bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2022‒08‒07
fifty-nine papers selected by
Christian Frezza, Universität zu Köln
  1. Regulation of mitochondrial proteostasis by the proton gradient.
  2. The mystery of mitochondrial plasticity: TMBIM5 integrates metabolic state and proteostasis.
  3. Nucleotide imbalance decouples cell growth from cell proliferation.
  4. T-bet B or not T-bet B, is that the question in obesity-related metabolic disease?
  5. Serine metabolism remodeling after platinum-based chemotherapy identifies vulnerabilities in a subgroup of resistant ovarian cancers.
  6. Roles of mitochondrial genetics in cancer metastasis.
  7. CMT2A-linked mitochondrial hyperfusion-driving mutant MFN2 perturbs ER-mitochondrial associations and Ca2+ homeostasis.
  8. cGAS-STING and the deadly CIN: how chronic inflammation represents a therapeutic vulnerability in chromosomally unstable cancers.
  9. Career pathways, part 9.
  10. Targeting acetyl-CoA metabolism attenuates the formation of fear memories through reduced activity-dependent histone acetylation.
  11. Nrf2 as a regulator of mitochondrial function: Energy metabolism and beyond.
  12. Rapamycin rescues mitochondrial dysfunction in cells carrying the m.8344A > G mutation in the mitochondrial tRNALys.
  13. Emerging metabolomic tools to study cancer metastasis.
  14. Connecting Metabolic Rewiring With Phenotype Switching in Melanoma.
  15. Tryptophan metabolism is a physiological integrator regulating circadian rhythms.
  16. DNA methyltransferase 3 alpha and TET methylcytosine dioxygenase 2 restrain mitochondrial DNA-mediated interferon signaling in macrophages.
  17. Novel DNM1L variants impair mitochondrial dynamics through divergent mechanisms.
  18. Mitochondrial remodeling and ischemic protection by G protein-coupled receptor 35 agonists.
  19. Aβ42 oligomers trigger synaptic loss through CAMKK2-AMPK-dependent effectors coordinating mitochondrial fission and mitophagy.
  20. 13C metabolic flux analysis clarifies distinct metabolic phenotypes of cancer cell spheroid mimicking tumor hypoxia.
  21. Role of the cystathionine β-synthase / H2S pathway in the development of cellular metabolic dysfunction and pseudohypoxia in down syndrome.
  22. PI3K-AKT Inhibits PANK4 to Promote De Novo Synthesis of Coenzyme A.
  23. Metabolic Rewiring in Glioblastoma Cancer: EGFR, IDH and Beyond.
  24. Acute exercise dynamically modulates the hepatic mitochondrial proteome.
  25. Using the urea cycle to shift astrocytes from harmful to helpful in Alzheimer's disease.
  26. Highly conserved shifts in ubiquitin-proteasome system (UPS) activity drive mitochondrial remodeling during quiescence.
  27. Segregated cation flux by TPC2 biases Ca2+ signaling through lysosomes.
  28. Glioblastoma hijacks neuronal mechanisms for brain invasion.
  29. The Delivery of Extracellular "Danger" Signals to Cytosolic Sensors in Phagocytes.
  30. Targeting strategies in the treatment of fumarate hydratase deficient renal cell carcinoma.
  31. Gluconeogenesis: Adding a new piece to the puzzle of malaria parasitism.
  32. Measuring Single-Cell Mitochondrial DNA Copy Number and Heteroplasmy using Digital Droplet Polymerase Chain Reaction.
  33. Ribosome impairment regulates intestinal stem cell identity via ZAKɑ activation.
  34. Aberrant iron distribution via hepatocyte-stellate cell axis drives liver lipogenesis and fibrosis.
  35. Cancer genes disfavoring T cell immunity identified via integrated systems approach.
  36. Outrunning obesity with Lac-Phe?
  37. De novo pyrimidine synthesis fuels glycolysis and confers chemoresistance in gastric cancer.
  38. Mitochondrial ROS promotes susceptibility to infection via gasdermin D-mediated necroptosis.
  39. Selenium modulates cancer cell response to pharmacologic ascorbate.
  40. Mitophagy and oral cancers.
  41. CD24-Siglec axis is an innate immune checkpoint against metaflammation and metabolic disorder.
  42. Targeting ASGR1 to lower cholesterol.
  43. The IRG1/itaconate/TFEB axis: A new weapon in macrophage antibacterial defense.
  44. PFKFB4 interacts with ICMT and activates RAS/AKT signaling-dependent cell migration in melanoma.
  45. Accurate determination of CRISPR-mediated gene fitness in transplantable tumours.
  46. Argininosuccinate synthase 1, arginine deprivation therapy and cancer management.
  47. Histone H3K36me2 and H3K36me3 form a chromatin platform essential for DNMT3A-dependent DNA methylation in mouse oocytes.
  48. PARP12 is required for mitochondrial function maintenance in thermogenic adipocytes.
  49. Maladaptive positive feedback production of ChREBPβ underlies glucotoxic β-cell failure.
  50. A non-canonical vitamin K cycle is a potent ferroptosis suppressor.
  51. Brown-fat-mediated tumour suppression by cold-altered global metabolism.
  52. Systems biochemistry to "deorphanize" human mitochondrial proteome.
  53. A new fluorescent sensor mitoferrofluor indicates the presence of chelatable iron in polarized and depolarized mitochondria.
  54. An immunogenic model of KRAS-mutant lung cancer enables evaluation of targeted therapy and immunotherapy combinations.
  55. Metabolic reprogramming from glycolysis to fatty acid uptake and beta-oxidation in platinum-resistant cancer cells.
  56. Balancing NAD+ deficits with nicotinamide riboside: therapeutic possibilities and limitations.
  57. FOXA1 inhibits hypoxia programs through transcriptional repression of HIF1A.
  58. Unique expression of the atypical mitochondrial subunit NDUFA4L2 in cerebral pericytes fine tunes HIF activity in response to hypoxia.
  59. Golgi stress induces SIRT2 to counteract Shigella infection via defatty-acylation.
  1. EMBO J. 2022 Aug 01. e110476
    Regulation of mitochondrial proteostasis by the proton gradient.
    Maria Patron, Daryna Tarasenko, Hendrik Nolte, Lara Kroczek, Mausumi Ghosh, Yohsuke Ohba, Yvonne Lasarzewski, Zeinab Alsadat Ahmadi, Alfredo Cabrera-Orefice, Akinori Eyiama, Tim Kellermann, Elena I Rugarli, Ulrich Brandt, Michael Meinecke, Thomas Langer.
      Mitochondria adapt to different energetic demands reshaping their proteome. Mitochondrial proteases are emerging as key regulators of these adaptive processes. Here, we use a multiproteomic approach to demonstrate the regulation of the m-AAA protease AFG3L2 by the mitochondrial proton gradient, coupling mitochondrial protein turnover to the energetic status of mitochondria. We identify TMBIM5 (previously also known as GHITM or MICS1) as a Ca2+ /H+ exchanger in the mitochondrial inner membrane, which binds to and inhibits the m-AAA protease. TMBIM5 ensures cell survival and respiration, allowing Ca2+ efflux from mitochondria and limiting mitochondrial hyperpolarization. Persistent hyperpolarization, however, triggers degradation of TMBIM5 and activation of the m-AAA protease. The m-AAA protease broadly remodels the mitochondrial proteome and mediates the proteolytic breakdown of respiratory complex I to confine ROS production and oxidative damage in hyperpolarized mitochondria. TMBIM5 thus integrates mitochondrial Ca2+ signaling and the energetic status of mitochondria with protein turnover rates to reshape the mitochondrial proteome and adjust the cellular metabolism.
    Keywords:  AFG3L2; TMBIM5; mitochondrial calcium; proton gradient; respiratory chain
    DOI:  https://doi.org/10.15252/embj.2021110476
  2. EMBO J. 2022 Aug 01. e111834
    The mystery of mitochondrial plasticity: TMBIM5 integrates metabolic state and proteostasis.
    Mindong Ren, Michael Schlame.
      Recent work identifies TMBIM5 as inner mitochondrial membrane Ca2+ /H+ exchanger, linking hyperpolarisation regulation to proteome control and energy metabolism.
    DOI:  https://doi.org/10.15252/embj.2022111834
  3. Nat Cell Biol. 2022 Aug 04.
    Nucleotide imbalance decouples cell growth from cell proliferation.
    Frances F Diehl, Teemu P Miettinen, Ryan Elbashir, Christopher S Nabel, Alicia M Darnell, Brian T Do, Scott R Manalis, Caroline A Lewis, Matthew G Vander Heiden.
      Nucleotide metabolism supports RNA synthesis and DNA replication to enable cell growth and division. Nucleotide depletion can inhibit cell growth and proliferation, but how cells sense and respond to changes in the relative levels of individual nucleotides is unclear. Moreover, the nucleotide requirement for biomass production changes over the course of the cell cycle, and how cells coordinate differential nucleotide demands with cell cycle progression is not well understood. Here we find that excess levels of individual nucleotides can inhibit proliferation by disrupting the relative levels of nucleotide bases needed for DNA replication and impeding DNA replication. The resulting purine and pyrimidine imbalances are not sensed by canonical growth regulatory pathways like mTORC1, Akt and AMPK signalling cascades, causing excessive cell growth despite inhibited proliferation. Instead, cells rely on replication stress signalling to survive during, and recover from, nucleotide imbalance during S phase. We find that ATR-dependent replication stress signalling is activated during unperturbed S phases and promotes nucleotide availability to support DNA replication. Together, these data reveal that imbalanced nucleotide levels are not detected until S phase, rendering cells reliant on replication stress signalling to cope with this metabolic problem and disrupting the coordination of cell growth and division.
    DOI:  https://doi.org/10.1038/s41556-022-00965-1
  4. Cell Metab. 2022 Aug 02. pii: S1550-4131(22)00307-2. [Epub ahead of print]34(8): 1081-1082
    T-bet B or not T-bet B, is that the question in obesity-related metabolic disease?
    Michael P Cancro.
      Obesity is linked to inflammation and downstream metabolic dysregulation. In this issue of Cell Metabolism, Hägglöf et al. show that iNKT cells enable the accumulation of T-bet+ B cells in white adipose tissue, which in turn produce chemokine and antibody mediators that exacerbate the onset and severity of metabolic disease.
    DOI:  https://doi.org/10.1016/j.cmet.2022.07.008
  5. Nat Commun. 2022 Aug 05. 13(1): 4578
    Serine metabolism remodeling after platinum-based chemotherapy identifies vulnerabilities in a subgroup of resistant ovarian cancers.
    Tom Van Nyen, Mélanie Planque, Lilian van Wagensveld, Joao A G Duarte, Esther A Zaal, Ali Talebi, Matteo Rossi, Pierre-René Körner, Lara Rizzotto, Stijn Moens, Wout De Wispelaere, Regina E M Baiden-Amissah, Gabe S Sonke, Hugo M Horlings, Guy Eelen, Emanuele Berardi, Johannes V Swinnen, Celia R Berkers, Peter Carmeliet, Diether Lambrechts, Ben Davidson, Reuven Agami, Sarah-Maria Fendt, Daniela Annibali, Frédéric Amant.
