a common pathway toward chronic kidney disease (CKD) and is the main pathological predecessor for end-stage renal disease; thus, preventing progressive CKD and renal fibrosis is essential to reducing their consequential morbidity and mortality. Emerging evidence has connected renal fibrosis to metabolic reprogramming; abnormalities in energy metabolism pathways, such as glycolysis, the tricarboxylic acid cycle, and lipid metabolism, are known to cause diseases of diverse etiologies. Cytokine interventions in affected metabolic pathways may significantly reduce the degree of fibrosis, highlighting therapeutic targets for drug development for renal fibrosis. Here, we discuss the relationship between glycolysis, lipid metabolism, mitochondrial and peroxisome dysfunction, and renal fibrosis in detail and propose that targeted therapies for specific metabolic pathways are expected to represent the next generation of treatments for renal fibrosis.
    Keywords:  Fatty acid oxidation; Glycolysis; Mitochondrial dysfunction; Peroxisomal dysfunction; Renal fibrosis
    DOI:  https://doi.org/10.1016/j.lfs.2022.121033
  41. Elife. 2022 Oct 20. pii: e82348. [Epub ahead of print]11
    Caveolae couple mechanical stress to integrin recycling and activation.
    Fidel-Nicolás Lolo, Dácil María Pavón, Araceli Grande, Alberto Elósegui Artola, Valeria Inés Segatori, Sara Sánchez, Xavier Trepat, Pere Roca-Cusachs, Miguel Ángel Del Pozo.
      Cells are subjected to multiple mechanical inputs throughout their lives. Their ability to detect these environmental cues is called mechanosensing, a process in which integrins play an important role. During cellular mechanosensing, plasma membrane (PM) tension is adjusted to mechanical stress through the buffering action of caveolae; however, little is known about the role of caveolae in early integrin mechanosensing regulation. Here, we show that Cav1KO fibroblasts increase adhesion to FN-coated beads when pulled with magnetic tweezers, as compared to wild type fibroblasts. This phenotype is Rho-independent and mainly derived from increased active b1-integrin content on the surface of Cav1KO fibroblasts. FRAP analysis and endocytosis/recycling assays revealed that active b1-integrin is mostly endocytosed through the CLIC/GEEC pathway and is more rapidly recycled to the PM in Cav1KO fibroblasts, in a Rab4 and PM tension-dependent manner. Moreover, the threshold for PM tension-driven b1-integrin activation is lower in Cav1KO MEFs than in wild type MEFs, through a mechanism dependent on talin activity. Our findings suggest that caveolae couple mechanical stress to integrin cycling and activation, thereby regulating the early steps of the cellular mechanosensing response.
    Keywords:  cell biology; mouse
    DOI:  https://doi.org/10.7554/eLife.82348
  42. Cell Metab. 2022 Oct 14. pii: S1550-4131(22)00450-8. [Epub ahead of print]
    Comprehensive single-cell transcriptional profiling defines shared and unique epithelial injury responses during kidney fibrosis.
    Haikuo Li, Eryn E Dixon, Haojia Wu, Benjamin D Humphreys.
      The underlying cellular events driving kidney fibrogenesis and metabolic dysfunction are incompletely understood. Here, we employed single-cell combinatorial indexing RNA sequencing to analyze 24 mouse kidneys from two fibrosis models. We profiled 309,666 cells in one experiment, representing 50 cell types/states encompassing epithelial, endothelial, immune, and stromal populations. Single-cell analysis identified diverse injury states of the proximal tubule, including two distinct early-phase populations with dysregulated lipid and amino acid metabolism, respectively. Lipid metabolism was defective in the chronic phase but was transiently activated in the very early stages of ischemia-induced injury, where we discovered increased lipid deposition and increased fatty acid β-oxidation. Perilipin 2 was identified as a surface marker of intracellular lipid droplets, and its knockdown in vitro disrupted cell energy state maintenance during lipid accumulation. Surveying epithelial cells across nephron segments identified shared and unique injury responses. Stromal cells exhibited high heterogeneity and contributed to fibrogenesis by epithelial-stromal crosstalk.
    Keywords:  PLIN2; acute kidney injury; cell differentiation; chronic kidney disease; fibrosis; kidney; lipid droplet; lipid metabolism; single-cell combinatorial indexing; tissue regeneration
    DOI:  https://doi.org/10.1016/j.cmet.2022.09.026
  43. Nat Commun. 2022 Oct 17. 13(1): 6132
    Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements.
    Victor Tobiasson, Ieva Berzina, Alexey Amunts.
