bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2024–06–02
sixty papers selected by
Christian Frezza, Universität zu Köln
  1. Cells dispose of cytoplasmic mitochondrial DNA by nucleoid-phagy.
  2. AspSnFR: A genetically encoded biosensor for real-time monitoring of aspartate in live cells.
  3. Transport activity regulates mitochondrial bioenergetics and biogenesis in renal tubules.
  4. TCAF1 promotes TRPV2-mediated Ca2+ release in response to cytosolic DNA to protect stressed replication forks.
  5. COX2-dependent suppression of anticancer immunity.
  6. 13C metabolite tracing reveals glutamine and acetate as critical in vivo fuels for CD8 T cells.
  7. HSDL2 links nutritional cues to bile acid and cholesterol homeostasis.
  8. ACLY alternative splicing correlates with cancer phenotypes.
  9. Ablation of Atp5if1 impairs metabolic reprogramming and proliferation of T lymphocytes and compromises mouse survival.
  10. Multifaceted mitochondria in innate immunity.
  11. CLUH maintains functional mitochondria and translation in motoneuronal axons and prevents peripheral neuropathy.
  12. Career pathways, part 14.
  13. PNPO-PLP axis senses prolonged hypoxia in macrophages by regulating lysosomal activity.
  14. CMTR-1 RNA methyltransferase mutations activate widespread expression of a dopaminergic neuron-specific mitochondrial complex I gene.
  15. Mechanical activation of VE-cadherin stimulates AMPK to increase endothelial cell metabolism and vasodilation.
  16. Breast cancer cell-secreted miR-199b-5p hijacks neurometabolic coupling to promote brain metastasis.
  17. Dynamic movement of the Golgi unit and its glycosylation enzyme zones.
  18. Pro-inflammatory macrophage activation does not require inhibition of mitochondrial respiration.
  19. mitoBKCa is functionally expressed in murine and human breast cancer cells and potentially contributes to metabolic reprogramming.
  20. The temporal progression of lung immune remodeling during breast cancer metastasis.
  21. Regulation of TSC2 lysosome translocation and mitochondrial turnover by TSC2 acetylation status.
  22. A mitochondrial-targeted activity-based sensing probe for ratiometric imaging of formaldehyde reveals key regulators of the mitochondrial one-carbon pool.
  23. Fasting alleviates metabolic alterations in mice with propionyl-CoA carboxylase deficiency due to Pcca mutation.
  24. The age-related decline of helicase function-how G-quadruplex structures promote genome instability.
  25. Hippo-YAP/TAZ signalling coordinates adipose plasticity and energy balance by uncoupling leptin expression from fat mass.
  26. Rab30 facilitates lipid homeostasis during fasting.
  27. Cystine/glutamate antiporter xCT controls skeletal muscle glutathione redox, bioenergetics and differentiation.
  28. No mutation, tumour initiation.
  29. Illuminating the path to pancreatic cancer.
  30. Dual sources of melatonin and evidence for different primary functions.
  31. The influence of circadian rhythms on CD8+ T cell activation upon vaccination: A mathematical modeling perspective.
  32. Phosphorylation of DNA-binding domains of CLOCK-BMAL1 complex for PER-dependent inhibition in circadian clock of mammalian cells.
  33. CPT2 mediated fatty acid oxidation is dispensable for humoral immunity.
  34. Reciprocal Regulation of Cardiac β-Oxidation and Pyruvate Dehydrogenase by Insulin.
  35. Chronic spindle assembly checkpoint activation causes myelosuppression and gastrointestinal atrophy.
  36. TBK1 is ubiquitinated by TRIM5α to assemble mitophagy machinery.
  37. METLIN-CCS Lipid Database: An authentic standards resource for lipid classification and identification.
  38. Phospholipid isotope tracing suggests β-catenin-driven suppression of phosphatidylcholine metabolism in hepatocellular carcinoma.
  39. Tissue-specific landscape of protein aggregation and quality control in an aging vertebrate.
  40. TRP14 is the rate-limiting enzyme for intracellular cystine reduction and regulates proteome cysteinylation.
  41. Novel somatic mutations in blood driving age-related clonal hematopoiesis.
  42. Drug screening in human physiologic medium identifies uric acid as an inhibitor of rigosertib efficacy.
  43. Epithelial aPKC deficiency leads to stem cell loss preceding metaplasia in colorectal cancer initiation.
  44. The glutamate/aspartate transporter EAAT1 is crucial for T-cell acute lymphoblastic leukemia proliferation and survival.
  45. Circadian control of tumor immunosuppression affects efficacy of immune checkpoint blockade.
  46. Aging atlas reveals cell-type-specific effects of pro-longevity strategies.
  47. Insights into the regulation of malate dehydrogenase: inhibitors, activators, and allosteric modulation by small molecules.
  48. Fluorescence Lifetime Imaging of Lipid Heterogeneity in the Inner Mitochondrial Membrane with a Super-photostable Environment-Sensitive Probe.
  49. Exploring the mystery of tumor metabolism: Warburg effect and mitochondrial metabolism fighting side by side.
  50. IL-4 Licenses B Cell Activation Through Cholesterol Synthesis.
  51. Germline-mediated immunoediting sculpts breast cancer subtypes and metastatic proclivity.
  52. Loss of temporal coherence in the circadian metabolome across multiple tissues during ageing in mice.
  53. Redistribution of defective mitochondria-mediated dihydroorotate dehydrogenase imparts 5-fluorouracil resistance in colorectal cancer.
  54. An alternative cell cycle coordinates multiciliated cell differentiation.
  55. YIPF3 and YIPF4 regulate autophagic turnover of the Golgi apparatus.
  56. Mycobacterium tuberculosis produces D-serine under hypoxia to limit CD8+ T cell-dependent immunity in mice.
  57. Nonlinear dynamics in phosphoinositide metabolism.
  58. Reprogramming of urea cycle in cancer: Mechanism, regulation and prospective therapeutic scopes.
  59. A prebiotic Krebs cycle analog generates amino acids with H2 and NH3 over nickel.
  60. Capturing heterogeneity in PDX models: representation matters.
  1. Nat Cell Biol. 2024 May 29.
    Cells dispose of cytoplasmic mitochondrial DNA by nucleoid-phagy.
      
    DOI:  https://doi.org/10.1038/s41556-024-01421-y
  2. Cell Chem Biol. 2024 May 20. pii: S2451-9456(24)00179-X. [Epub ahead of print]
    AspSnFR: A genetically encoded biosensor for real-time monitoring of aspartate in live cells.
    Lars Hellweg, Martin Pfeifer, Miroslaw Tarnawski, Shao Thing-Teoh, Lena Chang, Andrea Bergner, Jana Kress, Julien Hiblot, Tabea Wiedmer, Giulio Superti-Furga, Jürgen Reinhardt, Kai Johnsson, Philipp Leippe.
      Aspartate is crucial for nucleotide synthesis, ammonia detoxification, and maintaining redox balance via the malate-aspartate-shuttle (MAS). To disentangle these multiple roles of aspartate metabolism, tools are required that measure aspartate concentrations in real time and in live cells. We introduce AspSnFR, a genetically encoded green fluorescent biosensor for intracellular aspartate, engineered through displaying and screening biosensor libraries on mammalian cells. In live cells, AspSnFR is able to precisely and quantitatively measure cytosolic aspartate concentrations and dissect its production from glutamine. Combining high-content imaging of AspSnFR with pharmacological perturbations exposes differences in metabolic vulnerabilities of aspartate levels based on nutrient availability. Further, AspSnFR facilitates tracking of aspartate export from mitochondria through SLC25A12, the MAS' key transporter. We show that SLC25A12 is a rapidly responding and direct route to couple Ca2+ signaling with mitochondrial aspartate export. This establishes SLC25A12 as a crucial link between cellular signaling, mitochondrial respiration, and metabolism.
    DOI:  https://doi.org/10.1016/j.chembiol.2024.05.002
  3. FASEB J. 2024 May 31. 38(10): e23703
    Transport activity regulates mitochondrial bioenergetics and biogenesis in renal tubules.
    Chih-Jen Cheng, Jonathan M Nizar, Dao-Fu Dai, Chou-Long Huang.
      Renal tubules are featured with copious mitochondria and robust transport activity. Mutations in mitochondrial genes cause congenital renal tubulopathies, and changes in transport activity affect mitochondrial morphology, suggesting mitochondrial function and transport activity are tightly coupled. Current methods of using bulk kidney tissues or cultured cells to study mitochondrial bioenergetics are limited. Here, we optimized an extracellular flux analysis (EFA) to study mitochondrial respiration and energy metabolism using microdissected mouse renal tubule segments. EFA detects mitochondrial respiration and glycolysis by measuring oxygen consumption and extracellular acidification rates, respectively. We show that both measurements positively correlate with sample sizes of a few centimeter-length renal tubules. The thick ascending limbs (TALs) and distal convoluted tubules (DCTs) critically utilize glucose/pyruvate as energy substrates, whereas proximal tubules (PTs) are significantly much less so. Acute inhibition of TALs' transport activity by ouabain treatment reduces basal and ATP-linked mitochondrial respiration. Chronic inhibition of transport activity by 2-week furosemide treatment or deletion of with-no-lysine kinase 4 (Wnk4) decreases maximal mitochondrial capacity. In addition, chronic inhibition downregulates mitochondrial DNA mass and mitochondrial length/density in TALs and DCTs. Conversely, gain-of-function Wnk4 mutation increases maximal mitochondrial capacity and mitochondrial length/density without increasing mitochondrial DNA mass. In conclusion, EFA is a sensitive and reliable method to investigate mitochondrial functions in isolated renal tubules. Transport activity tightly regulates mitochondrial bioenergetics and biogenesis to meet the energy demand in renal tubules. The system allows future investigation into whether and how mitochondria contribute to tubular remodeling adapted to changes in transport activity.
    Keywords:  distal convoluted tubule; extracellular flux analysis; glycolysis; mitochondrial respiration; thick ascending limb; transport activity
    DOI:  https://doi.org/10.1096/fj.202400358RR
  4. Nat Commun. 2024 May 30. 15(1): 4609
    TCAF1 promotes TRPV2-mediated Ca2+ release in response to cytosolic DNA to protect stressed replication forks.
    Lingzhen Kong, Chen Cheng, Abigael Cheruiyot, Jiayi Yuan, Yichan Yang, Sydney Hwang, Daniel Foust, Ning Tsao, Emily Wilkerson, Nima Mosammaparast, Michael B Major, David W Piston, Shan Li, Zhongsheng You.
      The protection of the replication fork structure under stress conditions is essential for genome maintenance and cancer prevention. A key signaling pathway for fork protection involves TRPV2-mediated Ca2+ release from the ER, which is triggered after the generation of cytosolic DNA and the activation of cGAS/STING. This results in CaMKK2/AMPK activation and subsequent Exo1 phosphorylation, which prevent aberrant fork processing, thereby ensuring genome stability. However, it remains poorly understood how the TRPV2 channel is activated by the presence of cytosolic DNA. Here, through a genome-wide CRISPR-based screen, we identify TRPM8 channel-associated factor 1 (TCAF1) as a key factor promoting TRPV2-mediated Ca2+ release under replication stress or other conditions that activate cGAS/STING. Mechanistically, TCAF1 assists Ca2+ release by facilitating the dissociation of STING from TRPV2, thereby relieving TRPV2 repression. Consistent with this function, TCAF1 is required for fork protection, chromosomal stability, and cell survival after replication stress.
    DOI:  https://doi.org/10.1038/s41467-024-48988-6
  5. Trends Cancer. 2024 May 30. pii: S2405-8033(24)00096-7. [Epub ahead of print]
    COX2-dependent suppression of anticancer immunity.
    María Cecilia Lira, Lorenzo Galluzzi, Claire Vanpouille-Box.
      Prostaglandin E2 (PGE2) is well known to promote tumor progression by boosting cancer cell proliferation while inhibiting anticancer immunity. Recent data from Lacher et al. and Morotti et al. demonstrate that one of the mechanisms through which PGE2 suppresses tumor-targeting immune responses involves downregulation of interleukin 2 (IL2) receptors and consequent inhibition of mitochondrial metabolism in T cells.
    Keywords:  CASP3; NK cells; PTGER2; apoptosis; radiation therapy; tumor-infiltrating lymphocyte
    DOI:  https://doi.org/10.1016/j.trecan.2024.05.006
  6. Sci Adv. 2024 May 31. 10(22): eadj1431
    13C metabolite tracing reveals glutamine and acetate as critical in vivo fuels for CD8 T cells.