      Resistance to platinum-based chemotherapy represents a major clinical challenge for many tumors, including epithelial ovarian cancer. Patients often experience several response-relapse events, until tumors become resistant and life expectancy drops to 12-15 months. Despite improved knowledge of the molecular determinants of platinum resistance, the lack of clinical applicability limits exploitation of many potential targets, leaving patients with limited options. Serine biosynthesis has been linked to cancer growth and poor prognosis in various cancer types, however its role in platinum-resistant ovarian cancer is not known. Here, we show that a subgroup of resistant tumors decreases phosphoglycerate dehydrogenase (PHGDH) expression at relapse after platinum-based chemotherapy. Mechanistically, we observe that this phenomenon is accompanied by a specific oxidized nicotinamide adenine dinucleotide (NAD+) regenerating phenotype, which helps tumor cells in sustaining Poly (ADP-ribose) polymerase (PARP) activity under platinum treatment. Our findings reveal metabolic vulnerabilities with clinical implications for a subset of platinum resistant ovarian cancers.
    DOI:  https://doi.org/10.1038/s41467-022-32272-6
  6. Trends Cancer. 2022 Jul 29. pii: S2405-8033(22)00157-1. [Epub ahead of print]
    Roles of mitochondrial genetics in cancer metastasis.
    Danny R Welch, Christian Foster, Isidore Rigoutsos.
      The contributions of mitochondria to cancer have been recognized for decades. However, the focus on the metabolic role of mitochondria and the diminutive size of the mitochondrial genome compared to the nuclear genome have hindered discovery of the roles of mitochondrial genetics in cancer. This review summarizes recent data demonstrating the contributions of mitochondrial DNA (mtDNA) copy-number variants (CNVs), somatic mutations, and germline polymorphisms to cancer initiation, progression, and metastasis. The goal is to summarize accumulating data to establish a framework for exploring the contributions of mtDNA to neoplasia and metastasis.
    Keywords:  metabolism; metastasis; mitochondrial genetics; polymorphism; tumor progression
    DOI:  https://doi.org/10.1016/j.trecan.2022.07.004
  7. Biol Cell. 2022 Aug 04.
    CMT2A-linked mitochondrial hyperfusion-driving mutant MFN2 perturbs ER-mitochondrial associations and Ca2+ homeostasis.
    Rajdeep Das, Subhrangshu Das, Saikat Chakrabarti, Oishee Chakrabarti.
      Mitofusin2 (MFN2), an important molecular player that regulates mitochondrial fusion, also helps maintain the inter-organellar contact sites, referred as mitochondria associated membranes (MAMs) that exist between the ER and mitochondria. Here we show that a mutant of MFN2, R364W-MFN2, linked with the Charcot Marie Tooth disease, promotes mitochondrial hyperfusion, alters ER mitochondrial associations at the MAM junctions and perturbs inter-organellar calcium homeostasis. Such hyperfused mitochondria are also predisposed towards stress and undergo rapid fission upon induction of mild stress. Thus, here we report that presence of the R364W-MFN2 mutation makes cells susceptible towards stress, thus negatively affecting cellular health. This article is protected by copyright. All rights reserved.
    Keywords:  CMT2A-linked MFN2 mutant; DRP1; ER-mitochondrial associations; mitochondrial hyperfusion
    DOI:  https://doi.org/10.1111/boc.202100098
  8. Trends Cancer. 2022 Jul 29. pii: S2405-8033(22)00159-5. [Epub ahead of print]
    cGAS-STING and the deadly CIN: how chronic inflammation represents a therapeutic vulnerability in chromosomally unstable cancers.
    Samuel F Bakhoum.
      Chromosomal instability (CIN) is a key genomic driver of human cancer. CIN generates genomic copy-number heterogeneity and tumor-derived inflammation. In a recent paper, Hong et al. identify the cGAS-STING innate immune pathway as a crucial dependency in cancer cells with CIN and pinpoint the IL6/STAT3 axis as a therapeutic vulnerability in these difficult-to-treat tumors.
    DOI:  https://doi.org/10.1016/j.trecan.2022.07.006
  9. Nat Metab. 2022 Aug 05.
    Career pathways, part 9.
    Evanna L Mills, Edward T Chouchani.
      
    DOI:  https://doi.org/10.1038/s42255-022-00624-7
  10. Proc Natl Acad Sci U S A. 2022 Aug 09. 119(32): e2114758119
    Targeting acetyl-CoA metabolism attenuates the formation of fear memories through reduced activity-dependent histone acetylation.
    Desi C Alexander, Tanya Corman, Mariel Mendoza, Andrew Glass, Tal Belity, Ranran Wu, Rianne R Campbell, Joseph Han, Ashley A Keiser, Jeffrey Winkler, Marcelo A Wood, Thomas Kim, Benjamin A Garcia, Hagit Cohen, Philipp Mews, Gabor Egervari, Shelley L Berger.
      Histone acetylation is a key component in the consolidation of long-term fear memories. Histone acetylation is fueled by acetyl-coenzyme A (acetyl-CoA), and recently, nuclear-localized metabolic enzymes that produce this metabolite have emerged as direct and local regulators of chromatin. In particular, acetyl-CoA synthetase 2 (ACSS2) mediates histone acetylation in the mouse hippocampus. However, whether ACSS2 regulates long-term fear memory remains to be determined. Here, we show that Acss2 knockout is well tolerated in mice, yet the Acss2-null mouse exhibits reduced acquisition of long-term fear memory. Loss of Acss2 leads to reductions in both histone acetylation and expression of critical learning and memory-related genes in the dorsal hippocampus, specifically following fear conditioning. Furthermore, systemic administration of blood-brain barrier-permeable Acss2 inhibitors during the consolidation window reduces fear-memory formation in mice and rats and reduces anxiety in a predator-scent stress paradigm. Our findings suggest that nuclear acetyl-CoA metabolism via ACSS2 plays a critical, previously unappreciated, role in the formation of fear memories.
    Keywords:  epigenetics; fear conditioning; histone acetylation; learning and memory; mass spectrometry
    DOI:  https://doi.org/10.1073/pnas.2114758119
  11. Free Radic Biol Med. 2022 Jul 30. pii: S0891-5849(22)00496-8. [Epub ahead of print]
    Nrf2 as a regulator of mitochondrial function: Energy metabolism and beyond.
    Noemí Esteras, Andrey Y Abramov.
      Mitochondria are unique and essential organelles that mediate many vital cellular processes including energy metabolism and cell death. The transcription factor Nrf2 (NF-E2 p45-related factor 2) has emerged in the last few years as an important modulator of multiple aspects of mitochondrial function. Well-known for controlling cellular redox homeostasis, the cytoprotective effects of Nrf2 extend beyond its ability to regulate a diverse network of antioxidant and detoxification enzymes. Here, we review the role of Nrf2 in the regulation of mitochondrial function and structure. We focus on Nrf2 involvement in promoting mitochondrial quality control and regulation of basic aspects of mitochondrial function, including energy production, reactive oxygen species generation, calcium signalling, and cell death induction. Given the importance of mitochondria in the development of multiple diseases, these findings reinforce the pharmacological activation of Nrf2 as an attractive strategy to counteract mitochondrial dysfunction.
    Keywords:  Calcium; Dynamics; Energy; Fission; Fusion; Mitochondria; Mitochondrial biogenesis; Mitophagy; Nrf2; ROS; mPTP
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2022.07.013
  12. Mol Med. 2022 Aug 03. 28(1): 90
    Rapamycin rescues mitochondrial dysfunction in cells carrying the m.8344A > G mutation in the mitochondrial tRNALys.
    Mariantonietta Capristo, Valentina Del Dotto, Concetta Valentina Tropeano, Claudio Fiorini, Leonardo Caporali, Chiara La Morgia, Maria Lucia Valentino, Monica Montopoli, Valerio Carelli, Alessandra Maresca.
      BACKGROUND: Myoclonus, Epilepsy and Ragged-Red-Fibers (MERRF) is a mitochondrial encephalomyopathy due to heteroplasmic mutations in mitochondrial DNA (mtDNA) most frequently affecting the tRNALys gene at position m.8344A > G. Defective tRNALys severely impairs mitochondrial protein synthesis and respiratory chain when a high percentage of mutant heteroplasmy crosses the threshold for full-blown clinical phenotype. Therapy is currently limited to symptomatic management of myoclonic epilepsy, and supportive measures to counteract muscle weakness with co-factors/supplements.METHODS: We tested two therapeutic strategies to rescue mitochondrial function in cybrids and fibroblasts carrying different loads of the m.8344A > G mutation. The first strategy was aimed at inducing mitochondrial biogenesis directly, over-expressing the master regulator PGC-1α, or indirectly, through the treatment with nicotinic acid, a NAD+ precursor. The second was aimed at stimulating the removal of damaged mitochondria through prolonged rapamycin treatment.
    RESULTS: The first approach slightly increased mitochondrial protein expression and respiration in the wild type and intermediate-mutation load cells, but was ineffective in high-mutation load cell lines. This suggests that induction of mitochondrial biogenesis may not be sufficient to rescue mitochondrial dysfunction in MERRF cells with high-mutation load. The second approach, when administered chronically (4 weeks), induced a slight increase of mitochondrial respiration in fibroblasts with high-mutation load, and a significant improvement in fibroblasts with intermediate-mutation load, rescuing completely the bioenergetics defect. This effect was mediated by increased mitochondrial biogenesis, possibly related to the rapamycin-induced inhibition of the Mechanistic Target of Rapamycin Complex 1 (mTORC1) and the consequent activation of the Transcription Factor EB (TFEB).
    CONCLUSIONS: Overall, our results point to rapamycin-based therapy as a promising therapeutic option for MERRF.
    Keywords:  MERRF; Mitochondrial DNA; Mitochondrial biogenesis; Mitochondrial dysfunction; Niacin; PGC-1α; Rapamycin; mTORC1
    DOI:  https://doi.org/10.1186/s10020-022-00519-z
  13. Trends Cancer. 2022 Jul 28. pii: S2405-8033(22)00156-X. [Epub ahead of print]
    Emerging metabolomic tools to study cancer metastasis.
    Luiza Martins Nascentes Melo, Nicholas P Lesner, Marie Sabatier, Jessalyn M Ubellacker, Alpaslan Tasdogan.
      Metastasis is responsible for 90% of deaths in patients with cancer. Understanding the role of metabolism during metastasis has been limited by the development of robust and sensitive technologies that capture metabolic processes in metastasizing cancer cells. We discuss the current technologies available to study (i) metabolism in primary and metastatic cancer cells and (ii) metabolic interactions between cancer cells and the tumor microenvironment (TME) at different stages of the metastatic cascade. We identify advantages and disadvantages of each method and discuss how these tools and technologies will further improve our understanding of metastasis. Studies investigating the complex metabolic rewiring of different cells using state-of-the-art metabolomic technologies have the potential to reveal novel biological processes and therapeutic interventions for human cancers.
    Keywords:  analytical techniques; cancer metabolism; cancer metastasis; metabolomics
    DOI:  https://doi.org/10.1016/j.trecan.2022.07.003
  14. Front Cell Dev Biol. 2022 ;10 930250
    Connecting Metabolic Rewiring With Phenotype Switching in Melanoma.
    Paola Falletta, Colin R Goding, Yurena Vivas-García.
      Melanoma is a complex and aggressive cancer type that contains different cell subpopulations displaying distinct phenotypes within the same tumor. Metabolic reprogramming, a hallmark of cell transformation, is essential for melanoma cells to adopt different phenotypic states necessary for adaptation to changes arising from a dynamic milieu and oncogenic mutations. Increasing evidence demonstrates how melanoma cells can exhibit distinct metabolic profiles depending on their specific phenotype, allowing adaptation to hostile microenvironmental conditions, such as hypoxia or nutrient depletion. For instance, increased glucose consumption and lipid anabolism are associated with proliferation, while a dependency on exogenous fatty acids and an oxidative state are linked to invasion and metastatic dissemination. How these different metabolic dependencies are integrated with specific cell phenotypes is poorly understood and little is known about metabolic changes underpinning melanoma metastasis. Recent evidence suggests that metabolic rewiring engaging transitions to invasion and metastatic progression may be dependent on several factors, such as specific oncogenic programs or lineage-restricted mechanisms controlling cell metabolism, intra-tumor microenvironmental cues and anatomical location of metastasis. In this review we highlight how the main molecular events supporting melanoma metabolic rewiring and phenotype-switching are parallel and interconnected events that dictate tumor progression and metastatic dissemination through interplay with the tumor microenvironment.
