bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2022–11–20
fifty-two papers selected by
Christian Frezza, Universität zu Köln
  1. Cancer metabolite blunts immunity.
  2. Mitochondrial nucleoid trafficking regulated by the inner-membrane AAA-ATPase ATAD3A modulates respiratory complex formation.
  3. Suppression of CD8+ T cells by the metabolite itaconate.
  4. Myeloid-derived itaconate suppresses cytotoxic CD8+ T cells and promotes tumour growth.
  5. Iron Homeostasis and Energy Metabolism in Obesity.
  6. Non-mammalian metabolic models in the spotlight.
  7. Altered glycolysis triggers impaired mitochondrial metabolism and mTORC1 activation in diabetic β-cells.
  8. CD8+ T cell metabolic rewiring defined by scRNA-seq identifies a critical role of ASNS expression dynamics in T cell differentiation.
  9. Ribosome stalling is a signal for metabolic regulation by the ribotoxic stress response.
  10. Revealing de novo pyrimidine synthesis as a key vulnerability in brain tumors.
  11. From inulin to inflammation.
  12. Both ANT and ATPase are essential for mitochondrial permeability transition but not depolarization.
  13. Batokine neuregulin 4 promotes atherosclerotic resolution.
  14. Interruption of post-Golgi STING trafficking activates tonic interferon signaling.
  15. Ferroptosis of tumour neutrophils causes immune suppression in cancer.
  16. The NLRP3 inflammasome: regulation by metabolic signals.
  17. Identification of purine biosynthesis as an NADH-sensing pathway to mediate energy stress.
  18. mTOR inhibition attenuates chemosensitivity through the induction of chemotherapy resistant persisters.
  19. Crosstalk between glucose metabolism, lactate production and immune response modulation.
  20. Mitochondrial dysfunction compromises ciliary homeostasis in astrocytes.
  21. ATM inhibition drives metabolic adaptation via induction of macropinocytosis.
  22. OXPHOS promotes apoptotic resistance and cellular persistence in TH17 cells in the periphery and tumor microenvironment.
  23. mTORC1-c-Myc pathway rewires methionine metabolism for HCC progression through suppressing SIRT4 mediated ADP ribosylation of MAT2A.
  24. LUBAC assembles a ubiquitin signaling platform at mitochondria for signal amplification and transport of NF-κB to the nucleus.
  25. Short communication: Acute hypoxia does not alter mitochondrial abundance in naked mole-rats.
  26. Cellular and computational models reveal environmental and metabolic interactions in MMUT-type methylmalonic aciduria.
  27. Organelle homeostasis: from cellular mechanisms to disease.
  28. MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution.
  29. Mitochondrial Matrix Protease ClpP Agonists Inhibit Cancer Stem Cell Function in Breast Cancer Cells by Disrupting Mitochondrial Homeostasis.
  30. LUBAC and NF-κB trigger a nuclear response from mitochondria.
  31. Na+/H+-exchanger 1 enhances antitumor activity of engineered NK-92 natural killer cells.
  32. LACTB exerts tumor suppressor properties in epithelial ovarian cancer through regulation of Slug.
  33. Transcription factors TEAD2 and E2A globally repress acetyl-CoA synthesis to promote tumorigenesis.
  34. BCL6 is regulated by the MAPK/ELK1 axis and promotes KRAS-driven lung cancer.
  35. Tracing the electron flow in redox metabolism: The appropriate distribution of electrons is essential to maintain redox balance in cancer cells.
  36. IDH2, a novel target of OGT, facilitates glucose uptake and cellular bioenergy production via NF-κB signaling to promote colorectal cancer progression.
  37. Cytosolic and mitochondrial tRNA synthetase inhibitors increase lifespan in a GCN4/atf-4-dependent manner.
  38. Intestinal plasticity and metabolism as regulators of organismal energy homeostasis.
  39. Acetyl-CoA, protein acetylation, and liver cancer.
  40. A bioluminescent-based probe for in vivo non-invasive monitoring of nicotinamide riboside uptake reveals a link between metastasis and NAD+ metabolism.
  41. A Tale of Two Lipids: Lipid Unsaturation Commands Ferroptosis Sensitivity.
  42. Endogenous metabolism in endothelial and immune cells generates most of the tissue vitamin B3 (nicotinamide).
  43. PAHSAs reduce cellular senescence and protect pancreatic beta cells from metabolic stress through regulation of Mdm2/p53.
  44. Food odor perception promotes systemic lipid utilization.
  45. Running to Outcompete Metastasis.
  46. Cancer cell survival depends on collagen uptake into tumor-associated stroma.
  47. Tumour-derived D-2HG blocks T cell cytotoxicity.
  48. Macrophage mitochondrial levels of iron affect adipose tissue function in obesity.
  49. Alternative respiratory oxidases to study the animal electron transport chain.
  50. Inference of metabolic fluxes in nutrient-limited continuous cultures: A Maximum Entropy approach with the minimum information.
  51. The circadian rhythm regulates branched-chain amino acids metabolism in fast muscle of Chinese perch (Siniperca chuatsi) during short-term fasting by Clock-KLF15-Bcat2 pathway.
  52. A lineage tree-based hidden Markov model quantifies cellular heterogeneity and plasticity.
  1. Nat Metab. 2022 Nov 18.
    Cancer metabolite blunts immunity.
    Michael Attwaters.
      
    DOI:  https://doi.org/10.1038/s42255-022-00690-x
  2. Proc Natl Acad Sci U S A. 2022 Nov 22. 119(47): e2210730119
    Mitochondrial nucleoid trafficking regulated by the inner-membrane AAA-ATPase ATAD3A modulates respiratory complex formation.
    Takaya Ishihara, Reiko Ban-Ishihara, Azusa Ota, Naotada Ishihara.
      Mitochondria have their own DNA (mtDNA), which encodes essential respiratory subunits. Under live imaging, mitochondrial nucleoids, composed of several copies of mtDNA and DNA-binding proteins, such as mitochondrial transcription factor A (TFAM), actively move inside mitochondria and change the morphology, in concert with mitochondrial membrane fission. Here we found the mitochondrial inner membrane-anchored AAA-ATPase protein ATAD3A mediates the nucleoid dynamics. Its ATPase domain exposed to the matrix binds directly to TFAM and mediates nucleoid trafficking along mitochondria by ATP hydrolysis. Nucleoid trafficking also required ATAD3A oligomerization via an interaction between the coiled-coil domains in intermembrane space. In ATAD3A deficiency, impaired nucleoid trafficking repressed the clustered and enlarged nucleoids observed in mitochondrial fission-deficient cells resulted in dispersed distribution of small nucleoids observed throughout the mitochondrial network, and this enhanced respiratory complex formation. Thus, mitochondrial fission and nucleoid trafficking cooperatively determine the size, number, and distribution of nucleoids in mitochondrial network, which should modulate respiratory complex formation.
    Keywords:  ATAD3A; Drp1; mitochondrial fission; mtDNA nucleoid; respiratory complex
    DOI:  https://doi.org/10.1073/pnas.2210730119
  3. Nat Metab. 2022 Nov 14.
    Suppression of CD8+ T cells by the metabolite itaconate.
      
    DOI:  https://doi.org/10.1038/s42255-022-00694-7
  4. Nat Metab. 2022 Nov 14.
    Myeloid-derived itaconate suppresses cytotoxic CD8+ T cells and promotes tumour growth.
    Hongyun Zhao, Da Teng, Lifeng Yang, Xincheng Xu, Jiajia Chen, Tengjia Jiang, Austin Y Feng, Yaqing Zhang, Dennie T Frederick, Lei Gu, Li Cai, John M Asara, Marina Pasca di Magliano, Genevieve M Boland, Keith T Flaherty, Kenneth D Swanson, David Liu, Joshua D Rabinowitz, Bin Zheng.
      The tumour microenvironment possesses mechanisms that suppress anti-tumour immunity. Itaconate is a metabolite produced from the Krebs cycle intermediate cis-aconitate by the activity of immune-responsive gene 1 (IRG1). While it is known to be immune modulatory, the role of itaconate in anti-tumour immunity is unclear. Here, we demonstrate that myeloid-derived suppressor cells (MDSCs) secrete itaconate that can be taken up by CD8+ T cells and suppress their proliferation, cytokine production and cytolytic activity. Metabolite profiling, stable-isotope tracing and metabolite supplementation studies indicated that itaconate suppressed the biosynthesis of aspartate and serine/glycine in CD8+ T cells to attenuate their proliferation and function. Host deletion of Irg1 in female mice bearing allografted tumours resulted in decreased tumour growth, inhibited the immune-suppressive activities of MDSCs, promoted anti-tumour immunity of CD8+ T cells and enhanced the anti-tumour activity of anti-PD-1 antibody treatment. Furthermore, we found a significant negative correlation between IRG1 expression and response to PD-1 immune checkpoint blockade in patients with melanoma. Our findings not only reveal a previously unknown role of itaconate as an immune checkpoint metabolite secreted from MDSCs to suppress CD8+ T cells, but also establish IRG1 as a myeloid-selective target in immunometabolism whose inhibition promotes anti-tumour immunity and enhances the efficacy of immune checkpoint protein blockade.
    DOI:  https://doi.org/10.1038/s42255-022-00676-9
  5. Clin Nutr Res. 2022 Oct;11(4): 316-330
    Iron Homeostasis and Energy Metabolism in Obesity.
    Se Lin Kim, Sunhye Shin, Soo Jin Yang.
      Iron plays a role in energy metabolism as a component of vital enzymes and electron transport chains (ETCs) for adenosine triphosphate (ATP) synthesis. The tricarboxylic acid (TCA) cycle and oxidative phosphorylation are crucial in generating ATP in mitochondria. At the mitochondria matrix, heme and iron-sulfur clusters are synthesized. Iron-sulfur cluster is a part of the aconitase in the TCA cycle and a functional or structural component of electron transfer proteins. Heme is the prosthetic group for cytochrome c, a principal component of the respiratory ETC. Regarding fat metabolism, iron regulates mitochondrial fat oxidation and affects the thermogenesis of brown adipose tissue (BAT). Thermogenesis is a process that increases energy expenditure, and BAT is a tissue that generates heat via mitochondrial fuel oxidation. Iron deficiency may impair mitochondrial fuel oxidation by inhibiting iron-containing molecules, leading to decreased energy expenditure. Although it is expected that impaired mitochondrial fuel oxidation may be restored by iron supplementation, its underlying mechanisms have not been clearly identified. Therefore, this review summarizes the current evidence on how iron regulates energy metabolism considering the TCA cycle, oxidative phosphorylation, and thermogenesis. Additionally, we relate iron-mediated metabolic regulation to obesity and obesity-related complications.
