bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2023–09–10
forty-five papers selected by
Christian Frezza, Universität zu Köln
  1. Glycolytic Metabolon Assembly on Mitochondria via Hexokinase O-GlcNAcylation Promotes Metabolic Efficiency.
  2. Lysosomes mediate the mitochondrial UPR via mTORC1-dependent ATF4 phosphorylation.
  3. Peroxisomal compartmentalization of amino acid biosynthesis reactions imposes an upper limit on compartment size.
  4. Inhibition of mitochondrial fatty acid β-oxidation activates mTORC1 pathway and protein synthesis via Gcn5-dependent acetylation of raptor in zebrafish.
  5. Inflammatory mitochondrial nucleic acids as drivers of pathophysiology.
  6. Regulation with cell size ensures mitochondrial DNA homeostasis during cell growth.
  7. Secretion of mitochondrial DNA via exosomes promotes inflammation in Behçet's syndrome.
  8. Mitochondrial leak metabolism induces the Spemann-Mangold Organizer via Hif-1α in Xenopus.
  9. NAD(H) homeostasis underlies host protection mediated by glycolytic myeloid cells in tuberculosis.
  10. Vitamin B6 is governed by the local compartmentalization of metabolic enzymes during growth.
  11. GSK3α Regulates Temporally Dynamic Changes in Ribosomal Proteins upon Amino Acid Starvation in Cancer Cells.
  12. Personalised modelling of clinical heterogeneity between medium-chain acyl-CoA dehydrogenase patients.
  13. The paradox of aging: Aging-related shifts in T cell function and metabolism.
  14. Local and dynamic regulation of neuronal glycolysis in vivo.
  15. Intracellular BAPTA directly inhibits PFKFB3, thereby impeding mTORC1-driven Mcl-1 translation and killing MCL-1-addicted cancer cells.
  16. PTEN activates chaperone-mediated autophagy to regulate metabolism.
  17. METTL3 inhibition enhances anti-tumour immunity.
  18. Subcellular quantitative imaging of metabolites at the organelle level.
  19. eIF3d controls the persistent integrated stress response.
  20. Immunometabolic actions of trabectedin and lurbinectedin on human macrophages: relevance for their anti-tumor activity.
  21. C17orf80 binds the mitochondrial genome to promote its replication.
  22. Sensing mitochondrial DNA stress in cardiotoxicity.
  23. Antigen receptor stimulation induces purifying selection against pathogenic mitochondrial tRNA mutations.
  24. Serine-associated one-carbon metabolic reprogramming: a new anti-cancer therapeutic strategy.
  25. FoxO3 Modulates Circadian Rhythms in Neural Stem Cells.
  26. Metabolic elasticity: A new measure of age.
  27. Fatty acid oxidation regulates cellular senescence by modulating the autophagy-SIRT1 axis.
  28. Comprehensive sub-mitochondrial protein map of the parasitic protist Trypanosoma brucei defines critical features of organellar biology.
  29. A type 2 immune circuit in the stomach controls mammalian adaptation to dietary chitin.
  30. An integrative view on glucagon function and putative role in the progression of pancreatic neuroendocrine tumours (pNETs) and hepatocellular carcinomas (HCC).
  31. A mitochondrial EglN1-AMPKα axis drives breast cancer progression by enhancing metabolic adaptation to hypoxic stress.
  32. Enhanced mitochondrial buffering prevents Ca2+ overload in naked mole-rat brain.
  33. Metabolic FRET sensors in intact organs: Applying spectral unmixing to acquire reliable signals.
  34. Loss of attachment promotes proline accumulation and excretion in cancer cells.
  35. Positron emission tomography imaging of the sodium iodide symporter senses real-time energy stress in vivo.
  36. Epigenetic inheritance is unfaithful at intermediately methylated CpG sites.
  37. A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer.
  38. Creatine supplementation enhances anti-tumor immunity by promoting adenosine triphosphate production in macrophages.
  39. Reducing branched-chain amino acids improves cardiac stress response in mice by decreasing histone H3K23 propionylation.
  40. Advanced neurobiological tools to interrogate metabolism.
  41. Functional epigenomics: chromatin complexity untangled.
  42. Single-cell multi-omics identifies chronic inflammation as a driver of TP53-mutant leukemic evolution.
  43. Spatial metabolomics: from a niche field towards a driver of innovation.
  44. We need to shift the focus of aging research to aging itself.
  45. CLPX regulates mitochondrial fatty acid β-oxidation in liver cells.
  1. bioRxiv. 2023 Aug 26. pii: 2023.08.26.554955. [Epub ahead of print]
    Glycolytic Metabolon Assembly on Mitochondria via Hexokinase O-GlcNAcylation Promotes Metabolic Efficiency.
    Haoming Wang, John Vant, Youjun Wu, Richard Sánchez, Mary Lauren Micou, Andrew Zhang, Vincent Luczak, Seungyoon Blenda Yu, Mirna Jabbo, Seokjun Yoon, Ahmed Abdallah Abushawish, Majid Ghassemian, Eric Griffis, Marc Hammarlund, Abhishek Singharoy, Gulcin Pekkurnaz.
      Glucose is the primary cellular energy substrate and its metabolism via glycolysis is initiated by the rate-limiting enzyme Hexokinase (HK). In energy-demanding tissues like the brain, HK1 is the prominent isoform, primarily localized on mitochondria, crucial for the efficient coupling of glycolysis and oxidative phosphorylation, thereby ensuring optimal energy generation. Here, we reveal a novel regulatory mechanism whereby metabolic sensor enzyme O-GlcNAc transferase (OGT) modulates HK1 activity and its mitochondrial association. OGT catalyzes reversible O-GlcNAcylation, a post-translational modification, influenced by glucose flux-mediated intracellular UDP-GlcNAc concentrations. Dynamic O-GlcNAcylation of HK1's regulatory domain occurs with increased OGT activity, promoting glycolytic metabolon assembly on the outer mitochondrial membrane. This modification enhances HK1's mitochondrial localization, orchestrating glycolytic and mitochondrial ATP production. Mutations in HK1's O-GlcNAcylation site reduce ATP generation, affecting presynaptic vesicle release in neurons. Our findings reveal a new pathway linking neuronal metabolism to mitochondrial function through OGT and glycolytic metabolon formation, and provide important insight into the previously unknown metabolism plasticity mechanism.
    DOI:  https://doi.org/10.1101/2023.08.26.554955
  2. Cell Discov. 2023 Sep 07. 9(1): 92
    Lysosomes mediate the mitochondrial UPR via mTORC1-dependent ATF4 phosphorylation.
    Terytty Yang Li, Qi Wang, Arwen W Gao, Xiaoxu Li, Yu Sun, Adrienne Mottis, Minho Shong, Johan Auwerx.
      Lysosomes are central platforms for not only the degradation of macromolecules but also the integration of multiple signaling pathways. However, whether and how lysosomes mediate the mitochondrial stress response (MSR) remain largely unknown. Here, we demonstrate that lysosomal acidification via the vacuolar H+-ATPase (v-ATPase) is essential for the transcriptional activation of the mitochondrial unfolded protein response (UPRmt). Mitochondrial stress stimulates v-ATPase-mediated lysosomal activation of the mechanistic target of rapamycin complex 1 (mTORC1), which then directly phosphorylates the MSR transcription factor, activating transcription factor 4 (ATF4). Disruption of mTORC1-dependent ATF4 phosphorylation blocks the UPRmt, but not other similar stress responses, such as the UPRER. Finally, ATF4 phosphorylation downstream of the v-ATPase/mTORC1 signaling is indispensable for sustaining mitochondrial redox homeostasis and protecting cells from ROS-associated cell death upon mitochondrial stress. Thus, v-ATPase/mTORC1-mediated ATF4 phosphorylation via lysosomes links mitochondrial stress to UPRmt activation and mitochondrial function resilience.
    DOI:  https://doi.org/10.1038/s41421-023-00589-1
  3. Nat Commun. 2023 Sep 08. 14(1): 5544
    Peroxisomal compartmentalization of amino acid biosynthesis reactions imposes an upper limit on compartment size.
    Ying Gu, Sara Alam, Snezhana Oliferenko.
      Cellular metabolism relies on just a few redox cofactors. Selective compartmentalization may prevent competition between metabolic reactions requiring the same cofactor. Is such compartmentalization necessary for optimal cell function? Is there an optimal compartment size? Here we probe these fundamental questions using peroxisomal compartmentalization of the last steps of lysine and histidine biosynthesis in the fission yeast Schizosaccharomyces japonicus. We show that compartmentalization of these NAD+ dependent reactions together with a dedicated NADH/NAD+ recycling enzyme supports optimal growth when an increased demand for anabolic reactions taxes cellular redox balance. In turn, compartmentalization constrains the size of individual organelles, with larger peroxisomes accumulating all the required enzymes but unable to support both biosynthetic reactions at the same time. Our reengineering and physiological experiments indicate that compartmentalized biosynthetic reactions are sensitive to the size of the compartment, likely due to scaling-dependent changes within the system, such as enzyme packing density.