    Keywords:  MITF; drug resisitance; fatty acids; heterogeneity; melanoma; metabolic plasticity; mitochondria
    DOI:  https://doi.org/10.3389/fcell.2022.930250
  15. Mol Metab. 2022 Jul 29. pii: S2212-8778(22)00125-9. [Epub ahead of print] 101556
    Tryptophan metabolism is a physiological integrator regulating circadian rhythms.
    Paul Petrus, Marlene Cervantes, Muntaha Samad, Tomoki Sato, Alina Chao, Shogo Sato, Kevin B Koronowski, Grace Park, Yasmine Alam, Niklas Mejhert, Marcus M Seldin, José Manuel Monroy Kuhn, Kenneth A Dyar, Dominik Lutter, Pierre Baldi, Peter Kaiser, Cholsoon Jang, Paolo Sassone-Corsi.
      The circadian clock aligns physiology with the 24-hour rotation of Earth. Light and food are the main environmental cues (zeitgebers) regulating circadian rhythms in mammals. Yet, little is known about the interaction between specific dietary components and light in coordinating circadian homeostasis. Herein, we focused on essential amino acids and identified tryptophan as a key circadian modulator. Through a multi-omics approach and combinatory diet/light interventions, we demonstrated that tryptophan metabolism modulates temporal regulation of metabolism and transcription programs by buffering photic cues. Specifically, tryptophan metabolites regulate central circadian functions of the suprachiasmatic nucleus and the core clock machinery in the liver. Taken together, our findings propose tryptophan metabolism as a potential point for pharmacologic intervention to modulate phenotypes associated with disrupted circadian rhythms.
    DOI:  https://doi.org/10.1016/j.molmet.2022.101556
  16. Immunity. 2022 Aug 04. pii: S1074-7613(22)00295-3. [Epub ahead of print]
    DNA methyltransferase 3 alpha and TET methylcytosine dioxygenase 2 restrain mitochondrial DNA-mediated interferon signaling in macrophages.
    Isidoro Cobo, Tiffany N Tanaka, Kailash Chandra Mangalhara, Addison Lana, Calvin Yeang, Claudia Han, Johannes Schlachetzki, Jean Challcombe, Bethany R Fixsen, Mashito Sakai, Rick Z Li, Hannah Fields, Michal Mokry, Randy G Tsai, Rafael Bejar, Koen Prange, Menno de Winther, Gerald S Shadel, Christopher K Glass.
      Deleterious somatic mutations in DNA methyltransferase 3 alpha (DNMT3A) and TET mehtylcytosine dioxygenase 2 (TET2) are associated with clonal expansion of hematopoietic cells and higher risk of cardiovascular disease (CVD). Here, we investigated roles of DNMT3A and TET2 in normal human monocyte-derived macrophages (MDM), in MDM isolated from individuals with DNMT3A or TET2 mutations, and in macrophages isolated from human atherosclerotic plaques. We found that loss of function of DNMT3A or TET2 resulted in a type I interferon response due to impaired mitochondrial DNA integrity and activation of cGAS signaling. DNMT3A and TET2 normally maintained mitochondrial DNA integrity by regulating the expression of transcription factor A mitochondria (TFAM) dependent on their interactions with RBPJ and ZNF143 at regulatory regions of the TFAM gene. These findings suggest that targeting the cGAS-type I IFN pathway may have therapeutic value in reducing risk of CVD in patients with DNMT3A or TET2 mutations.
    Keywords:  DNMT3A; TET2; TFAM; atherosclerosis; clonal hematopoiesis; interferon; mitochondria DNA; transcriptional regulation
    DOI:  https://doi.org/10.1016/j.immuni.2022.06.022
  17. Life Sci Alliance. 2022 Dec;pii: e202101284. [Epub ahead of print]5(12):
    Novel DNM1L variants impair mitochondrial dynamics through divergent mechanisms.
    Kelsey A Nolden, John M Egner, Jack J Collier, Oliver M Russell, Charlotte L Alston, Megan C Harwig, Michael E Widlansky, Souphatta Sasorith, Inês A Barbosa, Andrew Gl Douglas, Julia Baptista, Mark Walker, Deirdre E Donnelly, Andrew A Morris, Hui Jeen Tan, Manju A Kurian, Kathleen Gorman, Santosh Mordekar, Charu Deshpande, Rajib Samanta, Robert McFarland, R Blake Hill, Robert W Taylor, Monika Oláhová.
      Imbalances in mitochondrial and peroxisomal dynamics are associated with a spectrum of human neurological disorders. Mitochondrial and peroxisomal fission both involve dynamin-related protein 1 (DRP1) oligomerisation and membrane constriction, although the precise biophysical mechanisms by which distinct DRP1 variants affect the assembly and activity of different DRP1 domains remains largely unexplored. We analysed four unreported de novo heterozygous variants in the dynamin-1-like gene DNM1L, affecting different highly conserved DRP1 domains, leading to developmental delay, seizures, hypotonia, and/or rare cardiac complications in infancy. Single-nucleotide DRP1 stalk domain variants were found to correlate with more severe clinical phenotypes, with in vitro recombinant human DRP1 mutants demonstrating greater impairments in protein oligomerisation, DRP1-peroxisomal recruitment, and both mitochondrial and peroxisomal hyperfusion compared to GTPase or GTPase-effector domain variants. Importantly, we identified a novel mechanism of pathogenesis, where a p.Arg710Gly variant uncouples DRP1 assembly from assembly-stimulated GTP hydrolysis, providing mechanistic insight into how assembly-state information is transmitted to the GTPase domain. Together, these data reveal that discrete, pathological DNM1L variants impair mitochondrial network maintenance by divergent mechanisms.
    DOI:  https://doi.org/10.26508/lsa.202101284
  18. Science. 2022 Aug 05. 377(6606): 621-629
    Mitochondrial remodeling and ischemic protection by G protein-coupled receptor 35 agonists.
    Gregory A Wyant, Wenyu Yu, IIias P Doulamis, Rio S Nomoto, Mossab Y Saeed, Thomas Duignan, James D McCully, William G Kaelin.
      Kynurenic acid (KynA) is tissue protective in cardiac, cerebral, renal, and retinal ischemia models, but the mechanism is unknown. KynA can bind to multiple receptors, including the aryl hydrocarbon receptor, the a7 nicotinic acetylcholine receptor (a7nAChR), multiple ionotropic glutamate receptors, and the orphan G protein-coupled receptor GPR35. Here, we show that GPR35 activation was necessary and sufficient for ischemic protection by KynA. When bound by KynA, GPR35 activated Gi- and G12/13-coupled signaling and trafficked to the outer mitochondria membrane, where it bound, apparantly indirectly, to ATP synthase inhibitory factor subunit 1 (ATPIF1). Activated GPR35, in an ATPIF1-dependent and pertussis toxin-sensitive manner, induced ATP synthase dimerization, which prevented ATP loss upon ischemia. These findings provide a rationale for the development of specific GPR35 agonists for the treatment of ischemic diseases.
    DOI:  https://doi.org/10.1126/science.abm1638
  19. Nat Commun. 2022 Aug 01. 13(1): 4444
    Aβ42 oligomers trigger synaptic loss through CAMKK2-AMPK-dependent effectors coordinating mitochondrial fission and mitophagy.
    Annie Lee, Chandana Kondapalli, Daniel M Virga, Tommy L Lewis, So Yeon Koo, Archana Ashok, Georges Mairet-Coello, Sebastien Herzig, Marc Foretz, Benoit Viollet, Reuben Shaw, Andrew Sproul, Franck Polleux.
      During the early stages of Alzheimer's disease (AD) in both mouse models and human patients, soluble forms of Amyloid-β 1-42 oligomers (Aβ42o) trigger loss of excitatory synapses (synaptotoxicity) in cortical and hippocampal pyramidal neurons (PNs) prior to the formation of insoluble amyloid plaques. In a transgenic AD mouse model, we observed a spatially restricted structural remodeling of mitochondria in the apical tufts of CA1 PNs dendrites corresponding to the dendritic domain where the earliest synaptic loss is detected in vivo. We also observed AMPK over-activation as well as increased fragmentation and loss of mitochondrial biomass in Ngn2-induced neurons derived from a new APPSwe/Swe knockin human ES cell line. We demonstrate that Aβ42o-dependent over-activation of the CAMKK2-AMPK kinase dyad mediates synaptic loss through coordinated phosphorylation of MFF-dependent mitochondrial fission and ULK2-dependent mitophagy. Our results uncover a unifying stress-response pathway causally linking Aβ42o-dependent structural remodeling of dendritic mitochondria to synaptic loss.
    DOI:  https://doi.org/10.1038/s41467-022-32130-5
  20. Metab Eng. 2022 Jul 31. pii: S1096-7176(22)00095-7. [Epub ahead of print]
    13C metabolic flux analysis clarifies distinct metabolic phenotypes of cancer cell spheroid mimicking tumor hypoxia.
    Shingo Noguchi, Kenichi Wakita, Fumio Matsuda, Hiroshi Shimizu.
      Cancer cells adapt their intracellular energy metabolism to the oxygen-deprived tumor microenvironment (TME) to ensure tumor progression. This adaptive mechanism has focused attention on the metabolic phenotypes of tumor cells under hypoxic TME for developing novel cancer therapies. Although widely used monolayer (2D) culture does not fully reflect in vivo hypoxic TME, spheroid (3D) culture can produce a milieu similar to the TME in vivo. However, how different metabolic phenotypes are expressed in 3D cultures mimicking tumor hypoxia compared with 2D cultures under hypoxia remains unclear. To address this issue, we investigated the metabolic phenotypes of 2D- and 3D-cultured cancer cells by 13C-metabolic flux analysis (13C-MFA). Principal component analysis of 13C mass isotopomer distributions clearly demonstrated distinct metabolic phenotypes of 3D-cultured cells. 13C-MFA clarified that 3D culture significantly upregulated pyruvate carboxylase flux in line with the pyruvate carboxylase protein expression level. On the other hand, 3D culture downregulated glutaminolytic flux. Consistent with our findings, 3D-cultured cells are more resistant to a glutaminase inhibitor than 2D-cultured cells. This study suggests the importance of considering the metabolic characteristics of the particular in vitro model used for research on cancer metabolism.
    Keywords:  (13)C-metabolic flux analysis; 3D culture; Cancer metabolism; Hypoxic tumor microenvironment; Spheroid
    DOI:  https://doi.org/10.1016/j.ymben.2022.07.008
  21. Redox Biol. 2022 Jul 21. pii: S2213-2317(22)00188-4. [Epub ahead of print]55 102416
    Role of the cystathionine β-synthase / H2S pathway in the development of cellular metabolic dysfunction and pseudohypoxia in down syndrome.
    Theodora Panagaki, Laszlo Pecze, Elisa B Randi, Anni I Nieminen, Csaba Szabo.
      BACKGROUND: Overexpression of the transsulfuration enzyme cystathionine-β-synthase (CBS), and overproduction of its product, hydrogen sulfide (H2S) are recognized as potential pathogenetic factors in Down syndrome (DS). The purpose of the study was to determine how the mitochondrial function and core metabolic pathways are affected by DS and how pharmacological inhibition of CBS affects these parameters.METHODS: 8 human control and 8 human DS fibroblast cell lines have been subjected to bioenergetic and fluxomic and proteomic analysis with and without treatment with a pharmacological inhibitor of CBS.