    Keywords:  Heme; Hepcidin; Iron-sulfur cluster; Obesity; Thermogenesis
    DOI:  https://doi.org/10.7762/cnr.2022.11.4.316
  6. Nat Metab. 2022 Nov 18.
    Non-mammalian metabolic models in the spotlight.
      
    DOI:  https://doi.org/10.1038/s42255-022-00704-8
  7. Nat Commun. 2022 Nov 14. 13(1): 6754
    Altered glycolysis triggers impaired mitochondrial metabolism and mTORC1 activation in diabetic β-cells.
    Elizabeth Haythorne, Matthew Lloyd, John Walsby-Tickle, Andrei I Tarasov, Jonas Sandbrink, Idoia Portillo, Raul Terron Exposito, Gregor Sachse, Malgorzata Cyranka, Maria Rohm, Patrik Rorsman, James McCullagh, Frances M Ashcroft.
      Chronic hyperglycaemia causes a dramatic decrease in mitochondrial metabolism and insulin content in pancreatic β-cells. This underlies the progressive decline in β-cell function in diabetes. However, the molecular mechanisms by which hyperglycaemia produces these effects remain unresolved. Using isolated islets and INS-1 cells, we show here that one or more glycolytic metabolites downstream of phosphofructokinase and upstream of GAPDH mediates the effects of chronic hyperglycemia. This metabolite stimulates marked upregulation of mTORC1 and concomitant downregulation of AMPK. Increased mTORC1 activity causes inhibition of pyruvate dehydrogenase which reduces pyruvate entry into the tricarboxylic acid cycle and partially accounts for the hyperglycaemia-induced reduction in oxidative phosphorylation and insulin secretion. In addition, hyperglycaemia (or diabetes) dramatically inhibits GAPDH activity, thereby impairing glucose metabolism. Our data also reveal that restricting glucose metabolism during hyperglycaemia prevents these changes and thus may be of therapeutic benefit. In summary, we have identified a pathway by which chronic hyperglycaemia reduces β-cell function.
    DOI:  https://doi.org/10.1038/s41467-022-34095-x
  8. Cell Rep. 2022 Nov 15. pii: S2211-1247(22)01510-8. [Epub ahead of print]41(7): 111639
    CD8+ T cell metabolic rewiring defined by scRNA-seq identifies a critical role of ASNS expression dynamics in T cell differentiation.
    Juan Fernández-García, Fabien Franco, Sweta Parik, Patricia Altea-Manzano, Antonino Alejandro Pane, Dorien Broekaert, Joke van Elsen, Ines Vermeire, Tessa Schalley, Mélanie Planque, Thomas van Brussel, Rogier Schepers, Elodie Modave, Tobias K Karakach, Peter Carmeliet, Diether Lambrechts, Ping-Chih Ho, Sarah-Maria Fendt.
      T cells dynamically rewire their metabolism during an immune response. We applied single-cell RNA sequencing to CD8+ T cells activated and differentiated in vitro in physiological medium to resolve these metabolic dynamics. We identify a differential time-dependent reliance of activating T cells on the synthesis versus uptake of various non-essential amino acids, which we corroborate with functional assays. We also identify metabolic genes that potentially dictate the outcome of T cell differentiation, by ranking them based on their expression dynamics. Among them, we find asparagine synthetase (Asns), whose expression peaks for effector T cells and decays toward memory formation. Disrupting these expression dynamics by ASNS overexpression promotes an effector phenotype, enhancing the anti-tumor response of adoptively transferred CD8+ T cells in a mouse melanoma model. We thus provide a resource of dynamic expression changes during CD8+ T cell activation and differentiation, and identify ASNS expression dynamics as a modulator of CD8+ T cell differentiation.
    Keywords:  ASNS; CD8(+) T cells; CP: Immunology; T-cell activation; T-cell differentiation; asparagine; dynamics; immunology; metabolism; physiological media; scRNA-seq
    DOI:  https://doi.org/10.1016/j.celrep.2022.111639
  9. Cell Metab. 2022 Nov 08. pii: S1550-4131(22)00489-2. [Epub ahead of print]
    Ribosome stalling is a signal for metabolic regulation by the ribotoxic stress response.
    Goda Snieckute, Aitana Victoria Genzor, Anna Constance Vind, Laura Ryder, Mark Stoneley, Sébastien Chamois, René Dreos, Cathrine Nordgaard, Frederike Sass, Melanie Blasius, Aida Rodríguez López, Sólveig Hlín Brynjólfsdóttir, Kasper Langebjerg Andersen, Anne E Willis, Lisa B Frankel, Steen Seier Poulsen, David Gatfield, Zachary Gerhart-Hines, Christoffer Clemmensen, Simon Bekker-Jensen.
      Impairment of translation can lead to collisions of ribosomes, which constitute an activation platform for several ribosomal stress-surveillance pathways. Among these is the ribotoxic stress response (RSR), where ribosomal sensing by the MAP3K ZAKα leads to activation of p38 and JNK kinases. Despite these insights, the physiological ramifications of ribosomal impairment and downstream RSR signaling remain elusive. Here, we show that stalling of ribosomes is sufficient to activate ZAKα. In response to amino acid deprivation and full nutrient starvation, RSR impacts on the ensuing metabolic responses in cells, nematodes, and mice. The RSR-regulated responses in these model systems include regulation of AMPK and mTOR signaling, survival under starvation conditions, stress hormone production, and regulation of blood sugar control. In addition, ZAK-/- male mice present a lean phenotype. Our work highlights impaired ribosomes as metabolic signals and demonstrates a role for RSR signaling in metabolic regulation.
    Keywords:  AMPK; FGF21; ZAK-alpha; amino acid starvation; mTOR; metabolic regulation; mouse models; ribosome collision; ribotoxic stress response
    DOI:  https://doi.org/10.1016/j.cmet.2022.10.011
  10. Cancer Cell. 2022 Nov 09. pii: S1535-6108(22)00520-7. [Epub ahead of print]
    Revealing de novo pyrimidine synthesis as a key vulnerability in brain tumors.
    Tanya Schild, Kayvan R Keshari.
      Brain tumors are notoriously difficult to treat. Three recent Cancer Cell articles aim to uncover novel druggable targets in IDH mutant gliomas, diffuse midline gliomas, and medulloblastomas, respectively, and show that these brain tumor types shift their metabolism to become reliant on de novo pyrimidine synthesis.
    DOI:  https://doi.org/10.1016/j.ccell.2022.10.023
  11. Nat Metab. 2022 Nov 18.
    From inulin to inflammation.
    Michael Attwaters.
      
    DOI:  https://doi.org/10.1038/s42255-022-00692-9
  12. iScience. 2022 Nov 18. 25(11): 105447
    Both ANT and ATPase are essential for mitochondrial permeability transition but not depolarization.
    M A Neginskaya, S E Morris, E V Pavlov.
      An increase in permeability of the mitochondrial inner membrane, mitochondrial permeability transition (PT), is the central event responsible for cell death and tissue damage in conditions such as stroke and heart attack. PT is caused by the cyclosporin A (CSA)-dependent calcium-induced pore, the permeability transition pore (PTP). The molecular details of PTP are incompletely understood. We utilized holographic and fluorescent microscopy to assess the contribution of ATP synthase and adenine nucleotide translocator (ANT) toward PTP. In cells lacking either ATP synthase or ANT, we observed CSA-sensitive membrane depolarization, but not high-conductance PTP. In wild-type cells, calcium-induced CSA-sensitive depolarization preceded opening of PTP, which occurred only after nearly complete mitochondrial membrane depolarization. We propose that both ATP synthase and ANT are required for high-conductance PTP but not depolarization, which presumably occurs through activation of the low-conductance PT, which has a molecular nature that is different from both complexes.
    Keywords:  Cell biology; Functional aspects of cell biology; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2022.105447
  13. Nat Metab. 2022 Nov 18.
    Batokine neuregulin 4 promotes atherosclerotic resolution.
    Ibrahim AlZaim, Joanna Kalucka.
      
    DOI:  https://doi.org/10.1038/s42255-022-00669-8
  14. Nat Commun. 2022 Nov 15. 13(1): 6977
    Interruption of post-Golgi STING trafficking activates tonic interferon signaling.
    Xintao Tu, Ting-Ting Chu, Devon Jeltema, Kennady Abbott, Kun Yang, Cong Xing, Jie Han, Nicole Dobbs, Nan Yan.
      Activation of the cGAS-STING pathway is traditionally considered a "trigger-release" mechanism where detection of microbial DNA or cyclic di-nucleotides sets off the type I interferon response. Whether this pathway can be activated without pathogenic ligand exposure is less well understood. Here we show that loss of Golgi-to-lysosome STING cofactors, but not ER-to-Golgi cofactors, selectively activates tonic interferon signalling. Impairment of post-Golgi trafficking extends STING Golgi-dwell time, resulting in elevated immune signalling and protection against infection. Mechanistically, trans-Golgi coiled coil protein GCC2 and several RAB GTPases act as key regulators of STING post-Golgi trafficking. Genomic deletion of these factors potently activates cGAS-STING signalling without instigating any pathogenic trigger for cGAS. Gcc2-/- mice develop STING-dependent serologic autoimmunity. Gcc2-deleted or Rab14-deleted cancer cells induce T-cell and IFN-dependent anti-tumour immunity and inhibit tumour growth in mice. In summary, we present a "basal flux" mechanism for tonic cGAS-STING signalling, regulated at the level of post-Golgi STING trafficking, which could be exploited for cancer immunotherapy.
    DOI:  https://doi.org/10.1038/s41467-022-33765-0
  15. Nature. 2022 Nov 16.
    Ferroptosis of tumour neutrophils causes immune suppression in cancer.