    DOI:  https://doi.org/10.1038/s41467-023-41347-x
  4. J Biol Chem. 2023 Sep 01. pii: S0021-9258(23)02248-2. [Epub ahead of print] 105220
    Inhibition of mitochondrial fatty acid β-oxidation activates mTORC1 pathway and protein synthesis via Gcn5-dependent acetylation of raptor in zebrafish.
    Wen-Hao Zhou, Yuan Luo, Rui-Xin Li, Pascal Degrace, Tony Jourdan, Fang Qiao, Li-Qiao Chen, Mei-Ling Zhang, Zhen-Yu Du.
      Pharmacological inhibition of mitochondrial fatty acid oxidation (FAO) has been clinically used to alleviate certain metabolic diseases by remodeling cellular metabolism. However, mitochondrial FAO inhibition also leads to mTORC1 activation-related protein synthesis and tissue hypertrophy, but the mechanism remains unclear. Here, by using a mitochondrial FAO inhibitor (Mildronate or Etomoxir) or knocking out carnitine palmitoyltransferase-1, we revealed that mitochondrial FAO inhibition activated the mTORC1 pathway through Gcn5-dependent Raptor acetylation. Mitochondrial FAO inhibition significantly promoted glucose catabolism and increased intracellular acetyl-CoA levels. In response to the increased intracellular acetyl-CoA, acetyltransferase Gcn5 activated mTORC1 by catalyzing Raptor acetylation through direct interaction. Further investigation also screened Raptor deacetylases HDAC class II and identified HDAC7 as a potential regulator of Raptor. These results provide a possible mechanistic explanation for the mTORC1 activation after mitochondrial FAO inhibition and also bring light to reveal the roles of nutrient metabolic remodeling in regulating protein acetylation by affecting acetyl-CoA production.
    Keywords:  Gcn5; Raptor; acetyl-CoA; mTORC1; mitochondrial FAO inhibition
    DOI:  https://doi.org/10.1016/j.jbc.2023.105220
  5. Clin Transl Med. 2023 Sep;13(9): e1403
    Inflammatory mitochondrial nucleic acids as drivers of pathophysiology.
    Christian G Peace, Alexander Hooftman, Dylan G Ryan.
      
    DOI:  https://doi.org/10.1002/ctm2.1403
  6. Nat Struct Mol Biol. 2023 Sep 07.
    Regulation with cell size ensures mitochondrial DNA homeostasis during cell growth.
    Anika Seel, Francesco Padovani, Moritz Mayer, Alissa Finster, Daniela Bureik, Felix Thoma, Christof Osman, Till Klecker, Kurt M Schmoller.
      To maintain stable DNA concentrations, proliferating cells need to coordinate DNA replication with cell growth. For nuclear DNA, eukaryotic cells achieve this by coupling DNA replication to cell-cycle progression, ensuring that DNA is doubled exactly once per cell cycle. By contrast, mitochondrial DNA replication is typically not strictly coupled to the cell cycle, leaving the open question of how cells maintain the correct amount of mitochondrial DNA during cell growth. Here, we show that in budding yeast, mitochondrial DNA copy number increases with cell volume, both in asynchronously cycling populations and during G1 arrest. Our findings suggest that cell-volume-dependent mitochondrial DNA maintenance is achieved through nuclear-encoded limiting factors, including the mitochondrial DNA polymerase Mip1 and the packaging factor Abf2, whose amount increases in proportion to cell volume. By directly linking mitochondrial DNA maintenance to nuclear protein synthesis and thus cell growth, constant mitochondrial DNA concentrations can be robustly maintained without a need for cell-cycle-dependent regulation.
    DOI:  https://doi.org/10.1038/s41594-023-01091-8
  7. EMBO J. 2023 Sep 04. e112573
    Secretion of mitochondrial DNA via exosomes promotes inflammation in Behçet's syndrome.
    Hachiro Konaka, Yasuhiro Kato, Toru Hirano, Kohei Tsujimoto, JeongHoon Park, Taro Koba, Wataru Aoki, Yusei Matsuzaki, Masayasu Taki, Shohei Koyama, Eri Itotagawa, Tatsunori Jo, Takehiro Hirayama, Taro Kawai, Ken J Ishii, Mitsuyoshi Ueda, Shigehiro Yamaguchi, Shizuo Akira, Takayoshi Morita, Yuichi Maeda, Masayuki Nishide, Sumiyuki Nishida, Yoshihito Shima, Masashi Narazaki, Hyota Takamatsu, Atsushi Kumanogoh.
      Mitochondrial DNA (mtDNA) leakage into the cytoplasm can occur when cells are exposed to noxious stimuli. Specific sensors recognize cytoplasmic mtDNA to promote cytokine production. Cytoplasmic mtDNA can also be secreted extracellularly, leading to sterile inflammation. However, the mode of secretion of mtDNA out of cells upon noxious stimuli and its relevance to human disease remain unclear. Here, we show that pyroptotic cells secrete mtDNA encapsulated within exosomes. Activation of caspase-1 leads to mtDNA leakage from the mitochondria into the cytoplasm via gasdermin-D. Caspase-1 also induces intraluminal membrane vesicle formation, allowing for cellular mtDNA to be taken up and secreted as exosomes. Encapsulation of mtDNA within exosomes promotes a strong inflammatory response that is ameliorated upon exosome biosynthesis inhibition in vivo. We further show that monocytes derived from patients with Behçet's syndrome (BS), a chronic systemic inflammatory disorder, show enhanced caspase-1 activation, leading to exosome-mediated mtDNA secretion and similar inflammation pathology as seen in BS patients. Collectively, our findings support that mtDNA-containing exosomes promote inflammation, providing new insights into the propagation and exacerbation of inflammation in human inflammatory diseases.
    Keywords:  Behçet's syndrome; caspase-1; exosome; mitochondrial DNA; pyroptosis
    DOI:  https://doi.org/10.15252/embj.2022112573
  8. Dev Cell. 2023 Sep 01. pii: S1534-5807(23)00411-2. [Epub ahead of print]
    Mitochondrial leak metabolism induces the Spemann-Mangold Organizer via Hif-1α in Xenopus.
    Alexandra MacColl Garfinkel, Nelli Mnatsakanyan, Jeet H Patel, Andrea E Wills, Amy Shteyman, Peter J S Smith, Kambiz N Alavian, Elizabeth Ann Jonas, Mustafa K Khokha.
      An instructive role for metabolism in embryonic patterning is emerging, although a role for mitochondria is poorly defined. We demonstrate that mitochondrial oxidative metabolism establishes the embryonic patterning center, the Spemann-Mangold Organizer, via hypoxia-inducible factor 1α (Hif-1α) in Xenopus. Hypoxia or decoupling ATP production from oxygen consumption expands the Organizer by activating Hif-1α. In addition, oxygen consumption is 20% higher in the Organizer than in the ventral mesoderm, indicating an elevation in mitochondrial respiration. To reconcile increased mitochondrial respiration with activation of Hif-1α, we discovered that the "free" c-subunit ring of the F1Fo ATP synthase creates an inner mitochondrial membrane leak, which decouples ATP production from respiration at the Organizer, driving Hif-1α activation there. Overexpression of either the c-subunit or Hif-1α is sufficient to induce Organizer cell fates even when β-catenin is inhibited. We propose that mitochondrial leak metabolism could be a general mechanism for activating Hif-1α and Wnt signaling.
    Keywords:  F(1)F(o) ATP synthase; Hif-1α; LRPPRC; Spemann-Mangold Organizer; Wnt/β-catenin signaling; Xenopus; free c-subunit; hypoxia; metabolism; mitochondria
    DOI:  https://doi.org/10.1016/j.devcel.2023.08.015
  9. Nat Commun. 2023 Sep 06. 14(1): 5472
    NAD(H) homeostasis underlies host protection mediated by glycolytic myeloid cells in tuberculosis.
    Hayden T Pacl, Krishna C Chinta, Vineel P Reddy, Sajid Nadeem, Ritesh R Sevalkar, Kievershen Nargan, Kapongo Lumamba, Threnesan Naidoo, Joel N Glasgow, Anupam Agarwal, Adrie J C Steyn.
      Mycobacterium tuberculosis (Mtb) disrupts glycolytic flux in infected myeloid cells through an unclear mechanism. Flux through the glycolytic pathway in myeloid cells is inextricably linked to the availability of NAD+, which is maintained by NAD+ salvage and lactate metabolism. Using lung tissue from tuberculosis (TB) patients and myeloid deficient LDHA (LdhaLysM-/-) mice, we demonstrate that glycolysis in myeloid cells is essential for protective immunity in TB. Glycolytic myeloid cells are essential for the early recruitment of multiple classes of immune cells and IFNγ-mediated protection. We identify NAD+ depletion as central to the glycolytic inhibition caused by Mtb. Lastly, we show that the NAD+ precursor nicotinamide exerts a host-dependent, antimycobacterial effect, and that nicotinamide prophylaxis and treatment reduce Mtb lung burden in mice. These findings provide insight into how Mtb alters host metabolism through perturbation of NAD(H) homeostasis and reprogramming of glycolysis, highlighting this pathway as a potential therapeutic target.