      Mitoribosomes of green algae display a great structural divergence from their tracheophyte relatives, with fragmentation of both rRNA and proteins as a defining feature. Here, we report a 2.9 Å resolution structure of the mitoribosome from the alga Polytomella magna harbouring a reduced rRNA split into 13 fragments. We found that the rRNA contains a non-canonical reduced form of the 5S, as well as a permutation of the LSU domain I. The mt-5S rRNA is stabilised by mL40 that is also found in mitoribosomes lacking the 5S, which suggests an evolutionary pathway. Through comparison to other ribosomes with fragmented rRNAs, we observe that the pattern is shared across large evolutionary distances, and between cellular compartments, indicating an evolutionary convergence and supporting the concept of a primordial fragmented ribosome. On the protein level, eleven peripherally associated HEAT-repeat proteins are involved in the binding of 3' rRNA termini, and the structure features a prominent pseudo-trimer of one of them (mL116). Finally, in the exit tunnel, mL128 constricts the tunnel width of the vestibular area, and mL105, a homolog of a membrane targeting component mediates contacts with an inner membrane bound insertase. Together, the structural analysis provides insight into the evolution of the ribosomal machinery in mitochondria.
    DOI:  https://doi.org/10.1038/s41467-022-33582-5
  44. Nat Rev Neurol. 2022 Oct 18.
    Gene therapy for primary mitochondrial diseases: experimental advances and clinical challenges.
    Micol Falabella, Michal Minczuk, Michael G Hanna, Carlo Viscomi, Robert D S Pitceathly.
      The variable clinical and biochemical manifestations of primary mitochondrial diseases (PMDs), and the complexity of mitochondrial genetics, have proven to be a substantial barrier to the development of effective disease-modifying therapies. Encouraging data from gene therapy trials in patients with Leber hereditary optic neuropathy and advances in DNA editing techniques have raised expectations that successful clinical transition of genetic therapies for PMDs is feasible. However, obstacles to the clinical application of genetic therapies in PMDs remain; the development of innovative, safe and effective genome editing technologies and vectors will be crucial to their future success and clinical approval. In this Perspective, we review progress towards the genetic treatment of nuclear and mitochondrial DNA-related PMDs. We discuss advances in mitochondrial DNA editing technologies alongside the unique challenges to targeting mitochondrial genomes. Last, we consider ongoing trials and regulatory requirements.
    DOI:  https://doi.org/10.1038/s41582-022-00715-9
  45. Proc Natl Acad Sci U S A. 2022 Oct 25. 119(43): e2207280119
    Endocytosis triggers V-ATPase-SYK-mediated priming of cGAS activation and innate immune response.
    Yu-Lin Yang, Li-Bo Cao, Wen-Rui He, Li Zhong, Yi Guo, Qing Yang, Hong-Bing Shu, Ming-Ming Hu.
      The current view of nucleic acid-mediated innate immunity is that binding of intracellular sensors to nucleic acids is sufficient for their activation. Here, we report that endocytosis of virus or foreign DNA initiates a priming signal for the DNA sensor cyclic GMP-AMP synthase (cGAS)-mediated innate immune response. Mechanistically, viral infection or foreign DNA transfection triggers recruitment of the spleen tyrosine kinase (SYK) and cGAS to the endosomal vacuolar H+ pump (V-ATPase), where SYK is activated and then phosphorylates human cGASY214/215 (mouse cGasY200/201) to prime its activation. Upon binding to DNA, the primed cGAS initiates robust cGAMP production and mediator of IRF3 activation/stimulator of interferon genes-dependent innate immune response. Consistently, blocking the V-ATPase-SYK axis impairs DNA virus- and transfected DNA-induced cGAMP production and expression of antiviral genes. Our findings reveal that V-ATPase-SYK-mediated tyrosine phosphorylation of cGAS following endocytosis of virus or other cargos serves as a priming signal for cGAS activation and innate immune response.
    Keywords:  DNA sensor cGAS; antiviral innate immunity; phosphorylation modification; signal transduction
    DOI:  https://doi.org/10.1073/pnas.2207280119
  46. EMBO Rep. 2022 Oct 17. e202153552
    Parkin drives pS65-Ub turnover independently of canonical autophagy in Drosophila.
    Joanne L Usher, Alvaro Sanchez-Martinez, Ana Terriente-Felix, Po-Lin Chen, Juliette J Lee, Chun-Hong Chen, Alexander J Whitworth.