    Rina Kim, Ayumi Hashimoto, Nune Markosyan, Vladimir A Tyurin, Yulia Y Tyurina, Gozde Kar, Shuyu Fu, Mohit Sehgal, Laura Garcia-Gerique, Andrew Kossenkov, Bereket A Gebregziabher, John W Tobias, Kristin Hicks, Rebecca A Halpin, Nevena Cvetesic, Hui Deng, Laxminarasimha Donthireddy, Andrew Greenberg, Brian Nam, Robert H Vonderheide, Yulia Nefedova, Valerian E Kagan, Dmitry I Gabrilovich.
      Ferroptosis is a non-apoptotic form of regulated cell death that is triggered by the discoordination of regulatory redox mechanisms culminating in massive peroxidation of polyunsaturated phospholipids. Ferroptosis inducers have shown considerable effectiveness in killing tumour cells in vitro, yet there has been no obvious success in experimental animal models, with the notable exception of immunodeficient mice1,2. This suggests that the effect of ferroptosis on immune cells remains poorly understood. Pathologically activated neutrophils (PMNs), termed myeloid-derived suppressor cells (PMN-MDSCs), are major negative regulators of anti-tumour immunity3-5. Here we found that PMN-MDSCs in the tumour microenvironment spontaneously die by ferroptosis. Although decreasing the presence of PMN-MDSCs, ferroptosis induces the release of oxygenated lipids and limits the activity of human and mouse T cells. In immunocompetent mice, genetic and pharmacological inhibition of ferroptosis abrogates suppressive activity of PMN-MDSCs, reduces tumour progression and synergizes with immune checkpoint blockade to suppress the tumour growth. By contrast, induction of ferroptosis in immunocompetent mice promotes tumour growth. Thus, ferroptosis is a unique and targetable immunosuppressive mechanism of PMN-MDSCs in the tumour microenvironment that can be pharmacologically modulated to limit tumour progression.
    DOI:  https://doi.org/10.1038/s41586-022-05443-0
  16. Trends Immunol. 2022 Nov 09. pii: S1471-4906(22)00211-3. [Epub ahead of print]
    The NLRP3 inflammasome: regulation by metabolic signals.
    Antoni Olona, Stuart Leishman, Paras K Anand.
      Macrophages undergo profound metabolic reprogramming upon sensing infectious and sterile stimuli. This metabolic shift supports and regulates essential innate immune functions, including activation of the NLRP3 inflammasome. Within distinct metabolic networks, key enzymes play pivotal roles to control flux restraining detrimental inflammasome signaling. However, depending on the metabolic cues, specific enzymes and metabolites result in inflammasome activation outcomes which contrast other metabolic steps in the pathway. We posit that understanding which metabolic steps commit to discrete inflammasome fates will broaden our understanding of metabolic checkpoints to maintain homeostasis and offer better therapeutic options in human disease.
    Keywords:  NLRP3; TCA cycle; glycolysis; inflammasome; lipids; metabolism
    DOI:  https://doi.org/10.1016/j.it.2022.10.003
  17. Nat Commun. 2022 Nov 17. 13(1): 7031
    Identification of purine biosynthesis as an NADH-sensing pathway to mediate energy stress.
    Ronghui Yang, Chuanzhen Yang, Lingdi Ma, Yiliang Zhao, Zihao Guo, Jing Niu, Qiaoyun Chu, Yingmin Ma, Binghui Li.
      An enhanced NADH/NAD+ ratio, termed reductive stress, is associated with many diseases. However, whether a downstream sensing pathway exists to mediate pathogenic outcomes remains unclear. Here, we generate a soluble pyridine nucleotide transhydrogenase from Escherichia coli (EcSTH), which can elevate the NADH/NAD+ ratio and meantime reduce the NADPH/NADP+ ratio. Additionally, we fuse EcSTH with previously described LbNOX (a water-forming NADH oxidase from Lactobacillus brevis) to resume the NADH/NAD+ ratio. With these tools and by using genome-wide CRISPR/Cas9 library screens and metabolic profiling in mammalian cells, we find that accumulated NADH deregulates PRPS2 (Ribose-phosphate pyrophosphokinase 2)-mediated downstream purine biosynthesis to provoke massive energy consumption, and therefore, the induction of energy stress. Blocking purine biosynthesis prevents NADH accumulation-associated cell death in vitro and tissue injury in vivo. These results underscore the pathophysiological role of deregulated purine biosynthesis in NADH accumulation-associated disorders and demonstrate the utility of EcSTH in manipulating NADH/NAD+ and NADPH/NADP+.
    DOI:  https://doi.org/10.1038/s41467-022-34850-0
  18. Nat Commun. 2022 Nov 17. 13(1): 7047
    mTOR inhibition attenuates chemosensitivity through the induction of chemotherapy resistant persisters.
    Yuanhui Liu, Nancy G Azizian, Delaney K Sullivan, Yulin Li.
      Chemotherapy can eradicate a majority of cancer cells. However, a small population of tumor cells often survives drug treatments through genetic and/or non-genetic mechanisms, leading to tumor recurrence. Here we report a reversible chemoresistance phenotype regulated by the mTOR pathway. Through a genome-wide CRISPR knockout library screen in pancreatic cancer cells treated with chemotherapeutic agents, we have identified the mTOR pathway as a prominent determinant of chemosensitivity. Pharmacological suppression of mTOR activity in cancer cells from diverse tissue origins leads to the persistence of a reversibly resistant population, which is otherwise eliminated by chemotherapeutic agents. Conversely, activation of the mTOR pathway increases chemosensitivity in vitro and in vivo and predicts better survival among various human cancers. Persister cells display a senescence phenotype. Inhibition of mTOR does not induce cellular senescence per se, but rather promotes the survival of senescent cells through regulation of autophagy and G2/M cell cycle arrest, as revealed by a small-molecule chemical library screen. Thus, mTOR plays a causal yet paradoxical role in regulating chemotherapeutic response; inhibition of the mTOR pathway, while suppressing tumor expansion, facilitates the development of a reversible drug-tolerant senescence state.
    DOI:  https://doi.org/10.1038/s41467-022-34890-6
  19. Cytokine Growth Factor Rev. 2022 Nov 07. pii: S1359-6101(22)00079-X. [Epub ahead of print]
    Crosstalk between glucose metabolism, lactate production and immune response modulation.
    Lei Ye, Yi Jiang, Mingming Zhang.
      Metabolites of glycolytic metabolism have been identified as signaling molecules and regulators of gene expression, in addition to their basic function as major energy and biosynthetic source. Immune cells reprogram metabolic pathways to cater to energy and biosynthesis demands upon activation. Most lymphocytes, including inflammatory M1 macrophages, mainly shift from oxidative phosphorylation to glycolysis, whereas regulatory T cells and M2 macrophages preferentially use the tricarboxylic acid (TCA) cycle and have reduced glycolysis. Recent studies have revealed the "non-metabolic" signaling functions of intermediates of the mitochondrial pathway and glycolysis. The roles of citrate, succinate and itaconate in immune response, including post-translational modifications of proteins and macrophages activation, have been highlighted. As an end product of glycolysis, lactate has received considerable interest from researchers. In this review, we specifically focused on studies exploring the integration of lactate into immune cell biology and associated pathologies. Lactate can act as a double-edged sword. On one hand, activated immune cells prefer to use lactate to support their function. On the other hand, accumulated lactate in the tissue microenvironment acts as a signaling molecule that restricts immune cell function. Recently, a novel epigenetic change mediated by histone lysine lactylation has been proposed. The burgeoning researches support the idea that histone lactylation participates in diverse cellular events. This review describes glycolytic metabolism, including the immunoregulation of metabolites of the TCA cycle and lactate. These latest findings strengthen our understanding on tumor and chronic inflammatory diseases and offer potential therapeutic options.
    Keywords:  Glucose metabolism; Immune cell function; Lactate; Lactylation; TCA cycle
    DOI:  https://doi.org/10.1016/j.cytogfr.2022.11.001
  20. J Cell Biol. 2023 Jan 02. pii: e202203019. [Epub ahead of print]222(1):
    Mitochondrial dysfunction compromises ciliary homeostasis in astrocytes.
    Olesia Ignatenko, Satu Malinen, Sofiia Rybas, Helena Vihinen, Joni Nikkanen, Aleksander Kononov, Eija S Jokitalo, Gulayse Ince-Dunn, Anu Suomalainen.
      Astrocytes, often considered as secondary responders to neurodegeneration, are emerging as primary drivers of brain disease. Here we show that mitochondrial DNA depletion in astrocytes affects their primary cilium, the signaling organelle of a cell. The progressive oxidative phosphorylation deficiency in astrocytes induces FOXJ1 and RFX transcription factors, known as master regulators of motile ciliogenesis. Consequently, a robust gene expression program involving motile cilia components and multiciliated cell differentiation factors are induced. While the affected astrocytes still retain a single cilium, these organelles elongate and become remarkably distorted. The data suggest that chronic activation of the mitochondrial integrated stress response (ISRmt) in astrocytes drives anabolic metabolism and promotes ciliary elongation. Collectively, our evidence indicates that an active signaling axis involving mitochondria and primary cilia exists and that ciliary signaling is part of ISRmt in astrocytes. We propose that metabolic ciliopathy is a novel pathomechanism for mitochondria-related neurodegenerative diseases.
    DOI:  https://doi.org/10.1083/jcb.202203019
  21. J Cell Biol. 2023 Jan 02. pii: e202007026. [Epub ahead of print]222(1):
    ATM inhibition drives metabolic adaptation via induction of macropinocytosis.
    Zhentai Huang, Chi-Wei Chen, Raquel Buj, Naveen Kumar Tangudu, Richard S Fang, Kelly E Leon, Erika S Dahl, Erika L Varner, Eliana von Krusenstiern, Aidan R Cole, Nathaniel W Snyder, Katherine M Aird.