    DOI:  https://doi.org/10.1038/s41467-023-40545-x
  10. Sci Adv. 2023 Sep 08. 9(36): eadi2232
    Vitamin B6 is governed by the local compartmentalization of metabolic enzymes during growth.
    Carolina N Franco, Laurence J Seabrook, Steven T Nguyen, Ying Yang, Melissa Campos, Qi Fan, Andrew C Cicchetto, Mei Kong, Heather R Christofk, Lauren V Albrecht.
      Vitamin B6 is a vital micronutrient across cell types and tissues, and dysregulated B6 levels contribute to human disease. Despite its importance, how B6 vitamer levels are regulated is not well understood. Here, we provide evidence that B6 dynamics are rapidly tuned by precise compartmentation of pyridoxal kinase (PDXK), the rate-limiting B6 enzyme. We show that canonical Wnt rapidly led to the accumulation of inactive B6 by shunting cytosolic PDXK into lysosomes. PDXK was modified with methyl-arginine Degron (MrDegron), a protein tag for lysosomes, which enabled delivery via microautophagy. Hyperactive lysosomes resulted in the continuous degradation of PDXK and B6 deficiency that promoted proliferation in Wnt-driven colorectal cancer (CRC) cells. Pharmacological or genetic disruption of the coordinated MrDegron proteolytic pathway was sufficient to reduce CRC survival in cells and organoid models. In sum, this work contributes to the repertoire of micronutrient-regulated processes that enable cancer cell growth and provides insight into the functional impact of B6 deficiencies for survival.
    DOI:  https://doi.org/10.1126/sciadv.adi2232
  11. Int J Mol Sci. 2023 Aug 26. pii: 13260. [Epub ahead of print]24(17):
    GSK3α Regulates Temporally Dynamic Changes in Ribosomal Proteins upon Amino Acid Starvation in Cancer Cells.
    Lorent Loxha, Nurul Khalida Ibrahim, Anna Sophie Stasche, Büsra Cinar, Tim Dolgner, Julia Niessen, Sabine Schreek, Beate Fehlhaber, Michael Forster, Martin Stanulla, Laura Hinze.
      Amino acid availability is crucial for cancer cells' survivability. Leukemia and colorectal cancer cells have been shown to resist asparagine depletion by utilizing GSK3-dependent proteasomal degradation, termed the Wnt-dependent stabilization of proteins (Wnt/STOP), to replenish their amino acid pool. The inhibition of GSK3α halts the sourcing of amino acids, which subsequently leads to cancer cell vulnerability toward asparaginase therapy. However, resistance toward GSK3α-mediated protein breakdown can occur, whose underlying mechanism is poorly understood. Here, we set out to define the mechanisms driving dependence toward this degradation machinery upon asparagine starvation in cancer cells. We show the independence of known stress response pathways including the integrated stress response mediated with GCN2. Additionally, we demonstrate the independence of changes in cell cycle progression and expression levels of the asparagine-synthesizing enzyme ASNS. Instead, RNA sequencing revealed that GSK3α inhibition and asparagine starvation leads to the temporally dynamic downregulation of distinct ribosomal proteins, which have been shown to display anti-proliferative functions. Using a CRISPR/Cas9 viability screen, we demonstrate that the downregulation of these specific ribosomal proteins can rescue cell death upon GSK3α inhibition and asparagine starvation. Thus, our findings suggest the vital role of the previously unrecognized regulation of ribosomal proteins in bridging GSK3α activity and tolerance of asparagine starvation.
    Keywords:  GSK3α; Wnt/STOP; acute leukemia; amino acid starvation; asparaginase; cancer; colorectal cancer; gene regulation; metabolism; ribosomal proteins
    DOI:  https://doi.org/10.3390/ijms241713260
  12. BMC Biol. 2023 Sep 04. 21(1): 184
    Personalised modelling of clinical heterogeneity between medium-chain acyl-CoA dehydrogenase patients.
    Christoff Odendaal, Emmalie A Jager, Anne-Claire M F Martines, Marcel A Vieira-Lara, Nicolette C A Huijkman, Ligia A Kiyuna, Albert Gerding, Justina C Wolters, Rebecca Heiner-Fokkema, Karen van Eunen, Terry G J Derks, Barbara M Bakker.
       BACKGROUND: Monogenetic inborn errors of metabolism cause a wide phenotypic heterogeneity that may even differ between family members carrying the same genetic variant. Computational modelling of metabolic networks may identify putative sources of this inter-patient heterogeneity. Here, we mainly focus on medium-chain acyl-CoA dehydrogenase deficiency (MCADD), the most common inborn error of the mitochondrial fatty acid oxidation (mFAO). It is an enigma why some MCADD patients-if untreated-are at risk to develop severe metabolic decompensations, whereas others remain asymptomatic throughout life. We hypothesised that an ability to maintain an increased free mitochondrial CoA (CoASH) and pathway flux might distinguish asymptomatic from symptomatic patients.
    RESULTS: We built and experimentally validated, for the first time, a kinetic model of the human liver mFAO. Metabolites were partitioned according to their water solubility between the bulk aqueous matrix and the inner membrane. Enzymes are also either membrane-bound or in the matrix. This metabolite partitioning is a novel model attribute and improved predictions. MCADD substantially reduced pathway flux and CoASH, the latter due to the sequestration of CoA as medium-chain acyl-CoA esters. Analysis of urine from MCADD patients obtained during a metabolic decompensation showed an accumulation of medium- and short-chain acylcarnitines, just like the acyl-CoA pool in the MCADD model. The model suggested some rescues that increased flux and CoASH, notably increasing short-chain acyl-CoA dehydrogenase (SCAD) levels. Proteome analysis of MCADD patient-derived fibroblasts indeed revealed elevated levels of SCAD in a patient with a clinically asymptomatic state. This is a rescue for MCADD that has not been explored before. Personalised models based on these proteomics data confirmed an increased pathway flux and CoASH in the model of an asymptomatic patient compared to those of symptomatic MCADD patients.
    CONCLUSIONS: We present a detailed, validated kinetic model of mFAO in human liver, with solubility-dependent metabolite partitioning. Personalised modelling of individual patients provides a novel explanation for phenotypic heterogeneity among MCADD patients. Further development of personalised metabolic models is a promising direction to improve individualised risk assessment, management and monitoring for inborn errors of metabolism.
    Keywords:  Inborn error of metabolism; Kinetic modelling; Medium-chain acyl-CoA dehydrogenase deficiency; Metabolite partitioning; Mitochondrial fatty acid oxidation; Personalised medicine; Phenotypic heterogeneity
    DOI:  https://doi.org/10.1186/s12915-023-01652-9
  13. Semin Immunol. 2023 Aug 31. pii: S1044-5323(23)00125-2. [Epub ahead of print]70 101834
    The paradox of aging: Aging-related shifts in T cell function and metabolism.
    Kylie M Quinn, Daniela M Vicencio, Nicole L La Gruta.
      T cell survival, differentiation after stimulation, and function are intrinsically linked to distinct cellular metabolic states. The ability of T cells to readily transition between metabolic states enables flexibility to meet the changing energy demands defined by distinct effector states or T cell lineages. Immune aging is characterized, in part, by the loss of naïve T cells, accumulation of senescent T cells, severe dysfunction in memory phenotype T cells in particular, and elevated levels of inflammatory cytokines, or 'inflammaging'. Here, we review our current understanding of the phenotypic and functional changes that occur with aging in T cells, and how they relate to metabolic changes in the steady state and after T cell activation. We discuss the apparent contradictions in the aging T cell phenotype - where enhanced differentiation states and metabolic profiles in the steady state can correspond to a diminished capacity to adapt metabolically and functionally after T cell activation. Finally, we discuss key recent studies that indicate the enormous potential for aged T cell metabolism to induce systemic inflammaging and organism-wide multimorbidity, resulting in premature death.
    Keywords:  Aging; Metabolism; Organismal aging; T cell dysfunction; T cells; Unconventional T cells
    DOI:  https://doi.org/10.1016/j.smim.2023.101834
  14. bioRxiv. 2023 Aug 26. pii: 2023.08.25.554774. [Epub ahead of print]
    Local and dynamic regulation of neuronal glycolysis in vivo.
    Aaron D Wolfe, John N Koberstein, Chadwick B Smith, Melissa L Stewart, Marc Hammarlund, Anthony Hyman, Philip Js Stork, Richard Goodman, Daniel A Colón-Ramos.