    RESULTS: DS cells exhibited a significantly higher CBS expression than control cells, and produced more H2S. They also exhibited suppressed mitochondrial electron transport and oxygen consumption and suppressed Complex IV activity, impaired cell proliferation and increased ROS generation. Inhibition of H2S biosynthesis with aminooxyacetic acid reduced cellular H2S, improved cellular bioenergetics, attenuated ROS and improved proliferation. 13C glucose fluxomic analysis revealed that DS cells exhibit a suppression of the Krebs cycle activity with a compensatory increase in glycolysis. CBS inhibition restored the flux from glycolysis to the Krebs cycle and reactivated oxidative phosphorylation. Proteomic analysis revealed no CBS-dependent alterations in the expression level of the enzymes involved in glycolysis, oxidative phosphorylation and the pentose phosphate pathway. DS was associated with the dysregulation of several components of the autophagy network; CBS inhibition normalized several of these parameters.
    CONCLUSIONS: Increased H2S generation in DS promotes pseudohypoxia and contributes to cellular metabolic dysfunction by causing a shift from oxidative phosphorylation to glycolysis.
    Keywords:  Down syndrome; Glycolysis; Hydrogen sulfide; Metabolism; Oxidative phosphorylation
    DOI:  https://doi.org/10.1016/j.redox.2022.102416
  22. Cancer Discov. 2022 Aug 05. OF1
    PI3K-AKT Inhibits PANK4 to Promote De Novo Synthesis of Coenzyme A.
      AKT inhibits the metabolic enzyme PANK4 to promote the de novo synthesis of coenzyme A (CoA).
    DOI:  https://doi.org/10.1158/2159-8290.CD-RW2022-140
  23. Front Oncol. 2022 ;12 901951
    Metabolic Rewiring in Glioblastoma Cancer: EGFR, IDH and Beyond.
    Abdellatif El Khayari, Najat Bouchmaa, Bouchra Taib, Zhiyun Wei, Ailiang Zeng, Rachid El Fatimy.
      Glioblastoma multiforme (GBM), a highly invasive and incurable tumor, is the humans' foremost, commonest, and deadliest brain cancer. As in other cancers, distinct combinations of genetic alterations (GA) in GBM induce a diversity of metabolic phenotypes resulting in enhanced malignancy and altered sensitivity to current therapies. Furthermore, GA as a hallmark of cancer, dysregulated cell metabolism in GBM has been recently linked to the acquired GA. Indeed, Numerous point mutations and copy number variations have been shown to drive glioma cells' metabolic state, affecting tumor growth and patient outcomes. Among the most common, IDH mutations, EGFR amplification, mutation, PTEN loss, and MGMT promoter mutation have emerged as key patterns associated with upregulated glycolysis and OXPHOS glutamine addiction and altered lipid metabolism in GBM. Therefore, current Advances in cancer genetic and metabolic profiling have yielded mechanistic insights into the metabolism rewiring of GBM and provided potential avenues for improved therapeutic modalities. Accordingly, actionable metabolic dependencies are currently used to design new treatments for patients with glioblastoma. Herein, we capture the current knowledge of genetic alterations in GBM, provide a detailed understanding of the alterations in metabolic pathways, and discuss their relevance in GBM therapy.
    Keywords:  GBM; genetic alteration; glioma therapy; glycolysis; metabolic genes
    DOI:  https://doi.org/10.3389/fonc.2022.901951
  24. Mol Omics. 2022 Aug 05.
    Acute exercise dynamically modulates the hepatic mitochondrial proteome.
    Colin S McCoin, Edziu Franczak, Michael P Washburn, Mihaela E Sardiu, John P Thyfault.
      Exercise powerfully increases energy metabolism and substrate flux in tissues, a process reliant on dramatic changes in mitochondrial energetics. Liver mitochondria play a multi-factorial role during exercise to fuel hepatic glucose output. We previously showed acute exercise activates hepatic mitophagy, a pathway to recycle low-functioning/damaged mitochondria, however little is known how individual bouts of exercise alters the hepatic mitochondrial proteome. Here we leveraged proteomics to examine changes in isolated hepatic mitochondria both immediately after and 2 hours post an acute, 1 hour bout of treadmill exercise in female mice. Further, we utilized leupeptin, a lysosomal inhibitor, to capture and measure exercise-induced changes in mitochondrial proteins that would have been unmeasured due to their targeting for lysosomal degradation. Proteomic analysis of enriched hepatic mitochondria identified 3241 total proteins. Functional enrichment analysis revealed robust enrichment for proteins critical to the mitochondria including metabolic pathways, tricarboxylic acid cycle, and electron transport system. Compared to the sedentary condition, exercise elevated processes regulating lipid localization, Il-5 signaling, and protein phosphorylation in isolated mitochondria. t-SNE analysis identified 4 unique expressional clusters driven by time-dependent changes in protein expression. Isolation of proteins significantly altered with exercise from each cluster revealed influences of leupeptin and exercise both independently and cooperatively modulating mitochondrial protein expressional profiles. Overall, we provide evidence that acute exercise rapidly modulates changes in the proteins/pathways of isolated hepatic mitochondria that include fatty acid metabolism/storage, post-translational protein modification, inflammation, and oxidative stress. In conclusion, the hepatic mitochondrial proteome undergoes extensive remodeling with a bout of exercise.
    DOI:  https://doi.org/10.1039/d2mo00143h
  25. Cell Metab. 2022 Aug 02. pii: S1550-4131(22)00300-X. [Epub ahead of print]34(8): 1079-1081
    Using the urea cycle to shift astrocytes from harmful to helpful in Alzheimer's disease.
    Ariel K Frame, Robert C Cumming.
      Astrocytes are brain cells that react to Alzheimer's disease pathology in ways that can have either beneficial or detrimental effects. In this issue of Cell Metabolism, Ju et al. outline a novel strategy for coercing astrocytes to a neuroprotective state by maintaining liver-like detoxification in the brain without producing damaging byproducts.
    DOI:  https://doi.org/10.1016/j.cmet.2022.07.001
  26. Nat Commun. 2022 Aug 01. 13(1): 4462
    Highly conserved shifts in ubiquitin-proteasome system (UPS) activity drive mitochondrial remodeling during quiescence.
    Sibiao Yue, Lei Wang, George N DeMartino, FangZhou Zhao, Yi Liu, Matthew H Sieber.
      Defects in cellular proteostasis and mitochondrial function drive many aspects of infertility, cancer, and other age-related diseases. All of these conditions rely on quiescent cells, such as oocytes and adult stem cells, that reduce their activity and remain dormant as part of their roles in tissue homeostasis, reproduction, and even cancer recurrence. Using a multi-organism approach, we show that dynamic shifts in the ubiquitin proteasome system drive mitochondrial remodeling during cellular quiescence. In contrast to the commonly held view that the ubiquitin-proteasome system (UPS) is primarily regulated by substrate ubiquitination, we find that increasing proteasome number and their recruitment to mitochondria support mitochondrial respiratory quiescence (MRQ). GSK3 triggers proteasome recruitment to the mitochondria by phosphorylating outer membrane proteins, such as VDAC, and suppressing mitochondrial fatty acid oxidation. This work defines a process that couples dynamic regulation of UPS activity to coordinated shifts in mitochondrial metabolism in fungi, Drosophila, and mammals during quiescence.
    DOI:  https://doi.org/10.1038/s41467-022-32206-2
  27. Nat Commun. 2022 Aug 02. 13(1): 4481
    Segregated cation flux by TPC2 biases Ca2+ signaling through lysosomes.
    Yu Yuan, Dawid Jaślan, Taufiq Rahman, Stephen R Bolsover, Vikas Arige, Larry E Wagner, Carla Abrahamian, Rachel Tang, Marco Keller, Jonas Hartmann, Anna S Rosato, Eva-Maria Weiden, Franz Bracher, David I Yule, Christian Grimm, Sandip Patel.
      Two-pore channels are endo-lysosomal cation channels with malleable selectivity filters that drive endocytic ion flux and membrane traffic. Here we show that TPC2 can differentially regulate its cation permeability when co-activated by its endogenous ligands, NAADP and PI(3,5)P2. Whereas NAADP rendered the channel Ca2+-permeable and PI(3,5)P2 rendered the channel Na+-selective, a combination of the two increased Ca2+ but not Na+ flux. Mechanistically, this was due to an increase in Ca2+ permeability independent of changes in ion selectivity. Functionally, we show that cell permeable NAADP and PI(3,5)P2 mimetics synergistically activate native TPC2 channels in live cells, globalizing cytosolic Ca2+ signals and regulating lysosomal pH and motility. Our data reveal that flux of different ions through the same pore can be independently controlled and identify TPC2 as a likely coincidence detector that optimizes lysosomal Ca2+ signaling.
    DOI:  https://doi.org/10.1038/s41467-022-31959-0
  28. Cell. 2022 Aug 04. pii: S0092-8674(22)00847-9. [Epub ahead of print]185(16): 2899-2917.e31
    Glioblastoma hijacks neuronal mechanisms for brain invasion.
    Varun Venkataramani, Yvonne Yang, Marc Cicero Schubert, Ekin Reyhan, Svenja Kristin Tetzlaff, Niklas Wißmann, Michael Botz, Stella Judith Soyka, Carlo Antonio Beretta, Rangel Lyubomirov Pramatarov, Laura Fankhauser, Luciano Garofano, Alexander Freudenberg, Julia Wagner, Dimitar Ivanov Tanev, Miriam Ratliff, Ruifan Xie, Tobias Kessler, Dirk C Hoffmann, Ling Hai, Yvette Dörflinger, Simone Hoppe, Yahaya A Yabo, Anna Golebiewska, Simone P Niclou, Felix Sahm, Anna Lasorella, Martin Slowik, Leif Döring, Antonio Iavarone, Wolfgang Wick, Thomas Kuner, Frank Winkler.
      Glioblastomas are incurable tumors infiltrating the brain. A subpopulation of glioblastoma cells forms a functional and therapy-resistant tumor cell network interconnected by tumor microtubes (TMs). Other subpopulations appear unconnected, and their biological role remains unclear. Here, we demonstrate that whole-brain colonization is fueled by glioblastoma cells that lack connections with other tumor cells and astrocytes yet receive synaptic input from neurons. This subpopulation corresponds to neuronal and neural-progenitor-like tumor cell states, as defined by single-cell transcriptomics, both in mouse models and in the human disease. Tumor cell invasion resembled neuronal migration mechanisms and adopted a Lévy-like movement pattern of probing the environment. Neuronal activity induced complex calcium signals in glioblastoma cells followed by the de novo formation of TMs and increased invasion speed. Collectively, superimposing molecular and functional single-cell data revealed that neuronal mechanisms govern glioblastoma cell invasion on multiple levels. This explains how glioblastoma's dissemination and cellular heterogeneity are closely interlinked.
    Keywords:  cancer neuroscience; cell heterogeneity; glioblastoma; glutamatergic synapse; neurogliomal synapses; neuron-tumor interaction; tumor cell networks; tumor microtubes
    DOI:  https://doi.org/10.1016/j.cell.2022.06.054
  29. Front Immunol. 2022 ;13 944142
    The Delivery of Extracellular "Danger" Signals to Cytosolic Sensors in Phagocytes.
    Gerone A Gonzales, Johnathan Canton.