      Macropinocytosis is a nonspecific endocytic process that may enhance cancer cell survival under nutrient-poor conditions. Ataxia-Telangiectasia mutated (ATM) is a tumor suppressor that has been previously shown to play a role in cellular metabolic reprogramming. We report that the suppression of ATM increases macropinocytosis to promote cancer cell survival in nutrient-poor conditions. Combined inhibition of ATM and macropinocytosis suppressed proliferation and induced cell death both in vitro and in vivo. Supplementation of ATM-inhibited cells with amino acids, branched-chain amino acids (BCAAs) in particular, abrogated macropinocytosis. Analysis of ATM-inhibited cells in vitro demonstrated increased BCAA uptake, and metabolomics of ascites and interstitial fluid from tumors indicated decreased BCAAs in the microenvironment of ATM-inhibited tumors. These data reveal a novel basis of ATM-mediated tumor suppression whereby loss of ATM stimulates protumorigenic uptake of nutrients in part via macropinocytosis to promote cancer cell survival and reveal a potential metabolic vulnerability of ATM-inhibited cells.
    DOI:  https://doi.org/10.1083/jcb.202007026
  22. Sci Immunol. 2022 Nov 25. 7(77): eabm8182
    OXPHOS promotes apoptotic resistance and cellular persistence in TH17 cells in the periphery and tumor microenvironment.
    Hanna S Hong, Nneka E Mbah, Mengrou Shan, Kristen Loesel, Lin Lin, Peter Sajjakulnukit, Luis O Correa, Anthony Andren, Jason Lin, Atsushi Hayashi, Brian Magnuson, Judy Chen, Zhaoheng Li, Yuying Xie, Li Zhang, Daniel R Goldstein, Shannon A Carty, Yu Leo Lei, Anthony W Opipari, Rafael J Argüello, Ilona Kryczek, Nobuhiko Kamada, Weiping Zou, Luigi Franchi, Costas A Lyssiotis.
      T cell proliferation and cytokine production are bioenergetically and biosynthetically costly. The inability to meet these metabolic demands results in altered differentiation, accompanied by impaired effector function, and attrition of the immune response. Interleukin-17-producing CD4 T cells (TH17s) are mediators of host defense, autoimmunity, and antitumor immunity in the setting of adoptive T cell therapy. TH17s are long-lived cells that require mitochondrial oxidative phosphorylation (OXPHOS) for effector function in vivo. Considering that TH17s polarized under standardized culture conditions are predominately glycolytic, little is known about how OXPHOS regulates TH17 processes, such as their ability to persist and thus contribute to protracted immune responses. Here, we modified standardized culture medium and identified a culture system that reliably induces OXPHOS dependence in TH17s. We found that TH17s cultured under OXPHOS conditions metabolically resembled their in vivo counterparts, whereas glycolytic cultures were dissimilar. OXPHOS TH17s exhibited increased mitochondrial fitness, glutamine anaplerosis, and an antiapoptotic phenotype marked by high BCL-XL and low BIM. Limited mitophagy, mediated by mitochondrial fusion regulator OPA-1, was critical to apoptotic resistance in OXPHOS TH17s. By contrast, glycolytic TH17s exhibited more mitophagy and an imbalance in BCL-XL to BIM, thereby priming them for apoptosis. In addition, through adoptive transfer experiments, we demonstrated that OXPHOS protected TH17s from apoptosis while enhancing their persistence in the periphery and tumor microenvironment in a murine model of melanoma. Together, our work demonstrates how metabolism regulates TH17 cell fate and highlights the potential for therapies that target OXPHOS in TH17-driven diseases.
    DOI:  https://doi.org/10.1126/sciimmunol.abm8182
  23. Cell Biosci. 2022 Nov 12. 12(1): 183
    mTORC1-c-Myc pathway rewires methionine metabolism for HCC progression through suppressing SIRT4 mediated ADP ribosylation of MAT2A.
    Liang Zhao, Huizhao Su, Xiaomeng Liu, Hongquan Wang, Yukuan Feng, Yan Wang, Haiqiang Chen, Luo Dai, Shihui Lai, Siqi Xu, Chong Li, Jihui Hao, Bo Tang.
       BACKGROUND: Exploiting cancer metabolism during nutrient availability holds immense potential for the clinical and therapeutic benefits of hepatocellular carcinoma (HCC) patients. Dietary methionine is a metabolic dependence of cancer development, but how the signal transduction integrates methionine status to achieve the physiological demand of cancer cells remains unknown.
    METHODS: Low or high levels of dietary methionine was fed to mouse models with patient-derived xenograft or diethyl-nitrosamine induced liver cancer. RNA sequence and metabolomics were performed to reveal the profound effect of methionine restriction on gene expression and metabolite changes. Immunostaining, sphere formation assays, in vivo tumourigenicity, migration and self-renewal ability were conducted to demonstrate the efficacy of methionine restriction and sorafenib.
    RESULTS: We discovered that mTORC1-c-Myc-SIRT4 axis was abnormally regulated in a methionine-dependent manner and affected the HCC progression. c-Myc rewires methionine metabolism through TRIM32 mediated degradation of SIRT4, which regulates MAT2A activity by ADP-ribosylation on amino acid residue glutamic acid 111. MAT2A is a key enzyme to generate S-adenosylmethionine (SAM). Loss of SIRT4 activates MAT2A, thereby increasing SAM level and dynamically regulating gene expression, which triggers the high proliferation rate of tumour cells. SIRT4 exerts its tumour suppressive function with targeted therapy (sorafenib) by affecting methionine, redox and nucleotide metabolism.
    CONCLUSIONS: These findings establish a novel characterization of the signaling transduction and the metabolic consequences of dietary methionine restriction in malignant liver tissue of mice. mTORC1, c-Myc, SIRT4 and ADP ribosylation site of MAT2A are promising clinical and therapeutic targets for the HCC treatment.
    Keywords:  ADP ribosylation; Cancer; MAT2A; Methionine metabolism; SIRT4; TRIM32; c-Myc; mTOR
    DOI:  https://doi.org/10.1186/s13578-022-00919-y
  24. EMBO J. 2022 Nov 18. e112006
    LUBAC assembles a ubiquitin signaling platform at mitochondria for signal amplification and transport of NF-κB to the nucleus.
    Zhixiao Wu, Lena A Berlemann, Verian Bader, Dominik A Sehr, Eva Dawin, Alberto Covallero, Jens Meschede, Lena Angersbach, Cathrin Showkat, Jonas B Michaelis, Christian Münch, Bettina Rieger, Dmitry Namgaladze, Maria Georgina Herrera, Fabienne C Fiesel, Wolfdieter Springer, Marta Mendes, Jennifer Stepien, Katalin Barkovits, Katrin Marcus, Albert Sickmann, Gunnar Dittmar, Karin B Busch, Dietmar Riedel, Marisa Brini, Jörg Tatzelt, Tito Cali, Konstanze F Winklhofer.
      Mitochondria are increasingly recognized as cellular hubs to orchestrate signaling pathways that regulate metabolism, redox homeostasis, and cell fate decisions. Recent research revealed a role of mitochondria also in innate immune signaling; however, the mechanisms of how mitochondria affect signal transduction are poorly understood. Here, we show that the NF-κB pathway activated by TNF employs mitochondria as a platform for signal amplification and shuttling of activated NF-κB to the nucleus. TNF treatment induces the recruitment of HOIP, the catalytic component of the linear ubiquitin chain assembly complex (LUBAC), and its substrate NEMO to the outer mitochondrial membrane, where M1- and K63-linked ubiquitin chains are generated. NF-κB is locally activated and transported to the nucleus by mitochondria, leading to an increase in mitochondria-nucleus contact sites in a HOIP-dependent manner. Notably, TNF-induced stabilization of the mitochondrial kinase PINK1 furthermore contributes to signal amplification by antagonizing the M1-ubiquitin-specific deubiquitinase OTULIN. Overall, our study reveals a role for mitochondria in amplifying TNF-mediated NF-κB activation, both serving as a signaling platform, as well as a transport mode for activated NF-κB to the nuclear.
    Keywords:  HOIP; NEMO; OTULIN; PINK1; ubiquitin
    DOI:  https://doi.org/10.15252/embj.2022112006
  25. Comp Biochem Physiol A Mol Integr Physiol. 2022 Nov 12. pii: S1095-6433(22)00201-X. [Epub ahead of print] 111343
    Short communication: Acute hypoxia does not alter mitochondrial abundance in naked mole-rats.
    Nathalie C Marks de Chabris, Soulene Sabir, Guy Perkins, Hang Cheng, Marc H Ellisman, Matthew E Pamenter.
      Hypoxia poses a significant energetic challenge and most species exhibit metabolic remodelling when exposed to prolonged hypoxia. One component of this remodelling is mitochondrial biogenesis/mitophagy, which alter mitochondrial abundance and helps to adjust metabolic throughput to match changes in energy demands in hypoxia. However, how acute hypoxia impacts mitochondrial abundance in hypoxia-tolerant species is poorly understood. To help address this gap, we exposed hypoxia-tolerant naked mole-rats to 3 h of normoxia or acute hypoxia (5% O2) and measured changes in mitochondrial abundance using two well-established markers: citrate synthase (CS) enzyme activity and mitochondrial DNA (mtDNA) abundance. We found that neither marker changed with hypoxia in brain, liver, or kidney, suggesting that mitochondrial biogenesis is not initiated during acute hypoxia in these tissues. Conversely in skeletal muscle, the ratio of CS activity to total protein decreased 50% with hypoxia. However, this change was likely driven by an increase in soluble protein density in hypoxia because CS activity was unchanged relative to wet tissue weight and the mtDNA copy number was unchanged. To confirm this, we examined skeletal muscle mitochondria using transmission electron microscopy and found no change in mitochondrial volume density. Taken together with previous studies of mitochondrial respiratory function, our present findings suggest that naked mole-rats primarily rely on tissue-specific functional remodelling of metabolic pathways and mitochondrial respiratory throughput, and not physical changes in mitochondrial number or volume, to adjust to short-term hypoxic exposure.
    Keywords:  Brain; Citrate synthase; Kidney; Liver; Mitochondrial DNA; Skeletal muscle
    DOI:  https://doi.org/10.1016/j.cbpa.2022.111343
  26. J Inherit Metab Dis. 2022 Nov 13.
    Cellular and computational models reveal environmental and metabolic interactions in MMUT-type methylmalonic aciduria.
    Charlotte Ramon, Florian Traversi, Céline Bürer, D Sean Froese, Jörg Stelling.