      Energy metabolism supports neuronal function. While it is well established that changes in energy metabolism underpin brain plasticity and function, less is known about how individual neurons modulate their metabolic states to meet varying energy demands. This is because most approaches used to examine metabolism in living organisms lack the resolution to visualize energy metabolism within individual circuits, cells, or subcellular regions. Here we adapted a biosensor for glycolysis, HYlight, for use in C. elegans to image dynamic changes in glycolysis within individual neurons and in vivo . We determined that neurons perform glycolysis cell-autonomously, and modulate glycolytic states upon energy stress. By examining glycolysis in specific neurons, we documented a neuronal energy landscape comprising three general observations: 1) glycolytic states in neurons are diverse across individual cell types; 2) for a given condition, glycolytic states within individual neurons are reproducible across animals; and 3) for varying conditions of energy stress, glycolytic states are plastic and adapt to energy demands. Through genetic analyses, we uncovered roles for regulatory enzymes and mitochondrial localization in the cellular and subcellular dynamic regulation of glycolysis. Our study demonstrates the use of a single-cell glycolytic biosensor to examine how energy metabolism is distributed across cells and coupled to dynamic states of neuronal function, and uncovers new relationships between neuronal identities and metabolic landscapes in vivo .
    Significance statement: While it is generally accepted that energy metabolism underpins neuronal function, how it is distributed and dynamically regulated in different tissues of the brain to meet varying energy demands is not well understood. Here we utilized a fluorescent biosensor, HYlight, to observe glycolytic metabolism at cellular and subcellular scales in vivo . By leveraging both the stereotyped identities of individual neurons in C. elegans, and genetic tools for manipulating glycolytic metabolism, we determined that neurons perform and dynamically regulate glycolysis to match changing cellular demands for energy. Our findings support a model whereby glycolytic states should be considered distinct and related to individual neuron identities in vivo , and introduce new questions about the interconnected nature of metabolism and neuronal function.
    DOI:  https://doi.org/10.1101/2023.08.25.554774
  15. Cell Death Dis. 2023 Sep 08. 14(9): 600
    Intracellular BAPTA directly inhibits PFKFB3, thereby impeding mTORC1-driven Mcl-1 translation and killing MCL-1-addicted cancer cells.
    Flore Sneyers, Martijn Kerkhofs, Femke Speelman-Rooms, Kirsten Welkenhuyzen, Rita La Rovere, Ahmed Shemy, Arnout Voet, Guy Eelen, Mieke Dewerchin, Stephen W G Tait, Bart Ghesquière, Martin D Bootman, Geert Bultynck.
      Intracellular Ca2+ signals control several physiological and pathophysiological processes. The main tool to chelate intracellular Ca2+ is intracellular BAPTA (BAPTAi), usually introduced into cells as a membrane-permeant acetoxymethyl ester (BAPTA-AM). Previously, we demonstrated that BAPTAi enhanced apoptosis induced by venetoclax, a BCL-2 antagonist, in diffuse large B-cell lymphoma (DLBCL). This finding implied a novel interplay between intracellular Ca2+ signaling and anti-apoptotic BCL-2 function. Hence, we set out to identify the underlying mechanisms by which BAPTAi enhances cell death in B-cell cancers. In this study, we discovered that BAPTAi alone induced apoptosis in hematological cancer cell lines that were highly sensitive to S63845, an MCL-1 antagonist. BAPTAi provoked a rapid decline in MCL-1-protein levels by inhibiting mTORC1-driven Mcl-1 translation. These events were not a consequence of cell death, as BAX/BAK-deficient cancer cells exhibited similar downregulation of mTORC1 activity and MCL-1-protein levels. Next, we investigated how BAPTAi diminished mTORC1 activity and identified its ability to impair glycolysis by directly inhibiting 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3) activity, a previously unknown effect of BAPTAi. Notably, these effects were also induced by a BAPTAi analog with low affinity for Ca2+. Consequently, our findings uncover PFKFB3 inhibition as an Ca2+-independent mechanism through which BAPTAi impairs cellular metabolism and ultimately compromises the survival of MCL-1-dependent cancer cells. These findings hold two important implications. Firstly, the direct inhibition of PFKFB3 emerges as a key regulator of mTORC1 activity and a promising target in MCL-1-dependent cancers. Secondly, cellular effects caused by BAPTAi are not necessarily related to Ca2+ signaling. Our data support the need for a reassessment of the role of Ca2+ in cellular processes when findings were based on the use of BAPTAi.
    DOI:  https://doi.org/10.1038/s41419-023-06120-4
  16. Autophagy. 2023 Sep 08. 1-2
    PTEN activates chaperone-mediated autophagy to regulate metabolism.
    S Joseph Endicott, Richard A Miller.
      PTEN is a negative modulator of the INS-PI3K-AKT pathway and is an essential regulator of metabolism and cell growth. PTEN is one of the most commonly mutated tumor suppressors in cancer. However, PTEN overexpression extends the lifespan of both sexes of mice. We recently showed that PTEN is necessary and sufficient to activate chaperone-mediated autophagy (CMA) in the mouse liver and cultured cells. Selective protein degradation via CMA is required to suppress glycolysis and fatty acid synthesis when PTEN is overexpressed. Thus, activation of CMA downstream of PTEN might modulate health and metabolism through selective degradation of key metabolic enzymes.
    Keywords:  Aging; PTEN; autophagy; chaperone-mediated autophagy; metabolism
    DOI:  https://doi.org/10.1080/15548627.2023.2255966
  17. Nat Rev Cancer. 2023 Sep 05.
    METTL3 inhibition enhances anti-tumour immunity.
    Gabrielle Brewer.
      
    DOI:  https://doi.org/10.1038/s41568-023-00621-2
  18. Nat Metab. 2023 Sep 07.
    Subcellular quantitative imaging of metabolites at the organelle level.
    Gary Siuzdak.
      
    DOI:  https://doi.org/10.1038/s42255-023-00882-z
  19. Mol Cell. 2023 Aug 30. pii: S1097-2765(23)00643-3. [Epub ahead of print]
    eIF3d controls the persistent integrated stress response.
    Shaoni Mukhopadhyay, Maria E Amodeo, Amy S Y Lee.
      Cells respond to intrinsic and extrinsic stresses by reducing global protein synthesis and activating gene programs necessary for survival. Here, we show that the integrated stress response (ISR) is driven by the non-canonical cap-binding protein eIF3d that acts as a critical effector to control core stress response orchestrators, the translation factor eIF2α and the transcription factor ATF4. We find that during persistent stress, eIF3d activates the translation of the kinase GCN2, inducing eIF2α phosphorylation and inhibiting general protein synthesis. In parallel, eIF3d upregulates the m6A demethylase ALKBH5 to drive 5' UTR-specific demethylation of stress response genes, including ATF4. Ultimately, this cascade converges on ATF4 expression by increasing mRNA engagement of translation machinery and enhancing ribosome bypass of upstream open reading frames (uORFs). Our results reveal that eIF3d acts in a life-or-death decision point during chronic stress and uncover a synergistic signaling mechanism in which translational cascades complement transcriptional amplification to control essential cellular processes.
    Keywords:  ATF4; GCN2; RNA methylation; eIF3d; integrated stress response; m(6)A; translation regulation
    DOI:  https://doi.org/10.1016/j.molcel.2023.08.008
  20. Front Immunol. 2023 ;14 1211068
    Immunometabolic actions of trabectedin and lurbinectedin on human macrophages: relevance for their anti-tumor activity.
    Adrián Povo-Retana, Marco Fariñas, Rodrigo Landauro-Vera, Marina Mojena, Carlota Alvarez-Lucena, Miguel A Fernández-Moreno, Antonio Castrillo, Juan Vladimir de la Rosa Medina, Sergio Sánchez-García, Carles Foguet, Francesc Mas, Silvia Marin, Marta Cascante, Lisardo Boscá.
      In recent years, the central role of cell bioenergetics in regulating immune cell function and fate has been recognized, giving rise to the interest in immunometabolism, an area of research focused on the interaction between metabolic regulation and immune function. Thus, early metabolic changes associated with the polarization of macrophages into pro-inflammatory or pro-resolving cells under different stimuli have been characterized. Tumor-associated macrophages are among the most abundant cells in the tumor microenvironment; however, it exists an unmet need to study the effect of chemotherapeutics on macrophage immunometabolism. Here, we use a systems biology approach that integrates transcriptomics and metabolomics to unveil the immunometabolic effects of trabectedin (TRB) and lurbinectedin (LUR), two DNA-binding agents with proven antitumor activity. Our results show that TRB and LUR activate human macrophages toward a pro-inflammatory phenotype by inducing a specific metabolic rewiring program that includes ROS production, changes in the mitochondrial inner membrane potential, increased pentose phosphate pathway, lactate release, tricarboxylic acids (TCA) cycle, serine and methylglyoxal pathways in human macrophages. Glutamine, aspartate, histidine, and proline intracellular levels are also decreased, whereas oxygen consumption is reduced. The observed immunometabolic changes explain additional antitumor activities of these compounds and open new avenues to design therapeutic interventions that specifically target the immunometabolic landscape in the treatment of cancer.
    Keywords:  ROS; immunometabolism; lurbinectedin; macrophages; trabectedin
    DOI:  https://doi.org/10.3389/fimmu.2023.1211068
  21. J Cell Biol. 2023 Oct 02. pii: e202302037. [Epub ahead of print]222(10):
    C17orf80 binds the mitochondrial genome to promote its replication.
    Hao Wu, Wenshuo Zhang, Fengli Xu, Kun Peng, Xiaoyu Liu, Wanqiu Ding, Qi Ma, Heping Cheng, Xianhua Wang.