      Parkinson's disease-related proteins, PINK1 and Parkin, act in a common pathway to maintain mitochondrial quality control. While the PINK1-Parkin pathway can promote autophagic mitochondrial turnover (mitophagy) following mitochondrial toxification in cell culture, alternative quality control pathways are suggested. To analyse the mechanisms by which the PINK1-Parkin pathway operates in vivo, we developed methods to detect Ser65-phosphorylated ubiquitin (pS65-Ub) in Drosophila. Exposure to the oxidant paraquat led to robust, Pink1-dependent pS65-Ub production, while pS65-Ub accumulates in unstimulated parkin-null flies, consistent with blocked degradation. Additionally, we show that pS65-Ub specifically accumulates on disrupted mitochondria in vivo. Depletion of the core autophagy proteins Atg1, Atg5 and Atg8a did not cause pS65-Ub accumulation to the same extent as loss of parkin, and overexpression of parkin promoted turnover of both basal and paraquat-induced pS65-Ub in an Atg5-null background. Thus, we have established that pS65-Ub immunodetection can be used to analyse Pink1-Parkin function in vivo as an alternative to reporter constructs. Moreover, our findings suggest that the Pink1-Parkin pathway can promote mitochondrial turnover independently of canonical autophagy in vivo.
    Keywords:   in vivo ; Parkinson's disease; mitochondria; mitophagy; phospho-ubiquitin
    DOI:  https://doi.org/10.15252/embr.202153552
  47. Mol Cell. 2022 Oct 20. pii: S1097-2765(22)00958-3. [Epub ahead of print]82(20): 3760-3762
    Vitamin K: A new guardian against ferroptosis.
    Tal Hirschhorn, Brent R Stockwell.
      The dietary factor vitamin K has been found to protect against ferroptosis, a form of cell death driven by lipid peroxidation. This reveals new dietary links to cancers and degenerative conditions and a key factor involved in warfarin poisoning.
    DOI:  https://doi.org/10.1016/j.molcel.2022.10.001
  48. Biochim Biophys Acta Mol Basis Dis. 2022 Oct 14. pii: S0925-4439(22)00243-5. [Epub ahead of print] 166572
    Proximal tubular Bmal1 protects against chronic kidney injury and renal fibrosis by maintaining of cellular metabolic homeostasis.
    Chengcheng Liu, Shuyao Li, Shuang Ji, Jiayang Zhang, Feng Zheng, Youfei Guan, Guangrui Yang, Lihong Chen.
      Recent studies suggest that deletion of the core clock gene Bmal1 in the kidney has a significant influence on renal physiological functions. However, the role of renal Bmal1 in chronic kidney disease (CKD) remains poorly understood. Here by generating mice lacking Bmal1 in proximal tubule (Bmal1flox/flox-KAP-Cre+, ptKO) and inducing CKD with the adenine diet model, we found that lack of Bmal1 in proximal tubule did not alter renal water and electrolyte homeostasis. However, adenine-induced renal injury indexes, including blood urea nitrogen, serum creatinine, and proteinuria, were markedly augmented in the ptKO mice. The ptKO kidneys also developed aggravated tubulointerstitial fibrosis and epithelial-mesenchymal transformation. Mechanistically, RNAseq analysis revealed significant downregulation of the expression of genes related to energy and substance metabolism, in particular fatty acid oxidation and glutathione/homocysteine metabolism, in the ptKO kidneys. Consistently, the renal contents of ATP and glutathione were markedly reduced in the ptKO mice, suggesting the disruption of cellular metabolic homeostasis. Moreover, we demonstrated that Bmal1 can activate the transcription of cystathionine β-synthase (CBS), a key enzyme for homocysteine metabolism and glutathione biosynthesis, through direct recruitment to the E-box motifs of its promoter. Supporting the in vivo findings, knockdown of Bmal1 in cultured proximal tubular cells inhibited CBS expression and amplified albumin-induced cell injury and fibrogenesis, while glutathione supplementation remarkably reversed these changes. Taken together, we concluded that deletion of Bmal1 in proximal tubule may aggravate chronic kidney injury and exacerbate renal fibrosis, the mechanism is related to suppressing CBS transcription and disturbing glutathione related metabolic homeostasis. These findings suggest a protective role of Bmal1 in chronic tubular injury and offer a novel target for treating CKD.
    Keywords:  Bmal1; Chronic kidney disease; Circadian clock; Metabolic homeostasis
    DOI:  https://doi.org/10.1016/j.bbadis.2022.166572
  49. Proc Biol Sci. 2022 Oct 26. 289(1985): 20221605
    Variable metabolic scaling breaks the law: from 'Newtonian' to 'Darwinian' approaches.
    Douglas S Glazier.