      MMUT-type methylmalonic aciduria is a rare inherited metabolic disease caused by the loss of function of the methylmalonyl-CoA mutase (MMUT) enzyme. Patients develop symptoms resembling those of primary mitochondrial disorders, but the underlying causes of mitochondrial dysfunction remain unclear. Here, we examined environmental and genetic interactions in MMUT deficiency using a combination of computational modeling and cellular models to decipher pathways interacting with MMUT. Immortalized fibroblast (hTERT BJ5ta) MMUT-KO (MUTKO) clones displayed a mild mitochondrial impairment in standard glucose-based medium, but they did not to show increased reliance on respiratory metabolism nor reduced growth or viability. Consistently, our modeling predicted MUTKO specific growth phenotypes only for lower extracellular glutamine concentrations. Indeed, two of three MMUT-deficient BJ5ta cell lines showed a reduced viability in glutamine-free medium. Further, growth on 183 different carbon and nitrogen substrates identified increased NADH (nicotinamide adenine dinucleotide) metabolism of BJ5ta and HEK293 MUTKO cells compared to controls on purine- and glutamine-based substrates. With this knowledge, our modeling predicted 13 reactions interacting with MMUT that potentiate an effect on growth, primarily those of secondary oxidation of propionyl-CoA, oxidative phosphorylation and oxygen diffusion. Of these, we validated 3-hydroxyisobutytyl-CoA hydrolase (HIBCH) in the secondary propionyl-CoA oxidation pathway. Altogether, these results suggest compensation for the loss of MMUT function by increasing anaplerosis through glutamine or by diverting flux away from MMUT through the secondary propionyl-CoA oxidation pathway, which may have therapeutic relevance.
    Keywords:  CRISPR-Cas9; Rare disease; constraint-based modeling; genetic interaction; metabolism; methylmalonic aciduria
    DOI:  https://doi.org/10.1002/jimd.12575
  27. FEBS J. 2022 Nov;289(22): 6822-6831
    Organelle homeostasis: from cellular mechanisms to disease.
    Emma Burbridge, Colin Adrain.
      The major criterion that distinguishes eukaryotes from prokaryotes is the presence of organelles in the former. Organelles provide a compartment in which biochemical processes are corralled within bespoke biophysical conditions and act as storage depots, powerhouses, waste storage/recycling units and innate immune signalling hubs. A key challenge faced by organelles is to define, and then retain, their identity; this is mediated by complex proteostasis mechanisms including the import of an organelle-specific proteome, the exclusion of non-organellar proteins and the removal of misfolded proteins via dedicated quality control mechanisms. This Special Issue on Organelle Homeostasis provides an engaging, eclectic, yet integrative, perspective on organelle homeostasis in a range of organelles including those from the secretory and endocytic pathways, mitochondria, the autophagy-lysosomal pathway and the nucleus and its sub-compartments. Some lesser-known organelles including migrasomes (organelles that are released by migrating cells) and GOMED (a Golgi-specific form of autophagy) are also introduced. In the spirit of the principles of organelle biology, we hope you find the reviews in this Issue both encapsulating and captivating, and we thank the authors for their excellent contributions.
    Keywords:  endoplasmic reticulum; mitochondria; nucleus; organelle homeostasis; quality control
    DOI:  https://doi.org/10.1111/febs.16667
  28. Genome Biol. 2022 Nov 14. 23(1): 241
    MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution.
    Tom L Kaufmann, Marina Petkovic, Thomas B K Watkins, Emma C Colliver, Sofya Laskina, Nisha Thapa, Darlan C Minussi, Nicholas Navin, Charles Swanton, Peter Van Loo, Kerstin Haase, Maxime Tarabichi, Roland F Schwarz.
      Aneuploidy, chromosomal instability, somatic copy-number alterations, and whole-genome doubling (WGD) play key roles in cancer evolution and provide information for the complex task of phylogenetic inference. We present MEDICC2, a method for inferring evolutionary trees and WGD using haplotype-specific somatic copy-number alterations from single-cell or bulk data. MEDICC2 eschews simplifications such as the infinite sites assumption, allowing multiple mutations and parallel evolution, and does not treat adjacent loci as independent, allowing overlapping copy-number events. Using simulations and multiple data types from 2780 tumors, we use MEDICC2 to demonstrate accurate inference of phylogenies, clonal and subclonal WGD, and ancestral copy-number states.
    Keywords:  Aneuploidy; Cancer evolution; Chromosomal instability; Intratumor heterogeneity; Phylogenetic reconstruction; Single-cell sequencing; Somatic copy-number alterations; Whole-genome doubling
    DOI:  https://doi.org/10.1186/s13059-022-02794-9
  29. Cancer Res Commun. 2022 Oct 10. 2(10): 1144-1161
    Mitochondrial Matrix Protease ClpP Agonists Inhibit Cancer Stem Cell Function in Breast Cancer Cells by Disrupting Mitochondrial Homeostasis.
    Yoshimi Endo Greer, Lidia Hernandez, Emily M J Fennell, Manjari Kundu, Donna Voeller, Raj Chari, Samuel F Gilbert, Thomas S K Gilbert, Shashikala Ratnayake, Binwu Tang, Markus Hafner, Qingrong Chen, Daoud Meerzaman, Edwin Iwanowicz, Christina M Annunziata, Lee M Graves, Stanley Lipkowitz.
      Mitochondria are multifaceted organelles which are important for bioenergetics, biosynthesis and signaling in metazoans. Mitochondrial functions are frequently altered in cancer to promote both the energy and the necessary metabolic intermediates for biosynthesis required for tumor growth. Cancer stem cells (CSCs) contribute to chemotherapy resistance, relapse, and metastasis. Recent studies have shown that while non-stem, bulk cancer cells utilize glycolysis, breast CSCs are more dependent on oxidative phosphorylation (OxPhos) and therefore targeting mitochondria may inhibit CSC function. We previously reported that small molecule ONC201, which is an agonist for the mitochondrial caseinolytic protease (ClpP), induces mitochondrial dysfunction in breast cancer cells. In this study, we report that ClpP agonists inhibit breast cancer cell proliferation and CSC function in vitro and in vivo. Mechanistically, we found that OxPhos inhibition downregulates multiple pathways required for CSC function, such as the mevalonate pathway, YAP, Myc, and the HIF pathway. ClpP agonists showed significantly greater inhibitory effect on CSC functions compared with other mitochondria-targeting drugs. Further studies showed that ClpP agonists deplete NAD(P)+ and NAD(P)H, induce redox imbalance, dysregulate one-carbon metabolism and proline biosynthesis. Downregulation of these pathways by ClpP agonists further contribute to the inhibition of CSC function. In conclusion, ClpP agonists inhibit breast CSC functions by disrupting mitochondrial homeostasis in breast cancer cells and inhibiting multiple pathways critical to CSC function.
    Significance: ClpP agonists disrupt mitochondrial homeostasis by activating mitochondrial matrix protease ClpP. We report that ClpP agonists inhibit cell growth and cancer stem cell functions in breast cancer models by modulating multiple metabolic pathways essential to cancer stem cell function.
    DOI:  https://doi.org/10.1158/2767-9764.CRC-22-0142
  30. EMBO J. 2022 Nov 18. e112920
    LUBAC and NF-κB trigger a nuclear response from mitochondria.
    Junsheng Chen, Thomas Simmen.
      Mitochondria are key signaling hubs for innate immune responses. In this issue, Wu et al (2022) report that remodeling of the outer mitochondrial membrane by the linear ubiquiting chain assembly complex (LUBAC) facilitates transport of activated NF-κB to the nucleus in response to TNF signaling.
    DOI:  https://doi.org/10.15252/embj.2022112920
  31. Cancer Res Commun. 2022 Aug;2(8): 842-856
    Na+/H+-exchanger 1 enhances antitumor activity of engineered NK-92 natural killer cells.
    Yao-Yu Gong, Hongguang Shao, Yu Li, Patricia Brafford, Zachary E Stine, Jing Sun, Dean W Felsher, Jordan S Orange, Steven M Albelda, Chi V Dang.
      Adoptive cell transfer (ACT) immunotherapy has remarkable efficacy against some hematological malignancies. However, its efficacy in solid tumors is limited by the adverse tumor microenvironment (TME) conditions, most notably that acidity inhibits T and natural killer (NK) cell mTOR complex 1 (mTORC1) activity and impairs cytotoxicity. In several reported studies, systemic buffering of tumor acidity enhanced the efficacy of immune checkpoint inhibitors. Paradoxically, we found in a c-Myc-driven hepatocellular carcinoma model that systemic buffering increased tumor mTORC1 activity, negating inhibition of tumor growth by anti-PD1 treatment. Therefore, in this proof-of-concept study, we tested the metabolic engineering of immune effector cells to mitigate the inhibitory effect of tumor acidity while avoiding side effects associated with systemic buffering. We first overexpressed an activated RHEB in the human NK cell line NK-92, thereby rescuing acid-blunted mTORC1 activity and enhancing cytolytic activity. Then, to directly mitigate the effect of acidity, we ectopically expressed acid extruder proteins. Whereas ectopic expression of carbonic anhydrase IX (CA9) moderately increased mTORC1 activity, it did not enhance effector function. In contrast, overexpressing a constitutively active Na+/H+-exchanger 1 (NHE1; SLC9A1) in NK-92 did not elevate mTORC1 but enhanced degranulation, target engagement, in vitro cytotoxicity, and in vivo antitumor activity. Our findings suggest the feasibility of overcoming the inhibitory effect of the TME by metabolically engineering immune effector cells, which can enhance ACT for better efficacy against solid tumors.
    Keywords:  Na+/H+-exchanger 1 (NHE1/SLC9A1); immunotherapy; natural killer (NK) cell; solid tumor; tumor acidosis; tumor microenvironment (TME)
    DOI:  https://doi.org/10.1158/2767-9764.crc-22-0270
  32. Life Sci Alliance. 2023 Jan;pii: e202201510. [Epub ahead of print]6(1):
    LACTB exerts tumor suppressor properties in epithelial ovarian cancer through regulation of Slug.