    Eric H Ma, Michael S Dahabieh, Lisa M DeCamp, Irem Kaymak, Susan M Kitchen-Goosen, Brandon M Oswald, Joseph Longo, Dominic G Roy, Mark J Verway, Radia M Johnson, Bozena Samborska, Lauren R Duimstra, Catherine A Scullion, Mya Steadman, Matthew Vos, Thomas P Roddy, Connie M Krawczyk, Kelsey S Williams, Ryan D Sheldon, Russell G Jones.
      Infusion of 13C-labeled metabolites provides a gold standard for understanding the metabolic processes used by T cells during immune responses in vivo. Through infusion of 13C-labeled metabolites (glucose, glutamine, and acetate) in Listeria monocytogenes-infected mice, we demonstrate that CD8 T effector (Teff) cells use metabolites for specific pathways during specific phases of activation. Highly proliferative early Teff cells in vivo shunt glucose primarily toward nucleotide synthesis and leverage glutamine anaplerosis in the tricarboxylic acid (TCA) cycle to support adenosine triphosphate and de novo pyrimidine synthesis. In addition, early Teff cells rely on glutamic-oxaloacetic transaminase 1 (Got1)-which regulates de novo aspartate synthesis-for effector cell expansion in vivo. CD8 Teff cells change fuel preference over the course of infection, switching from glutamine- to acetate-dependent TCA cycle metabolism late in infection. This study provides insights into the dynamics of Teff metabolism, illuminating distinct pathways of fuel consumption associated with CD8 Teff cell function in vivo.
    DOI:  https://doi.org/10.1126/sciadv.adj1431
  7. Sci Adv. 2024 May 31. 10(22): eadk9681
    HSDL2 links nutritional cues to bile acid and cholesterol homeostasis.
    Nolwenn Samson, Cristina R Bosoi, Christian Roy, Laurie Turcotte, Laura Tribouillard, Mathilde Mouchiroud, Line Berthiaume, Jocelyn Trottier, Heitor C G Silva, Thomas Guerbette, Ana Belén Plata-Gómez, Aurèle Besse-Patin, Alicia Montoni, Nicolò Ilacqua, Jennifer Lamothe, Yemima R Citron, Yves Gélinas, Stéphane Gobeil, Roberto Zoncu, Alexandre Caron, Mathieu Morissette, Luca Pellegrini, Patrick J Rochette, Jennifer L Estall, Alejo Efeyan, Michael Shum, Étienne Audet-Walsh, Olivier Barbier, André Marette, Mathieu Laplante.
      In response to energy and nutrient shortage, the liver triggers several catabolic processes to promote survival. Despite recent progress, the precise molecular mechanisms regulating the hepatic adaptation to fasting remain incompletely characterized. Here, we report the identification of hydroxysteroid dehydrogenase-like 2 (HSDL2) as a mitochondrial protein highly induced by fasting. We show that the activation of PGC1α-PPARα and the inhibition of the PI3K-mTORC1 axis stimulate HSDL2 expression in hepatocytes. We found that HSDL2 depletion decreases cholesterol conversion to bile acids (BAs) and impairs FXR activity. HSDL2 knockdown also reduces mitochondrial respiration, fatty acid oxidation, and TCA cycle activity. Bioinformatics analyses revealed that hepatic Hsdl2 expression positively associates with the postprandial excursion of various BA species in mice. We show that liver-specific HSDL2 depletion affects BA metabolism and decreases circulating cholesterol levels upon refeeding. Overall, our report identifies HSDL2 as a fasting-induced mitochondrial protein that links nutritional signals to BAs and cholesterol homeostasis.
    DOI:  https://doi.org/10.1126/sciadv.adk9681
  8. J Biol Chem. 2024 May 28. pii: S0021-9258(24)01919-7. [Epub ahead of print] 107418
    ACLY alternative splicing correlates with cancer phenotypes.
    Julianna G Supplee, Hayley C Affronti, Richard Duan, Rebekah C Brooks, Zachary E Stine, Phuong T T Nguyen, Laura V Pinheiro, Michael C Noji, Jack M Drummond, Kevin Huang, Kollin Schultz, Chi V Dang, Ronen Marmorstein, Kathryn E Wellen.
      ATP-citrate lyase (ACLY) links carbohydrate and lipid metabolism and provides nucleocytosolic acetyl-CoA necessary for protein acetylation. ACLY has two major splice isoforms: the full-length canonical "long" isoform and an uncharacterized "short" isoform in which exon 14 is spliced out. Exon 14 encodes 10 amino acids within a disordered region of the protein and includes at least 1 site that is dynamically phosphorylated. Both isoforms are expressed in healthy tissues to varying degrees. Analysis of human transcriptomic data revealed that the Percent Spliced In (PSI) of exon 14, i.e., the proportion of long isoform, is increased in several cancers and correlated with poorer overall survival in a pan-cancer analysis, though not in individual tumor types, which prompted us to explore potential biochemical and functional differences between ACLY isoforms. Here, we show that there are no discernible differences in enzymatic activity or stability between isoforms or phosphomutants of ACLY in vitro. Similarly, both isoforms and phosphomutants were able to rescue ACLY functions, including fatty acid synthesis and bulk histone acetylation, when re-expressed in Acly knockout cells. Deletion of Acly exon 14 in mice did not overtly impact development or metabolic physiology, nor did it attenuate tumor burden in a genetic model of intestinal cancer. Notably, expression of epithelial splicing regulatory protein 1 (ESRP1) is highly correlated with ACLY PSI. We report that ACLY splicing is regulated by ESRP1. In turn, both ESRP1 expression and ACLY PSI are correlated with specific immune signatures in tumors. Despite these intriguing patterns of ACLY splicing in healthy and cancer tissues, functional differences between the isoforms remain elusive.
    DOI:  https://doi.org/10.1016/j.jbc.2024.107418
  9. iScience. 2024 Jun 21. 27(6): 109863
    Ablation of Atp5if1 impairs metabolic reprogramming and proliferation of T lymphocytes and compromises mouse survival.
    Inés Romero-Carramiñana, Sonia Dominguez-Zorita, Pau B Esparza-Moltó, José M Cuezva.
      T cells experience metabolic reprogramming to an enhanced glycolysis upon activation. Herein, we have investigated whether ATPase Inhibitory Factor 1 (IF1), the physiological inhibitor of mitochondrial ATP synthase, participates in rewiring T cells to a particular metabolic phenotype. We show that the activation of naive CD4+ T lymphocytes both in vitro and in vivo is accompanied by a sharp upregulation of IF1, which is expressed only in Th1 effector cells. T lymphocytes of conditional CD4+-IF1-knockout mice display impaired glucose uptake and flux through glycolysis, reducing the biogenesis of mitochondria and cellular proliferation after activation. Consequently, mice devoid of IF1 in T lymphocytes cannot mount an effective Th1 response against bacterial infection compromising their survival. Overall, we show that the inhibition of a fraction of ATP synthase by IF1 regulates metabolic reprogramming and functionality of T cells, highlighting the essential role of IF1 in adaptive immune responses.
    Keywords:  Biological sciences; Immunology; Molecular biology; Physiology
    DOI:  https://doi.org/10.1016/j.isci.2024.109863
  10. NPJ Metab Health Dis. 2024 ;2(1): 6
    Multifaceted mitochondria in innate immunity.
    Eloïse Marques, Robbin Kramer, Dylan G Ryan.
      The ability of mitochondria to transform the energy we obtain from food into cell phosphorylation potential has long been appreciated. However, recent decades have seen an evolution in our understanding of mitochondria, highlighting their significance as key signal-transducing organelles with essential roles in immunity that extend beyond their bioenergetic function. Importantly, mitochondria retain bacterial motifs as a remnant of their endosymbiotic origin that are recognised by innate immune cells to trigger inflammation and participate in anti-microbial defence. This review aims to explore how mitochondrial physiology, spanning from oxidative phosphorylation (OxPhos) to signalling of mitochondrial nucleic acids, metabolites, and lipids, influences the effector functions of phagocytes. These myriad effector functions include macrophage polarisation, efferocytosis, anti-bactericidal activity, antigen presentation, immune signalling, and cytokine regulation. Strict regulation of these processes is critical for organismal homeostasis that when disrupted may cause injury or contribute to disease. Thus, the expanding body of literature, which continues to highlight the central role of mitochondria in the innate immune system, may provide insights for the development of the next generation of therapies for inflammatory diseases.
    Keywords:  Energy metabolism; Mitochondria
    DOI:  https://doi.org/10.1038/s44324-024-00008-3
  11. Sci Adv. 2024 May 31. 10(22): eadn2050
    CLUH maintains functional mitochondria and translation in motoneuronal axons and prevents peripheral neuropathy.
    Marta Zaninello, Tim Schlegel, Hendrik Nolte, Mujeeb Pirzada, Elisa Savino, Esther Barth, Ines Klein, Hauke Wüstenberg, Tesmin Uddin, Lisa Wolff, Brunhilde Wirth, Helmar C Lehmann, Jean-Michel Cioni, Thomas Langer, Elena I Rugarli.
      Transporting and translating mRNAs in axons is crucial for neuronal viability. Local synthesis of nuclear-encoded mitochondrial proteins protects long-lived axonal mitochondria from damage; however, the regulatory factors involved are largely unknown. We show that CLUH, which binds mRNAs encoding mitochondrial proteins, prevents peripheral neuropathy and motor deficits in the mouse. CLUH is enriched in the growth cone of developing spinal motoneurons and is required for their growth. The lack of CLUH affects the abundance of target mRNAs and the corresponding mitochondrial proteins more prominently in axons, leading to ATP deficits in the growth cone. CLUH interacts with ribosomal subunits, translation initiation, and ribosome recycling components and preserves axonal translation. Overexpression of the ribosome recycling factor ABCE1 rescues the mRNA and translation defects, as well as the growth cone size, in CLUH-deficient motoneurons. Thus, we demonstrate a role for CLUH in mitochondrial quality control and translational regulation in axons, which is essential for their development and long-term integrity and function.
    DOI:  https://doi.org/10.1126/sciadv.adn2050
  12. Nat Metab. 2024 May 31.
    Career pathways, part 14.
    Angelika Rambold, Santiago Vernia.
      
    DOI:  https://doi.org/10.1038/s42255-024-01056-1
  13. Nat Metab. 2024 May 31.
    PNPO-PLP axis senses prolonged hypoxia in macrophages by regulating lysosomal activity.
    Hiroki Sekine, Haruna Takeda, Norihiko Takeda, Akihiro Kishino, Hayato Anzawa, Takayuki Isagawa, Nao Ohta, Shohei Murakami, Hideya Iwaki, Nobufumi Kato, Shu Kimura, Zun Liu, Koichiro Kato, Fumiki Katsuoka, Masayuki Yamamoto, Fumihito Miura, Takashi Ito, Masatomo Takahashi, Yoshihiro Izumi, Hiroyuki Fujita, Hitoshi Yamagata, Takeshi Bamba, Takaaki Akaike, Norio Suzuki, Kengo Kinoshita, Hozumi Motohashi.
      Oxygen is critical for all metazoan organisms on the earth and impacts various biological processes in physiological and pathological conditions. While oxygen-sensing systems inducing acute hypoxic responses, including the hypoxia-inducible factor pathway, have been identified, those operating in prolonged hypoxia remain to be elucidated. Here we show that pyridoxine 5'-phosphate oxidase (PNPO), which catalyses bioactivation of vitamin B6, serves as an oxygen sensor and regulates lysosomal activity in macrophages. Decreased PNPO activity under prolonged hypoxia reduced an active form of vitamin B6, pyridoxal 5'-phosphate (PLP), and inhibited lysosomal acidification, which in macrophages led to iron dysregulation, TET2 protein loss and delayed resolution of the inflammatory response. Among PLP-dependent metabolism, supersulfide synthesis was suppressed in prolonged hypoxia, resulting in the lysosomal inhibition and consequent proinflammatory phenotypes of macrophages. The PNPO-PLP axis creates a distinct layer of oxygen sensing that gradually shuts down PLP-dependent metabolism in response to prolonged oxygen deprivation.
    DOI:  https://doi.org/10.1038/s42255-024-01053-4
  14. Curr Biol. 2024 May 24. pii: S0960-9822(24)00593-1. [Epub ahead of print]
    CMTR-1 RNA methyltransferase mutations activate widespread expression of a dopaminergic neuron-specific mitochondrial complex I gene.