      Serving as the power plant and signaling hub of a cell, mitochondria contain their own genome which encodes proteins essential for energy metabolism and forms DNA-protein assemblies called nucleoids. Mitochondrial DNA (mtDNA) exists in multiple copies within each cell ranging from hundreds to tens of thousands. Maintaining mtDNA homeostasis is vital for healthy cells, and its dysregulation causes multiple human diseases. However, the players involved in regulating mtDNA maintenance are largely unknown though the core components of its replication machinery have been characterized. Here, we identify C17orf80, a functionally uncharacterized protein, as a critical player in maintaining mtDNA homeostasis. C17orf80 primarily localizes to mitochondrial nucleoid foci and exhibits robust double-stranded DNA binding activity throughout the mitochondrial genome, thus constituting a bona fide new mitochondrial nucleoid protein. It controls mtDNA levels by promoting mtDNA replication and plays important roles in mitochondrial metabolism and cell proliferation. Our findings provide a potential target for therapeutics of human diseases associated with defective mtDNA control.
    DOI:  https://doi.org/10.1083/jcb.202302037
  22. Trends Endocrinol Metab. 2023 Sep 04. pii: S1043-2760(23)00165-0. [Epub ahead of print]
    Sensing mitochondrial DNA stress in cardiotoxicity.
    Yang-Nan Ding, Xiaoqiang Tang.
      Cytoplasmic mitochondrial DNA (mtDNA) can trigger the interferon response to promote disease progression, but mtDNA sensing mechanisms remain elusive. Lei et al. have shown that Z-DNA binding protein1 (ZBP1) cooperates with cyclic GMP-AMP synthase (cGAS) to sense Z-form mtDNA and transmit mtDNA stress signals to promote diseases such as cardiotoxicity, providing an important piece of the mtDNA stress landscape.
    Keywords:  Z-DNA; ZBP1; cGAS; cardiotoxicity; mtDNA
    DOI:  https://doi.org/10.1016/j.tem.2023.08.012
  23. JCI Insight. 2023 Sep 08. pii: e167656. [Epub ahead of print]8(17):
    Antigen receptor stimulation induces purifying selection against pathogenic mitochondrial tRNA mutations.
    Jingdian Zhang, Camilla Koolmeister, Jinming Han, Roberta Filograna, Leo Hanke, Monika Àdori, Daniel J Sheward, Sina Teifel, Shreekara Gopalakrishna, Qiuya Shao, Yong Liu, Keying Zhu, Robert A Harris, Gerald McInerney, Ben Murrell, Mike Aoun, Liselotte Bäckdahl, Rikard Holmdahl, Marcin Pekalski, Anna Wedell, Martin Engvall, Anna Wredenberg, Gunilla B Karlsson Hedestam, Xaquin Castro Dopico, Joanna Rorbach.
      Pathogenic mutations in mitochondrial (mt) tRNA genes that compromise oxidative phosphorylation (OXPHOS) exhibit heteroplasmy and cause a range of multisyndromic conditions. Although mitochondrial disease patients are known to suffer from abnormal immune responses, how heteroplasmic mtDNA mutations affect the immune system at the molecular level is largely unknown. Here, in mice carrying pathogenic C5024T in mt-tRNAAla and in patients with mitochondrial encephalomyopathy, lactic acidosis, stroke-like episodes (MELAS) syndrome carrying A3243G in mt-tRNALeu, we found memory T and B cells to have lower pathogenic mtDNA mutation burdens than their antigen-inexperienced naive counterparts, including after vaccination. Pathogenic burden reduction was less pronounced in myeloid compared with lymphoid lineages, despite C5024T compromising macrophage OXPHOS capacity. Rapid dilution of the C5024T mutation in T and B cell cultures could be induced by antigen receptor-triggered proliferation and was accelerated by metabolic stress conditions. Furthermore, we found C5024T to dysregulate CD8+ T cell metabolic remodeling and IFN-γ production after activation. Together, our data illustrate that the generation of memory lymphocytes shapes the mtDNA landscape, wherein pathogenic variants dysregulate the immune response.
    Keywords:  Adaptive immunity; Immunology; Metabolism; Mitochondria
    DOI:  https://doi.org/10.1172/jci.insight.167656
  24. Front Oncol. 2023 ;13 1184626
    Serine-associated one-carbon metabolic reprogramming: a new anti-cancer therapeutic strategy.
    Jing Zhang, Jian Bai, Chen Gong, Jianhua Wang, Yi Cheng, Jing Zhao, Huihua Xiong.
      Tumour metabolism is a major focus of cancer research, and metabolic reprogramming is an important feature of malignant tumours. Serine is an important non-essential amino acid, which is a main resource of one-carbon units in tumours. Cancer cells proliferate more than normal cells and require more serine for proliferation. The cancer-related genes that are involved in serine metabolism also show changes corresponding to metabolic alterations. Here, we reviewed the serine-associated one-carbon metabolism and its potential as a target for anti-tumour therapeutic strategies.
    Keywords:  SERINE; immunotherapy; metabolism reprogramming; molecular targeted therapy; one-carbon units
    DOI:  https://doi.org/10.3389/fonc.2023.1184626
  25. Int J Mol Sci. 2023 Sep 04. pii: 13662. [Epub ahead of print]24(17):
    FoxO3 Modulates Circadian Rhythms in Neural Stem Cells.
    Swip Draijer, Raissa Timmerman, Jesse Pannekeet, Alexandra van Harten, Elham Aida Farshadi, Julius Kemmer, Demy van Gilst, Inês Chaves, Marco F M Hoekman.
      Both FoxO transcription factors and the circadian clock act on the interface of metabolism and cell cycle regulation and are important regulators of cellular stress and stem cell homeostasis. Importantly, FoxO3 preserves the adult neural stem cell population by regulating cell cycle and cellular metabolism and has been shown to regulate circadian rhythms in the liver. However, whether FoxO3 is a regulator of circadian rhythms in neural stem cells remains unknown. Here, we show that loss of FoxO3 disrupts circadian rhythmicity in cultures of neural stem cells, an effect that is mediated via regulation of Clock transcriptional levels. Using Rev-Erbα-VNP as a reporter, we then demonstrate that loss of FoxO3 does not disrupt circadian rhythmicity at the single cell level. A meta-analysis of published data revealed dynamic co-occupancy of multiple circadian clock components within FoxO3 regulatory regions, indicating that FoxO3 is a Clock-controlled gene. Finally, we examined proliferation in the hippocampus of FoxO3-deficient mice and found that loss of FoxO3 delayed the circadian phase of hippocampal proliferation, indicating that FoxO3 regulates correct timing of NSC proliferation. Taken together, our data suggest that FoxO3 is an integral part of circadian regulation of neural stem cell homeostasis.
    Keywords:  FoxO3; cell cycle; circadian rhythms; liver; metabolism; neural stem cell
    DOI:  https://doi.org/10.3390/ijms241713662
  26. Cell Metab. 2023 09 05. pii: S1550-4131(23)00301-7. [Epub ahead of print]35(9): 1495-1497
    Metabolic elasticity: A new measure of age.
    Samuel Bennett, Shogo Sato.
      Promoting healthy aging is contingent on understanding the underlying mechanisms for the age-associated decline in metabolic physiology. Through developing a novel concept of "metabolic elasticity" to evaluate metabolic adaptability in response to cyclical changes in energy balance, Zhou et al. present an impactful gauge of metabolic health that is particularly relevant to aging.
    DOI:  https://doi.org/10.1016/j.cmet.2023.08.006
  27. BMB Rep. 2023 Sep 08. pii: 5938. [Epub ahead of print]
    Fatty acid oxidation regulates cellular senescence by modulating the autophagy-SIRT1 axis.
    Seungyeon Yang, Subin Moon, Soojung Claire Hur, Seung Min Jeong.
      Senescence, a cellular process through which damaged or dysfunctional cells suppress their cell cycle, contributes to aging or age-related functional declines. Cell metabolism has been closely correlated with aging processes and it is widely recognized that metabolic changes underlie cellular alterations with aging. Here, we report that fatty acid oxidation (FAO) serves as a critical regulator of cellular senescence and uncover the underlying mechanism by which FAO inhibition induces senescence. Pharmacological or genetic ablation of FAO results in a p53-dependent induction of cellular senescence in human fibroblasts, whereas enhancing FAO suppresses replicative senescence. We find that FAO inhibition promotes cellular senescence through acetyl-CoA, independent of energy depletion. Mechanistically, the increased formation of autophagosome following FAO inhibition leads to a reduction in SIRT1 protein levels, thereby contributing to senescence induction. Finally, we find that the inhibition of autophagy or the enforced expression of SIRT1 can rescue the induction of senescence as a result of FAO inhibition. Collectively, our study reveals a distinctive role for the FAO-autophagy-SIRT1 axis in the regulation of cellular senescence.
  28. Cell Rep. 2023 Sep 04. pii: S2211-1247(23)01094-X. [Epub ahead of print]42(9): 113083
    Comprehensive sub-mitochondrial protein map of the parasitic protist Trypanosoma brucei defines critical features of organellar biology.