    Valentina Cutano, Jessica Marianne Ferreira Mendes, Sara Escudeiro-Lopes, Susana Machado, Judith Vinaixa Forner, Juan M Gonzales-Morena, Martin Prevorovsky, Viacheslav Zemlianski, Yuxiong Feng, Petra Kralova Viziova, Andrea Hartmanova, Beata Malcekova, Pavel Jakoube, Sonia Iyer, Zuzana Keckesova.
      Epithelial-mesenchymal transition (EMT) is a cellular mechanism used by cancer cells to acquire migratory and stemness properties. In this study, we show, through in vitro, in vivo, and 3D culture experiments, that the mitochondrial protein LACTB manifests tumor suppressor properties in ovarian cancer. We show that LACTB is significantly down-regulated in epithelial ovarian cancer cells and clinical tissues. Re-expression of LACTB negatively effects the growth of cancer cells but not of non-tumorigenic cells. Mechanistically, we show that LACTB leads to differentiation of ovarian cancer cells and loss of their stemness properties, which is achieved through the inhibition of the EMT program and the LACTB-dependent down-regulation of Snail2/Slug transcription factor. This study uncovers a novel role of LACTB in ovarian cancer and proposes new ways of counteracting the oncogenic EMT program in this model system.
    DOI:  https://doi.org/10.26508/lsa.202201510
  33. Mol Cell. 2022 Nov 17. pii: S1097-2765(22)01055-3. [Epub ahead of print]82(22): 4246-4261.e11
    Transcription factors TEAD2 and E2A globally repress acetyl-CoA synthesis to promote tumorigenesis.
    Sujin Park, Dirk Mossmann, Qian Chen, Xueya Wang, Eva Dazert, Marco Colombi, Alexander Schmidt, Brendan Ryback, Charlotte K Y Ng, Luigi M Terracciano, Markus H Heim, Michael N Hall.
      Acetyl-coenzyme A (acetyl-CoA) plays an important role in metabolism, gene expression, signaling, and other cellular processes via transfer of its acetyl group to proteins and metabolites. However, the synthesis and usage of acetyl-CoA in disease states such as cancer are poorly characterized. Here, we investigated global acetyl-CoA synthesis and protein acetylation in a mouse model and patient samples of hepatocellular carcinoma (HCC). Unexpectedly, we found that acetyl-CoA levels are decreased in HCC due to transcriptional downregulation of all six acetyl-CoA biosynthesis pathways. This led to hypo-acetylation specifically of non-histone proteins, including many enzymes in metabolic pathways. Importantly, repression of acetyl-CoA synthesis promoted oncogenic dedifferentiation and proliferation. Mechanistically, acetyl-CoA synthesis was repressed by the transcription factors TEAD2 and E2A, previously unknown to control acetyl-CoA synthesis. Knockdown of TEAD2 and E2A restored acetyl-CoA levels and inhibited tumor growth. Our findings causally link transcriptional reprogramming of acetyl-CoA metabolism, dedifferentiation, and cancer.
    Keywords:  E2A; HCC; TEAD2; acetyl-CoA metabolism; dedifferentiation; hepatocellular carcinoma; protein acetylation; transcriptional reprogramming
    DOI:  https://doi.org/10.1016/j.molcel.2022.10.027
  34. J Clin Invest. 2022 Nov 15. pii: e161308. [Epub ahead of print]132(22):
    BCL6 is regulated by the MAPK/ELK1 axis and promotes KRAS-driven lung cancer.
    Kun Li, Yanan Liu, Yi Ding, Zhengwei Zhang, Juanjuan Feng, Jiaxin Hu, Jiwei Chen, Zhengke Lian, Yiliang Chen, Kewen Hu, Zhi Chen, Zhenyu Cai, Mingyao Liu, Xiufeng Pang.
      Mutational activation of KRAS is a common oncogenic event in lung cancer, yet effective therapies are still lacking. Here, we identify B cell lymphoma 6 (BCL6) as a lynchpin in KRAS-driven lung cancer. BCL6 expression was increased upon KRAS activation in lung tumor tissue in mice and was positively correlated with the expression of KRAS-GTP, the active form of KRAS, in various human cancer cell lines. Moreover, BCL6 was highly expressed in human KRAS-mutant lung adenocarcinomas and was associated with poor patient survival. Mechanistically, the MAPK/ERK/ELK1 signaling axis downstream of mutant KRAS directly regulated BCL6 expression. BCL6 maintained the global expression of prereplication complex components; therefore, BCL6 inhibition induced stalling of the replication fork, leading to DNA damage and growth arrest in KRAS-mutant lung cancer cells. Importantly, BCL6-specific knockout in lungs significantly reduced the tumor burden and mortality in the LSL-KrasG12D/+ lung cancer mouse model. Likewise, pharmacological inhibition of BCL6 significantly impeded the growth of KRAS-mutant lung cancer cells both in vitro and in vivo. In summary, our findings reveal a crucial role of BCL6 in promoting KRAS-addicted lung cancer and suggest BCL6 as a therapeutic target for the treatment of this intractable disease.
    Keywords:  Lung cancer; Oncology; Therapeutics
    DOI:  https://doi.org/10.1172/JCI161308
  35. Semin Cancer Biol. 2022 Oct 28. pii: S1044-579X(22)00209-7. [Epub ahead of print]87 32-47
    Tracing the electron flow in redox metabolism: The appropriate distribution of electrons is essential to maintain redox balance in cancer cells.
    Minfeng Ying, Xun Hu.
      Cancer cells are characterized by sustained proliferation, which requires a huge demand of fuels to support energy production and biosynthesis. Energy is produced by the oxidation of the fuels during catabolism, and biosynthesis is achieved by the reduction of smaller units or precursors. Therefore, the oxidation-reduction (redox) reactions in cancer cells are more active compared to those in the normal counterparts. The higher activity of redox metabolism also induces a more severe oxidative stress, raising the question of how cancer cells maintain the redox balance. In this review, we overview the redox metabolism of cancer cells in an electron-tracing view. The electrons are derived from the nutrients in the tumor microenvironment and released during catabolism. Most of the electrons are transferred to NAD(P) system and then directed to four destinations: energy production, ROS generation, reductive biosynthesis and antioxidant system. The appropriate distribution of these electrons achieved by the function of redox regulation network is essential to maintain redox homeostasis in cancer cells. Interfering with the electron distribution and disrupting redox balance by targeting the redox regulation network may provide therapeutic implications for cancer treatment.
    Keywords:  Antioxidant system; Cancer metabolism; NADPH; ROS; Redox balance
    DOI:  https://doi.org/10.1016/j.semcancer.2022.10.005
  36. Cell Oncol (Dordr). 2022 Nov 19.
    IDH2, a novel target of OGT, facilitates glucose uptake and cellular bioenergy production via NF-κB signaling to promote colorectal cancer progression.
    Xiaoli He, Nan Wu, Renlong Li, Haohao Zhang, Yu Zhao, Yongzhan Nie, Jing Wu.
       BACKGROUND: Although isocitrate dehydrogenase 2 (IDH2) mutations have been the hotspots in recent anticancer studies, the impact of wild-type IDH2 on cancer cell growth and metabolic alterations is still elusive.
    METHODS: IDH2 expression in CRC tissues was evaluated by immunohistochemistry, and the correlation between the expression level and the patient's survival rate was analyzed. Cell functional assays included CCK8 and colony formation for cell proliferation in vitro and ectopic xenograft as in vivo experimental model for tumor progression. A targeted metabolomic procedure was performed by liquid chromatography/tandem mass spectrometry to profile the metabolites from glycolysis and tricarboxylic acid (TCA) cycle. Mitochondrial function was assessed by measuring cellular oxygen consumption (OCR) and mitochondrial membrane potential (ΔΨ). Confocal microscope analysis and Western blotting were applied to detect the expression of GLUT1 and NF-κB signaling. O-GlcNAcylation and the interaction of IDH2 with OGT were confirmed by co-immunoprecipitation, followed by Western blotting analysis.
    RESULTS: IDH2 protein was highly expressed in CRC tissues, and correlated with poor survival of CRC patients. Wild-type IDH2 promoted CRC cell growth in vitro and tumor progression in xenograft mice. Overexpression of wild-type IDH2 significantly increased glycolysis and TCA cycle metabolites, the ratios of NADH/NAD+ and ATP/ADP, OCR and mitochondrial membrane potential (ΔΨ) in CRC cells. Furthermore, α-KG activated NF-κB signaling to promote glucose uptake by upregulating GLUT1. Interesting, O-GlcNAcylation enhanced the protein half-time of IDH2 by inhibiting ubiquitin-mediated proteasome degradation. The O-GlcNAc transferase (OGT)-IDH2 axis promoted CRC progression.
    CONCLUSION: Wild-type IDH2 reprogrammed glucose metabolism and bioenergetic production via the NF-κB signaling pathway to promote CRC development and progression. O-GlcNAcylation of IDH2 elevated the stability of IDH2 protein. And the axis of OGT-IDH2 played an essential promotive role in tumor progression, suggesting a novel potential therapeutic strategy in CRC treatment.
    Keywords:  Glucose uptake; Isocitrate dehydrogenase 2; Mitochondrial bioenergetics; NF-κB signaling; O-GlcNAc transferase; O-GlcNAcylation; Redox status
    DOI:  https://doi.org/10.1007/s13402-022-00740-2
  37. iScience. 2022 Nov 18. 25(11): 105410
    Cytosolic and mitochondrial tRNA synthetase inhibitors increase lifespan in a GCN4/atf-4-dependent manner.
    Christine E Robbins, Bhumil Patel, Danielle L Sawyer, Barrie Wilkinson, Brian K Kennedy, Mark A McCormick.
      Deletion of genes encoding ribosomal proteins extends lifespan in yeast. This increases translation of the functionally conserved transcription factor Gcn4, and lifespan extension in these mutants is GCN4-dependent. Gcn4 is also translationally upregulated by uncharged tRNAs, as are its C aenorhabditis elegans and mammalian functional orthologs. Here, we show that cytosolic tRNA synthetase inhibitors upregulate Gcn4 translation and extend yeast lifespan in a Gcn4-dependent manner. This cytosolic tRNA synthetase inhibitor is also able to extend the lifespan of C. elegans in an atf-4-dependent manner. We show that mitochondrial tRNA synthetase inhibitors greatly extend the lifespan of C. elegans, and this depends on atf-4. This suggests that perturbations of both cytosolic and mitochondrial translation may act in part via the same downstream pathway. These findings establish GCN4 orthologs as conserved longevity factors and, as long-lived mice exhibit elevated ATF4, leave open the possibility that tRNA synthetase inhibitors could also extend lifespan in mammals.