    Joshua D Meisel, Presli P Wiesenthal, Vamsi K Mootha, Gary Ruvkun.
      The mitochondrial proteome is comprised of approximately 1,100 proteins,1 all but 12 of which are encoded by the nuclear genome in C. elegans. The expression of nuclear-encoded mitochondrial proteins varies widely across cell lineages and metabolic states,2,3,4 but the factors that specify these programs are not known. Here, we identify mutations in two nuclear-localized mRNA processing proteins, CMTR1/CMTR-1 and SRRT/ARS2/SRRT-1, which we show act via the same mechanism to rescue the mitochondrial complex I mutant NDUFS2/gas-1(fc21). CMTR-1 is an FtsJ-family RNA methyltransferase that, in mammals, 2'-O-methylates the first nucleotide 3' to the mRNA CAP to promote RNA stability and translation5,6,7,8. The mutations isolated in cmtr-1 are dominant and lie exclusively in the regulatory G-patch domain. SRRT-1 is an RNA binding partner of the nuclear cap-binding complex and determines mRNA transcript fate.9 We show that cmtr-1 and srrt-1 mutations activate embryonic expression of NDUFS2/nduf-2.2, a paralog of NDUFS2/gas-1 normally expressed only in dopaminergic neurons, and that nduf-2.2 is necessary for the complex I rescue by the cmtr-1 G-patch mutant. Additionally, we find that loss of the cmtr-1 G-patch domain cause ectopic localization of CMTR-1 protein to processing bodies (P bodies), phase-separated organelles involved in mRNA storage and decay.10 P-body localization of the G-patch mutant CMTR-1 contributes to the rescue of the hyperoxia sensitivity of the NDUFS2/gas-1 mutant. This study suggests that mRNA methylation at P bodies may control nduf-2.2 gene expression, with broader implications for how the mitochondrial proteome is translationally remodeled in the face of tissue-specific metabolic requirements and stress.
    Keywords:  C. elegans; CMTR1; G-patch domain; Mitochondria; NADH:ubiquinone oxidoreductase; SRRT; complex I; hyperoxia; mRNA methylation; processing bodies
    DOI:  https://doi.org/10.1016/j.cub.2024.04.079
  15. bioRxiv. 2024 May 13. pii: 2024.05.09.593171. [Epub ahead of print]
    Mechanical activation of VE-cadherin stimulates AMPK to increase endothelial cell metabolism and vasodilation.
    Nicholas M Cronin, Logan W Dawson, Kris A DeMali.
      Endothelia cells respond to mechanical force by stimulating cellular signaling, but how these pathways are linked to elevations in cell metabolism and whether metabolism supports the mechanical response remains poorly understood. Here, we show that application of force to VE-cadherin stimulates liver kinase B1 (LKB1) to activate AMP-activated protein kinase (AMPK), a master regulator of energy homeostasis. VE-cadherin stimulated AMPK increases eNOS activity and localization to the plasma membrane as well as reinforcement of the actin cytoskeleton and cadherin adhesion complex, and glucose uptake. We present evidence for the increase in metabolism being necessary to fortify the adhesion complex, actin cytoskeleton, and cellular alignment. Together these data extend the paradigm for how mechanotransduction and metabolism are linked to include a connection to vasodilation, thereby providing new insight into how diseases involving contractile, metabolic, and vasodilatory disturbances arise.
    DOI:  https://doi.org/10.1101/2024.05.09.593171
  16. Nat Commun. 2024 May 29. 15(1): 4549
    Breast cancer cell-secreted miR-199b-5p hijacks neurometabolic coupling to promote brain metastasis.
    Xianhui Ruan, Wei Yan, Minghui Cao, Ray Anthony M Daza, Miranda Y Fong, Kaifu Yang, Jun Wu, Xuxiang Liu, Melanie Palomares, Xiwei Wu, Arthur Li, Yuan Chen, Rahul Jandial, Nicholas C Spitzer, Robert F Hevner, Shizhen Emily Wang.
      Breast cancer metastasis to the brain is a clinical challenge rising in prevalence. However, the underlying mechanisms, especially how cancer cells adapt a distant brain niche to facilitate colonization, remain poorly understood. A unique metabolic feature of the brain is the coupling between neurons and astrocytes through glutamate, glutamine, and lactate. Here we show that extracellular vesicles from breast cancer cells with a high potential to develop brain metastases carry high levels of miR-199b-5p, which shows higher levels in the blood of breast cancer patients with brain metastases comparing to those with metastatic cancer in other organs. miR-199b-5p targets solute carrier transporters (SLC1A2/EAAT2 in astrocytes and SLC38A2/SNAT2 and SLC16A7/MCT2 in neurons) to hijack the neuron-astrocyte metabolic coupling, leading to extracellular retention of these metabolites and promoting cancer cell growth. Our findings reveal a mechanism through which cancer cells of a non-brain origin reprogram neural metabolism to fuel brain metastases.
    DOI:  https://doi.org/10.1038/s41467-024-48740-0
  17. Nat Commun. 2024 May 27. 15(1): 4514
    Dynamic movement of the Golgi unit and its glycosylation enzyme zones.
    Akihiro Harada, Masataka Kunii, Kazuo Kurokawa, Takuya Sumi, Satoshi Kanda, Yu Zhang, Satomi Nadanaka, Koichiro M Hirosawa, Kazuaki Tokunaga, Takuro Tojima, Manabu Taniguchi, Kenta Moriwaki, Shin-Ichiro Yoshimura, Miki Yamamoto-Hino, Satoshi Goto, Toyomasa Katagiri, Satoshi Kume, Mitsuko Hayashi-Nishino, Miyako Nakano, Eiji Miyoshi, Kenichi G N Suzuki, Hiroshi Kitagawa, Akihiko Nakano.
      Knowledge on the distribution and dynamics of glycosylation enzymes in the Golgi is essential for better understanding this modification. Here, using a combination of CRISPR/Cas9 knockin technology and super-resolution microscopy, we show that the Golgi complex is assembled by a number of small 'Golgi units' that have 1-3 μm in diameter. Each Golgi unit contains small domains of glycosylation enzymes which we call 'zones'. The zones of N- and O-glycosylation enzymes are colocalised. However, they are less colocalised with the zones of a glycosaminoglycan synthesizing enzyme. Golgi units change shapes dynamically and the zones of glycosylation enzymes rapidly move near the rim of the unit. Photobleaching analysis indicates that a glycosaminoglycan synthesizing enzyme moves between units. Depletion of giantin dissociates units and prevents the movement of glycosaminoglycan synthesizing enzymes, which leads to insufficient glycosaminoglycan synthesis. Thus, we show the structure-function relationship of the Golgi and its implications in human pathogenesis.
    DOI:  https://doi.org/10.1038/s41467-024-48901-1
  18. bioRxiv. 2024 May 14. pii: 2024.05.10.593451. [Epub ahead of print]
    Pro-inflammatory macrophage activation does not require inhibition of mitochondrial respiration.
    Andréa B Ball, Anthony E Jones, Kaitlyn B Nguyễn, Amy Rios, Nico Marx, Wei Yuan Hsieh, Krista Yang, Brandon R Desousa, Kristen K O Kim, Michaela Veliova, Zena Marie Del Mundo, Orian S Shirihai, Cristiane Benincá, Linsey Stiles, Steven J Bensinger, Ajit S Divakaruni.
      Pro-inflammatory macrophage activation is a hallmark example of how mitochondria serve as signaling organelles. Upon classical macrophage activation, oxidative phosphorylation sharply decreases and mitochondria are repurposed to accumulate signals that amplify effector function. However, evidence is conflicting as to whether this collapse in respiration is essential or largely dispensable. Here we systematically examine this question and show that reduced oxidative phosphorylation is not required for pro-inflammatory macrophage activation. Only stimuli that engage both MyD88- and TRIF-linked pathways decrease mitochondrial respiration, and different pro-inflammatory stimuli have varying effects on other bioenergetic parameters. Additionally, pharmacologic and genetic models of electron transport chain inhibition show no direct link between respiration and pro-inflammatory activation. Studies in mouse and human macrophages also reveal accumulation of the signaling metabolites succinate and itaconate can occur independently of characteristic breaks in the TCA cycle. Finally, in vivo activation of peritoneal macrophages further demonstrates that a pro-inflammatory response can be elicited without reductions to oxidative phosphorylation. Taken together, the results suggest the conventional model of mitochondrial reprogramming upon macrophage activation is incomplete.
    DOI:  https://doi.org/10.1101/2024.05.10.593451
  19. Elife. 2024 May 29. pii: RP92511. [Epub ahead of print]12
    mitoBKCa is functionally expressed in murine and human breast cancer cells and potentially contributes to metabolic reprogramming.
    Helmut Bischof, Selina Maier, Piotr Koprowski, Bogusz Kulawiak, Sandra Burgstaller, Joanna Jasińska, Kristian Serafimov, Monika Zochowska, Dominic Gross, Werner Schroth, Lucas Matt, David Arturo Juarez Lopez, Ying Zhang, Irina Bonzheim, Florian A Büttner, Falko Fend, Matthias Schwab, Andreas L Birkenfeld, Roland Malli, Michael Lämmerhofer, Piotr Bednarczyk, Adam Szewczyk, Robert Lukowski.
      Alterations in the function of K+ channels such as the voltage- and Ca2+-activated K+ channel of large conductance (BKCa) reportedly promote breast cancer (BC) development and progression. Underlying molecular mechanisms remain, however, elusive. Here, we provide electrophysiological evidence for a BKCa splice variant localized to the inner mitochondrial membrane of murine and human BC cells (mitoBKCa). Through a combination of genetic knockdown and knockout along with a cell permeable BKCa channel blocker, we show that mitoBKCa modulates overall cellular and mitochondrial energy production, and mediates the metabolic rewiring referred to as the 'Warburg effect', thereby promoting BC cell proliferation in the presence and absence of oxygen. Additionally, we detect mitoBKCa and BKCa transcripts in low or high abundance, respectively, in clinical BC specimens. Together, our results emphasize, that targeting mitoBKCa could represent a treatment strategy for selected BC patients in future.
    Keywords:  K+ channels; Kcnma1; Slo1; Warburg effect; biosensors; breast cancer; cancer biology; cell biology; human; metabolic reprogramming; mitoBKCa; mouse
    DOI:  https://doi.org/10.7554/eLife.92511
  20. Cancer Cell. 2024 May 24. pii: S1535-6108(24)00167-3. [Epub ahead of print]
    The temporal progression of lung immune remodeling during breast cancer metastasis.
    Christopher S McGinnis, Zhuang Miao, Daphne Superville, Winnie Yao, Andrei Goga, Nathan E Reticker-Flynn, Juliane Winkler, Ansuman T Satpathy.
      Tumor metastasis requires systemic remodeling of distant organ microenvironments that impacts immune cell phenotypes, population structure, and intercellular communication. However, our understanding of immune phenotypic dynamics in the metastatic niche remains incomplete. Here, we longitudinally assayed lung immune transcriptional profiles in the polyomavirus middle T antigen (PyMT) and 4T1 metastatic breast cancer models from primary tumorigenesis, through pre-metastatic niche formation, to the final stages of metastatic outgrowth at single-cell resolution. Computational analyses of these data revealed a TLR-NFκB inflammatory program enacted by both peripherally derived and tissue-resident myeloid cells that correlated with pre-metastatic niche formation and mirrored CD14+ "activated" myeloid cells in the primary tumor. Moreover, we observed that primary tumor and metastatic niche natural killer (NK) cells are differentially regulated in mice and human patient samples, with the metastatic niche featuring elevated cytotoxic NK cell proportions. Finally, we identified cell-type-specific dynamic regulation of IGF1 and CCL6 signaling during metastatic progression that represents anti-metastatic immunotherapy candidate pathways.
    Keywords:  NF-κB; TLR; cancer immunology; immunosuppression; inflammation; metastasis; myeloid; natural killer cells; single-cell genomics
    DOI:  https://doi.org/10.1016/j.ccell.2024.05.004
  21. Sci Rep. 2024 May 31. 14(1): 12521
    Regulation of TSC2 lysosome translocation and mitochondrial turnover by TSC2 acetylation status.
    Patricia Marqués, Jesús Burillo, Carlos González-Blanco, Beatriz Jiménez, Gema García, Ana García-Aguilar, Sarai Iglesias-Fortes, Ángela Lockwood, Carlos Guillén.