    Jan Pyrih, Michael Hammond, Aline Alves, Samuel Dean, Jack Daniel Sunter, Richard John Wheeler, Keith Gull, Julius Lukeš.
      We have generated a high-confidence mitochondrial proteome (MitoTag) of the Trypanosoma brucei procyclic stage containing 1,239 proteins. For 337 of these, a mitochondrial localization had not been described before. We use the TrypTag dataset as a foundation and take advantage of the properties of the fluorescent protein tag that causes aberrant but fortuitous accumulation of tagged matrix and inner membrane proteins near the kinetoplast (mitochondrial DNA). Combined with transmembrane domain predictions, this characteristic allowed categorization of 1,053 proteins into mitochondrial sub-compartments, the detection of unique matrix-localized fucose and methionine synthesis, and the identification of new kinetoplast proteins, which showed kinetoplast-linked pyrimidine synthesis. Moreover, disruption of targeting signals by tagging allowed mapping of the mode of protein targeting to these sub-compartments, identifying a set of C-tail anchored outer mitochondrial membrane proteins and mitochondrial carriers likely employing multiple target peptides. This dataset represents a comprehensive, updated mapping of the mitochondrion.
    Keywords:  CP: Cell biology; Trypanosoma; fucose; inner mitochondrial membrane; kinetoplast; mitochondrion; protein targeting
    DOI:  https://doi.org/10.1016/j.celrep.2023.113083
  29. Science. 2023 Sep 08. 381(6662): 1092-1098
    A type 2 immune circuit in the stomach controls mammalian adaptation to dietary chitin.
    Do-Hyun Kim, Yilin Wang, Haerin Jung, Rachael L Field, Xinya Zhang, Ta-Chiang Liu, Changqing Ma, James S Fraser, Jonathan R Brestoff, Steven J Van Dyken.
      Dietary fiber improves metabolic health, but host-encoded mechanisms for digesting fibrous polysaccharides are unclear. In this work, we describe a mammalian adaptation to dietary chitin that is coordinated by gastric innate immune activation and acidic mammalian chitinase (AMCase). Chitin consumption causes gastric distension and cytokine production by stomach tuft cells and group 2 innate lymphoid cells (ILC2s) in mice, which drives the expansion of AMCase-expressing zymogenic chief cells that facilitate chitin digestion. Although chitin influences gut microbial composition, ILC2-mediated tissue adaptation and gastrointestinal responses are preserved in germ-free mice. In the absence of AMCase, sustained chitin intake leads to heightened basal type 2 immunity, reduced adiposity, and resistance to obesity. These data define an endogenous metabolic circuit that enables nutrient extraction from an insoluble dietary constituent by enhancing digestive function.
    DOI:  https://doi.org/10.1126/science.add5649
  30. Mol Cell Endocrinol. 2023 Sep 05. pii: S0303-7207(23)00214-9. [Epub ahead of print] 112063
    An integrative view on glucagon function and putative role in the progression of pancreatic neuroendocrine tumours (pNETs) and hepatocellular carcinomas (HCC).
    Bárbara Ferreira, Adrián Heredia, Jacinta Serpa.
      Cancer metabolism research area evolved greatly, however, is still unknown the impact of systemic metabolism control and diet on cancer. It makes sense that systemic regulators of metabolism can act directly on cancer cells and activate signalling, prompting metabolic remodelling needed to sustain cancer cell survival, tumour growth and disease progression. In the present review, we describe the main glucagon functions in the control of glycaemia and of metabolic pathways overall. Furthermore, an integrative view on how glucagon and related signalling pathways can contribute for pancreatic neuroendocrine tumours (pNETs) and hepatocellular carcinomas (HCC) progression, since pancreas and liver are the major organs exposed to higher levels of glucagon, pancreas as a producer and liver as a scavenger. The main objective is to bring to discussion some glucagon-dependent mechanisms by presenting an integrative view on microenvironmental and systemic aspects in pNETs and HCC biology.
    Keywords:  GCGR; Glucagon; HCC; Metabolic remodelling; Signalling pathways; pNETs
    DOI:  https://doi.org/10.1016/j.mce.2023.112063
  31. EMBO J. 2023 Sep 04. e113743
    A mitochondrial EglN1-AMPKα axis drives breast cancer progression by enhancing metabolic adaptation to hypoxic stress.
    Weiwei Jiang, Mengyao Zhang, Chuan Gao, Chaojun Yan, Ronghui Gao, Ziwei He, Xin Wei, Jingjing Xiong, Zilun Ruan, Qian Yang, Jinpeng Li, Qifang Li, Ziyi Zhong, Mengna Zhang, Qianqian Yuan, Hankun Hu, Shuang Wang, Ming-Ming Hu, Cheguo Cai, Gao-Song Wu, Chao Jiang, Ya-Lin Zhang, Chen-Song Zhang, Jing Zhang.
      Mitochondria play essential roles in cancer cell adaptation to hypoxia, but the underlying mechanisms remain elusive. Through mitochondrial proteomic profiling, we here find that the prolyl hydroxylase EglN1 (PHD2) accumulates on mitochondria under hypoxia. EglN1 substrate-binding region in the β2β3 loop is responsible for its mitochondrial translocation and contributes to breast tumor growth. Furthermore, we identify AMP-activated protein kinase alpha (AMPKα) as an EglN1 substrate on mitochondria. The EglN1-AMPKα interaction is essential for their mutual mitochondrial translocation. After EglN1 prolyl-hydroxylates AMPKα under normoxia, they rapidly dissociate following prolyl-hydroxylation, leading to their immediate release from mitochondria. In contrast, hypoxia results in constant EglN1-AMPKα interaction and their accumulation on mitochondria, leading to the formation of a Ca2+ /calmodulin-dependent protein kinase 2 (CaMKK2)-EglN1-AMPKα complex to activate AMPKα phosphorylation, ensuring metabolic homeostasis and breast tumor growth. Our findings identify EglN1 as an oxygen-sensitive metabolic checkpoint signaling hypoxic stress to mitochondria through its β2β3 loop region, suggesting a potential therapeutic target for breast cancer.
    Keywords:  AMPKα; EglN1; hypoxia; metabolic homeostasis; mitochondrial translocation
    DOI:  https://doi.org/10.15252/embj.2023113743
  32. J Physiol. 2023 Sep 05.
    Enhanced mitochondrial buffering prevents Ca2+ overload in naked mole-rat brain.
    Hang Cheng, Guy A Perkins, Saeyeon Ju, Keunyoung Kim, Mark H Ellisman, Matthew E Pamenter.
      Deleterious Ca2+ accumulation is central to hypoxic cell death in the brain of most mammals. Conversely, hypoxia-mediated increases in cytosolic Ca2+ are retarded in hypoxia-tolerant naked mole-rat brain. We hypothesized that naked mole-rat brain mitochondria have an enhanced capacity to buffer exogenous Ca2+ and examined Ca2+ handling in naked mole-rat cortical tissue. We report that naked mole-rat brain mitochondria buffer >2-fold more exogenous Ca2+ than mouse brain mitochondria, and that the half-maximal inhibitory concentration (IC50 ) at which Ca2+ inhibits aerobic oxidative phosphorylation is >2-fold higher in naked mole-rat brain. The primary driving force of Ca2+ uptake is the mitochondrial membrane potential (Δψm ), and the IC50 at which Ca2+ decreases Δψm is ∼4-fold higher in naked mole-rat than mouse brain. The ability of naked mole-rat brain mitochondria to safely retain large volumes of Ca2+ may be due to ultrastructural differences that support the uptake and physical storage of Ca2+ in mitochondria. Specifically, and relative to mouse brain, naked mole-rat brain mitochondria are larger and have higher crista density and increased physical interactions between adjacent mitochondrial membranes, all of which are associated with improved energetic homeostasis and Ca2+ management. We propose that excessive Ca2+ influx into naked mole-rat brain is buffered by physical storage in large mitochondria, which would reduce deleterious Ca2+ overload and may thus contribute to the hypoxia and ischaemia-tolerance of naked mole-rat brain. KEY POINTS: Unregulated Ca2+ influx is a hallmark of hypoxic brain death; however, hypoxia-mediated Ca2+ influx into naked mole-rat brain is markedly reduced relative to mice. This is important because naked mole-rat brain is robustly tolerant against in vitro hypoxia, and because Ca2+ is a key driver of hypoxic cell death in brain. We show that in hypoxic naked mole-rat brain, oxidative capacity and mitochondrial membrane integrity are better preserved following exogenous Ca2+ stress. This is due to mitochondrial buffering of exogenous Ca2+ and is driven by a mitochondrial membrane potential-dependant mechanism. The unique ultrastructure of naked mole-rat brain mitochondria, as a large physical storage space, may support increased Ca2+ buffering and thus hypoxia-tolerance.
    Keywords:  electron transport system; membrane potential; mitochondrial permeability transition pore; oxidative phosphorylation
    DOI:  https://doi.org/10.1113/JP285002
  33. Biol Open. 2023 Sep 06. pii: bio.060030. [Epub ahead of print]
    Metabolic FRET sensors in intact organs: Applying spectral unmixing to acquire reliable signals.