    Keywords:  Biochemistry; Biological sciences; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2022.105410
  38. Nat Metab. 2022 Nov 17.
    Intestinal plasticity and metabolism as regulators of organismal energy homeostasis.
    Ozren Stojanović, Irene Miguel-Aliaga, Mirko Trajkovski.
      The small intestine displays marked anatomical and functional plasticity that includes adaptive alterations in adult gut morphology, enteroendocrine cell profile and their hormone secretion, as well as nutrient utilization and storage. In this Perspective, we examine how shifts in dietary and environmental conditions bring about changes in gut size, and describe how the intestine adapts to changes in internal state, bowel resection and gastric bypass surgery. We highlight the critical importance of these intestinal remodelling processes in maintaining energy balance of the organism, and in protecting the metabolism of other organs. The intestinal resizing is supported by changes in the microbiota composition, and by activation of carbohydrate and fatty acid metabolism, which govern the intestinal stem cell proliferation, intestinal cell fate, as well as survivability of differentiated epithelial cells. The discovery that intestinal remodelling is part of the normal physiological adaptation to various triggers, and the potential for harnessing the reversible gut plasticity, in our view, holds extraordinary promise for developing therapeutic approaches against metabolic and inflammatory diseases.
    DOI:  https://doi.org/10.1038/s42255-022-00679-6
  39. Mol Cell. 2022 Nov 17. pii: S1097-2765(22)01015-2. [Epub ahead of print]82(22): 4196-4198
    Acetyl-CoA, protein acetylation, and liver cancer.
    Zhengming Wu, Kun-Liang Guan.
      Using multi-omics approaches, Park et al. show that reduced cellular acetyl-CoA and protein hypoacetylation promote liver cancer growth and dedifferentiation.
    DOI:  https://doi.org/10.1016/j.molcel.2022.10.015
  40. Biosens Bioelectron. 2022 Oct 29. pii: S0956-5663(22)00866-1. [Epub ahead of print]220 114826
    A bioluminescent-based probe for in vivo non-invasive monitoring of nicotinamide riboside uptake reveals a link between metastasis and NAD+ metabolism.
    Tamara Maric, Arkadiy Bazhin, Pavlo Khodakivskyi, Georgy Mikhaylov, Ekaterina Solodnikova, Aleksey Yevtodiyenko, Greta Maria Paola Giordano Attianese, George Coukos, Melita Irving, Magali Joffraud, Carles Cantó, Elena Goun.
      Nicotinamide riboside (NR) is a form of vitamin B3 and is one of the most studied compounds for the restoration of cellular NAD+ levels demonstrating clinical potential in many metabolic and age-related disorders. Despite its wide commercial availability as a powerful nutraceutical, our understanding of NR uptake by different cells and tissues is greatly limited by the lack of noninvasive in vivo imaging tools limiting its clinical translation. Here, we report the development and validation of a bioluminescent NR uptake probe (BiNR) for non-invasive longitudinal imaging of NR uptake both in vitro and in vivo. In addition, we optimized an assay that allows monitoring of NR flux without the need to transfect cells with the luciferase gene, enabling the use of the BiNR probe in clinical samples, as demonstrated with human T cells. Lastly, we used BiNR to investigate the role of NR uptake in cancer prevalence and metastases formation in triple negative breast cancer (TNBC) animal model. Our results demonstrate that NR supplementation results in a significant increase in cancer prevalence and metastases of TNBC to the brain. These results outline the important role of powerful nutraceuticals like NR in cancer metabolism and the need to personalize their use in certain patient populations.
    Keywords:  Brain metastases; Cancer prevalence; Human T cells; In vivo noninvasive bioluminescent imaging; NR supplementation; Nicotinamide riboside (NR) uptake
    DOI:  https://doi.org/10.1016/j.bios.2022.114826
  41. Proteomics. 2022 Nov 18. e2100308
    A Tale of Two Lipids: Lipid Unsaturation Commands Ferroptosis Sensitivity.
    Jason Rodencal, Scott J Dixon.
      Membrane lipids play important roles in the regulation of cell fate, including the execution of ferroptosis. Ferroptosis is a non-apoptotic cell death mechanism defined by iron-dependent membrane lipid peroxidation. Phospholipids containing polyunsaturated fatty acids (PUFAs) are highly vulnerable to peroxidation and are essential for ferroptosis execution. By contrast, the incorporation of less oxidizable monounsaturated fatty acids (MUFAs) in membrane phospholipids protects cells from ferroptosis. The enzymes and pathways that govern PUFA and MUFA metabolism therefore play a critical role in determining cellular sensitivity to ferroptosis. Here, we review three lipid metabolic processes fatty acid biosynthesis, ether lipid biosynthesis, and phospholipid remodeling-that govern ferroptosis sensitivity by regulating the balance of PUFAs and MUFAs in membrane phospholipids. This article is protected by copyright. All rights reserved.
    Keywords:  PUFA; ether lipid; ferroptosis; iron; membrane; necrosis
    DOI:  https://doi.org/10.1002/pmic.202100308
  42. iScience. 2022 Nov 18. 25(11): 105431
    Endogenous metabolism in endothelial and immune cells generates most of the tissue vitamin B3 (nicotinamide).
    Julianna D Zeidler, Claudia C S Chini, Karina S Kanamori, Sonu Kashyap, Jair M Espindola-Netto, Katie Thompson, Gina Warner, Fernanda S Cabral, Thais R Peclat, Lilian Sales Gomez, Sierra A Lopez, Miles K Wandersee, Renee A Schoon, Kimberly Reid, Keir Menzies, Felipe Beckedorff, Joel M Reid, Sebastian Brachs, Ralph G Meyer, Mirella L Meyer-Ficca, Eduardo Nunes Chini.
      In mammals, nicotinamide (NAM) is the primary NAD precursor available in circulation, a signaling molecule, and a precursor for methyl-nicotinamide (M-NAM) synthesis. However, our knowledge about how the body regulates tissue NAM levels is still limited. Here we demonstrate that dietary vitamin B3 partially regulates plasma NAM and NAM-derived metabolites, but not their tissue levels. We found that NAD de novo synthesis from tryptophan contributes to plasma and tissue NAM, likely by providing substrates for NAD-degrading enzymes. We also demonstrate that tissue NAM is mainly generated by endogenous metabolism and that the NADase CD38 is the main enzyme that produces tissue NAM. Tissue-specific CD38-floxed mice revealed that CD38 activity on endothelial and immune cells is the major contributor to tissue steady-state levels of NAM in tissues like spleen and heart. Our findings uncover the presence of different pools of NAM in the body and a central role for CD38 in regulating tissue NAM levels.
    Keywords:  Biochemistry; Biological sciences; Immunology; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2022.105431
  43. Proc Natl Acad Sci U S A. 2022 Nov 22. 119(47): e2206923119
    PAHSAs reduce cellular senescence and protect pancreatic beta cells from metabolic stress through regulation of Mdm2/p53.
    Maria F Rubin de Celis, Ruben Garcia-Martin, Ismail Syed, Jennifer Lee, Cristina Aguayo-Mazzucato, Susan Bonner-Weir, Barbara B Kahn.
      Senescence in pancreatic beta cells plays a major role in beta cell dysfunction, which leads to impaired glucose homeostasis and diabetes. Therefore, prevention of beta cell senescence could reduce the risk of diabetes. Treatment of nonobese diabetic (NOD) mice, a model of type 1 autoimmune diabetes (T1D), with palmitic acid hydroxy stearic acids (PAHSAs), a novel class of endogenous lipids with antidiabetic and antiinflammatory effects, delays the onset and reduces the incidence of T1D from 82% with vehicle treatment to 35% with PAHSAs. Here, we show that a major mechanism by which PAHSAs protect islets of the NOD mice is by directly preventing and reversing the initial steps of metabolic stress-induced senescence. In vitro PAHSAs increased Mdm2 expression, which decreases the stability of p53, a key inducer of senescence-related genes. In addition, PAHSAs enhanced expression of protective genes, such as those regulating DNA repair and glutathione metabolism and promoting autophagy. We demonstrate the translational relevance by showing that PAHSAs prevent and reverse early stages of senescence in metabolically stressed human islets by the same Mdm2 mechanism. Thus, a major mechanism for the dramatic effect of PAHSAs in reducing the incidence of type 1 diabetes in NOD mice is decreasing cellular senescence; PAHSAs may have a similar benefit in humans.
    Keywords:  cellular senescence; diabetes; lipids; metabolic stress; pancreatic islets
    DOI:  https://doi.org/10.1073/pnas.2206923119
  44. Nat Metab. 2022 Nov 14.
    Food odor perception promotes systemic lipid utilization.
    Hiroshi Tsuneki, Masanori Sugiyama, Toshihiro Ito, Kiyofumi Sato, Hiroki Matsuda, Kengo Onishi, Koharu Yubune, Yukina Matsuoka, Sanaka Nagai, Towa Yamagishi, Takahiro Maeda, Kosuke Honda, Akira Okekawa, Shiro Watanabe, Keisuke Yaku, Daisuke Okuzaki, Ryota Otsubo, Masanori Nomoto, Kaoru Inokuchi, Takashi Nakagawa, Tsutomu Wada, Teruhito Yasui, Toshiyasu Sasaoka.
      Food cues during fasting elicit Pavlovian conditioning to adapt for anticipated food intake. However, whether the olfactory system is involved in metabolic adaptations remains elusive. Here we show that food-odor perception promotes lipid metabolism in male mice. During fasting, food-odor stimulation is sufficient to increase serum free fatty acids via adipose tissue lipolysis in an olfactory-memory-dependent manner, which is mediated by the central melanocortin and sympathetic nervous systems. Additionally, stimulation with a food odor prior to refeeding leads to enhanced whole-body lipid utilization, which is associated with increased sensitivity of the central agouti-related peptide system, reduced sympathetic activity and peripheral tissue-specific metabolic alterations, such as an increase in gastrointestinal lipid absorption and hepatic cholesterol turnover. Finally, we show that intermittent fasting coupled with food-odor stimulation improves glycemic control and prevents insulin resistance in diet-induced obese mice. Thus, olfactory regulation is required for maintaining metabolic homeostasis in environments with either an energy deficit or energy surplus, which could be considered as part of dietary interventions against metabolic disorders.
