bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2023–05–28
fifty papers selected by
Christian Frezza, Universität zu Köln
  1. Electron transport chain inhibition increases cellular dependence on purine transport and salvage.
  2. Anaplerotic nutrient stress drives synergy of angiogenesis inhibitors with therapeutics targeting tumor metabolism.
  3. AKT activation because of PTEN loss upregulates xCT via GSK3β/NRF2, leading to inhibition of ferroptosis in PTEN-mutant tumor cells.
  4. Mitoprotease LONP1 controls white-to-beige adipocyte conversion via metabolic enzyme turnover.
  5. Glycolytically impaired Drosophila glial cells fuel neural metabolism via β-oxidation.
  6. Oxidization of optic atrophy 1 cysteines occurs during heart ischemia-reperfusion and amplifies cell death by oxidative stress.
  7. The KEAP1-NRF2 pathway regulates TFEB/TFE3-dependent lysosomal biogenesis.
  8. A coordinated multiorgan metabolic response contributes to human mitochondrial myopathy.
  9. Gene and protein expression and metabolic flux analysis reveals metabolic scaling in liver ex vivo and in vivo.
  10. Mitochondrial dynamics and cristae shape changes during metabolic reprogramming.
  11. Phospholipase D3 degrades mitochondrial DNA to regulate nucleotide signaling and APP metabolism.
  12. AMPK is a mechano-metabolic sensor linking cell adhesion and mitochondrial dynamics to Myosin-dependent cell migration.
  13. Regulatory mechanisms of mitochondrial calcium uptake by the calcium uniporter complex.
  14. Ca2+ signaling and cell death.
  15. The AE4 transporter mediates kidney acid-base sensing.
  16. High-Throughput Image-Based Quantification of Mitochondrial DNA Synthesis and Distribution.
  17. Senescence-induced immune remodeling facilitates metastatic adrenal cancer in a sex-dimorphic manner.
  18. Chronic kidney disease promotes ageing in a multiorgan disease network.
  19. Metabolic landscape of the male mouse gut identifies different niches determined by microbial activities.
  20. Redefining the role of AMPK in autophagy and the energy stress response.
  21. Suppression of the human malic enzyme 2 modifies energy metabolism and inhibits cellular respiration.
  22. Succinylation of a KEAP1 sensor lysine promotes NRF2 activation.
  23. Exercise metabolism and adaptation in skeletal muscle.
  24. CDKN2A deletion remodels lipid metabolism to prime glioblastoma for ferroptosis.
  25. The metabolic state of the heart regulates mitochondrial supercomplex abundance in mice.
  26. Alanine supplementation exploits glutamine dependency induced by SMARCA4/2-loss.
  27. Identifying Redox-Sensitive Cysteine Residues in Mitochondria.
  28. γ-Linolenic acid in maternal milk drives cardiac metabolic maturation.
  29. Divergent metabolic programmes control two populations of MAIT cells that protect the lung.
  30. Crucial neuroprotective roles of the metabolite BH4 in dopaminergic neurons.
  31. Real-Time Assessment of Intracellular Metabolites in Single Cells through RNA-Based Sensors.
  32. Canagliflozin impairs T cell effector function via metabolic suppression in autoimmunity.
  33. Emerging frontiers in regenerative medicine.
  34. Mitophagy restricts BAX/BAK-independent, Parkin-mediated apoptosis.
  35. Cystine rather than cysteine is the preferred substrate for β-elimination by cystathionine γ-lyase: implications for dietary methionine restriction.
  36. PROX1 induction by autolysosomal activity stabilizes persister-like state of colon cancer via feedback repression of the NOX1-mTORC1 pathway.
  37. Proteolytic rewiring of mitochondria by LONP1 directs cell identity switching of adipocytes.
  38. mTORC1 activity negatively regulates human hair follicle growth and pigmentation.
  39. IL-10 constrains sphingolipid metabolism via fatty acid desaturation to limit inflammation.
  40. Ferroptosis: mechanisms and implications for cancer development and therapy response.
  41. Hypoxia extends lifespan and neurological function in a mouse model of aging.
  42. Mechanobiology of organelles: illuminating their roles in mechanosensing and mechanotransduction.
  43. Context-dependent activation of STING-interferon signaling by CD11b agonists enhances anti-tumor immunity.
  44. Genetically encoded photocatalytic protein labeling enables spatially-resolved profiling of intracellular proteome.
  45. Tetrahydrobiopterin: Beyond Its Traditional Role as a Cofactor.
  46. Establishment of gastrointestinal assembloids to study the interplay between epithelial crypts and their mesenchymal niche.
  47. Non-canonical and developmental roles of the TCA cycle in plants.
  48. Strand-selective base editing of human mitochondrial DNA using mitoBEs.
  49. Genome-scale functional genomics identify genes preferentially essential for multiple myeloma cells compared to other neoplasias.