    Lautaro Gándara, Lucía Durrieu, Pablo Wappner.
      In multicellular organisms, metabolic coordination across multiple tissues and cell types is essential to satisfy regionalized energetic requirements and respond coherently to changing environmental conditions. However, most metabolic assays require the destruction of the biological sample, with a concomitant loss of spatial information. Fluorescent metabolic sensors and probes are among the most user-friendly techniques for collecting metabolic information with spatial resolution. In a previous work, we have adapted to an animal system, Drosophila melanogaster, genetically encoded metabolic FRET-based sensors that had been previously developed in single-cell systems. These sensors provide semi-quantitative data on the stationary concentrations of key metabolites of the bioenergetic metabolism: lactate, pyruvate, and 2-oxoglutarate. The use of these sensors in intact organs required the development of an image processing method that minimizes the contribution of spatially complex autofluorescence patterns, that would obscure the FRET signals. In this article, we show step by step how to design FRET-based sensor experiments and how to process the fluorescence signal to obtain reliable FRET values.
    Keywords:  Autofluorescence; Drosophila; FRET; Metabolic sensors; Spectral unmixing
    DOI:  https://doi.org/10.1242/bio.060030
  34. Sci Adv. 2023 Sep 08. 9(36): eadh2023
    Loss of attachment promotes proline accumulation and excretion in cancer cells.
    Steven E Pilley, Marc Hennequart, Anke Vandekeere, Julianna Blagih, Nathalie M Legrave, Sarah-Maria Fendt, Karen H Vousden, Christiaan F Labuschagne.
      Previous studies have revealed a role for proline metabolism in supporting cancer development and metastasis. In this study, we show that many cancer cells respond to loss of attachment by accumulating and secreting proline. Detached cells display reduced proliferation accompanied by a general decrease in overall protein production and de novo amino acid synthesis compared to attached cells. However, proline synthesis was maintained under detached conditions. Furthermore, while overall proline incorporation into proteins was lower in detached cells compared to other amino acids, there was an increased production of the proline-rich protein collagen. The increased excretion of proline from detached cells was also shown to be used by macrophages, an abundant and important component of the tumor microenvironment. Our study suggests that detachment induced accumulation and secretion of proline may contribute to tumor progression by supporting increased production of extracellular matrix and providing proline to surrounding stromal cells.
    DOI:  https://doi.org/10.1126/sciadv.adh2023
  35. Cancer Metab. 2023 Sep 07. 11(1): 14
    Positron emission tomography imaging of the sodium iodide symporter senses real-time energy stress in vivo.
    Piotr Dzien, Agata Mackintosh, Gaurav Malviya, Emma Johnson, Dmitry Soloviev, Gavin Brown, Alejandro Huerta Uribe, Colin Nixon, Scott K Lyons, Oliver Maddocks, Karen Blyth, David Y Lewis.
       BACKGROUND: Tissue environment is critical in determining tumour metabolic vulnerability. However, in vivo drug testing is slow and waiting for tumour growth delay may not be the most appropriate endpoint for metabolic treatments. An in vivo method for measuring energy stress would rapidly determine tumour targeting in a physiologically relevant environment. The sodium-iodide symporter (NIS) is an imaging reporter gene whose protein product co-transports sodium and iodide, and positron emission tomography (PET) radiolabelled anions into the cell. Here, we show that PET imaging of NIS-mediated radiotracer uptake can rapidly visualise tumour energy stress within minutes following in vivo treatment.
    METHODS: We modified HEK293T human embryonic kidney cells, and A549 and H358 lung cancer cells to express transgenic NIS. Next, we subjected these cells and implanted tumours to drugs known to induce metabolic stress to observe the impact on NIS activity and energy charge. We used [18F]tetrafluoroborate positron emission tomography (PET) imaging to non-invasively image NIS activity in vivo.
    RESULTS: NIS activity was ablated by treating HEK293T cells in vitro, with the Na+/K+ ATPase inhibitor digoxin, confirming that radiotracer uptake was dependent on the sodium-potassium concentration gradient. NIS-mediated radiotracer uptake was significantly reduced (- 58.2%) following disruptions to ATP re-synthesis by combined glycolysis and oxidative phosphorylation inhibition in HEK293T cells and by oxidative phosphorylation inhibition (- 16.6%) in A549 cells in vitro. PET signal was significantly decreased (- 56.5%) within 90 min from the onset of treatment with IACS-010759, an oxidative phosphorylation inhibitor, in subcutaneous transgenic A549 tumours in vivo, showing that NIS could rapidly and sensitively detect energy stress non-invasively, before more widespread changes to phosphorylated AMP-activated protein kinase, phosphorylated pyruvate dehydrogenase, and GLUT1 were detectable.
    CONCLUSIONS: NIS acts as a rapid metabolic sensor for drugs that lead to ATP depletion. PET imaging of NIS could facilitate in vivo testing of treatments targeting energetic pathways, determine drug potency, and expedite metabolic drug development.
    Keywords:  2-DG; Energy charge; IACS-010759; Metabolic sensor; Oligomycin A; Positron emission tomography; Reporter genes
    DOI:  https://doi.org/10.1186/s40170-023-00314-2
  36. Nat Commun. 2023 Sep 02. 14(1): 5336
    Epigenetic inheritance is unfaithful at intermediately methylated CpG sites.
    Amir D Hay, Noah J Kessler, Daniel Gebert, Nozomi Takahashi, Hugo Tavares, Felipe K Teixeira, Anne C Ferguson-Smith.
      DNA methylation at the CpG dinucleotide is considered a stable epigenetic mark due to its presumed long-term inheritance through clonal expansion. Here, we perform high-throughput bisulfite sequencing on clonally derived somatic cell lines to quantitatively measure methylation inheritance at the nucleotide level. We find that although DNA methylation is generally faithfully maintained at hypo- and hypermethylated sites, this is not the case at intermediately methylated CpGs. Low fidelity intermediate methylation is interspersed throughout the genome and within genes with no or low transcriptional activity, and is not coordinately maintained between neighbouring sites. We determine that the probabilistic changes that occur at intermediately methylated sites are likely due to DNMT1 rather than DNMT3A/3B activity. The observed lack of clonal inheritance at intermediately methylated sites challenges the current epigenetic inheritance model and has direct implications for both the functional relevance and general interpretability of DNA methylation as a stable epigenetic mark.
    DOI:  https://doi.org/10.1038/s41467-023-40845-2
  37. Nat Commun. 2023 Sep 06. 14(1): 5195
    A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer.
    Corina E Antal, Tae Gyu Oh, Stefan Aigner, En-Ching Luo, Brian A Yee, Tania Campos, Hervé Tiriac, Katherine L Rothamel, Zhang Cheng, Henry Jiao, Allen Wang, Nasun Hah, Elizabeth Lenkiewicz, Jan C Lumibao, Morgan L Truitt, Gabriela Estepa, Ester Banayo, Senada Bashi, Edgar Esparza, Ruben M Munoz, Jolene K Diedrich, Nicole M Sodir, Jasmine R Mueller, Cory R Fraser, Erkut Borazanci, David Propper, Daniel D Von Hoff, Christopher Liddle, Ruth T Yu, Annette R Atkins, Haiyong Han, Andrew M Lowy, Michael T Barrett, Dannielle D Engle, Gerard I Evan, Gene W Yeo, Michael Downes, Ronald M Evans.
      Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy in need of new therapeutic options. Using unbiased analyses of super-enhancers (SEs) as sentinels of core genes involved in cell-specific function, here we uncover a druggable SE-mediated RNA-binding protein (RBP) cascade that supports PDAC growth through enhanced mRNA translation. This cascade is driven by a SE associated with the RBP heterogeneous nuclear ribonucleoprotein F, which stabilizes protein arginine methyltransferase 1 (PRMT1) to, in turn, control the translational mediator ubiquitin-associated protein 2-like. All three of these genes and the regulatory SE are essential for PDAC growth and coordinately regulated by the Myc oncogene. In line with this, modulation of the RBP network by PRMT1 inhibition reveals a unique vulnerability in Myc-high PDAC patient organoids and markedly reduces tumor growth in male mice. Our study highlights a functional link between epigenetic regulation and mRNA translation and identifies components that comprise unexpected therapeutic targets for PDAC.
    DOI:  https://doi.org/10.1038/s41467-023-40798-6
  38. Front Immunol. 2023 ;14 1176956
    Creatine supplementation enhances anti-tumor immunity by promoting adenosine triphosphate production in macrophages.
    Zhenzi Peng, Suguru Saito.