      Life's size and tempo are intimately linked. The rate of metabolism varies with body mass in remarkably regular ways that can often be described by a simple power function, where the scaling exponent (b, slope in a log-linear plot) is typically less than 1. Traditional theory based on physical constraints has assumed that b is 2/3 or 3/4, following natural law, but hundreds of studies have documented extensive, systematic variation in b. This overwhelming, law-breaking, empirical evidence is causing a paradigm shift in metabolic scaling theory and methodology from 'Newtonian' to 'Darwinian' approaches. A new wave of studies focuses on the adaptable regulation and evolution of metabolic scaling, as influenced by diverse intrinsic and extrinsic factors, according to multiple context-dependent mechanisms, and within boundary limits set by physical constraints.
    Keywords:  adaptive evolution; biological regulation; body size scaling; metabolic rate; natural laws; physical constraints
    DOI:  https://doi.org/10.1098/rspb.2022.1605
  50. Nat Cell Biol. 2022 Oct 20.
    Fructose-1,6-bisphosphatase 1 functions as a protein phosphatase to dephosphorylate histone H3 and suppresses PPARα-regulated gene transcription and tumour growth.
    Zheng Wang, Min Li, Hongfei Jiang, Shudi Luo, Fei Shao, Yan Xia, Mengke Yang, Xiangle Ren, Tong Liu, Meisi Yan, Xu Qian, Haiyan He, Dong Guo, Yuran Duan, Ke Wu, Lei Wang, Guimei Ji, Yuli Shen, Lin Li, Peixiang Zheng, Bofei Dong, Jing Fang, Min Zheng, Tingbo Liang, Haitao Li, Rilei Yu, Daqian Xu, Zhimin Lu.
      Tumour cells exhibit greater metabolic plasticity than normal cells and possess selective advantages for survival and proliferation with unclearly defined mechanisms. Here we demonstrate that glucose deprivation in normal hepatocytes induces PERK-mediated fructose-1,6-bisphosphatase 1 (FBP1) S170 phosphorylation, which converts the FBP1 tetramer to monomers and exposes its nuclear localization signal for nuclear translocation. Importantly, nuclear FBP1 binds PPARα and functions as a protein phosphatase that dephosphorylates histone H3T11 and suppresses PPARα-mediated β-oxidation gene expression. In contrast, FBP1 S124 is O-GlcNAcylated by overexpressed O-linked N-acetylglucosamine transferase in hepatocellular carcinoma cells, leading to inhibition of FBP1 S170 phosphorylation and enhancement of β-oxidation for tumour growth. In addition, FBP1 S170 phosphorylation inversely correlates with β-oxidation gene expression in hepatocellular carcinoma specimens and patient survival duration. These findings highlight the differential role of FBP1 in gene regulation in normal and tumour cells through direct chromatin modulation and underscore the inactivation of its protein phosphatase function in tumour growth.
    DOI:  https://doi.org/10.1038/s41556-022-01009-4
  51. EMBO Rep. 2022 Oct 21. e55839
    Human ZBP1 induces cell death-independent inflammatory signaling via RIPK3 and RIPK1.
    Ruoshi Peng, Chris Kedong Wang, Xuan Wang-Kan, Manja Idorn, Majken Kjaer, Felix Y Zhou, Berthe Katrine Fiil, Frederik Timmermann, Susana L Orozco, Julia McCarthy, Carol S Leung, Xin Lu, Katrin Bagola, Jan Rehwinkel, Andrew Oberst, Jonathan Maelfait, Søren R Paludan, Mads Gyrd-Hansen.
      ZBP1 is an interferon-induced cytosolic nucleic acid sensor that facilitates antiviral responses via RIPK3. Although ZBP1-mediated programmed cell death is widely described, whether and how it promotes inflammatory signaling is unclear. Here, we report a ZBP1-induced inflammatory signaling pathway mediated by K63- and M1-linked ubiquitin chains, which depends on RIPK1 and RIPK3 as scaffolds independently of cell death. In human HT29 cells, ZBP1 associated with RIPK1 and RIPK3 as well as ubiquitin ligases cIAP1 and LUBAC. ZBP1-induced K63- and M1-linked ubiquitination of RIPK1 and ZBP1 to promote TAK1- and IKK-mediated inflammatory signaling and cytokine production. Inhibition of caspase activity suppressed ZBP1-induced cell death but enhanced cytokine production in a RIPK1- and RIPK3 kinase activity-dependent manner. Lastly, we provide evidence that ZBP1 signaling contributes to SARS-CoV-2-induced cytokine production. Taken together, we describe a ZBP1-RIPK3-RIPK1-mediated inflammatory signaling pathway relayed by the scaffolding role of RIPKs and regulated by caspases, which may induce inflammation when ZBP1 is activated below the threshold needed to trigger a cell death response.