      Phagocytes, such as macrophages and dendritic cells, possess the ability to ingest large quantities of exogenous material into membrane-bound endocytic organelles such as macropinosomes and phagosomes. Typically, the ingested material, which consists of diverse macromolecules such as proteins and nucleic acids, is delivered to lysosomes where it is digested into smaller molecules like amino acids and nucleosides. These smaller molecules can then be exported out of the lysosomes by transmembrane transporters for incorporation into the cell's metabolic pathways or for export from the cell. There are, however, exceptional instances when undigested macromolecules escape degradation and are instead delivered across the membrane of endocytic organelles into the cytosol of the phagocyte. For example, double stranded DNA, a damage associated molecular pattern shed by necrotic tumor cells, is endocytosed by phagocytes in the tumor microenvironment and delivered to the cytosol for detection by the cytosolic "danger" sensor cGAS. Other macromolecular "danger" signals including lipopolysaccharide, intact proteins, and peptidoglycans can also be actively transferred from within endocytic organelles to the cytosol. Despite the obvious biological importance of these processes, we know relatively little of how macromolecular "danger" signals are transferred across endocytic organelle membranes for detection by cytosolic sensors. Here we review the emerging evidence for the active cytosolic transfer of diverse macromolecular "danger" signals across endocytic organelle membranes. We will highlight developing trends and discuss the potential molecular mechanisms driving this emerging phenomenon.
    Keywords:  DAMP; PAMP; dendritic cell; endocytic organelle; macrophage; pattern recognition receptor; phagocyte; phagocytosis
    DOI:  https://doi.org/10.3389/fimmu.2022.944142
  30. Front Oncol. 2022 ;12 906014
    Targeting strategies in the treatment of fumarate hydratase deficient renal cell carcinoma.
    Andrea Katharina Lindner, Gennadi Tulchiner, Andreas Seeber, Peter J Siska, Martin Thurnher, Renate Pichler.
      Fumarate hydratase (FH) - deficient renal cell carcinoma (FHdRCC) is a rare aggressive subtype of RCC caused by a germline or sporadic loss-of-function mutation in the FH gene. Here, we summarize how FH deficiency results in the accumulation of fumarate, which in turn leads to activation of hypoxia-inducible factor (HIF) through inhibition of prolyl hydroxylases. HIF promotes tumorigenesis by orchestrating a metabolic switch to glycolysis even under normoxia, a phenomenon well-known as the Warburg effect. HIF activates the transcription of many genes, including vascular endothelial growth factor (VEGF). Crosstalk between HIF and epidermal growth factor receptor (EGFR) has also been described as a tumor-promoting mechanism. In this review we discuss therapeutic options for FHdRCC with a focus on anti-angiogenesis and EGFR-blockade. We also address potential targets that arise within the metabolic escape routes taken by FH-deficient cells for cell growth and survival.
    Keywords:  bevacizumab; erlotinib; fumarate hydratase; fumarate hydratase deficient renal cell carcinoma; glucose; hereditary leiomyomatosis and renal cell cancer; metabolism; renal cell carcinoma (RCC)
    DOI:  https://doi.org/10.3389/fonc.2022.906014
  31. Cell Metab. 2022 Aug 02. pii: S1550-4131(22)00303-5. [Epub ahead of print]34(8): 1083-1085
    Gluconeogenesis: Adding a new piece to the puzzle of malaria parasitism.
    Kely C Matteucci, Theresa R Ramalho, Isabella C Hirako, Ricardo T Gazzinelli.
      Disorders of carbohydrate metabolism, including hypoglycemia and lactic acidosis, are common features of malaria. In this issue of Cell Metabolism, Ramos et al. report that regulation of gluconeogenesis and glycemia by the host glucose-6-phosphatase catalytic subunit 1 (G6Pc1) is a key metabolic step that affects both Plasmodium replication and clinical outcome of disease.
    DOI:  https://doi.org/10.1016/j.cmet.2022.07.004
  32. J Vis Exp. 2022 Jul 12.
    Measuring Single-Cell Mitochondrial DNA Copy Number and Heteroplasmy using Digital Droplet Polymerase Chain Reaction.
    Stephen P Burr, Patrick F Chinnery.
      The mammalian mitochondrial (mt)DNA is a small, circular, double-stranded, intra-mitochondrial DNA molecule, encoding 13 subunits of the electron transport chain. Unlike the diploid nuclear genome, most cells contain many more copies of mtDNA, ranging from less than 100 to over 200,000 copies depending on cell type. MtDNA copy number is increasingly used as a biomarker for a number of age-related degenerative conditions and diseases, and thus, accurate measurement of the mtDNA copy number is becoming a key tool in both research and diagnostic settings. Mutations in the mtDNA, often occurring as single nucleotide polymorphisms (SNPs) or deletions, can either exist in all copies of the mtDNA within the cell (termed homoplasmy) or as a mixture of mutated and WT mtDNA copies (termed heteroplasmy). Heteroplasmic mtDNA mutations are a major cause of clinical mitochondrial pathology, either in rare diseases or in a growing number of common late-onset diseases such as Parkinson's disease. Determining the level of heteroplasmy present in cells is a critical step in the diagnosis of rare mitochondrial diseases and in research aimed at understanding common late-onset disorders where mitochondria may play a role. MtDNA copy number and heteroplasmy have traditionally been measured by quantitative (q)PCR-based assays or deep sequencing. However, the recent introduction of ddPCR technology has provided an alternative method for measuring both parameters. It offers several advantages over existing methods, including the ability to measure absolute mtDNA copy number and sufficient sensitivity to make accurate measurements from single cells even at low copy numbers. Presented here is a detailed protocol describing the measurement of mtDNA copy number in single cells using ddPCR, referred to as droplet generation PCR henceforth, with the option for simultaneous measurement of heteroplasmy in cells with mtDNA deletions. The possibility of expanding this method to measure heteroplasmy in cells with mtDNA SNPs is also discussed.
    DOI:  https://doi.org/10.3791/63870
  33. Nat Commun. 2022 Aug 02. 13(1): 4492
    Ribosome impairment regulates intestinal stem cell identity via ZAKɑ activation.
    Joana Silva, Ferhat Alkan, Sofia Ramalho, Goda Snieckute, Stefan Prekovic, Ana Krotenberg Garcia, Santiago Hernández-Pérez, Rob van der Kammen, Danielle Barnum, Liesbeth Hoekman, Maarten Altelaar, Wilbert Zwart, Saskia Jacoba Elisabeth Suijkerbuijk, Simon Bekker-Jensen, William James Faller.
      The small intestine is a rapidly proliferating organ that is maintained by a small population of Lgr5-expressing intestinal stem cells (ISCs). However, several Lgr5-negative ISC populations have been identified, and this remarkable plasticity allows the intestine to rapidly respond to both the local environment and to damage. However, the mediators of such plasticity are still largely unknown. Using intestinal organoids and mouse models, we show that upon ribosome impairment (driven by Rptor deletion, amino acid starvation, or low dose cyclohexamide treatment) ISCs gain an Lgr5-negative, fetal-like identity. This is accompanied by a rewiring of metabolism. Our findings suggest that the ribosome can act as a sensor of nutrient availability, allowing ISCs to respond to the local nutrient environment. Mechanistically, we show that this phenotype requires the activation of ZAKɑ, which in turn activates YAP, via SRC. Together, our data reveals a central role for ribosome dynamics in intestinal stem cells, and identify the activation of ZAKɑ as a critical mediator of stem cell identity.
    DOI:  https://doi.org/10.1038/s41467-022-32220-4
  34. Cell Metab. 2022 Aug 02. pii: S1550-4131(22)00305-9. [Epub ahead of print]34(8): 1201-1213.e5
    Aberrant iron distribution via hepatocyte-stellate cell axis drives liver lipogenesis and fibrosis.
    Hong Gao, Zhongmou Jin, Gautam Bandyopadhyay, Gaowei Wang, Dinghong Zhang, Karina Cunha E Rocha, Xiao Liu, Huayi Zhao, Tatiana Kisseleva, David A Brenner, Michael Karin, Wei Ying.
      Hepatocytes have important roles in liver iron homeostasis, abnormalities in which are tightly associated with liver steatosis and fibrosis. Here, we show that non-alcoholic fatty liver disease (NAFLD) and steatohepatitis (NASH) are characterized by iron-deficient hepatocytes and iron overload in hepatic stellate cells (HSCs). Iron deficiency enhances hepatocyte lipogenesis and insulin resistance through HIF2α-ATF4 signaling. Elevated secretion of iron-containing hepatocyte extracellular vesicles (EVs), which are normally cleared by Kupffer cells, accounts for hepatocyte iron deficiency and HSC iron overload in NAFLD/NASH livers. Iron accumulation results in overproduction of reactive oxygen species that promote HSC fibrogenic activation. Conversely, blocking hepatocyte EV secretion or depleting EV iron cargo restores liver iron homeostasis, concomitant with mitigation of NAFLD/NASH-associated liver steatosis and fibrosis. Taken together, these studies show that iron distribution disorders contribute to the development of liver metabolic diseases.
    Keywords:  NAFLD; NASH; extracellular vesicle; hepatic stellate cell; hepatocyte; iron; liver fibrosis; liver steatosis
    DOI:  https://doi.org/10.1016/j.cmet.2022.07.006
  35. Cell Rep. 2022 Aug 02. pii: S2211-1247(22)00962-7. [Epub ahead of print]40(5): 111153
    Cancer genes disfavoring T cell immunity identified via integrated systems approach.
    Rigel J Kishton, Shashank J Patel, Amy E Decker, Suman K Vodnala, Maggie Cam, Tori N Yamamoto, Yogin Patel, Madhusudhanan Sukumar, Zhiya Yu, Michelle Ji, Amanda N Henning, Devikala Gurusamy, Douglas C Palmer, Roxana A Stefanescu, Andrew T Girvin, Winifred Lo, Anna Pasetto, Parisa Malekzadeh, Drew C Deniger, Kris C Wood, Neville E Sanjana, Nicholas P Restifo.
      Adoptive T cell therapies (ACT) have been curative for a limited number of cancer patients. The sensitization of cancer cells to T cell killing may expand the benefit of these therapies for more patients. To this end, we use a three-step approach to identify cancer genes that disfavor T cell immunity. First, we profile gene transcripts upregulated by cancer under selection pressure from T cell killing. Second, we identify potential tumor gene targets and pathways that disfavor T cell killing using signaling pathway activation libraries and genome-wide loss-of-function CRISPR-Cas9 screens. Finally, we implement pharmacological perturbation screens to validate these targets and identify BIRC2, ITGAV, DNPEP, BCL2, and ERRα as potential ACT-drug combination candidates. Here, we establish that BIRC2 limits antigen presentation and T cell recognition of tumor cells by suppressing IRF1 activity and provide evidence that BIRC2 inhibition in combination with ACT is an effective strategy to increase efficacy.
    Keywords:  CP: Cancer; CP: Immunology; CRISPR screen; cell therapy; combination immunotherapy; gain-of-function screen; immunotherapy resistance
    DOI:  https://doi.org/10.1016/j.celrep.2022.111153
  36. Cell Metab. 2022 Aug 02. pii: S1550-4131(22)00306-0. [Epub ahead of print]34(8): 1085-1087
    Outrunning obesity with Lac-Phe?
    Jens Lund, Christoffer Clemmensen, Thue W Schwartz.
      Lactate released from skeletal muscle during high-intensity exercise gives rise to a surge in circulating lactate-derived pseudo-dipeptide metabolites including N-lactoyl-phenylalanine (Lac-Phe). In a recent Nature paper, Li et al. use genetic and pharmacological evidence to now propose Lac-Phe to be an "exercise hormone" that suppresses appetite and obesity.