      Creatine is an indispensable organic compound utilized in physiological environments; however, its role in immunity is still poorly understood. Here, we show that creatine supplementation enhances anti-tumor immunity through the functional upregulation of macrophages by increasing adenosine triphosphate (ATP) production. Creatine supplementation significantly suppressed B16-F10-originated tumor growth in mice compared with the control treatment. Under these conditions, intratumor macrophages polarized towards the M1 phenotype rather than the M2 phenotype, and there was an increase in tumor antigen-specific CD8+ T cells in the mice. The cytokine production and antigen-presenting activity in the macrophages were enhanced by creatine supplementation, resulting in a substantial increase in tumor antigen-specific CD8+ T cells. ATP upregulation was achieved through the cytosolic phosphocreatine (PCr) system via extracellular creatine uptake, rather than through glycolysis and mitochondrial oxidative phosphorylation in the macrophages. Blockade of the creatine transporter (CrT) failed to upregulate ATP and enhance the immunological activity of macrophages in creatine supplementation, which also impaired CD8+ T cell activity. Consequently, CrT blockade failed to suppress tumor growth in the creatine-supplemented mice. Thus, creatine is an important nutrient that promotes macrophage function by increasing ATP levels, ultimately contributing to enhanced anti-tumor immunity orchestrated by CD8+ T cells.
    Keywords:  ATP; CD8+ T cells; anti-tumor immunity; creatine; macrophages
    DOI:  https://doi.org/10.3389/fimmu.2023.1176956
  39. J Clin Invest. 2023 Sep 05. pii: e169399. [Epub ahead of print]
    Reducing branched-chain amino acids improves cardiac stress response in mice by decreasing histone H3K23 propionylation.
    Zhi Yang, Minzhen He, Julianne Austin, Danish Sayed, Maha Abdellatif.
      Identifying branched-chain amino acid (BCAA) oxidation enzymes in the nucleus led us to predict that they are a source of propionyl-CoA that are utilized for histone propionylation and, thereby, regulate gene expression. To investigate the effects of BCAA on the development of cardiac hypertrophy and failure, we applied pressure overload on the heart in mice maintained on a diet with standard levels of BCAA (BCAA-control) versus a BCAA-free diet. The former was associated with an increase in histone H3K23-propionyl (H3K23Pr) at the promoters of upregulated genes [e.g., cell signaling and extracellular matrix genes] and a decrease at the promoters of downregulated genes [e.g., electron transfer complex (ETC I-V) and metabolic genes]. Intriguingly, the BCAA-free diet tempered the increases in promoter-H3K23Pr, thus, reducing collagen gene expression and fibrosis during cardiac hypertrophy. Conversely, the BCAA-free diet inhibited the reductions in promoter-H3K23Pr and abolished the downregulation of ETC I-V subunits, enhanced mitochondrial respiration, and curbed progression of cardiac hypertrophy. Thus, lowering the intake of BCAA reduces pressure overload-induced changes in histone propionylation-dependent gene expression in the heart, which retards the development of cardiomyopathy.
    Keywords:  Cardiology; Cardiovascular disease; Epigenetics; Metabolism; Transcription
    DOI:  https://doi.org/10.1172/JCI169399
  40. Nat Rev Endocrinol. 2023 Sep 06.
    Advanced neurobiological tools to interrogate metabolism.
    Paul Nicholas Mirabella, Henning Fenselau.
      Engineered neurobiological tools for the manipulation of cellular activity, such as chemogenetics and optogenetics, have become a cornerstone of modern neuroscience research. These tools are invaluable for the interrogation of the central control of metabolism as they provide a direct means to establish a causal relationship between brain activity and biological processes at the cellular, tissue and organismal levels. The utility of these methods has grown substantially due to advances in cellular-targeting strategies, alongside improvements in the resolution and potency of such tools. Furthermore, the potential to recapitulate endogenous cellular signalling has been enriched by insights into the molecular signatures and activity dynamics of discrete brain cell types. However, each modulatory tool has a specific set of advantages and limitations; therefore, tool selection and suitability are of paramount importance to optimally interrogate the cellular and circuit-based underpinnings of metabolic outcomes within the organism. Here, we describe the key principles and uses of engineered neurobiological tools. We also highlight inspiring applications and outline critical considerations to be made when using these tools within the field of metabolism research. We contend that the appropriate application of these biotechnological advances will enable the delineation of the central circuitry regulating systemic metabolism with unprecedented potential.
    DOI:  https://doi.org/10.1038/s41574-023-00885-6
  41. Nat Struct Mol Biol. 2023 Sep 08.
    Functional epigenomics: chromatin complexity untangled.
    Ricardo Mack, Or Gozani.
      
    DOI:  https://doi.org/10.1038/s41594-023-01088-3
  42. Nat Genet. 2023 Sep;55(9): 1531-1541
    Single-cell multi-omics identifies chronic inflammation as a driver of TP53-mutant leukemic evolution.
    Alba Rodriguez-Meira, Ruggiero Norfo, Sean Wen, Agathe L Chédeville, Haseeb Rahman, Jennifer O'Sullivan, Guanlin Wang, Eleni Louka, Warren W Kretzschmar, Aimee Paterson, Charlotte Brierley, Jean-Edouard Martin, Caroline Demeule, Matthew Bashton, Nikolaos Sousos, Daniela Moralli, Lamia Subha Meem, Joana Carrelha, Bishan Wu, Angela Hamblin, Helene Guermouche, Florence Pasquier, Christophe Marzac, François Girodon, William Vainchenker, Mark Drummond, Claire Harrison, J Ross Chapman, Isabelle Plo, Sten Eirik W Jacobsen, Bethan Psaila, Supat Thongjuea, Iléana Antony-Debré, Adam J Mead.
      Understanding the genetic and nongenetic determinants of tumor protein 53 (TP53)-mutation-driven clonal evolution and subsequent transformation is a crucial step toward the design of rational therapeutic strategies. Here we carry out allelic resolution single-cell multi-omic analysis of hematopoietic stem/progenitor cells (HSPCs) from patients with a myeloproliferative neoplasm who transform to TP53-mutant secondary acute myeloid leukemia (sAML). All patients showed dominant TP53 'multihit' HSPC clones at transformation, with a leukemia stem cell transcriptional signature strongly predictive of adverse outcomes in independent cohorts, across both TP53-mutant and wild-type (WT) AML. Through analysis of serial samples, antecedent TP53-heterozygous clones and in vivo perturbations, we demonstrate a hitherto unrecognized effect of chronic inflammation, which suppressed TP53 WT HSPCs while enhancing the fitness advantage of TP53-mutant cells and promoted genetic evolution. Our findings will facilitate the development of risk-stratification, early detection and treatment strategies for TP53-mutant leukemia, and are of broad relevance to other cancer types.
    DOI:  https://doi.org/10.1038/s41588-023-01480-1
  43. Nat Metab. 2023 Sep 07.
    Spatial metabolomics: from a niche field towards a driver of innovation.
    Theodore Alexandrov.
      
    DOI:  https://doi.org/10.1038/s42255-023-00881-0
  44. Proc Natl Acad Sci U S A. 2023 Sep 12. 120(37): e2307449120
    We need to shift the focus of aging research to aging itself.
    Jesse R Poganik, Vadim N Gladyshev.
      
    DOI:  https://doi.org/10.1073/pnas.2307449120
  45. J Biol Chem. 2023 Sep 01. pii: S0021-9258(23)02238-X. [Epub ahead of print] 105210
    CLPX regulates mitochondrial fatty acid β-oxidation in liver cells.
    Ko Suzuki, Yoshiko Kubota, Kiriko Kaneko, Costantine Chasama Kamata, Kazumichi Furuyama.
      Mitochondrial fatty acid oxidation (β-oxidation) is an essential metabolic process for energy production in eukaryotic cells, but the regulatory mechanisms of this pathway are largely unknown. In the present study, we found that several enzymes involved in β-oxidation are associated with CLPX, the AAA+ unfoldase that is a component of the mitochondrial matrix protease ClpXP. The suppression of CLPX expression increased β-oxidation activity in the HepG2 cell line and in primary human hepatocytes without glucagon treatment. However, the protein levels of enzymes involved in β-oxidation did not significantly increase in CLPX-deleted HepG2 cells (CLPX-KO cells). Coimmunoprecipitation experiments revealed that the protein level in the immunoprecipitates of each antibody changed after the treatment of wild-type cells with glucagon, and a part of these changes was also observed in the comparison of wild-type and CLPX-KO cells without glucagon treatment. Although the exogenous expression of wild-type or ATP-hydrolysis mutant CLPX suppressed β-oxidation activity in CLPX-KO cells, glucagon treatment induced β-oxidation activity only in CLPX-KO cells expressing wild-type CLPX. These results suggest that the dissociation of CLPX from its target proteins is essential for the induction of β-oxidation in HepG2 cells. Moreover, specific phosphorylation of AMP-activated protein kinase (AMPK) and a decrease in the expression of acetyl-CoA carboxylase 2 were observed in CLPX-KO cells, suggesting that CLPX might participate in the regulation of the cytosolic signaling pathway for β-oxidation. The mechanism for AMPK phosphorylation remains elusive; however, our results uncovered the hitherto unknown role of CLPX in mitochondrial β-oxidation in human liver cells.
    Keywords:  CLPX; beta-oxidation; glucagon; hepatocyte; mitochondria; protein‒protein interaction
    DOI:  https://doi.org/10.1016/j.jbc.2023.105210
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