      Sirtuin1 (SIRT1) activity decreases the tuberous sclerosis complex 2 (TSC2) lysine acetylation status, inhibiting the mechanistic target of rapamycin complex 1 (mTORC1) signalling and concomitantly, activating autophagy. This study analyzes the role of TSC2 acetylation levels in its translocation to the lysosome and the mitochondrial turnover in both mouse embryonic fibroblast (MEF) and in mouse insulinoma cells (MIN6) as a model of pancreatic β cells. Resveratrol (RESV), an activator of SIRT1 activity, promotes TSC2 deacetylation and its translocation to the lysosome, inhibiting mTORC1 activity. An improvement in mitochondrial turnover was also observed in cells treated with RESV, associated with an increase in the fissioned mitochondria, positive autophagic and mitophagic fluxes and an enhancement of mitochondrial biogenesis. This study proves that TSC2 in its deacetylated form is essential for regulating mTORC1 signalling and the maintenance of the mitochondrial quality control, which is involved in the homeostasis of pancreatic beta cells and prevents from several metabolic disorders such as Type 2 Diabetes Mellitus.
    Keywords:  Acetylation; Lysosome; Mitophagy; Pancreatic β cells; TSC2; mTORC1
    DOI:  https://doi.org/10.1038/s41598-024-63525-7
  22. Chem Sci. 2024 May 29. 15(21): 8080-8088
    A mitochondrial-targeted activity-based sensing probe for ratiometric imaging of formaldehyde reveals key regulators of the mitochondrial one-carbon pool.
    Logan Tenney, Vanha N Pham, Thomas F Brewer, Christopher J Chang.
      Formaldehyde (FA) is both a highly reactive environmental genotoxin and an endogenously produced metabolite that functions as a signaling molecule and one-carbon (1C) store to regulate 1C metabolism and epigenetics in the cell. Owing to its signal-stress duality, cells have evolved multiple clearance mechanisms to maintain FA homeostasis, acting to avoid the established genotoxicity of FA while also redirecting FA-derived carbon units into the biosynthesis of essential nucleobases and amino acids. The highly compartmentalized nature of FA exposure, production, and regulation motivates the development of chemical tools that enable monitoring of transient FA fluxes with subcellular resolution. Here we report a mitochondrial-targeted, activity-based sensing probe for ratiometric FA detection, MitoRFAP-2, and apply this reagent to monitor endogenous mitochondrial sources and sinks of this 1C unit. We establish the utility of subcellular localization by showing that MitoRFAP-2 is sensitive enough to detect changes in mitochondrial FA pools with genetic and pharmacological modulation of enzymes involved in 1C and amino acid metabolism, including the pervasive, less active genetic mutant aldehyde dehydrogenase 2*2 (ALDH2*2), where previous, non-targeted versions of FA sensors are not. Finally, we used MitoRFAP-2 to comparatively profile basal levels of FA across a panel of breast cancer cell lines, finding that FA-dependent fluorescence correlates with expression levels of enzymes involved in 1C metabolism. By showcasing the ability of MitoRFAP-2 to identify new information on mitochondrial FA homeostasis, this work provides a starting point for the design of a broader range of chemical probes for detecting physiologically important aldehydes with subcellular resolution and a useful reagent for further studies of 1C biology.
    DOI:  https://doi.org/10.1039/d4sc01183j
  23. Commun Biol. 2024 May 29. 7(1): 659
    Fasting alleviates metabolic alterations in mice with propionyl-CoA carboxylase deficiency due to Pcca mutation.
    Wentao He, Hannah Marchuk, Dwight Koeberl, Takhar Kasumov, Xiaoxin Chen, Guo-Fang Zhang.
      Propionic acidemia (PA), resulting from Pcca or Pccb gene mutations, impairs propionyl-CoA metabolism and induces metabolic alterations. While speculation exists that fasting might exacerbate metabolic crises in PA patients by accelerating the breakdown of odd-chain fatty acids and amino acids into propionyl-CoA, direct evidence is lacking. Our investigation into the metabolic effects of fasting in Pcca-/-(A138T) mice, a PA model, reveals surprising outcomes. Propionylcarnitine, a PA biomarker, decreases during fasting, along with the C3/C2 (propionylcarnitine/acetylcarnitine) ratio, ammonia, and methylcitrate. Although moderate amino acid catabolism to propionyl-CoA occurs with a 23-h fasting, a significant reduction in microbiome-produced propionate and increased fatty acid oxidation mitigate metabolic alterations by decreasing propionyl-CoA synthesis and enhancing acetyl-CoA synthesis. Fasting-induced gluconeogenesis further facilitates propionyl-CoA catabolism without changing propionyl-CoA carboxylase activity. These findings suggest that fasting may alleviate metabolic alterations in Pcca-/-(A138T) mice, prompting the need for clinical evaluation of its potential impact on PA patients.
    DOI:  https://doi.org/10.1038/s42003-024-06362-8
  24. FEBS Lett. 2024 May 27.
    The age-related decline of helicase function-how G-quadruplex structures promote genome instability.
    Joana Frobel, Robert Hänsel-Hertsch.
      The intricate mechanisms underlying transcription-dependent genome instability involve G-quadruplexes (G4) and R-loops. This perspective elucidates the potential link between these structures and genome instability in aging. The co-occurrence of G4 DNA and RNA-DNA hybrid structures (G-loop) underscores a complex interplay in genome regulation and instability. Here, we hypothesize that the age-related decline of sirtuin function leads to an increase in acetylated helicases that bind to G4 DNA and RNA-DNA hybrid structures, but are less efficient in resolving them. We propose that acetylated, less active, helicases induce persistent G-loop structures, promoting transcription-dependent genome instability in aging.
    Keywords:  G4; G‐quadruplex; RNA–DNA hybrids; R‐loops; aging; double‐strand breaks; epigenetics; genome instability; helicases; sirtuins
    DOI:  https://doi.org/10.1002/1873-3468.14939
  25. Nat Metab. 2024 May;6(5): 847-860
    Hippo-YAP/TAZ signalling coordinates adipose plasticity and energy balance by uncoupling leptin expression from fat mass.
    Sungwoo Choi, Ju-Gyeong Kang, Yen T H Tran, Sun-Hye Jeong, Kun-Young Park, Hyemi Shin, Young Hoon Kim, Myungsun Park, Hahn Nahmgoong, Taejun Seol, Haeyon Jeon, Yeongmin Kim, Sanghee Park, Hee-Joo Kim, Min-Seob Kim, Xiaoxu Li, Maroun Bou Sleiman, Eries Lee, Jinhyuk Choi, David Eisenbarth, Sang Heon Lee, Suhyeon Cho, David D Moore, Johan Auwerx, Il-Young Kim, Jae Bum Kim, Jong-Eun Park, Dae-Sik Lim, Jae Myoung Suh.
      Adipose tissues serve as an energy reservoir and endocrine organ, yet the mechanisms that coordinate these functions remain elusive. Here, we show that the transcriptional coregulators, YAP and TAZ, uncouple fat mass from leptin levels and regulate adipocyte plasticity to maintain metabolic homeostasis. Activating YAP/TAZ signalling in adipocytes by deletion of the upstream regulators Lats1 and Lats2 results in a profound reduction in fat mass by converting mature adipocytes into delipidated progenitor-like cells, but does not cause lipodystrophy-related metabolic dysfunction, due to a paradoxical increase in circulating leptin levels. Mechanistically, we demonstrate that YAP/TAZ-TEAD signalling upregulates leptin expression by directly binding to an upstream enhancer site of the leptin gene. We further show that YAP/TAZ activity is associated with, and functionally required for, leptin regulation during fasting and refeeding. These results suggest that adipocyte Hippo-YAP/TAZ signalling constitutes a nexus for coordinating adipose tissue lipid storage capacity and systemic energy balance through the regulation of adipocyte plasticity and leptin gene transcription.
    DOI:  https://doi.org/10.1038/s42255-024-01045-4
  26. Nat Commun. 2024 May 25. 15(1): 4469
    Rab30 facilitates lipid homeostasis during fasting.
    Danielle M Smith, Brian Y Liu, Michael J Wolfgang.
      To facilitate inter-tissue communication and the exchange of proteins, lipoproteins, and metabolites with the circulation, hepatocytes have an intricate and efficient intracellular trafficking system regulated by small Rab GTPases. Here, we show that Rab30 is induced in the mouse liver by fasting, which is amplified in liver-specific carnitine palmitoyltransferase 2 knockout mice (Cpt2L-/-) lacking the ability to oxidize fatty acids, in a Pparα-dependent manner. Live-cell super-resolution imaging and in vivo proximity labeling demonstrates that Rab30-marked vesicles are highly dynamic and interact with proteins throughout the secretory pathway. Rab30 whole-body, liver-specific, and Rab30; Cpt2 liver-specific double knockout (DKO) mice are viable with intact Golgi ultrastructure, although Rab30 deficiency in DKO mice suppresses the serum dyslipidemia observed in Cpt2L-/- mice. Corresponding with decreased serum triglyceride and cholesterol levels, DKO mice exhibit decreased circulating but not hepatic ApoA4 protein, indicative of a trafficking defect. Together, these data suggest a role for Rab30 in the selective sorting of lipoproteins to influence hepatocyte and circulating triglyceride levels, particularly during times of excessive lipid burden.
    DOI:  https://doi.org/10.1038/s41467-024-48959-x
  27. Redox Biol. 2024 May 25. pii: S2213-2317(24)00191-5. [Epub ahead of print]73 103213
    Cystine/glutamate antiporter xCT controls skeletal muscle glutathione redox, bioenergetics and differentiation.
    Michel N Kanaan, Chantal A Pileggi, Charbel Y Karam, Luke S Kennedy, Claire Fong-McMaster, Miroslava Cuperlovic-Culf, Mary-Ellen Harper.
      Cysteine, the rate-controlling amino acid in cellular glutathione synthesis is imported as cystine, by the cystine/glutamate antiporter, xCT, and subsequently reduced to cysteine. As glutathione redox is important in muscle regeneration in aging, we hypothesized that xCT exerts upstream control over skeletal muscle glutathione redox, metabolism and regeneration. Bioinformatic analyses of publicly available datasets revealed that expression levels of xCT and GSH-related genes are inversely correlated with myogenic differentiation genes. Muscle satellite cells (MuSCs) isolated from Slc7a11sut/sut mice, which harbour a mutation in the Slc7a11 gene encoding xCT, required media supplementation with 2-mercaptoethanol to support cell proliferation but not myotube differentiation, despite persistently lower GSH. Slc7a11sut/sut primary myotubes were larger compared to WT myotubes, and also exhibited higher glucose uptake and cellular oxidative capacities. Immunostaining of myogenic markers (Pax7, MyoD, and myogenin) in cardiotoxin-damaged tibialis anterior muscle fibres revealed greater MuSC activation and commitment to differentiation in Slc7a11sut/sut muscle compared to WT mice, culminating in larger myofiber cross-sectional areas at 21 days post-injury. Slc7a11sut/sut mice subjected to a 5-week exercise training protocol demonstrated enhanced insulin tolerance compared to WT mice, but blunted muscle mitochondrial biogenesis and respiration in response to exercise training. Our results demonstrate that the absence of xCT inhibits cell proliferation but promotes myotube differentiation by regulating cellular metabolism and glutathione redox. Altogether, these results support the notion that myogenesis is a redox-regulated process and may help inform novel therapeutic approaches for muscle wasting and dysfunction in aging and disease.
    Keywords:  Glutathione; Glycolysis; Mitochondria; Myogenesis; Oxidative phosphorylation; Redox
    DOI:  https://doi.org/10.1016/j.redox.2024.103213
  28. Nat Rev Cancer. 2024 May 29.
    No mutation, tumour initiation.
    Daniela Senft.
      
    DOI:  https://doi.org/10.1038/s41568-024-00711-9
  29. Cell Res. 2024 May 27.
    Illuminating the path to pancreatic cancer.
    Hiroyuki Kato, Nabeel Bardeesy.
      
    DOI:  https://doi.org/10.1038/s41422-024-00982-9
  30. Front Endocrinol (Lausanne). 2024 ;15 1414463
    Dual sources of melatonin and evidence for different primary functions.
    Russel J Reiter, Ramaswamy Sharma, Dun-Xian Tan, Luiz Gustavo de Almieda Chuffa, Danilo Grunig Humberto da Silva, Andrzej T Slominski, Kerstin Steinbrink, Konrad Kleszczynski.