  50. PGC-1α Is a Master Regulator of Mitochondrial Lifecycle and ROS Stress Response.
  1. bioRxiv. 2023 May 11. pii: 2023.05.11.540429. [Epub ahead of print]
    Electron transport chain inhibition increases cellular dependence on purine transport and salvage.
    Zheng Wu, Divya Bezwada, Robert C Harris, Chunxiao Pan, Phong T Nguyen, Brandon Faubert, Ling Cai, Feng Cai, Hieu S Vu, Hongli Chen, Misty Martin- Sandoval, Duyen Do, Wen Gu, Yuannyu Zhang, Bookyung Ko, Bailey Brooks, Sherwin Kelekar, Yuanyuan Zhang, Lauren G Zacharias, K Celeste Oaxaca, Thomas P Mathews, Javier Garcia-Bermudez, Min Ni, Ralph J DeBerardinis.
      Cancer cells reprogram their metabolism to support cell growth and proliferation in harsh environments. While many studies have documented the importance of mitochondrial oxidative phosphorylation (OXPHOS) in tumor growth, some cancer cells experience conditions of reduced OXPHOS in vivo and induce alternative metabolic pathways to compensate. To assess how human cells respond to mitochondrial dysfunction, we performed metabolomics in fibroblasts and plasma from patients with inborn errors of mitochondrial metabolism, and in cancer cells subjected to inhibition of the electron transport chain (ETC). All these analyses revealed extensive perturbations in purine-related metabolites; in non-small cell lung cancer (NSCLC) cells, ETC blockade led to purine metabolite accumulation arising from a reduced cytosolic NAD + /NADH ratio (NADH reductive stress). Stable isotope tracing demonstrated that ETC deficiency suppressed de novo purine nucleotide synthesis while enhancing purine salvage. Analysis of NSCLC patients infused with [U- 13 C]glucose revealed that tumors with markers of low oxidative mitochondrial metabolism exhibited high expression of the purine salvage enzyme HPRT1 and abundant levels of the HPRT1 product inosine monophosphate (IMP). ETC blockade also induced production of ribose-5' phosphate (R5P) by the pentose phosphate pathway (PPP) and import of purine nucleobases. Blocking either HPRT1 or nucleoside transporters sensitized cancer cells to ETC inhibition, and overexpressing nucleoside transporters was sufficient to drive growth of NSCLC xenografts. Collectively, this study mechanistically delineates how cells compensate for suppressed purine metabolism in response to ETC blockade, and uncovers a new metabolic vulnerability in tumors experiencing NADH excess.
    DOI:  https://doi.org/10.1101/2023.05.11.540429
  2. bioRxiv. 2023 May 09. pii: 2023.05.07.539744. [Epub ahead of print]
    Anaplerotic nutrient stress drives synergy of angiogenesis inhibitors with therapeutics targeting tumor metabolism.
    Sunada Khadka, Yu-Hsi Lin, Jeffrey Ackroyd, Yi-An Chen, Yanghui Sheng, Wubin Qian, Sheng Guo, Yining Chen, Eliot Behr, Yasaman Barekatain, Md Nasir Uddin, Kenisha Arthur, Victoria Yan, Wen-Hao Hsu, Edward Chang, Anton Poral, Theresa Tran, Surendra Chaurasia, Dimitra K Georgiou, John M Asara, Floris P Barthel, Steve W Millward, Ronald A DePinho, Florian L Muller.
      Tumor angiogenesis is a cancer hallmark, and its therapeutic inhibition has provided meaningful, albeit limited, clinical benefit. While anti-angiogenesis inhibitors deprive the tumor of oxygen and essential nutrients, cancer cells activate metabolic adaptations to diminish therapeutic response. Despite these adaptations, angiogenesis inhibition incurs extensive metabolic stress, prompting us to consider such metabolic stress as an induced vulnerability to therapies targeting cancer metabolism. Metabolomic profiling of angiogenesis-inhibited intracranial xenografts showed universal decrease in tricarboxylic acid cycle intermediates, corroborating a state of anaplerotic nutrient deficit or stress. Accordingly, we show strong synergy between angiogenesis inhibitors (Avastin, Tivozanib) and inhibitors of glycolysis or oxidative phosphorylation through exacerbation of anaplerotic nutrient stress in intracranial orthotopic xenografted gliomas. Our findings were recapitulated in GBM xenografts that do not have genetically predisposed metabolic vulnerabilities at baseline. Thus, our findings cement the central importance of the tricarboxylic acid cycle as the nexus of metabolic vulnerabilities and suggest clinical path hypothesis combining angiogenesis inhibitors with pharmacological cancer interventions targeting tumor metabolism for GBM tumors.
    DOI:  https://doi.org/10.1101/2023.05.07.539744
  3. Cell Rep. 2023 May 19. pii: S2211-1247(23)00547-8. [Epub ahead of print]42(5): 112536
    AKT activation because of PTEN loss upregulates xCT via GSK3β/NRF2, leading to inhibition of ferroptosis in PTEN-mutant tumor cells.