    Keywords:  RIPK1; RIPK3; SARS-CoV-2; ZBP1; inflammatory signaling
    DOI:  https://doi.org/10.15252/embr.202255839
  52. Nat Metab. 2022 Oct;4(10): 1336-1351
    COX7A2L genetic variants determine cardiorespiratory fitness in mice and human.
    Giorgia Benegiamo, Maroun Bou Sleiman, Martin Wohlwend, Sandra Rodríguez-López, Ludger J E Goeminne, Pirkka-Pekka Laurila, Marie Klevjer, Minna K Salonen, Jari Lahti, Pooja Jha, Sara Cogliati, José Antonio Enriquez, Ben M Brumpton, Anja Bye, Johan G Eriksson, Johan Auwerx.
      Mitochondrial respiratory complexes form superassembled structures called supercomplexes. COX7A2L is a supercomplex-specific assembly factor in mammals, although its implication for supercomplex formation and cellular metabolism remains controversial. Here we identify a role for COX7A2L for mitochondrial supercomplex formation in humans. By using human cis-expression quantitative trait loci data, we highlight genetic variants in the COX7A2L gene that affect its skeletal muscle expression specifically. The most significant cis-expression quantitative trait locus is a 10-bp insertion in the COX7A2L 3' untranslated region that increases messenger RNA stability and expression. Human myotubes harboring this insertion have more supercomplexes and increased respiration. Notably, increased COX7A2L expression in the muscle is associated with lower body fat and improved cardiorespiratory fitness in humans. Accordingly, specific reconstitution of Cox7a2l expression in C57BL/6J mice leads to higher maximal oxygen consumption, increased lean mass and increased energy expenditure. Furthermore, Cox7a2l expression in mice is induced specifically in the muscle upon exercise. These findings elucidate the genetic basis of mitochondrial supercomplex formation and function in humans and show that COX7A2L plays an important role in cardiorespiratory fitness, which could have broad therapeutic implications in reducing cardiovascular mortality.
    DOI:  https://doi.org/10.1038/s42255-022-00655-0
  53. EMBO J. 2022 Oct 17. e111173
    Prohibitin 1 regulates mtDNA release and downstream inflammatory responses.
    Hao Liu, Hualin Fan, Pengcheng He, Haixia Zhuang, Xiao Liu, Meiting Chen, Wenwei Zhong, Yi Zhang, Cien Zhen, Yanling Li, Huilin Jiang, Tian Meng, Yiming Xu, Guojun Zhao, Du Feng.
      Exposure of mitochondrial DNA (mtDNA) to the cytosol activates innate immune responses. But the mechanisms by which mtDNA crosses the inner mitochondrial membrane are unknown. Here, we found that the inner mitochondrial membrane protein prohibitin 1 (PHB1) plays a critical role in mtDNA release by regulating permeability across the mitochondrial inner membrane. Loss of PHB1 results in alterations in mitochondrial integrity and function. PHB1-deficient macrophages, serum from myeloid-specific PHB1 KO (Phb1MyeKO) mice, and peripheral blood mononuclear cells from neonatal sepsis patients show increased interleukin-1β (IL-1β) levels. PHB1 KO mice are also intolerant of lipopolysaccharide shock. Phb1-depleted macrophages show increased cytoplasmic release of mtDNA and inflammatory responses. This process is suppressed by cyclosporine A and VBIT-4, which inhibit the mitochondrial permeability transition pore (mPTP) and VDAC oligomerization. Inflammatory stresses downregulate PHB1 expression levels in macrophages. Under normal physiological conditions, the inner mitochondrial membrane proteins, AFG3L2 and SPG7, are tethered to PHB1 to inhibit mPTP opening. Downregulation of PHB1 results in enhanced interaction between AFG3L2 and SPG7, mPTP opening, mtDNA release, and downstream inflammatory responses.
    Keywords:  AFG3L2; MIMP; PHB; SPG7; mtDNA
    DOI:  https://doi.org/10.15252/embj.2022111173
  54. Cell Death Dis. 2022 Oct 15. 13(10): 872
    The Cancermuts software package for the prioritization of missense cancer variants: a case study of AMBRA1 in melanoma.
    Matteo Tiberti, Luca Di Leo, Mette Vixø Vistesen, Rikke Sofie Kuhre, Francesco Cecconi, Daniela De Zio, Elena Papaleo.