      This article discusses data showing that mammals, including humans, have two sources of melatonin that exhibit different functions. The best-known source of melatonin, herein referred to as Source #1, is the pineal gland. In this organ, melatonin production is circadian with maximal synthesis and release into the blood and cerebrospinal fluid occurring during the night. Of the total amount of melatonin produced in mammals, we speculate that less than 5% is synthesized by the pineal gland. The melatonin rhythm has the primary function of influencing the circadian clock at the level of the suprachiasmatic nucleus (the CSF melatonin) and the clockwork in all peripheral organs (the blood melatonin) via receptor-mediated actions. A second source of melatonin (Source # 2) is from multiple tissues throughout the body, probably being synthesized in the mitochondria of these cells. This constitutes the bulk of the melatonin produced in mammals and is concerned with metabolic regulation. This review emphasizes the action of melatonin from peripheral sources in determining re-dox homeostasis, but it has other critical metabolic effects as well. Extrapineal melatonin synthesis does not exhibit a circadian rhythm and it is not released into the blood but acts locally in its cell of origin and possibly in a paracrine matter on adjacent cells. The factors that control/influence melatonin synthesis at extrapineal sites are unknown. We propose that the concentration of melatonin in these cells is determined by the subcellular redox state and that melatonin synthesis may be inducible under stressful conditions as in plant cells.
    Keywords:  cell metabolism; cerebrospinal fluid; circadian rhythms; extrapineal melatonin; free radicals; mitochondria; redox homeostasis; suprachiasmatic nucleus
    DOI:  https://doi.org/10.3389/fendo.2024.1414463
  31. J Theor Biol. 2024 May 23. pii: S0022-5193(24)00133-4. [Epub ahead of print]590 111852
    The influence of circadian rhythms on CD8+ T cell activation upon vaccination: A mathematical modeling perspective.
    Nasri Balit, Nicolas Cermakian, Anmar Khadra.
      Circadian rhythms have been implicated in the modulation of many physiological processes, including those associated with the immune system. For example, these rhythms influence CD8+ T cell responses within the adaptive immune system. The mechanism underlying this immune-circadian interaction, however, remains unclear, particularly in the context of vaccination. Here, we devise a molecularly-explicit gene regulatory network model of early signaling in the naïve CD8+ T cell activation pathway, comprised of three axes (or subsystems) labeled ZAP70, LAT and CD28, to elucidate the molecular details of this immune-circadian mechanism and its relation to vaccination. This is done by coupling the model to a periodic forcing function to identify the molecular players targeted by circadian rhythms, and analyzing how these rhythms subsequently affect CD8+ T cell activation under differing levels of T cell receptor (TCR) phosphorylation, which we designate as vaccine load. By performing both bifurcation and parameter sensitivity analyses on the model at the single cell and ensemble levels, we find that applying periodic forcing on molecular targets within the ZAP70 axis is sufficient to create a day-night discrepancy in CD8+ T cell activation in a manner that is dependent on the bistable switch inherent in CD8+ T cell early signaling. We also demonstrate that the resulting CD8+ T cell activation is dependent on the strength of the periodic coupling as well as on the level of TCR phosphorylation. Our results show that this day-night discrepancy is not transmitted to certain downstream molecules within the LAT subsystem, such as mTORC1, suggesting a secondary, independent circadian regulation on that protein complex. We also corroborate experimental results by showing that the circadian regulation of CD8+ T cell primarily acts at a baseline, pre-vaccination state, playing a facilitating role in priming CD8+ T cells to vaccine inputs according to the time of day. By applying an ensemble level analysis using bifurcation theory and by including several hypothesized molecular targets of this circadian rhythm, we further demonstrate an increased variability between CD8+ T cells (due to heterogeneity) induced by its circadian regulation, which may allow an ensemble of CD8+ T cells to activate at a lower vaccine load, improving its sensitivity. This modeling study thus provides insights into the immune targets of the circadian clock, and proposes an interaction between vaccine load and the influence of circadian rhythms on CD8+ T cell activation.
    Keywords:  Adaptive immunity; Bifurcation analysis; Bistable switch; CD8(＋) T cells; Circadian rhythm; Ensemble level bistable switch; Mathematical modeling; PRCC; Vaccination dynamics
    DOI:  https://doi.org/10.1016/j.jtbi.2024.111852
  32. Proc Natl Acad Sci U S A. 2024 Jun 04. 121(23): e2316858121
    Phosphorylation of DNA-binding domains of CLOCK-BMAL1 complex for PER-dependent inhibition in circadian clock of mammalian cells.
    Yuta Otobe, Eui Min Jeong, Shunsuke Ito, Yuta Shinohara, Nobuhiro Kurabayashi, Atsu Aiba, Yoshitaka Fukada, Jae Kyoung Kim, Hikari Yoshitane.
      In mammals, CLOCK and BMAL1 proteins form a heterodimer that binds to E-box sequences and activates transcription of target genes, including Period (Per). Translated PER proteins then bind to the CLOCK-BMAL1 complex to inhibit its transcriptional activity. However, the molecular mechanism and the impact of this PER-dependent inhibition on the circadian clock oscillation remain elusive. We previously identified Ser38 and Ser42 in a DNA-binding domain of CLOCK as phosphorylation sites at the PER-dependent inhibition phase. In this study, knockout rescue experiments showed that nonphosphorylatable (Ala) mutations at these sites shortened circadian period, whereas their constitutive-phospho-mimetic (Asp) mutations completely abolished the circadian rhythms. Similarly, we found that nonphosphorylatable (Ala) and constitutive-phospho-mimetic (Glu) mutations at Ser78 in a DNA-binding domain of BMAL1 also shortened the circadian period and abolished the rhythms, respectively. The mathematical modeling predicted that these constitutive-phospho-mimetic mutations weaken the DNA binding of the CLOCK-BMAL1 complex and that the nonphosphorylatable mutations inhibit the PER-dependent displacement (reduction of DNA-binding ability) of the CLOCK-BMAL1 complex from DNA. Biochemical experiments supported the importance of these phosphorylation sites for displacement of the complex in the PER2-dependent inhibition. Our results provide direct evidence that phosphorylation of CLOCK-Ser38/Ser42 and BMAL1-Ser78 plays a crucial role in the PER-dependent inhibition and the determination of the circadian period.
    Keywords:  CRISPR-Cas9; DNA binding; circadian rhythm; mathematical modeling; phosphorylation
    DOI:  https://doi.org/10.1073/pnas.2316858121
  33. bioRxiv. 2024 May 18. pii: 2024.05.15.594133. [Epub ahead of print]
    CPT2 mediated fatty acid oxidation is dispensable for humoral immunity.
    Meilu Li, Xian Zhou, Xingxing Zhu, Yanfeng Li, Taro Hitosugi, Yuzhen Li, Hu Zeng.
      B cell activation is accompanied by dynamic metabolic reprogramming, supported by a multitude of nutrients that include glucose, amino acids and fatty acids. While several studies have indicated that fatty acid mitochondrial oxidation is critical for immune cell functions, contradictory findings have been reported. Carnitine palmitoyltransferase II (CPT2) is a critical enzyme for long-chain fatty acid oxidation in mitochondria. Here, we test the requirement of CPT2 for humoral immunity using a mouse model with a lymphocyte specific deletion of CPT2. Stable 13 C isotope tracing reveals highly reduced fatty acid-derived citrate production in CPT2 deficient B cells. Yet, CPT2 deficiency has no significant impact on B cell development, B cell activation, germinal center formation, and antibody production upon either thymus-dependent or -independent antigen challenges. Together, our findings indicate that CPT2 mediated fatty acid oxidation is dispensable for humoral immunity, highlighting the metabolic flexibility of lymphocytes.
    DOI:  https://doi.org/10.1101/2024.05.15.594133
  34. J Biol Chem. 2024 May 23. pii: S0021-9258(24)01913-6. [Epub ahead of print] 107412
    Reciprocal Regulation of Cardiac β-Oxidation and Pyruvate Dehydrogenase by Insulin.
    Abdallah Elnwasany, Heba A Ewida, Ivan Menendez-Montes, Monika Mizerska, Xiaorong Fu, Chai-Wan Kim, Jay D Horton, Shawn C Burgess, Beverly A Rothermel, Pamela A Szweda, Luke I Szweda.
      The heart alters the rate and relative oxidation of fatty acids and glucose based on availability and energetic demand. Insulin plays a crucial role in this process diminishing fatty acid and increasing glucose oxidation when glucose availability increases. Loss of insulin sensitivity and metabolic flexibility can result in cardiovascular disease. It is therefore important to identify mechanisms by which insulin regulates substrate utilization in the heart. Mitochondrial pyruvate dehydrogenase (PDH) is the key regulatory site for the oxidation of glucose for ATP production. Nevertheless, the impact of insulin on PDH activity has not been fully delineated, particularly in the heart. We sought in vivo evidence that insulin stimulates cardiac PDH and that this process is driven by inhibition of fatty acid oxidation. Mice injected with insulin exhibited dephosphorylation and activation of cardiac PDH. This was accompanied by an increase in the content of malonyl-CoA, an inhibitor of carnitine palmitoyltransferase 1 (CPT1) and, thus, mitochondrial import of fatty acids. Administration of the CPT1 inhibitor oxfenicine was sufficient to activate PDH. Malonyl-CoA is produced by acetyl-CoA carboxylase (ACC). Pharmacologic inhibition or knockout of cardiac ACC diminished insulin-dependent production of malonyl-CoA and activation of PDH. Finally, circulating insulin and cardiac glucose utilization exhibit daily rhythms reflective of nutritional status. We demonstrate that time of day-dependent changes in PDH activity are mediated, in part, by ACC-dependent production of malonyl-CoA. Thus, by inhibiting fatty acid oxidation, insulin reciprocally activates PDH. These studies identify potential molecular targets to promote cardiac glucose oxidation and treat heart disease.
    Keywords:  Acetyl-CoA Carboxylase; Heart; Insulin; Malonyl-CoA; Mitochondria; Pyruvate Dehydrogenase; β-Oxidation
    DOI:  https://doi.org/10.1016/j.jbc.2024.107412
  35. EMBO Rep. 2024 May 28.
    Chronic spindle assembly checkpoint activation causes myelosuppression and gastrointestinal atrophy.
    Gerlinde Karbon, Fabian Schuler, Vincent Z Braun, Felix Eichin, Manuel Haschka, Mathias Drach, Rocio Sotillo, Stephan Geley, Diana Cj Spierings, Andrea E Tijhuis, Floris Foijer, Andreas Villunger.
      Interference with microtubule dynamics in mitosis activates the spindle assembly checkpoint (SAC) to prevent chromosome segregation errors. The SAC induces mitotic arrest by inhibiting the anaphase-promoting complex (APC) via the mitotic checkpoint complex (MCC). The MCC component MAD2 neutralizes the critical APC cofactor, CDC20, preventing exit from mitosis. Extended mitotic arrest can promote mitochondrial apoptosis and caspase activation. However, the impact of mitotic cell death on tissue homeostasis in vivo is ill-defined. By conditional MAD2 overexpression, we observe that chronic SAC activation triggers bone marrow aplasia and intestinal atrophy in mice. While myelosuppression can be compensated for, gastrointestinal atrophy is detrimental. Remarkably, deletion of pro-apoptotic Bim/Bcl2l11 prevents gastrointestinal syndrome, while neither loss of Noxa/Pmaip or co-deletion of Bid and Puma/Bbc3 has such a protective effect, identifying BIM as rate-limiting apoptosis effector in mitotic cell death of the gastrointestinal epithelium. In contrast, only overexpression of anti-apoptotic BCL2, but none of the BH3-only protein deficiencies mentioned above, can mitigate myelosuppression. Our findings highlight tissue and cell-type-specific survival dependencies in response to SAC perturbation in vivo.
    Keywords:  Apoptosis; BH3-only Proteins; MAD2; Mitosis; Spindle Assembly Checkpoint
    DOI:  https://doi.org/10.1038/s44319-024-00160-3
  36. Cell Rep. 2024 May 29. pii: S2211-1247(24)00622-3. [Epub ahead of print]43(6): 114294
    TBK1 is ubiquitinated by TRIM5α to assemble mitophagy machinery.
    Bhaskar Saha, Hallvard Olsvik, Geneva L Williams, Seeun Oh, Gry Evjen, Eva Sjøttem, Michael A Mandell.