    DOI:  https://doi.org/10.1038/s42255-022-00673-y
  45. Cancer Res. 2022 Nov 15. 82(22): 4124-4125
    Running to Outcompete Metastasis.
    Marwa Zerhouni, Elena Piskounova.
      The role of exercise in cancer progression is an emerging field of research, with intriguing evidence for physical activity playing an inhibitory role in cancer onset. In their recent publication, Sheinboim and colleagues demonstrate the impact of physical exercise on melanoma primary tumor growth and metastasis. They establish that physical exercise decreases metastatic spread, using both human epidemiologic data and in vivo models of melanoma metastasis. Systemic metabolic reprogramming of organs, induced by exercise, leads to a decrease in melanoma growth and progression as healthy organs are able to outcompete melanoma cells for nutrients. Exercise led to systemic metabolic changes in carbohydrate metabolism, glycolysis, and oxidative phosphorylation as well as mitochondrial biogenesis. Interestingly, the "metabolic shield" created by exercise could be reversed using the mTOR inhibitor rapamycin. This study highlights the importance of metabolic plasticity in metastasis and uncovers a direct link between systemic metabolic reprogramming and mTOR signaling. Overall, the study by Sheinboim and colleagues provides a more detailed understanding of the metastatic requirements in the context of energy and nutrient availability and the impact of exercise on cancer progression, highlighting novel opportunities for therapeutic intervention. See related article by Sheinboim et al., p. 4164.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-2898
  46. Nat Commun. 2022 Nov 18. 13(1): 7078
    Cancer cell survival depends on collagen uptake into tumor-associated stroma.
    Kuo-Sheng Hsu, James M Dunleavey, Christopher Szot, Liping Yang, Mary Beth Hilton, Karen Morris, Steven Seaman, Yang Feng, Emily M Lutz, Robert Koogle, Francesco Tomassoni-Ardori, Saurabh Saha, Xiaoyan M Zhang, Enrique Zudaire, Pradip Bajgain, Joshua Rose, Zhongyu Zhu, Dimiter S Dimitrov, Frank Cuttitta, Nancy J Emenaker, Lino Tessarollo, Brad St Croix.
      Collagen I, the most abundant protein in humans, is ubiquitous in solid tumors where it provides a rich source of exploitable metabolic fuel for cancer cells. While tumor cells were unable to exploit collagen directly, here we show they can usurp metabolic byproducts of collagen-consuming tumor-associated stroma. Using genetically engineered mouse models, we discovered that solid tumor growth depends upon collagen binding and uptake mediated by the TEM8/ANTXR1 cell surface protein in tumor-associated stroma. Tumor-associated stromal cells processed collagen into glutamine, which was then released and internalized by cancer cells. Under chronic nutrient starvation, a condition driven by the high metabolic demand of tumors, cancer cells exploited glutamine to survive, an effect that could be reversed by blocking collagen uptake with TEM8 neutralizing antibodies. These studies reveal that cancer cells exploit collagen-consuming stromal cells for survival, exposing an important vulnerability across solid tumors with implications for developing improved anticancer therapy.
    DOI:  https://doi.org/10.1038/s41467-022-34643-5
  47. Nat Rev Cancer. 2022 Nov 14.
    Tumour-derived D-2HG blocks T cell cytotoxicity.
    Joseph Willson.
      
    DOI:  https://doi.org/10.1038/s41568-022-00534-6
  48. Nat Rev Endocrinol. 2022 Nov 17.
    Macrophage mitochondrial levels of iron affect adipose tissue function in obesity.
    Olivia Tysoe.
      
    DOI:  https://doi.org/10.1038/s41574-022-00781-5
  49. Biochim Biophys Acta Bioenerg. 2022 Nov 14. pii: S0005-2728(22)00406-6. [Epub ahead of print] 148936
    Alternative respiratory oxidases to study the animal electron transport chain.
    Pablo Hernansanz-Agustín, José Antonio Enríquez.
      Oxidative phosphorylation is a common process to most organisms in which the main function is to generate an electrochemical gradient across the inner mitochondrial membrane (IMM) and to make energy available to the cell. However, plants, many fungi and some animals maintain non-energy conserving oxidases which serve as a bypass to coupled respiration. Namely, the alternative NADH:ubiquinone oxidoreductase NDI1, present in the complex I (CI)-lacking Saccharomyces cerevisiae, and the alternative oxidase, ubiquinol:oxygen oxidoreductase AOX, present in many organisms across different kingdoms. In the last few years, these alternative oxidases have been used to dissect previously indivisible processes in bioenergetics and have helped to discover, understand, and corroborate important processes in mitochondria. Here, we review how the use of alternative oxidases have contributed to the knowledge in CI stability, bioenergetics, redox biology, and the implications of their use in current and future research.
    Keywords:  AOX; Alternative oxidase; CoQ pool; Oxphos; ROS
    DOI:  https://doi.org/10.1016/j.bbabio.2022.148936
  50. iScience. 2022 Dec 22. 25(12): 105450
    Inference of metabolic fluxes in nutrient-limited continuous cultures: A Maximum Entropy approach with the minimum information.
    José Antonio Pereiro-Morejón, Jorge Fernandez-de-Cossio-Diaz, Roberto Mulet.
      The study of cellular metabolism is limited by the amount of experimental data available. Formulations able to extract relevant predictions from accessible measurements are needed. Maximum Entropy (ME) inference has been successfully applied to genome-scale models of cellular metabolism, and recent data-driven studies have suggested that in chemostat cultures of Escherichia coli (E. coli), the growth rate and uptake rates of limiting nutrients are the most informative observables. We propose the thesis that this can be explained by the chemostat dynamics, which typically drives nutrient-limited cultures toward observable metabolic states maximally restricted in the dimensions of those fluxes. A practical consequence is that relevant flux observables can now be replaced by culture parameters usually controlled. We test our model by using simulations, and then we apply it to E. coli experimental data where we evaluate the quality of the inference, comparing it to alternative formulations that rest on convex optimization.
    Keywords:  Bioinformatics; Metabolic flux analysis; Systems biology
    DOI:  https://doi.org/10.1016/j.isci.2022.105450
  51. Br J Nutr. 2022 Nov 14. 1-31
    The circadian rhythm regulates branched-chain amino acids metabolism in fast muscle of Chinese perch (Siniperca chuatsi) during short-term fasting by Clock-KLF15-Bcat2 pathway.
    Xin Zhu, Jingjie Liu, Minglang Cai, Lingsheng Bao, Yaxiong Pan, Ping Wu, Wuying Chu, Jianshe Zhang.
      As an internal time keeping mechanism, circadian rhythm plays crucial role in maintaining homeostasis when in response to nutrition change, meanwhile, branched-chain amino acids (BCAAs) in skeletal muscle play an important role in preserving energy homeostasis during fasting. Previous results from our lab suggested that fasting can influence peripheral circadian rhythm and BCAAs metabolism in fish, but the relationship between circadian rhythm and BCAAs metabolism, and whether circadian rhythm regulates BCAAs metabolism to maintain physiological homeostasis during fasting remains unclear. This study shows that the expression of 15 core clock genes, as well as KLF15 and Bcat2 is highly responsive to short-term fasting in fast muscle of Siniperca chuatsi, and the correlation coefficient between Clock and KLF15 expression is enhanced after fasting treatment. Furthermore, we demonstrate that the transcriptional expression of KLF15 is regulated by Clock, and the transcriptional expression of Bcat2 is regulated by KLF15 by using dual-luciferase reporter gene assay and Vivo-Morpholinos mediated gene knockdown technique. Therefore, fasting imposes a dynamic coordination of transcription between the circadian rhythm and BCAAs metabolic pathways. The findings highlight the interaction between circadian rhythm and BCAAs metabolism, and suggest that fasting induces a switch in KLF15 expression through affecting the rhythmic expression of Clock, and then KLF15 promotes the transcription of Bcat2 to enhance the metabolism of BCAAs, thus maintaining energy homeostasis and providing energy for skeletal muscle as well as other tissues.
    Keywords:  Branched-chain amino acids; Catabolism; Circadian rhythm; Energy homeostasis; Short-term fasting
    DOI:  https://doi.org/10.1017/S0007114522003646
  52. Commun Biol. 2022 Nov 17. 5(1): 1258
    A lineage tree-based hidden Markov model quantifies cellular heterogeneity and plasticity.
    Farnaz Mohammadi, Shakthi Visagan, Sean M Gross, Luka Karginov, J C Lagarde, Laura M Heiser, Aaron S Meyer.
      Individual cells can assume a variety of molecular and phenotypic states and recent studies indicate that cells can rapidly adapt in response to therapeutic stress. Such phenotypic plasticity may confer resistance, but also presents opportunities to identify molecular programs that could be targeted for therapeutic benefit. Approaches to quantify tumor-drug responses typically focus on snapshot, population-level measurements. While informative, these methods lack lineage and temporal information, which are particularly critical for understanding dynamic processes such as cell state switching. As new technologies have become available to measure lineage relationships, modeling approaches will be needed to identify the forms of cell-to-cell heterogeneity present in these data. Here we apply a lineage tree-based adaptation of a hidden Markov model that employs single cell lineages as input to learn the characteristic patterns of phenotypic heterogeneity and state transitions. In benchmarking studies, we demonstrated that the model successfully classifies cells within experimentally-tractable dataset sizes. As an application, we analyzed experimental measurements in cancer and non-cancer cell populations under various treatments. We find evidence of multiple phenotypically distinct states, with considerable heterogeneity and unique drug responses. In total, this framework allows for the flexible modeling of single cell heterogeneity across lineages to quantify, understand, and control cell state switching.
    DOI:  https://doi.org/10.1038/s42003-022-04208-9
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