      Cancer genomics and cancer mutation databases have made an available wealth of information about missense mutations found in cancer patient samples. Contextualizing by means of annotation and predicting the effect of amino acid change help identify which ones are more likely to have a pathogenic impact. Those can be validated by means of experimental approaches that assess the impact of protein mutations on the cellular functions or their tumorigenic potential. Here, we propose the integrative bioinformatic approach Cancermuts, implemented as a Python package. Cancermuts is able to gather known missense cancer mutations from databases such as cBioPortal and COSMIC, and annotate them with the pathogenicity score REVEL as well as information on their source. It is also able to add annotations about the protein context these mutations are found in, such as post-translational modification sites, structured/unstructured regions, presence of short linear motifs, and more. We applied Cancermuts to the intrinsically disordered protein AMBRA1, a key regulator of many cellular processes frequently deregulated in cancer. By these means, we classified mutations of AMBRA1 in melanoma, where AMBRA1 is highly mutated and displays a tumor-suppressive role. Next, based on REVEL score, position along the sequence, and their local context, we applied cellular and molecular approaches to validate the predicted pathogenicity of a subset of mutations in an in vitro melanoma model. By doing so, we have identified two AMBRA1 mutations which show enhanced tumorigenic potential and are worth further investigation, highlighting the usefulness of the tool. Cancermuts can be used on any protein targets starting from minimal information, and it is available at https://www.github.com/ELELAB/cancermuts as free software.
    DOI:  https://doi.org/10.1038/s41419-022-05318-2
  55. Front Cell Dev Biol. 2022 ;10 942579
    The proneural transcription factor ASCL1 regulates cell proliferation and primes for differentiation in neuroblastoma.
    Lydia M Parkinson, Sarah L Gillen, Laura M Woods, Lewis Chaytor, Daniel Marcos, Fahad R Ali, Jason S Carroll, Anna Philpott.
      Neuroblastoma is believed to arise from sympathetic neuroblast precursors that fail to engage the neuronal differentiation programme, but instead become locked in a pro-proliferative developmental state. Achaete-scute homolog 1 (ASCL1) is a proneural master regulator of transcription which modulates both proliferation and differentiation of sympathetic neuroblast precursor cells during development, while its expression has been implicated in the maintenance of an oncogenic programme in MYCN-amplified neuroblastoma. However, the role of ASCL1 expression in neuroblastoma is not clear, especially as its levels vary considerably in different neuroblastoma cell lines. Here, we have investigated the role of ASCL1 in maintaining proliferation and controlling differentiation in both MYCN amplified and Anaplastic Lymphoma Kinase (ALK)-driven neuroblastoma cells. Using CRISPR deletion, we generated neuroblastoma cell lines lacking ASCL1 expression, and these grew more slowly than parental cells, indicating that ASCL1 contributes to rapid proliferation of MYCN amplified and non-amplified neuroblastoma cells. Genome-wide analysis after ASCL1 deletion revealed reduced expression of genes associated with neuronal differentiation, while chromatin accessibility at regulatory regions associated with differentiation genes was also attenuated by ASCL1 knock-out. In neuroblastoma, ASCL1 has been described as part of a core regulatory circuit of developmental regulators whose high expression is maintained by mutual cross-activation of a network of super enhancers and is further augmented by the activity of MYC/MYCN. Surprisingly, ASCL1 deletion had little effect on the transcription of CRC gene transcripts in these neuroblastoma cell lines, but the ability of MYC/MYCN and CRC component proteins, PHOX2B and GATA3, to bind to chromatin was compromised. Taken together, our results demonstrate several roles for endogenous ASCL1 in neuroblastoma cells: maintaining a highly proliferative phenotype, regulating DNA binding of the core regulatory circuit genes to chromatin, while also controlling accessibility and transcription of differentiation targets. Thus, we propose a model where ASCL1, a key developmental regulator of sympathetic neurogenesis, plays a pivotal role in maintaining proliferation while simultaneously priming cells for differentiation in neuroblastoma.
    Keywords:  ASCL1; chromatin accessibility; differentiation; neuroblastoma; neurogenesis; proliferation
    DOI:  https://doi.org/10.3389/fcell.2022.942579
  56. Nature. 2022 Oct 19.
    Clathrin-associated AP-1 controls termination of STING signalling.
    Ying Liu, Pengbiao Xu, Sophie Rivara, Chong Liu, Jonathan Ricci, Xuefeng Ren, James H Hurley, Andrea Ablasser.