    Kaitlyn M Cahuzac, Abigail Lubin, Kaitlyn Bosch, Nicole Stokes, Sarah Mense Shoenfeld, Royce Zhou, Haddy Lemon, John Asara, Ramon E Parsons.
      Here, we show that the tumor suppressor phosphatase and tensin homolog deleted from chromosome 10 (PTEN) sensitizes cells to ferroptosis, an iron-dependent form of cell death, by restraining the expression and activity of the cystine/glutamate antiporter system Xc- (xCT). Loss of PTEN activates AKT kinase to inhibit GSK3β, increasing NF-E2 p45-related factor 2 (NRF2) along with transcription of one of its known target genes encoding xCT. Elevated xCT in Pten-null mouse embryonic fibroblasts increases the flux of cystine transport and synthesis of glutathione, which enhances the steady-state levels of these metabolites. A pan-cancer analysis finds that loss of PTEN shows evidence of increased xCT, and PTEN-mutant cells are resistant to ferroptosis as a consequence of elevated xCT. These findings suggest that selection of PTEN mutation during tumor development may be due to its ability to confer resistance to ferroptosis in the setting of metabolic and oxidative stress that occurs during tumor initiation and progression.
    Keywords:  Akt; CP: Cancer; CP: Metabolism; GSK3β; NRF2; PTEN; cancer; cysteine; ferroptosis; glutathione; xCT
    DOI:  https://doi.org/10.1016/j.celrep.2023.112536
  4. Nat Cell Biol. 2023 May 24.
    Mitoprotease LONP1 controls white-to-beige adipocyte conversion via metabolic enzyme turnover.
      
    DOI:  https://doi.org/10.1038/s41556-023-01161-5
  5. Nat Commun. 2023 May 24. 14(1): 2996
    Glycolytically impaired Drosophila glial cells fuel neural metabolism via β-oxidation.
    Ellen McMullen, Helen Hertenstein, Katrin Strassburger, Leon Deharde, Marko Brankatschk, Stefanie Schirmeier.
      Neuronal function is highly energy demanding and thus requires efficient and constant metabolite delivery by glia. Drosophila glia are highly glycolytic and provide lactate to fuel neuronal metabolism. Flies are able to survive for several weeks in the absence of glial glycolysis. Here, we study how Drosophila glial cells maintain sufficient nutrient supply to neurons under conditions of impaired glycolysis. We show that glycolytically impaired glia rely on mitochondrial fatty acid breakdown and ketone body production to nourish neurons, suggesting that ketone bodies serve as an alternate neuronal fuel to prevent neurodegeneration. We show that in times of long-term starvation, glial degradation of absorbed fatty acids is essential to ensure survival of the fly. Further, we show that Drosophila glial cells act as a metabolic sensor and can induce mobilization of peripheral lipid stores to preserve brain metabolic homeostasis. Our study gives evidence of the importance of glial fatty acid degradation for brain function, and survival, under adverse conditions in Drosophila.
    DOI:  https://doi.org/10.1038/s41467-023-38813-x
  6. Redox Biol. 2023 May 19. pii: S2213-2317(23)00156-8. [Epub ahead of print]63 102755
    Oxidization of optic atrophy 1 cysteines occurs during heart ischemia-reperfusion and amplifies cell death by oxidative stress.
    Martina Semenzato, Mark J Kohr, Charlotte Quirin, Roberta Menabò, Petra Alanova, Lukas Alan, Anna Pellattiero, Elizabeth Murphy, Fabio Di Lisa, Luca Scorrano.
      During cardiac ischemia-reperfusion, excess reactive oxygen species can damage mitochondrial, cellular and organ function. Here we show that cysteine oxidation of the mitochondrial protein Opa1 contributes to mitochondrial damage and cell death caused by oxidative stress. Oxy-proteomics of ischemic-reperfused hearts reveal oxidation of the C-terminal C786 of Opa1 and treatment of perfused mouse hearts, adult cardiomyocytes, and fibroblasts with H2O2 leads to the formation of a reduction-sensitive ∼180 KDa Opa1 complex, distinct from the ∼270 KDa one antagonizing cristae remodeling. This Opa1 oxidation process is curtailed by mutation of C786 and of the other 3 Cys residues of its C-terminal domain (Opa1TetraCys). When reintroduced in Opa1-/- cells, Opa1TetraCys is not efficiently processed into short Opa1TetraCys and hence fails to fuse mitochondria. Unexpectedly, Opa1TetraCys restores mitochondrial ultrastructure in Opa1-/- cells and protects them from H2O2-induced mitochondrial depolarization, cristae remodeling, cytochrome c release and cell death. Thus, preventing the Opa1 oxidation occurring during cardiac ischemia-reperfusion reduces mitochondrial damage and cell death induced by oxidative stress independent of mitochondrial fusion.