    DOI:  https://doi.org/10.1016/j.cmet.2022.07.007
  37. Cancer Lett. 2022 Jul 31. pii: S0304-3835(22)00321-4. [Epub ahead of print] 215837
    De novo pyrimidine synthesis fuels glycolysis and confers chemoresistance in gastric cancer.
    Daochuan He, Mengqian Chen, Lei Chang, Jianxin Gu, Fenglin Liu, Xiaodong Gao, Yuanyuan Ruan.
      Metabolic reprogramming is a hallmark in multiple types of malignancies. Fast-growing cancer cells require facilitated synthesis of essential metabolites and excessive energy production. However, whether they are internally coordinated remains largely unknown. Herein, we found that de novo pyrimidine synthesis enhanced aerobic glycolysis in cancer cells. Mechanistically, pyrimidine biosynthesis augmented Notch signaling and transcriptionally increased c-Myc expression, leading to up-regulation of critical glycolytic enzymes. Further studies revealed that pyrimidine synthesis could stabilize γ-secretase subunit Nicastrin at post-translational N-linked glycosylation level, thereby inducing the cleavage and activation of Notch. Besides, we found that up-regulation of the key enzymes for de novo pyrimidine synthesis CAD and DHODH conferred the chemotherapeutic resistance of gastric cancer via accelerating glycolysis, and pharmacologic inhibition of pyrimidine biosynthetic pathway sensitized cancer cells to chemotherapy in vitro and in vivo. Collectively, our findings provide more insights into the regulation of aerobic glycolysis and a metabolic vulnerability that can be exploited to enhance chemotherapy efficacy in gastric cancer.
    Keywords:  C-Myc; Chemotherapy; N-linked glycosylation; Nicastrin; Notch1
    DOI:  https://doi.org/10.1016/j.canlet.2022.215837
  38. Cell. 2022 Jul 29. pii: S0092-8674(22)00790-5. [Epub ahead of print]
    Mitochondrial ROS promotes susceptibility to infection via gasdermin D-mediated necroptosis.
    Chi G Weindel, Eduardo L Martinez, Xiao Zhao, Cory J Mabry, Samantha L Bell, Krystal J Vail, Aja K Coleman, Jordyn J VanPortfliet, Baoyu Zhao, Allison R Wagner, Sikandar Azam, Haley M Scott, Pingwei Li, A Phillip West, Jason Karpac, Kristin L Patrick, Robert O Watson.
      Although mutations in mitochondrial-associated genes are linked to inflammation and susceptibility to infection, their mechanistic contributions to immune outcomes remain ill-defined. We discovered that the disease-associated gain-of-function allele Lrrk2G2019S (leucine-rich repeat kinase 2) perturbs mitochondrial homeostasis and reprograms cell death pathways in macrophages. When the inflammasome is activated in Lrrk2G2019S macrophages, elevated mitochondrial ROS (mtROS) directs association of the pore-forming protein gasdermin D (GSDMD) to mitochondrial membranes. Mitochondrial GSDMD pore formation then releases mtROS, promoting a switch to RIPK1/RIPK3/MLKL-dependent necroptosis. Consistent with enhanced necroptosis, infection of Lrrk2G2019S mice with Mycobacterium tuberculosis elicits hyperinflammation and severe immunopathology. Our findings suggest a pivotal role for GSDMD as an executer of multiple cell death pathways and demonstrate that mitochondrial dysfunction can direct immune outcomes via cell death modality switching. This work provides insights into how LRRK2 mutations manifest or exacerbate human diseases and identifies GSDMD-dependent necroptosis as a potential target to limit Lrrk2G2019S-mediated immunopathology.
    Keywords:  Drosophila melanogaster; LRRK2; Mycobacterium tuberculosis; Parkinson’s disease; RIPK3; immunometabolism; inflammasome; inflammation; innate immunity; pyroptosis
    DOI:  https://doi.org/10.1016/j.cell.2022.06.038
  39. Cancer Res. 2022 Aug 02. pii: CAN-22-0408. [Epub ahead of print]
    Selenium modulates cancer cell response to pharmacologic ascorbate.
    Connor S R Jankowski, Joshua D Rabinowitz.
      High-dose ascorbate (vitamin C) has shown promising anti-cancer activity. Two redox mechanisms have been proposed: hydrogen peroxide generation by ascorbate itself or glutathione depletion by dehydroascorbate (formed by ascorbate oxidation). Here we show that the metabolic effects and cytotoxicity of high-dose ascorbate in vitro result from hydrogen peroxide independently of dehydroascorbate. These effects were suppressed by selenium through antioxidant selenoenzymes including glutathione peroxidase 1 (GPX1) but not the classic ferroptosis-inhibiting selenoenzyme GPX4. Selenium-mediated protection from ascorbate was powered by NADPH from the pentose phosphate pathway. In vivo, dietary selenium deficiency resulted in significant enhancement of ascorbate activity against glioblastoma xenografts. These data establish selenoproteins as key mediators of cancer redox homeostasis. Cancer sensitivity to free radical-inducing therapies, including ascorbate, may depend on selenium, providing a dietary approach for improving their anticancer efficacy.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-0408
  40. Natl J Maxillofac Surg. 2022 Jan-Apr;13(1):13(1): 11-19
    Mitophagy and oral cancers.
    Ripon Md Chowdhury.
      Mitophagy is a progressive process that selectively targets weakened, old and damaged mitochondria, by an autophagic pathway, causing its destruction. Mitophagy maintains normal cellular physiology and tissue development, thereby controlling the cohesiveness of the mitochondrial pool. The mechanisms of mitophagy, tumorogenesis, and cell death are usually interrelated with each other and could be initiated by definite stressful conditions like hypoxia and nutrient starvation, which leads to the overall reduction in mitochondrial mass. This impedes the production of reactive oxygen species, and conserves nutrition, leading to cell survival in such extreme conditions. The inability to harmonize and regulate mitochondrial outcome in response to oncogenic stress can either stimulate or suppress tumorogenesis. Therefore, the relationship between mitophagy, tumorogenesis, and cell death plays an important role in the identification of potential targets of cell death and selective wiping out of cancer cells. This review portrays the mechanism of mitophagy, along with its role in cancers especially on oral cancers, and its importance in cancer therapeutics.
    Keywords:  Autophagy; cell death; mitophagy; oral cancers; treatment; tumorogenesis
    DOI:  https://doi.org/10.4103/njms.NJMS_123_20
  41. Cell Metab. 2022 Aug 02. pii: S1550-4131(22)00304-7. [Epub ahead of print]34(8): 1088-1103.e6
    CD24-Siglec axis is an innate immune checkpoint against metaflammation and metabolic disorder.
    Xu Wang, Mingyue Liu, Jifeng Zhang, Nicholas K Brown, Peng Zhang, Yan Zhang, Heng Liu, Xuexiang Du, Wei Wu, Martin Devenport, Weng Tao, Yang Mao-Draayer, Guo-Yun Chen, Y Eugene Chen, Pan Zheng, Yang Liu.
      The molecular interactions that regulate chronic inflammation underlying metabolic disease remain largely unknown. Since the CD24-Siglec interaction regulates inflammatory response to danger-associated molecular patterns (DAMPs), we have generated multiple mouse strains with single or combined mutations of Cd24 or Siglec genes to explore the role of the CD24-Siglec interaction in metaflammation and metabolic disorder. Here, we report that the CD24-Siglec-E axis, but not other Siglecs, is a key suppressor of obesity-related metabolic dysfunction. Inactivation of the CD24-Siglec-E pathway exacerbates, while CD24Fc treatment alleviates, diet-induced metabolic disorders, including obesity, dyslipidemia, insulin resistance, and nonalcoholic steatohepatitis (NASH). Mechanistically, sialylation-dependent recognition of CD24 by Siglec-E induces SHP-1 recruitment and represses metaflammation to protect against metabolic syndrome. A first-in-human study of CD24Fc (NCT02650895) supports the significance of this pathway in human lipid metabolism and inflammation. These findings identify the CD24-Siglec-E axis as an innate immune checkpoint against metaflammation and metabolic disorder and suggest a promising therapeutic target for metabolic disease.
    Keywords:  CD24; NASH; Siglec-E; Siglecs; insulin resistance; metabolic syndrome; metaflammation; obesity; sialic acid-binding immunoglobulin-like lectins; sialylation
    DOI:  https://doi.org/10.1016/j.cmet.2022.07.005
  42. Nat Metab. 2022 Aug 04.
    Targeting ASGR1 to lower cholesterol.
    Daniel J Rader.
      
    DOI:  https://doi.org/10.1038/s42255-022-00623-8
  43. Mol Cell. 2022 Aug 04. pii: S1097-2765(22)00545-7. [Epub ahead of print]82(15): 2732-2734
    The IRG1/itaconate/TFEB axis: A new weapon in macrophage antibacterial defense.
    José A Martina, Rosa Puertollano.
      Zhang et al. (2022) report that itaconate, a mitochondrial metabolite produced by macrophages upon inflammatory stimuli, activates the master regulator of lysosomal biogenesis TFEB to facilitate clearance of invading bacteria and efficient immune response.
    DOI:  https://doi.org/10.1016/j.molcel.2022.06.009
  44. Life Sci Alliance. 2022 Dec;pii: e202201377. [Epub ahead of print]5(12):
    PFKFB4 interacts with ICMT and activates RAS/AKT signaling-dependent cell migration in melanoma.
    Méghane Sittewelle, Vincent Kappès, Chenxi Zhou, Déborah Lécuyer, Anne H Monsoro-Burq.
      Cell migration is a complex process, tightly regulated during embryonic development and abnormally activated during cancer metastasis. RAS-dependent signaling is a major nexus controlling essential cell parameters including proliferation, survival, and migration, utilizing downstream effectors such as the PI3K/AKT signaling pathway. In melanoma, oncogenic mutations frequently enhance RAS, PI3K/AKT, or MAP kinase signaling and trigger other cancer hallmarks among which the activation of metabolism regulators. PFKFB4 is one of these critical regulators of glycolysis and of the Warburg effect. Here, however, we explore a novel function of PFKFB4 in melanoma cell migration. We find that PFKFB4 interacts with ICMT, a posttranslational modifier of RAS. PFKFB4 promotes ICMT/RAS interaction, controls RAS localization at the plasma membrane, activates AKT signaling and enhances cell migration. We thus provide evidence of a novel and glycolysis-independent function of PFKFB4 in human cancer cells. This unconventional activity links the metabolic regulator PFKFB4 to RAS-AKT signaling and impacts melanoma cell migration.
    DOI:  https://doi.org/10.26508/lsa.202201377
  45. Nat Commun. 2022 Aug 04. 13(1): 4534
    Accurate determination of CRISPR-mediated gene fitness in transplantable tumours.
    Peter Eirew, Ciara O'Flanagan, Jerome Ting, Sohrab Salehi, Jazmine Brimhall, Beixi Wang, Justina Biele, Teresa Algara, So Ra Lee, Corey Hoang, Damian Yap, Steven McKinney, Cherie Bates, Esther Kong, Daniel Lai, Sean Beatty, Mirela Andronescu, Elena Zaikova, Tyler Funnell, Nicholas Ceglia, Stephen Chia, Karen Gelmon, Colin Mar, Sohrab Shah, Andrew Roth, Alexandre Bouchard-Côté, Samuel Aparicio.