      Ubiquitination of mitochondrial proteins provides a basis for the downstream recruitment of mitophagy machinery, yet whether ubiquitination of the machinery itself contributes to mitophagy is unknown. Here, we show that K63-linked polyubiquitination of the key mitophagy regulator TBK1 is essential for its mitophagy functions. This modification is catalyzed by the ubiquitin ligase TRIM5α and is required for TBK1 to interact with and activate a set of ubiquitin-binding autophagy adaptors including NDP52, p62/SQSTM1, and NBR1. Autophagy adaptors, along with TRIM27, enable TRIM5α to engage with TBK1 following mitochondrial damage. TRIM5α's ubiquitin ligase activity is required for the accumulation of active TBK1 on damaged mitochondria in Parkin-dependent and Parkin-independent mitophagy pathways. Our data support a model in which TRIM5α provides a mitochondria-localized, ubiquitin-based, self-amplifying assembly platform for TBK1 and mitophagy adaptors that is ultimately necessary for the recruitment of the core autophagy machinery.
    Keywords:  CP: Cell biology; NBR1; NDP52; Optineurin; TAX1BP1; TBK1; TRIM27/RFP; autophagy; p62; tripartite motif; ubiquitin ligase
    DOI:  https://doi.org/10.1016/j.celrep.2024.114294
  37. Nat Metab. 2024 May 27.
    METLIN-CCS Lipid Database: An authentic standards resource for lipid classification and identification.
    Erin S Baker, Winnie Uritboonthai, Aries Aisporna, Corey Hoang, Heino M Heyman, Lisa Connell, Damien Olivier-Jimenez, Martin Giera, Gary Siuzdak.
      
    DOI:  https://doi.org/10.1038/s42255-024-01058-z
  38. Biochim Biophys Acta Mol Cell Biol Lipids. 2024 May 23. pii: S1388-1981(24)00064-7. [Epub ahead of print]1869(6): 159514
    Phospholipid isotope tracing suggests β-catenin-driven suppression of phosphatidylcholine metabolism in hepatocellular carcinoma.
    Chad VanSant-Webb, Hayden K Low, Junko Kuramoto, Claire E Stanley, Hantao Qiang, Audrey Y Su, Alexis N Ross, Chad G Cooper, James E Cox, Scott A Summers, Kimberley J Evason, Gregory S Ducker.
      Activating mutations in the CTNNB1 gene encoding β-catenin are among the most frequently observed oncogenic alterations in hepatocellular carcinoma (HCC). Profound alterations in lipid metabolism, including increases in fatty acid oxidation and transformation of the phospholipidome, occur in HCC with CTNNB1 mutations, but it is unclear what mechanisms give rise to these changes. We employed untargeted lipidomics and targeted isotope tracing to measure phospholipid synthesis activity in an inducible human liver cell line expressing mutant β-catenin, as well as in transgenic zebrafish with activated β-catenin-driven HCC. In both models, activated β-catenin expression was associated with large changes in the lipidome including conserved increases in acylcarnitines and ceramides and decreases in triglycerides. Lipid isotope tracing analysis in human cells revealed a reduction in phosphatidylcholine (PC) production rates as assayed by choline incorporation. We developed lipid isotope tracing analysis for zebrafish tumors and observed reductions in phosphatidylcholine synthesis by both the CDP-choline and PEMT pathways. The observed changes in the β-catenin-driven HCC phospholipidome suggest that zebrafish can recapitulate conserved features of HCC lipid metabolism and may serve as a model for identifying future HCC-specific lipid metabolic targets.
    Keywords:  Ceramides; Hepatocellular carcinoma; Isotope tracing; Lipid metabolism; Phospholipids; Zebrafish
    DOI:  https://doi.org/10.1016/j.bbalip.2024.159514
  39. Dev Cell. 2024 May 24. pii: S1534-5807(24)00266-1. [Epub ahead of print]
    Tissue-specific landscape of protein aggregation and quality control in an aging vertebrate.
    Yiwen R Chen, Itamar Harel, Param Priya Singh, Inbal Ziv, Eitan Moses, Uri Goshtchevsky, Ben E Machado, Anne Brunet, Daniel F Jarosz.
      Protein aggregation is a hallmark of age-related neurodegeneration. Yet, aggregation during normal aging and in tissues other than the brain is poorly understood. Here, we leverage the African turquoise killifish to systematically profile protein aggregates in seven tissues of an aging vertebrate. Age-dependent aggregation is strikingly tissue specific and not simply driven by protein expression differences. Experimental interrogation in killifish and yeast, combined with machine learning, indicates that this specificity is linked to protein-autonomous biophysical features and tissue-selective alterations in protein quality control. Co-aggregation of protein quality control machinery during aging may further reduce proteostasis capacity, exacerbating aggregate burden. A segmental progeria model with accelerated aging in specific tissues exhibits selectively increased aggregation in these same tissues. Intriguingly, many age-related protein aggregates arise in wild-type proteins that, when mutated, drive human diseases. Our data chart a comprehensive landscape of protein aggregation during vertebrate aging and identify strong, tissue-specific associations with dysfunction and disease.
    Keywords:  aggregates; aging; multi-tissue; protein homeostasis; proteomics; systems biology
    DOI:  https://doi.org/10.1016/j.devcel.2024.04.014
  40. EMBO J. 2024 May 29.
    TRP14 is the rate-limiting enzyme for intracellular cystine reduction and regulates proteome cysteinylation.
    Pablo Martí-Andrés, Isabela Finamor, Isabel Torres-Cuevas, Salvador Pérez, Sergio Rius-Pérez, Hildegard Colino-Lage, David Guerrero-Gómez, Esperanza Morato, Anabel Marina, Patrycja Michalska, Rafael León, Qing Cheng, Eszter Petra Jurányi, Klaudia Borbényi-Galambos, Iván Millán, Péter Nagy, Antonio Miranda-Vizuete, Edward E Schmidt, Antonio Martínez-Ruiz, Elias Sj Arnér, Juan Sastre.
      It has remained unknown how cells reduce cystine taken up from the extracellular space, which is a required step for further utilization of cysteine in key processes such as protein or glutathione synthesis. Here, we show that the thioredoxin-related protein of 14 kDa (TRP14, encoded by TXNDC17) is the rate-limiting enzyme for intracellular cystine reduction. When TRP14 is genetically knocked out, cysteine synthesis through the transsulfuration pathway becomes the major source of cysteine in human cells, and knockout of both pathways becomes lethal in C. elegans subjected to proteotoxic stress. TRP14 can also reduce cysteinyl moieties on proteins, rescuing their activities as here shown with cysteinylated peroxiredoxin 2. Txndc17 knockout mice were, surprisingly, protected in an acute pancreatitis model, concomitant with activation of Nrf2-driven antioxidant pathways and upregulation of transsulfuration. We conclude that TRP14 is the evolutionarily conserved enzyme principally responsible for intracellular cystine reduction in C. elegans, mice, and humans.
    Keywords:  Acute Pancreatitis; Cysteine Homeostasis; Protein Cysteinylation; Proteotoxic Stress; Transsulfuration
    DOI:  https://doi.org/10.1038/s44318-024-00117-1
  41. Nat Genet. 2024 May 28.
    Novel somatic mutations in blood driving age-related clonal hematopoiesis.
      
    DOI:  https://doi.org/10.1038/s41588-024-01756-0
  42. JCI Insight. 2024 May 30. pii: e174329. [Epub ahead of print]
    Drug screening in human physiologic medium identifies uric acid as an inhibitor of rigosertib efficacy.
    Vipin Rawat, Patrick DeLear, Prarthana Prashanth, Mete Emir Ozgurses, Anteneh Tebeje, Philippa A Burns, Kelly O Conger, Christopher Solís, Yasir Hasnain, Anna Novikova, Jennifer E Endress, Paloma González-Sánchez, Wentao Dong, Greg Stephanopoulos, Gina M DeNicola, Isaac Harris, David Sept, Frank M Mason, Jonathan L Coloff.
      The non-physiological nutrient levels found in traditional culture media have been shown to affect numerous aspects of cancer cell physiology, including how cells respond to certain therapeutic agents. Here, we comprehensively evaluated how physiological nutrient levels impact therapeutic response by performing drug screening in human plasma-like medium (HPLM). We observed dramatic nutrient-dependent changes in sensitivity to a variety of FDA-approved and clinically trialed compounds including rigosertib, an experimental cancer therapeutic that has recently failed in phase 3 clinical trials. Mechanistically, we found that the ability of rigosertib to destabilize microtubules is strongly inhibited by the purine metabolism end product uric acid, which is uniquely abundant in humans relative to traditional in vitro and in vivo cancer models. These results demonstrate the broad and dramatic effects nutrient levels can have on drug response, and how incorporation of human-specific physiological nutrient media might help to identify compounds whose efficacy could be impacted in humans.
    Keywords:  Cancer; Cell biology; Cytoskeleton; Drug screens; Oncology
    DOI:  https://doi.org/10.1172/jci.insight.174329
  43. Dev Cell. 2024 May 23. pii: S1534-5807(24)00299-5. [Epub ahead of print]
    Epithelial aPKC deficiency leads to stem cell loss preceding metaplasia in colorectal cancer initiation.
    Hiroto Kinoshita, Anxo Martinez-Ordoñez, Tania Cid-Diaz, Qixiu Han, Angeles Duran, Yu Muta, Xiao Zhang, Juan F Linares, Yuki Nakanishi, Hiroaki Kasashima, Masakazu Yashiro, Kiyoshi Maeda, Ana Albaladejo-Gonzalez, Daniel Torres-Moreno, José García-Solano, Pablo Conesa-Zamora, Giorgio Inghirami, Maria T Diaz-Meco, Jorge Moscat.
      The early mechanisms of spontaneous tumor initiation that precede malignancy are largely unknown. We show that reduced aPKC levels correlate with stem cell loss and the induction of revival and metaplastic programs in serrated- and conventional-initiated premalignant lesions, which is perpetuated in colorectal cancers (CRCs). Acute inactivation of PKCλ/ι in vivo and in mouse organoids is sufficient to stimulate JNK in non-transformed intestinal epithelial cells (IECs), which promotes cell death and the rapid loss of the intestinal stem cells (ISCs), including those that are LGR5+. This is followed by the accumulation of revival stem cells (RSCs) at the bottom of the crypt and fetal-metaplastic cells (FMCs) at the top, creating two spatiotemporally distinct cell populations that depend on JNK-induced AP-1 and YAP. These cell lineage changes are maintained during cancer initiation and progression and determine the aggressive phenotype of human CRC, irrespective of their serrated or conventional origin.
    Keywords:  AP-1; JNK; Yap; aPKC; cell death; colorectal cancer; intestinal stem cell; metaplasia; preneoplasia; tumor initiation
    DOI:  https://doi.org/10.1016/j.devcel.2024.05.001
  44. Haematologica. 2024 May 30.
    The glutamate/aspartate transporter EAAT1 is crucial for T-cell acute lymphoblastic leukemia proliferation and survival.
    Vesna S Stanulović, Shorog Al Omair, Michelle A C Reed, Jennie Roberts, Sandeep Potluri, Taylor Fulton-Ward, Nancy Gudgeon, Emma L Bishop, Juliette Roels, Tracey A Perry, Sovan Sarkar, Guy Pratt, Tom Taghon, Sarah Dimeloe, Ulrich L Günther, Christian Ludwig, Maarten Hoogenkamp.
      T-cell acute lymphoblastic leukemia (T-ALL) is a cancer of the immune system. Approximately 20% of paediatric and 50% of adult T-ALL patients have refractory disease or relapse and die from the disease. To improve patient outcome new therapeutics are needed. With the aim to identify new therapeutic targets, we combined the analysis of T-ALL gene expression and metabolism to identify the metabolic adaptations that T-ALL cells exhibit. We found that glutamine uptake is essential for T-ALL proliferation. Isotope tracing experiments showed that glutamine fuels aspartate synthesis through the TCA cycle and that glutamine and glutamine-derived aspartate together supply three nitrogen atoms in purines and all but one atom in pyrimidine rings. We show that the glutamate-aspartate transporter EAAT1 (SLC1A3), which is normally expressed in the central nervous system, is crucial for glutamine conversion to aspartate and nucleotides and that T-ALL cell proliferation depends on EAAT1 function. Through this work, we identify EAAT1 as a novel therapeutic target for T-ALL treatment.
    DOI:  https://doi.org/10.3324/haematol.2023.283471
  45. Nat Immunol. 2024 May 28.
    Circadian control of tumor immunosuppression affects efficacy of immune checkpoint blockade.