    DOI:  https://doi.org/10.1016/j.redox.2023.102755
  7. Proc Natl Acad Sci U S A. 2023 05 30. 120(22): e2217425120
    The KEAP1-NRF2 pathway regulates TFEB/TFE3-dependent lysosomal biogenesis.
    Athena Jessica S Ong, Cerys E Bladen, Tara A Tigani, Anthony P Karamalakis, Kimberley J Evason, Kristin K Brown, Andrew G Cox.
      The maintenance of redox and metabolic homeostasis is integral to embryonic development. Nuclear factor erythroid 2-related factor 2 (NRF2) is a stress-induced transcription factor that plays a central role in the regulation of redox balance and cellular metabolism. Under homeostatic conditions, NRF2 is repressed by Kelch-like ECH-associated protein 1 (KEAP1). Here, we demonstrate that Keap1 deficiency induces Nrf2 activation and postdevelopmental lethality. Loss of viability is preceded by severe liver abnormalities characterized by an accumulation of lysosomes. Mechanistically, we demonstrate that loss of Keap1 promotes aberrant activation of transcription factor EB (TFEB)/transcription factor binding to IGHM Enhancer 3 (TFE3)-dependent lysosomal biogenesis. Importantly, we find that NRF2-dependent regulation of lysosomal biogenesis is cell autonomous and evolutionarily conserved. These studies identify a role for the KEAP1-NRF2 pathway in the regulation of lysosomal biogenesis and suggest that maintenance of lysosomal homeostasis is required during embryonic development.
    Keywords:  KEAP1; NRF2; TFEB/TFE3; lysosome; zebrafish
    DOI:  https://doi.org/10.1073/pnas.2217425120
  8. EMBO Mol Med. 2023 May 24. e16951
    A coordinated multiorgan metabolic response contributes to human mitochondrial myopathy.
    Nneka Southwell, Guido Primiano, Viraj Nadkarni, Nabeel Attarwala, Emelie Beattie, Dawson Miller, Sumaitaah Alam, Irene Liparulo, Yevgeniya I Shurubor, Maria Lucia Valentino, Valerio Carelli, Serenella Servidei, Steven S Gross, Giovanni Manfredi, Qiuying Chen, Marilena D'Aurelio.
      Mitochondrial diseases are a heterogeneous group of monogenic disorders that result from impaired oxidative phosphorylation (OXPHOS). As neuromuscular tissues are highly energy-dependent, mitochondrial diseases often affect skeletal muscle. Although genetic and bioenergetic causes of OXPHOS impairment in human mitochondrial myopathies are well established, there is a limited understanding of metabolic drivers of muscle degeneration. This knowledge gap contributes to the lack of effective treatments for these disorders. Here, we discovered fundamental muscle metabolic remodeling mechanisms shared by mitochondrial disease patients and a mouse model of mitochondrial myopathy. This metabolic remodeling is triggered by a starvation-like response that evokes accelerated oxidation of amino acids through a truncated Krebs cycle. While initially adaptive, this response evolves in an integrated multiorgan catabolic signaling, lipid store mobilization, and intramuscular lipid accumulation. We show that this multiorgan feed-forward metabolic response involves leptin and glucocorticoid signaling. This study elucidates systemic metabolic dyshomeostasis mechanisms that underlie human mitochondrial myopathies and identifies potential new targets for metabolic intervention.
    Keywords:  amino acid metabolism; glucocorticoids; leptin; mitochondrial myopathy; muscle wasting
    DOI:  https://doi.org/10.15252/emmm.202216951
  9. Elife. 2023 May 23. pii: e78335. [Epub ahead of print]12
    Gene and protein expression and metabolic flux analysis reveals metabolic scaling in liver ex vivo and in vivo.
    Ngozi D Akingbesote, Brooks P Leitner, Daniel G Jovin, Reina Desrouleaux, Dennis Owusu, Wanling Zhu, Zongyu Li, Michael N Pollak, Rachel J Perry.
      Metabolic scaling, the inverse correlation of metabolic rates to body mass, has been appreciated for more than 80 years. Studies of metabolic scaling have largely been restricted to mathematical modeling of caloric intake and oxygen consumption, and mostly rely on computational modeling. The possibility that other metabolic processes scale with body size has not been comprehensively studied. To address this gap in knowledge, we employed a systems approach including transcriptomics, proteomics, and measurement of in vitro and in vivo metabolic fluxes. Gene expression in livers of five species spanning a 30,000-fold range in mass revealed differential expression according to body mass of genes related to cytosolic and mitochondrial metabolic processes, and to detoxication of oxidative damage. To determine whether flux through key metabolic pathways is ordered inversely to body size, we applied stable isotope tracer methodology to study multiple cellular compartments, tissues, and species. Comparing C57BL/6 J mice with Sprague-Dawley rats, we demonstrate that while ordering of metabolic fluxes is not observed in in vitro cell-autonomous settings, it is present in liver slices and in vivo. Together, these data reveal that metabolic scaling extends beyond oxygen consumption to other aspects of metabolism, and is regulated at the level of gene and protein expression, enzyme activity, and substrate supply.