      Assessing tumour gene fitness in physiologically-relevant model systems is challenging due to biological features of in vivo tumour regeneration, including extreme variations in single cell lineage progeny. Here we develop a reproducible, quantitative approach to pooled genetic perturbation in patient-derived xenografts (PDXs), by encoding single cell output from transplanted CRISPR-transduced cells in combination with a Bayesian hierarchical model. We apply this to 181 PDX transplants from 21 breast cancer patients. We show that uncertainty in fitness estimates depends critically on the number of transplant cell clones and the variability in clone sizes. We use a pathway-directed allelic series to characterize Notch signaling, and quantify TP53 / MDM2 drug-gene conditional fitness in outlier patients. We show that fitness outlier identification can be mirrored by pharmacological perturbation. Overall, we demonstrate that the gene fitness landscape in breast PDXs is dominated by inter-patient differences.
    DOI:  https://doi.org/10.1038/s41467-022-31830-2
  46. Front Pharmacol. 2022 ;13 935553
    Argininosuccinate synthase 1, arginine deprivation therapy and cancer management.
    Naihui Sun, Xing Zhao.
      Metabolic reprogramming is an emerging hallmark of tumor cells. In order to survive in the nutrient-deprived environment, tumor cells rewire their metabolic phenotype to provide sufficient energy and build biomass to sustain their transformed state and promote malignant behaviors. Amino acids are the main compositions of protein, which provide key intermediate substrates for the activation of signaling pathways. Considering that cells can synthesize arginine via argininosuccinate synthase 1 (ASS1), arginine is regarded as a non-essential amino acid, making arginine depletion as a promising therapeutic strategy for ASS1-silencing tumors. In this review, we summarize the current knowledge of expression pattern of ASS1 and related signaling pathways in cancer and its potential role as a novel therapeutic target in cancer. Besides, we outline how ASS1 affects metabolic regulation and tumor progression and further discuss the role of ASS1 in arginine deprivation therapy. Finally, we review approaches to target ASS1 for cancer therapies.
    Keywords:  amino acid; arginine; metabolic reprogramming; prognosis; resistance
    DOI:  https://doi.org/10.3389/fphar.2022.935553
  47. Nat Commun. 2022 Aug 03. 13(1): 4440
    Histone H3K36me2 and H3K36me3 form a chromatin platform essential for DNMT3A-dependent DNA methylation in mouse oocytes.
    Seiichi Yano, Takashi Ishiuchi, Shusaku Abe, Satoshi H Namekawa, Gang Huang, Yoshihiro Ogawa, Hiroyuki Sasaki.
      Establishment of the DNA methylation landscape of mammalian oocytes, mediated by the DNMT3A-DNMT3L complex, is crucial for reproduction and development. In mouse oocytes, high levels of DNA methylation occur exclusively in the transcriptionally active regions, with moderate to low levels of methylation in other regions. Histone H3K36me3 mediates the high levels of methylation in the transcribed regions; however, it is unknown which histone mark guides the methylation in the other regions. Here, we show that, in mouse oocytes, H3K36me2 is highly enriched in the X chromosome and is broadly distributed across all autosomes. Upon H3K36me2 depletion, DNA methylation in moderately methylated regions is selectively affected, and a methylation pattern unique to the X chromosome is switched to an autosome-like pattern. Furthermore, we find that simultaneous depletion of H3K36me2 and H3K36me3 results in global hypomethylation, comparable to that of DNMT3A depletion. Therefore, the two histone marks jointly provide the chromatin platform essential for guiding DNMT3A-dependent DNA methylation in mouse oocytes.
    DOI:  https://doi.org/10.1038/s41467-022-32141-2
  48. Adipocyte. 2022 Dec;11(1): 379-388
    PARP12 is required for mitochondrial function maintenance in thermogenic adipocytes.
    Fan Hu, Chang Li, Yafen Ye, Xuhong Lu, Miriayi Alimujiang, Ningning Bai, Jingjing Sun, Xiaojing Ma, Xiaohua Li, Ying Yang.
      PARP12 is a member of poly-ADP-ribosyl polymerase (PARPs), which has been characterized for its antiviral function. Yet its physiological implication in adipocytes remains unknown. Here, we report a central function of PARP12 in thermogenic adipocytes. We show that PARP12 is highly expressed in brown adipose tissue and is mainly localized to the mitochondria. Knockdown of PARP12 in vitro reduced UCP1 expression. In parallel, the deficiency of PARP12 reduced mitochondrial respiration in adipocytes, while overexpression of PARP12 reversed these effects.
    Keywords:  Adipocytes; mitochondria; poly(ADP-ribose) polymerases; thermogenesis
    DOI:  https://doi.org/10.1080/21623945.2022.2091206
  49. Nat Commun. 2022 Jul 30. 13(1): 4423
    Maladaptive positive feedback production of ChREBPβ underlies glucotoxic β-cell failure.
    Liora S Katz, Gabriel Brill, Pili Zhang, Anil Kumar, Sharon Baumel-Alterzon, Lee B Honig, Nicolás Gómez-Banoy, Esra Karakose, Marius Tanase, Ludivine Doridot, Alexandra Alvarsson, Bennett Davenport, Peng Wang, Luca Lambertini, Sarah A Stanley, Dirk Homann, Andrew F Stewart, James C Lo, Mark A Herman, Adolfo Garcia-Ocaña, Donald K Scott.
      Preservation and expansion of β-cell mass is a therapeutic goal for diabetes. Here we show that the hyperactive isoform of carbohydrate response-element binding protein (ChREBPβ) is a nuclear effector of hyperglycemic stress occurring in β-cells in response to prolonged glucose exposure, high-fat diet, and diabetes. We show that transient positive feedback induction of ChREBPβ is necessary for adaptive β-cell expansion in response to metabolic challenges. Conversely, chronic excessive β-cell-specific overexpression of ChREBPβ results in loss of β-cell identity, apoptosis, loss of β-cell mass, and diabetes. Furthermore, β-cell "glucolipotoxicity" can be prevented by deletion of ChREBPβ. Moreover, ChREBPβ-mediated cell death is mitigated by overexpression of the alternate CHREBP gene product, ChREBPα, or by activation of the antioxidant Nrf2 pathway in rodent and human β-cells. We conclude that ChREBPβ, whether adaptive or maladaptive, is an important determinant of β-cell fate and a potential target for the preservation of β-cell mass in diabetes.
    DOI:  https://doi.org/10.1038/s41467-022-32162-x
  50. Nature. 2022 Aug 03.
    A non-canonical vitamin K cycle is a potent ferroptosis suppressor.
    Eikan Mishima, Junya Ito, Zijun Wu, Toshitaka Nakamura, Adam Wahida, Sebastian Doll, Wulf Tonnus, Palina Nepachalovich, Elke Eggenhofer, Maceler Aldrovandi, Bernhard Henkelmann, Ken-Ichi Yamada, Jonas Wanninger, Omkar Zilka, Emiko Sato, Regina Feederle, Daniela Hass, Adriano Maida, André Santos Dias Mourão, Andreas Linkermann, Edward K Geissler, Kiyotaka Nakagawa, Takaaki Abe, Maria Fedorova, Bettina Proneth, Derek A Pratt, Marcus Conrad.
      Ferroptosis, a non-apoptotic form of cell death marked by iron-dependent lipid peroxidation1, has a key role in organ injury, degenerative disease and vulnerability of therapy-resistant cancers2. Although substantial progress has been made in understanding the molecular processes relevant to ferroptosis, additional cell-extrinsic and cell-intrinsic processes that determine cell sensitivity toward ferroptosis remain unknown. Here we show that the fully reduced forms of vitamin K-a group of naphthoquinones that includes menaquinone and phylloquinone3-confer a strong anti-ferroptotic function, in addition to the conventional function linked to blood clotting by acting as a cofactor for γ-glutamyl carboxylase. Ferroptosis suppressor protein 1 (FSP1), a NAD(P)H-ubiquinone reductase and the second mainstay of ferroptosis control after glutathione peroxidase-44,5, was found to efficiently reduce vitamin K to its hydroquinone, a potent radical-trapping antioxidant and inhibitor of (phospho)lipid peroxidation. The FSP1-mediated reduction of vitamin K was also responsible for the antidotal effect of vitamin K against warfarin poisoning. It follows that FSP1 is the enzyme mediating warfarin-resistant vitamin K reduction in the canonical vitamin K cycle6. The FSP1-dependent non-canonical vitamin K cycle can act to protect cells against detrimental lipid peroxidation and ferroptosis.
    DOI:  https://doi.org/10.1038/s41586-022-05022-3
  51. Nature. 2022 Aug 03.
    Brown-fat-mediated tumour suppression by cold-altered global metabolism.
    Takahiro Seki, Yunlong Yang, Xiaoting Sun, Sharon Lim, Sisi Xie, Ziheng Guo, Wenjing Xiong, Masashi Kuroda, Hiroshi Sakaue, Kayoko Hosaka, Xu Jing, Masahito Yoshihara, Lili Qu, Xin Li, Yuguo Chen, Yihai Cao.
      Glucose uptake is essential for cancer glycolysis and is involved in non-shivering thermogenesis of adipose tissues1-6. Most cancers use glycolysis to harness energy for their infinite growth, invasion and metastasis2,7,8. Activation of thermogenic metabolism in brown adipose tissue (BAT) by cold and drugs instigates blood glucose uptake in adipocytes4,5,9. However, the functional effects of the global metabolic changes associated with BAT activation on tumour growth are unclear. Here we show that exposure of tumour-bearing mice to cold conditions markedly inhibits the growth of various types of solid tumours, including clinically untreatable cancers such as pancreatic cancers. Mechanistically, cold-induced BAT activation substantially decreases blood glucose and impedes the glycolysis-based metabolism in cancer cells. The removal of BAT and feeding on a high-glucose diet under cold exposure restore tumour growth, and genetic deletion of Ucp1-the key mediator for BAT-thermogenesis-ablates the cold-triggered anticancer effect. In a pilot human study, mild cold exposure activates a substantial amount of BAT in both healthy humans and a patient with cancer with mitigated glucose uptake in the tumour tissue. These findings provide a previously undescribed concept and paradigm for cancer therapy that uses a simple and effective approach. We anticipate that cold exposure and activation of BAT through any other approach, such as drugs and devices either alone or in combination with other anticancer therapeutics, will provide a general approach for the effective treatment of various cancers.
    DOI:  https://doi.org/10.1038/s41586-022-05030-3
  52. Mol Cell. 2022 Aug 04. pii: S1097-2765(22)00662-1. [Epub ahead of print]82(15): 2735-2737
    Systems biochemistry to "deorphanize" human mitochondrial proteome.
    Francois Miros, Ran Liu, Hongying Shen.
      Rensvold, Shishkova, et al. (2022) apply an integrated systems biology approach spanning proteomics, lipidomics, and metabolomics to a collection of CRISPR knockout cells targeting 116 distinct human mitochondrial proteins, revealing new mitochondrial biology and guiding orphan disease diagnosis.
    DOI:  https://doi.org/10.1016/j.molcel.2022.07.005
  53. J Biol Chem. 2022 Aug 02. pii: S0021-9258(22)00778-5. [Epub ahead of print] 102336
    A new fluorescent sensor mitoferrofluor indicates the presence of chelatable iron in polarized and depolarized mitochondria.
    Andaleb Kholmukhamedov, Li Li, Christopher C Lindsey, Jiangting Hu, Anna-Liisa Nieminen, Kenji Takemoto, Gyda C Beeson, Chad M Beneker, Campbell McInnes, Craig C Beeson, John J Lemasters.