      Stimulator of interferon genes (STING) functions downstream of cyclic GMP-AMP synthase in DNA sensing or as a direct receptor for bacterial cyclic dinucleotides and small molecules to activate immunity during infection, cancer and immunotherapy1-10. Precise regulation of STING is essential to ensure balanced immune responses and prevent detrimental autoinflammation11-16. After activation, STING, a transmembrane protein, traffics from the endoplasmic reticulum to the Golgi, where its phosphorylation by the protein kinase TBK1 enables signal transduction17-20. The mechanism that ends STING signalling at the Golgi remains unknown. Here we show that adaptor protein complex 1 (AP-1) controls the termination of STING-dependent immune activation. We find that AP-1 sorts phosphorylated STING into clathrin-coated transport vesicles for delivery to the endolysosomal system, where STING is degraded21. We identify a highly conserved dileucine motif in the cytosolic C-terminal tail (CTT) of STING that, together with TBK1-dependent CTT phosphorylation, dictates the AP-1 engagement of STING. A cryo-electron microscopy structure of AP-1 in complex with phosphorylated STING explains the enhanced recognition of TBK1-activated STING. We show that suppression of AP-1 exacerbates STING-induced immune responses. Our results reveal a structural mechanism of negative regulation of STING and establish that the initiation of signalling is inextricably associated with its termination to enable transient activation of immunity.
    DOI:  https://doi.org/10.1038/s41586-022-05354-0
  57. Nat Commun. 2022 Oct 18. 13(1): 6168
    The hypoxia response pathway promotes PEP carboxykinase and gluconeogenesis in C. elegans.
    Mehul Vora, Stephanie M Pyonteck, Tatiana Popovitchenko, Tarmie L Matlack, Aparna Prashar, Nanci S Kane, John Favate, Premal Shah, Christopher Rongo.
      Actively dividing cells, including some cancers, rely on aerobic glycolysis rather than oxidative phosphorylation to generate energy, a phenomenon termed the Warburg effect. Constitutive activation of the Hypoxia Inducible Factor (HIF-1), a transcription factor known for mediating an adaptive response to oxygen deprivation (hypoxia), is a hallmark of the Warburg effect. HIF-1 is thought to promote glycolysis and suppress oxidative phosphorylation. Here, we instead show that HIF-1 can promote gluconeogenesis. Using a multiomics approach, we reveal the genomic, transcriptomic, and metabolomic landscapes regulated by constitutively active HIF-1 in C. elegans. We use RNA-seq and ChIP-seq under aerobic conditions to analyze mutants lacking EGL-9, a key negative regulator of HIF-1. We integrate these approaches to identify over two hundred genes directly and functionally upregulated by HIF-1, including the PEP carboxykinase PCK-1, a rate-limiting mediator of gluconeogenesis. This activation of PCK-1 by HIF-1 promotes survival in response to both oxidative and hypoxic stress. Our work identifies functional direct targets of HIF-1 in vivo, comprehensively describing the metabolome induced by HIF-1 activation in an organism.
    DOI:  https://doi.org/10.1038/s41467-022-33849-x
  58. Science. 2022 Oct 21. 378(6617): eabq4835
    Mammalian oocytes store mRNAs in a mitochondria-associated membraneless compartment.
    Shiya Cheng, Gerrit Altmeppen, Chun So, Luisa M Welp, Sarah Penir, Torben Ruhwedel, Katerina Menelaou, Katarina Harasimov, Alexandra Stützer, Martyn Blayney, Kay Elder, Wiebke Möbius, Henning Urlaub, Melina Schuh.
      Full-grown oocytes are transcriptionally silent and must stably maintain the messenger RNAs (mRNAs) needed for oocyte meiotic maturation and early embryonic development. However, where and how mammalian oocytes store maternal mRNAs is unclear. Here, we report that mammalian oocytes accumulate mRNAs in a mitochondria-associated ribonucleoprotein domain (MARDO). MARDO assembly around mitochondria was promoted by the RNA-binding protein ZAR1 and directed by an increase in mitochondrial membrane potential during oocyte growth. MARDO foci coalesced into hydrogel-like matrices that clustered mitochondria. Maternal mRNAs stored in the MARDO were translationally repressed. Loss of ZAR1 disrupted the MARDO, dispersed mitochondria, and caused a premature loss of MARDO-localized mRNAs. Thus, a mitochondria-associated membraneless compartment controls mitochondrial distribution and regulates maternal mRNA storage, translation, and decay to ensure fertility in mammals.
    DOI:  https://doi.org/10.1126/science.abq4835
  59. Nature. 2022 Oct 19.
    Borgs are giant genetic elements with potential to expand metabolic capacity.
    Basem Al-Shayeb, Marie C Schoelmerich, Jacob West-Roberts, Luis E Valentin-Alvarado, Rohan Sachdeva, Susan Mullen, Alexander Crits-Christoph, Michael J Wilkins, Kenneth H Williams, Jennifer A Doudna, Jillian F Banfield.