    Keywords:  biochemistry; chemical biology; liver metabolism; metabolic flux; metabolic scaling; mouse; rat
    DOI:  https://doi.org/10.7554/eLife.78335
  10. Antioxid Redox Signal. 2023 May 22.
    Mitochondrial dynamics and cristae shape changes during metabolic reprogramming.
    Ippei Kawano, Bazila Bazila, Petr Jezek, Andrea Dlasková.
       SIGNIFICANCE: The architecture of the mitochondrial network and cristae critically impact cell differentiation and identity. Cells undergoing metabolic reprogramming to aerobic glycolysis (Warburg effect), such as immune cells, stem cells, and cancer cells, go through controlled modifications in mitochondrial architecture, which is critical for achieving the resulting cellular phenotype.
    RECENT ADVANCES: Recent studies in immunometabolism have shown that the manipulation of mitochondrial network dynamics and cristae shape directly affects T cell phenotype and macrophage polarization through altering energy metabolism. Similar manipulations also alter the specific metabolic phenotypes that accompany somatic reprogramming, stem cell differentiation, and cancer cells. The modulation of OXPHOS activity, accompanied by changes in metabolite signaling, ROS generation, and ATP levels is the shared underlying mechanism.
    CRITICAL ISSUES: The plasticity of mitochondrial architecture is particularly vital for metabolic reprogramming. Consequently, failure to adapt the appropriate mitochondrial morphology often compromises the differentiation and identity of the cell. Immune, stem, and tumor cells exhibit striking similarities in their coordination of mitochondrial morphology with metabolic pathways. However, although many general unifying principles can be observed, their validity is not absolute, and the mechanistic links thus need to be further explored.
    FUTURE DIRECTIONS: Better knowledge of the molecular mechanisms involved and their relationships to both mitochondrial network and cristae morphology will not only further deepen our understanding of energy metabolism but may also contribute to improved therapeutic manipulation of cell viability, differentiation, proliferation, and identity in many different cell types.
    DOI:  https://doi.org/10.1089/ars.2023.0268
  11. Nat Commun. 2023 May 24. 14(1): 2847
    Phospholipase D3 degrades mitochondrial DNA to regulate nucleotide signaling and APP metabolism.
    Zoë P Van Acker, Anika Perdok, Ruben Hellemans, Katherine North, Inge Vorsters, Cedric Cappel, Jonas Dehairs, Johannes V Swinnen, Ragna Sannerud, Marine Bretou, Markus Damme, Wim Annaert.
      Phospholipase D3 (PLD3) polymorphisms are linked to late-onset Alzheimer's disease (LOAD). Being a lysosomal 5'-3' exonuclease, its neuronal substrates remained unknown as well as how a defective lysosomal nucleotide catabolism connects to AD-proteinopathy. We identified mitochondrial DNA (mtDNA) as a major physiological substrate and show its manifest build-up in lysosomes of PLD3-defective cells. mtDNA accretion creates a degradative (proteolytic) bottleneck that presents at the ultrastructural level as a marked abundance of multilamellar bodies, often containing mitochondrial remnants, which correlates with increased PINK1-dependent mitophagy. Lysosomal leakage of mtDNA to the cytosol activates cGAS-STING signaling that upregulates autophagy and induces amyloid precursor C-terminal fragment (APP-CTF) and cholesterol accumulation. STING inhibition largely normalizes APP-CTF levels, whereas an APP knockout in PLD3-deficient backgrounds lowers STING activation and normalizes cholesterol biosynthesis. Collectively, we demonstrate molecular cross-talks through feedforward loops between lysosomal nucleotide turnover, cGAS-STING and APP metabolism that, when dysregulated, result in neuronal endolysosomal demise as observed in LOAD.
    DOI:  https://doi.org/10.1038/s41467-023-38501-w
  12. Nat Commun. 2023 May 22. 14(1): 2740
    AMPK is a mechano-metabolic sensor linking cell adhesion and mitochondrial dynamics to Myosin-dependent cell migration.
    Eva Crosas-Molist, Vittoria Graziani, Oscar Maiques, Pahini Pandya, Joanne Monger, Remi Samain, Samantha L George, Saba Malik, Jerrine Salise, Valle Morales, Adrien Le Guennec, R Andrew Atkinson, Rosa M Marti, Xavier Matias-Guiu, Guillaume Charras, Maria R Conte, Alberto Elosegui-Artola, Mark Holt, Victoria Sanz-Moreno.