    Bridget M Fortin, Shannon M Pfeiffer, Jacob Insua-Rodríguez, Hamad Alshetaiwi, Alexander Moshensky, Wei A Song, Alisa L Mahieu, Sung Kook Chun, Amber N Lewis, Alex Hsu, Isam Adam, Oliver S Eng, Nicholas R Pannunzio, Marcus M Seldin, Ivan Marazzi, Francesco Marangoni, Devon A Lawson, Kai Kessenbrock, Selma Masri.
      The circadian clock is a critical regulator of immunity, and this circadian control of immune modulation has an essential function in host defense and tumor immunosurveillance. Here we use a single-cell RNA sequencing approach and a genetic model of colorectal cancer to identify clock-dependent changes to the immune landscape that control the abundance of immunosuppressive cells and consequent suppression of cytotoxic CD8+ T cells. Of these immunosuppressive cell types, PD-L1-expressing myeloid-derived suppressor cells (MDSCs) peak in abundance in a rhythmic manner. Disruption of the epithelial cell clock regulates the secretion of cytokines that promote heightened inflammation, recruitment of neutrophils and the subsequent development of MDSCs. We also show that time-of-day anti-PD-L1 delivery is most effective when synchronized with the abundance of immunosuppressive MDSCs. Collectively, these data indicate that circadian gating of tumor immunosuppression informs the timing and efficacy of immune checkpoint inhibitors.
    DOI:  https://doi.org/10.1038/s41590-024-01859-0
  46. Nat Aging. 2024 May 30.
    Aging atlas reveals cell-type-specific effects of pro-longevity strategies.
    Shihong Max Gao, Yanyan Qi, Qinghao Zhang, Youchen Guan, Yi-Tang Lee, Lang Ding, Lihua Wang, Aaron S Mohammed, Hongjie Li, Yusi Fu, Meng C Wang.
      Organismal aging involves functional declines in both somatic and reproductive tissues. Multiple strategies have been discovered to extend lifespan across species. However, how age-related molecular changes differ among various tissues and how those lifespan-extending strategies slow tissue aging in distinct manners remain unclear. Here we generated the transcriptomic Cell Atlas of Worm Aging (CAWA, http://mengwanglab.org/atlas ) of wild-type and long-lived strains. We discovered cell-specific, age-related molecular and functional signatures across all somatic and germ cell types. We developed transcriptomic aging clocks for different tissues and quantitatively determined how three different pro-longevity strategies slow tissue aging distinctively. Furthermore, through genome-wide profiling of alternative polyadenylation (APA) events in different tissues, we discovered cell-type-specific APA changes during aging and revealed how these changes are differentially affected by the pro-longevity strategies. Together, this study offers fundamental molecular insights into both somatic and reproductive aging and provides a valuable resource for in-depth understanding of the diversity of pro-longevity mechanisms.
    DOI:  https://doi.org/10.1038/s43587-024-00631-1
  47. Essays Biochem. 2024 May 30. pii: EBC20230087. [Epub ahead of print]
    Insights into the regulation of malate dehydrogenase: inhibitors, activators, and allosteric modulation by small molecules.
    Betsy M Martinez-Vaz, Alicia L Howard, Varuni K Jamburuthugoda, Kevin P Callahan.
      Cellular metabolism comprises a complex network of biochemical anabolic and catabolic processes that fuel the growth and survival of living organisms. The enzyme malate dehydrogenase (MDH) is most known for its role in oxidizing malate to oxaloacetate (OAA) in the last step of the tricarboxylic acid (TCA) cycle, but it also participates in the malate-aspartate shuttle in the mitochondria as well as the glyoxylate cycle in plants. These pathways and the specific reactions within them are dynamic and must be carefully calibrated to ensure a balance between nutrient/energy supply and demand. MDH structural and functional complexity requires a variety of regulatory mechanisms, including allosteric regulation, feedback, and competitive inhibition, which are often dependent on whether the enzyme is catalyzing its forward or reverse reaction. Given the role of MDH in central metabolism and its potential as a target for therapeutics in both cancer and infectious diseases, there is a need to better understand its regulation. The involvement of MDH in multiple pathways makes it challenging to identify which effectors are critical to its activity. Many of the in vitro experiments examining MDH regulation were done decades ago, and though allosteric sites have been proposed, none to date have been specifically mapped. This review aims to provide an overview of the current knowledge surrounding MDH regulation by its substrate, products, and other intermediates of the TCA cycle while highlighting all the gaps in our understanding of its regulatory mechanisms.
    Keywords:  Malate; activators; allosteric regulation; dehydrogenase; inhibitors; regulation
    DOI:  https://doi.org/10.1042/EBC20230087
  48. Angew Chem Int Ed Engl. 2024 May 28. e202404328
    Fluorescence Lifetime Imaging of Lipid Heterogeneity in the Inner Mitochondrial Membrane with a Super-photostable Environment-Sensitive Probe.
    Junwei Wang, Masayasu Taki, Yohsuke Ohba, Makoto Arita, Shigehiro Yamaguchi.
      The inner mitochondrial membrane (IMM) undergoes dynamic morphological changes, which are crucial for the maintenance of mitochondrial functions as well as cell survival. As the dynamics of the membrane are governed by its lipid components, a fluorescent probe that can sense spatiotemporal alterations in the lipid properties of the IMM over long periods of time is required to understand mitochondrial physiological functions in detail. Herein, we report a red-emissive IMM-labeling reagent with excellent photostability and sensitivity to its environment, which enables the visualization of the IMM ultrastructure using super-resolution microscopy as well as of the lipid heterogeneity based on the fluorescence lifetime at the single mitochondrion level. Combining the probe and fluorescence lifetime imaging microscopy (FLIM) showed that peroxidation of unsaturated lipids in the IMM by reactive oxygen species caused an increase in the membrane order, which took place prior to mitochondrial swelling.
    Keywords:  Fluorescence lifetime imaging; Imaging agents; Inner mitochondrial membrane; Lipid heterogeneity; Phosphorus heterocycles
    DOI:  https://doi.org/10.1002/anie.202404328
  49. Cell Signal. 2024 May 28. pii: S0898-6568(24)00207-9. [Epub ahead of print] 111239
    Exploring the mystery of tumor metabolism: Warburg effect and mitochondrial metabolism fighting side by side.
    Yongxin Yu, Yulang Jiang, Christian Glandorff, Mingyu Sun.
      The metabolic reconfiguration of tumor cells constitutes a pivotal aspect of tumor proliferation and advancement. This study delves into two primary facets of tumor metabolism: the Warburg effect and mitochondrial metabolism, elucidating their contributions to tumor dominance. The Warburg effect facilitates efficient energy acquisition by tumor cells through aerobic glycolysis and lactic acid fermentation, offering metabolic advantages conducive to growth and proliferation. Simultaneously, mitochondrial metabolism, serving as the linchpin of sustained tumor vitality, orchestrates the tricarboxylic acid cycle and electron transport chain, furnishing a steadfast and dependable wellspring of biosynthesis for tumor cells. Regarding targeted therapy, this discourse examines extant strategies targeting tumor glycolysis and mitochondrial metabolism, underscoring their potential efficacy in modulating tumor metabolism while envisaging future research trajectories and treatment paradigms in the realm of tumor metabolism. By means of a thorough exploration of tumor metabolism, this study aspires to furnish crucial insights into the regulation of tumor metabolic processes, thereby furnishing valuable guidance for the development of novel therapeutic modalities. This comprehensive deliberation is poised to catalyze advancements in tumor metabolism research and offer novel perspectives and pathways for the formulation of cancer treatment strategies in the times ahead.
    Keywords:  Metabolic reprogramming; Mitochondria; Targeted therapy; Tumor; Warburg effect
    DOI:  https://doi.org/10.1016/j.cellsig.2024.111239
  50. bioRxiv. 2024 May 15. pii: 2024.05.13.593964. [Epub ahead of print]
    IL-4 Licenses B Cell Activation Through Cholesterol Synthesis.
    Holly R Steach, Autumn G York, Mathias H Skadow, Shuting Chen, Jun Zhao, Kevin J Williams, Quan Zhou, Weu-Yuan Hsieh, J Richard Brewer, Rihao Qu, Justin A Shyer, Christian Harman, Esen Sefik, Walter K Mowell, Will Bailis, Can Cui, Yuval Kluger, Steven J Bensinger, Joe Craft, Richard A Flavell.
      Lymphocyte activation involves a transition from quiescence and associated catabolic metabolism to a metabolic state with noted similarities to cancer cells such as heavy reliance on aerobic glycolysis for energy demands and increased nutrient requirements for biomass accumulation and cell division 1-3 . Following antigen receptor ligation, lymphocytes require spatiotemporally distinct "second signals". These include costimulatory receptor or cytokine signaling, which engage discrete programs that often involve remodeling of organelles and increased nutrient uptake or synthesis to meet changing biochemical demands 4-6 . One such signaling molecule, IL-4, is a highly pleiotropic cytokine that was first identified as a B cell co-mitogen over 30 years ago 7 . However, how IL-4 signaling mechanistically supports B cell proliferation is incompletely understood. Here, using single cell RNA sequencing we find that the cholesterol biosynthetic program is transcriptionally upregulated following IL-4 signaling during the early B cell response to influenza virus infection, and is required for B cell activation in vivo . By limiting lipid availability in vitro , we determine cholesterol to be essential for B cells to expand their endoplasmic reticulum, progress through cell cycle, and proliferate. In sum, we demonstrate that the well-known ability of IL-4 to act as a B cell growth factor is through a previously unknown rewiring of specific lipid anabolic programs, relieving sensitivity of cells to environmental nutrient availability.
    DOI:  https://doi.org/10.1101/2024.05.13.593964
  51. Science. 2024 May 31. 384(6699): eadh8697
    Germline-mediated immunoediting sculpts breast cancer subtypes and metastatic proclivity.
    Kathleen E Houlahan, Aziz Khan, Noah F Greenwald, Cristina Sotomayor Vivas, Robert B West, Michael Angelo, Christina Curtis.
      Tumors with the same diagnosis can have different molecular profiles and response to treatment. It remains unclear when and why these differences arise. Somatic genomic aberrations occur within the context of a highly variable germline genome. Interrogating 5870 breast cancer lesions, we demonstrated that germline-derived epitopes in recurrently amplified genes influence somatic evolution by mediating immunoediting. Individuals with a high germline-epitope burden in human epidermal growth factor receptor 2 (HER2/ERBB2) are less likely to develop HER2-positive breast cancer compared with other subtypes. The same holds true for recurrent amplicons defining three aggressive estrogen receptor (ER)-positive subgroups. Tumors that overcome such immune-mediated negative selection are more aggressive and demonstrate an "immune cold" phenotype. These data show that the germline genome plays a role in dictating somatic evolution.
    DOI:  https://doi.org/10.1126/science.adh8697
  52. Eur J Neurosci. 2024 May 27.
    Loss of temporal coherence in the circadian metabolome across multiple tissues during ageing in mice.
    M Renate Buijink, Michel van Weeghel, Amy Harms, Devika S Murli, Johanna H Meijer, Thomas Hankemeier, Stephan Michel, Laura Kervezee.
      Circadian clock function declines with ageing, which can aggravate ageing-related diseases such as type 2 diabetes and neurodegenerative disorders. Understanding age-related changes in the circadian system at a systemic level can contribute to the development of strategies to promote healthy ageing. The goal of this study was to investigate the impact of ageing on 24-h rhythms in amine metabolites across four tissues in young (2 months of age) and old (22-25 months of age) mice using a targeted metabolomics approach. Liver, plasma, the suprachiasmatic nucleus (SCN; the location of the central circadian clock in the hypothalamus) and the paraventricular nucleus (PVN; a downstream target of the SCN) were collected from young and old mice every 4 h during a 24-h period (n = 6-7 mice per group). Differential rhythmicity analysis revealed that ageing impacts 24-h rhythms in the amine metabolome in a tissue-specific manner. Most profound changes were observed in the liver, in which rhythmicity was lost in 60% of the metabolites in aged mice. Furthermore, we found strong correlations in metabolite levels between the liver and plasma and between the SCN and the PVN in young mice. These correlations were almost completely abolished in old mice. These results indicate that ageing is accompanied by a severe loss of the circadian coordination between tissues and by disturbed rhythmicity of metabolic processes. The tissue-specific impact of ageing may help to differentiate mechanisms of ageing-related disorders in the brain versus peripheral tissues and thereby contribute to the development of potential therapies for these disorders.