      Anaerobic methane oxidation exerts a key control on greenhouse gas emissions1, yet factors that modulate the activity of microorganisms performing this function remain poorly understood. Here we discovered extraordinarily large, diverse DNA sequences that primarily encode hypothetical proteins through studying groundwater, sediments and wetland soil where methane production and oxidation occur. Four curated, complete genomes are linear, up to approximately 1 Mb in length and share genome organization, including replichore structure, long inverted terminal repeats and genome-wide unique perfect tandem direct repeats that are intergenic or generate amino acid repeats. We infer that these are highly divergent archaeal extrachromosomal elements with a distinct evolutionary origin. Gene sequence similarity, phylogeny and local divergence of sequence composition indicate that many of their genes were assimilated from methane-oxidizing Methanoperedens archaea. We refer to these elements as 'Borgs'. We identified at least 19 different Borg types coexisting with Methanoperedens spp. in four distinct ecosystems. Borgs provide methane-oxidizing Methanoperedens archaea access to genes encoding proteins involved in redox reactions and energy conservation (for example, clusters of multihaem cytochromes and methyl coenzyme M reductase). These data suggest that Borgs might have previously unrecognized roles in the metabolism of this group of archaea, which are known to modulate greenhouse gas emissions, but further studies are now needed to establish their functional relevance.
    DOI:  https://doi.org/10.1038/s41586-022-05256-1
  60. Curr Top Microbiol Immunol. 2022 ;436 95-115
    PTEN in Immunity.
    Antonella Papa, Pier Paolo Pandolfi.
      The tumor suppressor PTEN (Phosphatase and Tensin homolog deleted on Chromosome 10) executes critical biological functions that limit cellular growth and proliferation. PTEN inhibits activation of the proto-oncogenic PI3K pathway and is required during embryogenesis and to suppress tumor formation and cancer progression throughout life. The critical role that PTEN plays in restraining cellular growth has been validated through the generation of a number of animal models whereby PTEN inactivation invariably leads to tumor formation in a cell-autonomous fashion. However, the increasing understanding of the mechanisms through which the immune system contributes to suppressing tumor progression has highlighted how, in a cell non-autonomous fashion, cancer-associated mutations can indirectly enhance oncogenesis by evading immune cell recognition. Here, in light of the essential role of PTEN in the regulation of immune cell development and function, and based on recent findings showing that PTEN loss can promote resistance to immune checkpoint inhibitors in various tumor types, we re-evaluate our understanding of the mechanisms through which PTEN functions as a tumor suppressor and postulate that this task is achieved through a combination of cell autonomous and non-autonomous effects. We highlight some of the critical studies that have delineated the functional role of PTEN in immune cell development and blood malignancies and propose new strategies for the treatment of PTEN loss-driven diseases.
    Keywords:  Cancer resistance; Immune cell development; Immunotherapy; PTEN; Tumor suppression
    DOI:  https://doi.org/10.1007/978-3-031-06566-8_4
  61. Nature. 2022 Oct 19.
    HRG-9 homologues regulate haem trafficking from haem-enriched compartments.
    Fengxiu Sun, Zhenzhen Zhao, Mathilda M Willoughby, Shuaiqi Shen, Yu Zhou, Yiyan Shao, Jing Kang, Yongtian Chen, Mengying Chen, Xiaojing Yuan, Iqbal Hamza, Amit R Reddi, Caiyong Chen.
      Haem is an iron-containing tetrapyrrole that is critical for a variety of cellular and physiological processes1-3. Haem binding proteins are present in almost all cellular compartments, but the molecular mechanisms that regulate the transport and use of haem within the cell remain poorly understood2,3. Here we show that haem-responsive gene 9 (HRG-9) (also known as transport and Golgi organization 2 (TANGO2)) is an evolutionarily conserved haem chaperone with a crucial role in trafficking haem out of haem storage or synthesis sites in eukaryotic cells. Loss of Caenorhabditis elegans hrg-9 and its paralogue hrg-10 results in the accumulation of haem in lysosome-related organelles, the haem storage site in worms. Similarly, deletion of the hrg-9 homologue TANGO2 in yeast and mammalian cells induces haem overload in mitochondria, the site of haem synthesis. We demonstrate that TANGO2 binds haem and transfers it from cellular membranes to apo-haemoproteins. Notably, homozygous tango2-/- zebrafish larvae develop pleiotropic symptoms including encephalopathy, cardiac arrhythmia and myopathy, and die during early development. These defects partially resemble the symptoms of human TANGO2-related metabolic encephalopathy and arrhythmias, a hereditary disease caused by mutations in TANGO24-8. Thus, the identification of HRG-9 as an intracellular haem chaperone provides a biological basis for exploring the aetiology and treatment of TANGO2-related disorders.
    DOI:  https://doi.org/10.1038/s41586-022-05347-z
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