      Cell migration is crucial for cancer dissemination. We find that AMP-activated protein kinase (AMPK) controls cell migration by acting as an adhesion sensing molecular hub. In 3-dimensional matrices, fast-migrating amoeboid cancer cells exert low adhesion/low traction linked to low ATP/AMP, leading to AMPK activation. In turn, AMPK plays a dual role controlling mitochondrial dynamics and cytoskeletal remodelling. High AMPK activity in low adhering migratory cells, induces mitochondrial fission, resulting in lower oxidative phosphorylation and lower mitochondrial ATP. Concurrently, AMPK inactivates Myosin Phosphatase, increasing Myosin II-dependent amoeboid migration. Reducing adhesion or mitochondrial fusion or activating AMPK induces efficient rounded-amoeboid migration. AMPK inhibition suppresses metastatic potential of amoeboid cancer cells in vivo, while a mitochondrial/AMPK-driven switch is observed in regions of human tumours where amoeboid cells are disseminating. We unveil how mitochondrial dynamics control cell migration and suggest that AMPK is a mechano-metabolic sensor linking energetics and the cytoskeleton.
    DOI:  https://doi.org/10.1038/s41467-023-38292-0
  13. Biophys Physicobiol. 2023 ;20(1): e200004
    Regulatory mechanisms of mitochondrial calcium uptake by the calcium uniporter complex.
    Akiko Yamada, Akira Watanabe, Takenori Yamamoto.
      Mitochondria play an important role in energy conversion as well as in intracellular calcium (Ca2+) storage. Ca2+ uptake from the cytosol to the mitochondria is mediated by the calcium uniporter, which functions as a Ca2+ ion channel. However, the molecular composition of this uniporter has remained unclear until recently. The Ca2+ ion channel consists of seven subunits. The yeast reconstitution technique revealed that the mitochondrial calcium uniporter (MCU) and essential MCU regulatory element (EMRE) are the core subunits of the complex. Furthermore, detailed structure-function analyses of the core subunits (MCU and EMRE) were performed. In this review, the regulatory mechanism of mitochondrial Ca2+ uptake is discussed.
    Keywords:  calcium; ion channel; mitochondria; yeast
    DOI:  https://doi.org/10.2142/biophysico.bppb-v20.0004
  14. Cell Calcium. 2023 May 19. pii: S0143-4160(23)00071-4. [Epub ahead of print]113 102759
    Ca2+ signaling and cell death.
    Nada Dhaouadi, Veronica Angela Maria Vitto, Paolo Pinton, Lorenzo Galluzzi, Saverio Marchi.
      Multiple forms of regulated cell death (RCD) have been characterized, each of which originates from the activation of a dedicated molecular machinery. RCD can occur in purely physiological settings or upon failing cellular adaptation to stress. Ca2+ions have been shown to physically interact with - and hence regulate - various components of the RCD machinery. Moreover, intracellular Ca2+ accumulation can promote organellar dysfunction to degree that can be overtly cytotoxic or sensitize cells to RCD elicited by other stressors. Here, we provide an overview of the main links between Ca2+and different forms of RCD, including apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, lysosome-dependent cell death, and parthanatos.
    Keywords:  Apoptosis; Bcl2; Endoplasmic reticulum, immunogenic cell death; Lysosomes; MPT-driven necrosis
    DOI:  https://doi.org/10.1016/j.ceca.2023.102759
  15. Nat Commun. 2023 May 26. 14(1): 3051
    The AE4 transporter mediates kidney acid-base sensing.
    H Vitzthum, M Koch, L Eckermann, S L Svendsen, P Berg, C A Hübner, C A Wagner, J Leipziger, C Meyer-Schwesinger, H Ehmke.
      The kidney plays a key role in the correction of systemic acid-base imbalances. Central for this regulation are the intercalated cells in the distal nephron, which secrete acid or base into the urine. How these cells sense acid-base disturbances is a long-standing question. Intercalated cells exclusively express the Na+-dependent Cl-/HCO3- exchanger AE4 (Slc4a9). Here we show that AE4-deficient mice exhibit a major dysregulation of acid-base balance. By combining molecular, imaging, biochemical and integrative approaches, we demonstrate that AE4-deficient mice are unable to sense and appropriately correct metabolic alkalosis and acidosis. Mechanistically, a lack of adaptive base secretion via the Cl-/HCO3- exchanger pendrin (Slc26a4) is the key cellular cause of this derailment. Our findings identify AE4 as an essential part of the renal sensing mechanism for changes in acid-base status.
    DOI:  https://doi.org/10.1038/s41467-023-38562-x
  16. J Vis Exp. 2023 05 05.
    High-Throughput Image-Based Quantification of Mitochondrial DNA Synthesis and Distribution.
    Lukasz S Borowski, Karolina Kasztelan, Jolanta Czerwinska-Kostrzewska, Roman J Szczesny.