      Mitochondrial chelatable iron contributes to the severity of several injury processes, including ischemia/reperfusion, oxidative stress, and drug toxicity. However, methods to measure this species in living cells are lacking. To measure mitochondrial chelatable iron in living cells, here we synthesized a new fluorescent indicator, mitoferrofluor (MFF). We designed cationic MFF to accumulate electrophoretically in polarized mitochondria, where a reactive group then forms covalent adducts with mitochondrial proteins to retain MFF even after subsequent depolarization. We also show in cell-free medium that Fe2+ (and Cu2+), but not Fe3+, Ca2+, or other biologically relevant divalent cations, strongly quenched MFF fluorescence. Using confocal microscopy, we demonstrate in hepatocytes that red MFF fluorescence co-localized with the green fluorescence of the mitochondrial membrane potential (ΔΨm) indicator, rhodamine 123 (Rh123), indicating selective accumulation into mitochondria. Unlike Rh123, mitochondria retained MFF after ΔΨm collapse. Furthermore, intracellular delivery of iron with membrane-permeant Fe3+/8-hydroxyquinoline (FeHQ) quenched MFF fluorescence by ∼80% in hepatocytes and other cell lines, which was substantially restored by the membrane-permeant transition metal chelator pyridoxal isonicotinoyl hydrazone. We also show FeHQ quenched the fluorescence of cytosolically co-loaded calcein, another Fe2+ indicator, confirming that Fe3+ in FeHQ undergoes intracellular reduction to Fe2+. Finally, MFF fluorescence did not change after addition of the calcium mobilizer thapsigargin, which shows MFF is insensitive to physiologically relevant increases of mitochondrial Ca2+. In conclusion, the new sensor reagent MFF fluorescence is an indicator of mitochondrial chelatable Fe2+ in normal hepatocytes with polarized mitochondria as well as in cells undergoing loss of ΔΨm.
    Keywords:  iron sensor; ischemia/reperfusion; membrane potential; mitochondria
    DOI:  https://doi.org/10.1016/j.jbc.2022.102336
  54. Cancer Res. 2022 Aug 05. pii: CAN-22-0325. [Epub ahead of print]
    An immunogenic model of KRAS-mutant lung cancer enables evaluation of targeted therapy and immunotherapy combinations.
    Jesse Boumelha, Sophie de Carné Trécesson, Emily K Law, Pablo Romero-Clavijo, Matthew Coelho, Kevin Ng, Edurne Mugarza, Christopher Moore, Sareena Rana, Deborah R Caswell, Miguel Murillo, David C Hancock, Prokopios P Argyris, William L Brown, Cameron Durfee, Lindsay K Larson, Rachel I Vogel, Alejandro Suarez-Bonnet, Simon L Priestnall, Philip East, Sarah J Ross, George Kassiotis, Miriam Molina-Arcas, Charles Swanton, Reuben Harris, Julian Downward.
      Mutations in oncogenes such as KRAS and EGFR cause a high proportion of lung cancers. Drugs targeting these proteins cause tumor regression but ultimately fail to elicit cures. As a result, there is an intense interest in how to best combine targeted therapies with other treatments, such as immunotherapies. However, preclinical systems for studying the interaction of lung tumors with the host immune system are inadequate, in part due to the low tumor mutational burden in genetically engineered mouse models. Here we set out to develop mouse models of mutant KRAS-driven lung cancer with an elevated tumor mutational burden by expressing the human DNA cytosine deaminase, APOBEC3B, to mimic the mutational signature seen in human lung cancer. This failed to substantially increase clonal tumor mutational burden and autochthonous tumors remained refractory to immunotherapy. However, establishing clonal cell lines from these tumors enabled the generation of an immunogenic syngeneic transplantation model of KRAS-mutant lung adenocarcinoma that was sensitive to immunotherapy. Unexpectedly, anti-tumor immune responses were not directed against neoantigens but instead targeted derepressed endogenous retroviral antigens. The ability of KRASG12C inhibitors to cause regression of KRASG12C-expressing tumors was markedly potentiated by the adaptive immune system, highlighting the importance of using immunocompetent models for evaluating targeted therapies. Overall, this model provides a unique opportunity for the study of combinations of targeted and immunotherapies in immune-hot lung cancer.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-0325
  55. Nat Commun. 2022 Aug 05. 13(1): 4554
    Metabolic reprogramming from glycolysis to fatty acid uptake and beta-oxidation in platinum-resistant cancer cells.
    Yuying Tan, Junjie Li, Guangyuan Zhao, Kai-Chih Huang, Horacio Cardenas, Yinu Wang, Daniela Matei, Ji-Xin Cheng.
      Increased glycolysis is considered as a hallmark of cancer. Yet, cancer cell metabolic reprograming during therapeutic resistance development is under-studied. Here, through high-throughput stimulated Raman scattering imaging and single cell analysis, we find that cisplatin-resistant cells exhibit increased fatty acids (FA) uptake, accompanied by decreased glucose uptake and lipogenesis, indicating reprogramming from glucose to FA dependent anabolic and energy metabolism. A metabolic index incorporating glucose derived anabolism and FA uptake correlates linearly to the level of cisplatin resistance in ovarian cancer (OC) cell lines and primary cells. The increased FA uptake facilitates cancer cell survival under cisplatin-induced oxidative stress by enhancing beta-oxidation. Consequently, blocking beta-oxidation by a small molecule inhibitor combined with cisplatin or carboplatin synergistically suppresses OC proliferation in vitro and growth of patient-derived xenografts in vivo. Collectively, these findings support a rapid detection method of cisplatin-resistance at single cell level and a strategy for treating cisplatin-resistant tumors.
    DOI:  https://doi.org/10.1038/s41467-022-32101-w
  56. Cell Mol Life Sci. 2022 Aug 02. 79(8): 463
    Balancing NAD+ deficits with nicotinamide riboside: therapeutic possibilities and limitations.
    Angelique Cercillieux, Eleonora Ciarlo, Carles Canto.
      Alterations in cellular nicotinamide adenine dinucleotide (NAD+) levels have been observed in multiple lifestyle and age-related medical conditions. This has led to the hypothesis that dietary supplementation with NAD+ precursors, or vitamin B3s, could exert health benefits. Among the different molecules that can act as NAD+ precursors, Nicotinamide Riboside (NR) has gained most attention due to its success in alleviating and treating disease conditions at the pre-clinical level. However, the clinical outcomes for NR supplementation strategies have not yet met the expectations generated in mouse models. In this review we aim to provide a comprehensive view on NAD+ biology, what causes NAD+ deficits and the journey of NR from its discovery to its clinical development. We also discuss what are the current limitations in NR-based therapies and potential ways to overcome them. Overall, this review will not only provide tools to understand NAD+ biology and assess its changes in disease situations, but also to decide which NAD+ precursor could have the best therapeutic potential.
    Keywords:  Metabolic disease; NAD+; Nicotinamide; Nicotinamide riboside; Vitamin B3
    DOI:  https://doi.org/10.1007/s00018-022-04499-5
  57. Oncogene. 2022 Aug 05.
    FOXA1 inhibits hypoxia programs through transcriptional repression of HIF1A.
    Xiaohai Wang, Lourdes Brea, Xiaodong Lu, Galina Gritsina, Su H Park, Wanqing Xie, Jonathan C Zhao, Jindan Yu.
      Intratumoral hypoxia is associated with castration-resistant prostate cancer (CRPC), a lethal disease. FOXA1 is an epithelial transcription factor that is down-regulated in CRPC. We have previously reported that FOXA1 loss induces epithelial-mesenchymal transition (EMT) and cell motility through elevated TGFβ signaling. However, whether FOXA1 directly regulates hypoxia pathways of CRPC tumors has not been previously studied. Here we report that FOXA1 down-regulation induces hypoxia transcriptional programs, and FOXA1 level is negatively correlated with hypoxia markers in clinical prostate cancer (PCa) samples. Mechanistically, FOXA1 directly binds to an intragenic enhancer of HIF1A to inhibit its expression, and HIF1A, in turn, is critical in mediating FOXA1 loss-induced hypoxia gene expression. Further, we identify CCL2, a chemokine ligand that modulates tumor microenvironment and promotes cancer progression, as a crucial target of the FOXA1-HIF1A axis. We found that FOXA1 loss leads to immunosuppressive macrophage infiltration and increased cell invasion, dependent on HIF1A expression. Critically, therapeutic targeting of HIF1A-CCL2 using pharmacological inhibitors abolishes FOXA1 loss-induced macrophage infiltration and PCa cell invasion. In summary, our study reveals an essential role of FOXA1 in controlling the hypoxic tumor microenvironment and establishes the HIF1A-CCL2 axis as one mechanism of FOXA1 loss-induced CRPC progression.
    DOI:  https://doi.org/10.1038/s41388-022-02423-6
  58. J Cereb Blood Flow Metab. 2022 Aug 04. 271678X221118236
    Unique expression of the atypical mitochondrial subunit NDUFA4L2 in cerebral pericytes fine tunes HIF activity in response to hypoxia.
    Claudia Mesa-Ciller, Guillermo Turiel, Andrea Guajardo-Grence, Ana Belen Lopez-Rodriguez, Javier Egea, Katrien De Bock, Julián Aragonés, Andrés A Urrutia.
      A central response to insufficient cerebral oxygen delivery is a profound reprograming of metabolism, which is mainly regulated by the Hypoxia Inducible Factor (HIF). Among other responses, HIF induces the expression of the atypical mitochondrial subunit NDUFA4L2. Surprisingly, NDUFA4L2 is constitutively expressed in the brain in non-hypoxic conditions. Analysis of publicly available single cell transcriptomic (scRNA-seq) data sets coupled with high-resolution multiplexed fluorescence RNA in situ hybridization (RNA F.I.S.H.) revealed that in the murine and human brain NDUFA4L2 is exclusively expressed in mural cells with the highest levels found in pericytes and declining along the arteriole-arterial smooth muscle cell axis. This pattern was mirrored by COX4I2, another atypical mitochondrial subunit. High NDUFA4L2 expression was also observed in human brain pericytes in vitro, decreasing when pericytes are muscularized and further induced by HIF stabilization in a PHD2/PHD3 dependent manner. In vivo, Vhl conditional inactivation in pericyte targeting Ng2-cre transgenic mice dramatically induced NDUFA4L2 expression. Finally NDUFA4L2 inactivation in pericytes increased oxygen consumption and therefore the degree of HIF pathway induction in hypoxia. In conclusion our work reveals that NDUFA4L2 together with COX4I2 is a key hypoxic-induced metabolic marker constitutively expressed in pericytes coupling mitochondrial oxygen consumption and cellular hypoxia response.
    Keywords:  Brain; HIF; NDUFA4L2; oxygen; pericyte
    DOI:  https://doi.org/10.1177/0271678X221118236
  59. Nat Commun. 2022 Aug 02. 13(1): 4494
    Golgi stress induces SIRT2 to counteract Shigella infection via defatty-acylation.
    Miao Wang, Yugang Zhang, Garrison P Komaniecki, Xuan Lu, Ji Cao, Mingming Zhang, Tao Yu, Dan Hou, Nicole A Spiegelman, Ming Yang, Ian R Price, Hening Lin.
      Enzymes from pathogens often modulate host protein post-translational modifications (PTMs), facilitating survival and proliferation of pathogens. Shigella virulence factors IpaJ and IcsB induce proteolytic cleavage and lysine fatty acylation on host proteins, which cause Golgi stress and suppress innate immunity, respectively. However, it is unknown whether host enzymes could reverse such modifications introduced by pathogens' virulence factors to suppress pathogenesis. Herein, we report that SIRT2, a potent lysine defatty-acylase, is upregulated by the transcription factor CREB3 under Golgi stress induced by Shigella infection. SIRT2 in turn removes the lysine fatty acylation introduced by Shigella virulence factor IcsB to enhance host innate immunity. SIRT2 knockout mice are more susceptible to Shigella infection than wildtype mice, demonstrating the importance of SIRT2 to counteract Shigella infection.
    DOI:  https://doi.org/10.1038/s41467-022-32227-x
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