    Keywords:  ageing; amine metabolism; chronobiology; circadian rhythms; hypothalamus; liver; metabolomics; plasma
    DOI:  https://doi.org/10.1111/ejn.16428
  53. Redox Biol. 2024 May 23. pii: S2213-2317(24)00185-X. [Epub ahead of print]73 103207
    Redistribution of defective mitochondria-mediated dihydroorotate dehydrogenase imparts 5-fluorouracil resistance in colorectal cancer.
    Shuohui Dong, Mingguang Zhang, Zhiqiang Cheng, Xiang Zhang, Weili Liang, Songhan Li, Linchuan Li, Qian Xu, Siyi Song, Zitian Liu, Guangwei Yang, Xiang Zhao, Ze Tao, Shuo Liang, Kexin Wang, Guangyong Zhang, Sanyuan Hu.
      Although 5-fluorouracil (5-FU) is the primary chemotherapy treatment for colorectal cancer (CRC), its efficacy is limited by drug resistance. Ferroptosis activation is a promising treatment for 5-FU-resistant cancer cells; however, potential therapeutic targets remain elusive. This study investigated ferroptosis vulnerability and dihydroorotate dehydrogenase (DHODH) activity using stable, 5-FU-resistant CRC cell lines and xenograft models. Ferroptosis was characterized by measuring malondialdehyde levels, assessing lipid metabolism and peroxidation, and using mitochondrial imaging and assays. DHODH function is investigated through gene knockdown experiments, tumor behavior assays, mitochondrial import reactions, intramitochondrial localization, enzymatic activity analyses, and metabolomics assessments. Intracellular lipid accumulation and mitochondrial DHODH deficiency led to lipid peroxidation overload, weakening the defense system of 5-FU-resistant CRC cells against ferroptosis. DHODH, primarily located within the inner mitochondrial membrane, played a crucial role in driving intracellular pyrimidine biosynthesis and was redistributed to the cytosol in 5-FU-resistant CRC cells. Cytosolic DHODH, like its mitochondrial counterpart, exhibited dihydroorotate catalytic activity and participated in pyrimidine biosynthesis. This amplified intracellular pyrimidine pools, thereby impeding the efficacy of 5-FU treatment through molecular competition. These findings contribute to the understanding of 5-FU resistance mechanisms and suggest that ferroptosis and DHODH are promising therapeutic targets for patients with CRC exhibiting resistance to 5-FU.
    Keywords:  Chemoresistance; Colorectal cancer; Dihydroorotate dehydrogenase; Ferroptosis; Lipid metabolic reprogramming
    DOI:  https://doi.org/10.1016/j.redox.2024.103207
  54. Nature. 2024 May 29.
    An alternative cell cycle coordinates multiciliated cell differentiation.
    Semil P Choksi, Lauren E Byrnes, Mia J Konjikusic, Benedict W H Tsai, Rachel Deleon, Quanlong Lu, Christopher J Westlake, Jeremy F Reiter.
      The canonical mitotic cell cycle coordinates DNA replication, centriole duplication and cytokinesis to generate two cells from one1. Some cells, such as mammalian trophoblast giant cells, use cell cycle variants like the endocycle to bypass mitosis2. Differentiating multiciliated cells, found in the mammalian airway, brain ventricles and reproductive tract, are post-mitotic but generate hundreds of centrioles, each of which matures into a basal body and nucleates a motile cilium3,4. Several cell cycle regulators have previously been implicated in specific steps of multiciliated cell differentiation5,6. Here we show that differentiating multiciliated cells integrate cell cycle regulators into a new alternative cell cycle, which we refer to as the multiciliation cycle. The multiciliation cycle redeploys many canonical cell cycle regulators, including cyclin-dependent kinases (CDKs) and their cognate cyclins. For example, cyclin D1, CDK4 and CDK6, which are regulators of mitotic G1-to-S progression, are required to initiate multiciliated cell differentiation. The multiciliation cycle amplifies some aspects of the canonical cell cycle, such as centriole synthesis, and blocks others, such as DNA replication. E2F7, a transcriptional regulator of canonical S-to-G2 progression, is expressed at high levels during the multiciliation cycle. In the multiciliation cycle, E2F7 directly dampens the expression of genes encoding DNA replication machinery and terminates the S phase-like gene expression program. Loss of E2F7 causes aberrant acquisition of DNA synthesis in multiciliated cells and dysregulation of multiciliation cycle progression, which disrupts centriole maturation and ciliogenesis. We conclude that multiciliated cells use an alternative cell cycle that orchestrates differentiation instead of controlling proliferation.
    DOI:  https://doi.org/10.1038/s41586-024-07476-z
  55. EMBO J. 2024 May 31.
    YIPF3 and YIPF4 regulate autophagic turnover of the Golgi apparatus.
    Shinri Kitta, Tatsuya Kaminishi, Momoko Higashi, Takayuki Shima, Kohei Nishino, Nobuhiro Nakamura, Hidetaka Kosako, Tamotsu Yoshimori, Akiko Kuma.
      The degradation of organelles by autophagy is essential for cellular homeostasis. The Golgi apparatus has recently been demonstrated to be degraded by autophagy, but little is known about how the Golgi is recognized by the forming autophagosome. Using quantitative proteomic analysis and two novel Golgiphagy reporter systems, we found that the five-pass transmembrane Golgi-resident proteins YIPF3 and YIPF4 constitute a Golgiphagy receptor. The interaction of this complex with LC3B, GABARAP, and GABARAPL1 is dependent on a LIR motif within YIPF3 and putative phosphorylation sites immediately upstream; the stability of the complex is governed by YIPF4. Expression of a YIPF3 protein containing a mutated LIR motif caused an elongated Golgi morphology, indicating the importance of Golgi turnover via selective autophagy. The reporter assays reported here may be readily adapted to different experimental contexts to help deepen our understanding of Golgiphagy.
    Keywords:  Autophagy Receptor; Golgi Turnover; Golgiphagy; Organelle Degradation; Selective Autophagy
    DOI:  https://doi.org/10.1038/s44318-024-00131-3
  56. Nat Microbiol. 2024 May 28.
    Mycobacterium tuberculosis produces D-serine under hypoxia to limit CD8+ T cell-dependent immunity in mice.
    Hongyu Cheng, Zhe Ji, Yang Wang, Shenzhi Li, Tianqi Tang, Fei Wang, Cheng Peng, Xiangyang Wu, Yuanna Cheng, Zhonghua Liu, Mingtong Ma, Jie Wang, Xiaochen Huang, Lin Wang, Lianhua Qin, Haipeng Liu, Jianxia Chen, Ruijuan Zheng, Carl G Feng, Xia Cai, Di Qu, Lilin Ye, Hua Yang, Baoxue Ge.
      Adaptation to hypoxia is a major challenge for the survival of Mycobacterium tuberculosis (Mtb) in vivo. Interferon (IFN)-γ-producing CD8+ T cells contribute to control of Mtb infection, in part by promoting antimicrobial activities of macrophages. Whether Mtb counters these responses, particularly during hypoxic conditions, remains unknown. Using metabolomic, proteomic and genetic approaches, here we show that Mtb induced Rv0884c (SerC), an Mtb phosphoserine aminotransferase, to produce D-serine. This activity increased Mtb pathogenesis in mice but did not directly affect intramacrophage Mtb survival. Instead, D-serine inhibited IFN-γ production by CD8+ T cells, which indirectly reduced the ability of macrophages to restrict Mtb upon co-culture. Mechanistically, D-serine interacted with WDR24 and inhibited mTORC1 activation in CD8+ T cells. This decreased T-bet expression and reduced IFN-γ production by CD8+ T cells. Our findings suggest an Mtb evasion mechanism where pathogen metabolic adaptation to hypoxia leads to amino acid-dependent suppression of adaptive anti-TB immunity.
    DOI:  https://doi.org/10.1038/s41564-024-01701-1
  57. Curr Opin Cell Biol. 2024 May 24. pii: S0955-0674(24)00052-8. [Epub ahead of print]88 102373
    Nonlinear dynamics in phosphoinositide metabolism.
    Suet Yin Sarah Fung, X J Xǔ, Min Wu.
      Phosphoinositides broadly impact membrane dynamics, signal transduction and cellular physiology. The orchestration of signaling complexity by this seemingly simple metabolic pathway remains an open question. It is increasingly evident that comprehending the complexity of the phosphoinositides metabolic network requires a systems view based on nonlinear dynamics, where the products of metabolism can either positively or negatively modulate enzymatic function. These feedback and feedforward loops may be paradoxical, leading to counterintuitive effects. In this review, we introduce the framework of nonlinear dynamics, emphasizing distinct dynamical regimes such as the excitable state, oscillations, and mixed-mode oscillations-all of which have been experimentally observed in phosphoinositide metabolisms. We delve into how these dynamical behaviors arise from one or multiple network motifs, including positive and negative feedback loops, coherent and incoherent feedforward loops. We explore the current understanding of the molecular circuits responsible for these behaviors. While mapping these circuits presents both conceptual and experimental challenges, redefining cellular behavior based on dynamical state, lipid fluxes, time delay, and network topology is likely essential for a comprehensive understanding of this fundamental metabolic network.
    DOI:  https://doi.org/10.1016/j.ceb.2024.102373
  58. Biochem Pharmacol. 2024 May 28. pii: S0006-2952(24)00309-5. [Epub ahead of print] 116326
    Reprogramming of urea cycle in cancer: Mechanism, regulation and prospective therapeutic scopes.
    Noyel Ghosh, Sushweta Mahalanobish, Parames C Sil.
      Hepatic urea cycle, previously known as ornithine cycle, is the chief biochemical pathway that deals with the disposal of excessive nitrogen in form of urea, resulted from protein breakdown and concomitant condensation of ammonia. Enzymes involved in urea cycle are expressed differentially outside hepatic tissue and are mostly involved in production of arginine from citrulline in arginine-depleted condition. Inline, cancer cells frequently adapt metabolic rewiring to support sufficient biomass production in order to sustain tumor cell survival, multiplication and subsequent growth. For the accomplishment of this aim, metabolic reprogramming in cancer cells is set in way so that cellular nitrogen and carbon repertoire can be utilized and channelized maximally towards anabolic reactions. A strategy to meet such outcome is to cut down unnecessary catabolic reactions and nitrogen elimination. Thus, transfigured urea cycle is a hallmark of neoplasia. During oncogenesis, altered expression and regulation of enzymes involved in urea cycle is a revolutionary approach meet to maximum incorporation of nitrogen for sustaining tumor specific biogenesis. Currently, we have reviewed neoplasm-specific deregulations of urea cycle-enzymes in different types and stages of cancers suggesting its context-oriented dynamic nature. Considering such insight to be valuable in terms of prospective cancer diagnosis and therapeutics adaptive evolution of deregulated urea cycle has been enlightened.
    Keywords:  Arginine depletion therapy; Aspartate; Cancer; Carbamoyl phosphate; Urea cycle
    DOI:  https://doi.org/10.1016/j.bcp.2024.116326
  59. Chem. 2024 May 09. 10(5): 1528-1540
    A prebiotic Krebs cycle analog generates amino acids with H2 and NH3 over nickel.
    Harpreet Kaur, Sophia A Rauscher, Emilie Werner, Youngdong Song, Jing Yi, Wahnyalo Kazöne, William F Martin, Harun Tüysüz, Joseph Moran.
      Hydrogen (H2) has powered microbial metabolism for roughly 4 billion years. The recent discovery that it also fuels geochemical analogs of the most ancient biological carbon fixation pathway sheds light on the origin of metabolism. However, it remains unclear whether H2 can sustain more complex nonenzymatic reaction networks. Here, we show that H2 drives the nonenzymatic reductive amination of six biological ketoacids and glyoxylate to give the corresponding amino acids in good yields using ammonium concentrations ranging from 6 to 150 mM. Catalytic amounts of nickel or ground meteorites enable these reactions at 22°C and pH 8. The same conditions promote an H2-dependent ketoacid-forming reductive aldol chemistry that co-occurs with reductive amination, producing a continuous reaction network resembling amino acid synthesis in the metabolic core of ancient microbes. The results support the hypothesis that the earliest biochemical networks could have emerged without enzymes or RNA.
    DOI:  https://doi.org/10.1016/j.chempr.2024.02.001
  60. Nat Commun. 2024 May 31. 15(1): 4652
    Capturing heterogeneity in PDX models: representation matters.
    Hari Shankar Sunil, Kathryn A O'Donnell.
      
    DOI:  https://doi.org/10.1038/s41467-024-47607-8
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