      The vast majority of cellular processes require a continuous supply of energy, the most common carrier of which is the ATP molecule. Eukaryotic cells produce most of their ATP in the mitochondria by oxidative phosphorylation. Mitochondria are unique organelles because they have their own genome that is replicated and passed on to the next generation of cells. In contrast to the nuclear genome, there are multiple copies of the mitochondrial genome in the cell. The detailed study of the mechanisms responsible for the replication, repair, and maintenance of the mitochondrial genome is essential for understanding the proper functioning of mitochondria and whole cells under both normal and disease conditions. Here, a method that allows the high-throughput quantification of the synthesis and distribution of mitochondrial DNA (mtDNA) in human cells cultured in vitro is presented. This approach is based on the immunofluorescence detection of actively synthesized DNA molecules labeled by 5-bromo-2'-deoxyuridine (BrdU) incorporation and the concurrent detection of all the mtDNA molecules with anti-DNA antibodies. Additionally, the mitochondria are visualized with specific dyes or antibodies. The culturing of cells in a multi-well format and the utilization of an automated fluorescence microscope make it easier to study the dynamics of mtDNA and the morphology of mitochondria under a variety of experimental conditions in a relatively short time.
    DOI:  https://doi.org/10.3791/65236
  17. Nat Aging. 2023 May 25.
    Senescence-induced immune remodeling facilitates metastatic adrenal cancer in a sex-dimorphic manner.
    Kate M Warde, Lorenzo J Smith, Lihua Liu, Chris J Stubben, Brian K Lohman, Parker W Willett, Julia L Ammer, Guadalupe Castaneda-Hernandez, Sikiru O Imodoye, Chenge Zhang, Kara D Jones, Kimber Converso-Baran, H Atakan Ekiz, Marc Barry, Michael R Clay, Katja Kiseljak-Vassiliades, Thomas J Giordano, Gary D Hammer, Kaitlin J Basham.
      Aging markedly increases cancer risk, yet our mechanistic understanding of how aging influences cancer initiation is limited. Here we demonstrate that the loss of ZNRF3, an inhibitor of Wnt signaling that is frequently mutated in adrenocortical carcinoma, leads to the induction of cellular senescence that remodels the tissue microenvironment and ultimately permits metastatic adrenal cancer in old animals. The effects are sexually dimorphic, with males exhibiting earlier senescence activation and a greater innate immune response, driven in part by androgens, resulting in high myeloid cell accumulation and lower incidence of malignancy. Conversely, females present a dampened immune response and increased susceptibility to metastatic cancer. Senescence-recruited myeloid cells become depleted as tumors progress, which is recapitulated in patients in whom a low myeloid signature is associated with worse outcomes. Our study uncovers a role for myeloid cells in restraining adrenal cancer with substantial prognostic value and provides a model for interrogating pleiotropic effects of cellular senescence in cancer.
    DOI:  https://doi.org/10.1038/s43587-023-00420-2
  18. Nat Rev Nephrol. 2023 May 26.
    Chronic kidney disease promotes ageing in a multiorgan disease network.
    Thomas Benzing, Björn Schumacher.
      
    DOI:  https://doi.org/10.1038/s41581-023-00729-6
  19. Nat Metab. 2023 May 22.
    Metabolic landscape of the male mouse gut identifies different niches determined by microbial activities.
    Karin H U Meier, Julian Trouillon, Hai Li, Melanie Lang, Tobias Fuhrer, Nicola Zamboni, Shinichi Sunagawa, Andrew J Macpherson, Uwe Sauer.
      Distinct niches of the mammalian gut are populated by diverse microbiota, but the contribution of spatial variation to intestinal metabolism remains unclear. Here we present a map of the longitudinal metabolome along the gut of healthy colonized and germ-free male mice. With this map, we reveal a general shift from amino acids in the small intestine to organic acids, vitamins and nucleotides in the large intestine. We compare the metabolic landscapes in colonized versus germ-free mice to disentangle the origin of many metabolites in different niches, which in some cases allows us to infer the underlying processes or identify the producing species. Beyond the known impact of diet on the small intestinal metabolic niche, distinct spatial patterns suggest specific microbial influence on the metabolome in the small intestine. Thus, we present a map of intestinal metabolism and identify metabolite-microbe associations, which provide a basis to connect the spatial occurrence of bioactive compounds to host or microorganism metabolism.
    DOI:  https://doi.org/10.1038/s42255-023-00802-1
  20. Nat Commun. 2023 May 24. 14(1): 2994
    Redefining the role of AMPK in autophagy and the energy stress response.
    Ji-Man Park, Da-Hye Lee, Do-Hyung Kim.
      Autophagy maintains cellular homeostasis during low energy states. According to the current understanding, glucose-depleted cells induce autophagy through AMPK, the primary energy-sensing kinase, to acquire energy for survival. However, contrary to the prevailing concept, our study demonstrates that AMPK inhibits ULK1, the kinase responsible for autophagy initiation, thereby suppressing autophagy. We found that glucose starvation suppresses amino acid starvation-induced stimulation of ULK1-Atg14-Vps34 signaling via AMPK activation. During an energy crisis caused by mitochondrial dysfunction, the LKB1-AMPK axis inhibits ULK1 activation and autophagy induction, even under amino acid starvation. Despite its inhibitory effect, AMPK protects the ULK1-associated autophagy machinery from caspase-mediated degradation during energy deficiency, preserving the cellular ability to initiate autophagy and restore homeostasis once the stress subsides. Our findings reveal that dual functions of AMPK, restraining abrupt induction of autophagy upon energy shortage while preserving essential autophagy components, are crucial to maintain cellular homeostasis and survival during energy stress.
    DOI:  https://doi.org/10.1038/s41467-023-38401-z
  21. Commun Biol. 2023 May 22. 6(1): 548
    Suppression of the human malic enzyme 2 modifies energy metabolism and inhibits cellular respiration.
    Ju-Yi Hsieh, Kun-Chi Chen, Chun-Hsiung Wang, Guang-Yaw Liu, Jie-An Ye, Yu-Tung Chou, Yi-Chun Lin, Cheng-Jhe Lyu, Rui-Ying Chang, Yi-Liang Liu, Yen-Hsien Li, Mau-Rong Lee, Meng-Chiao Ho, Hui-Chih Hung.
      Human mitochondrial NAD(P)+-dependent malic enzyme (ME2) is well-known for its role in cell metabolism, which may be involved in cancer or epilepsy. We present potent ME2 inhibitors based on cyro-EM structures that target ME2 enzyme activity. Two structures of ME2-inhibitor complexes demonstrate that 5,5'-Methylenedisalicylic acid (MDSA) and embonic acid (EA) bind allosterically to ME2's fumarate-binding site. Mutagenesis studies demonstrate that Asn35 and the Gln64-Tyr562 network are required for both inhibitors' binding. ME2 overexpression increases pyruvate and NADH production while decreasing the cell's NAD+/NADH ratio; however, ME2 knockdown has the opposite effect. MDSA and EA inhibit pyruvate synthesis and thus increase the NAD+/NADH ratio, implying that these two inhibitors interfere with metabolic changes by inhibiting cellular ME2 activity. ME2 silence or inhibiting ME2 activity with MDSA or EA decreases cellular respiration and ATP synthesis. Our findings suggest that ME2 is crucial for mitochondrial pyruvate and energy metabolism, as well as cellular respiration, and that ME2 inhibitors could be useful in the treatment of cancer or other diseases that involve these processes.
    DOI:  https://doi.org/10.1038/s42003-023-04930-y
  22. bioRxiv. 2023 May 09. pii: 2023.05.08.539908. [Epub ahead of print]
    Succinylation of a KEAP1 sensor lysine promotes NRF2 activation.
    Lara Ibrahim, Caroline Stanton, Kayla Nutsch, Thu Nguyen, Chloris Li-Ma, Yeonjin Ko, Gabriel C Lander, R Luke Wiseman, Michael J Bollong.
      Crosstalk between metabolism and stress-responsive signaling is essential to maintaining cellular homeostasis. One way this crosstalk is achieved is through the covalent modification of proteins by endogenous, reactive metabolites that regulate the activity of key stress-responsive transcription factors such as NRF2. Several metabolites including methylglyoxal, glyceraldehyde 3-phosphate, fumarate, and itaconate covalently modify sensor cysteines of the NRF2 regulatory protein KEAP1, resulting in stabilization of NRF2 and activation of its cytoprotective transcriptional program. Here, we employed a shRNA-based screen targeting the enzymes of central carbon metabolism to identify additional regulatory nodes bridging metabolic pathways to NRF2 activation. We found that succinic anhydride, increased by genetic depletion of the TCA cycle enzyme succinyl-CoA synthetase or by direct administration, results in N-succinylation of lysine 131 of KEAP1 to activate NRF2 transcriptional signaling. This study identifies KEAP1 as capable of sensing reactive metabolites not only by several cysteine residues but also by a conserved lysine residue, indicating its potential to sense an expanded repertoire of reactive metabolic messengers.
    DOI:  https://doi.org/10.1101/2023.05.08.539908
  23. Nat Rev Mol Cell Biol. 2023 May 24.
    Exercise metabolism and adaptation in skeletal muscle.
    Jonathon A B Smith, Kevin A Murach, Kenneth A Dyar, Juleen R Zierath.
      Viewing metabolism through the lens of exercise biology has proven an accessible and practical strategy to gain new insights into local and systemic metabolic regulation. Recent methodological developments have advanced understanding of the central role of skeletal muscle in many exercise-associated health benefits and have uncovered the molecular underpinnings driving adaptive responses to training regimens. In this Review, we provide a contemporary view of the metabolic flexibility and functional plasticity of skeletal muscle in response to exercise. First, we provide background on the macrostructure and ultrastructure of skeletal muscle fibres, highlighting the current understanding of sarcomeric networks and mitochondrial subpopulations. Next, we discuss acute exercise skeletal muscle metabolism and the signalling, transcriptional and epigenetic regulation of adaptations to exercise training. We address knowledge gaps throughout and propose future directions for the field. This Review contextualizes recent research of skeletal muscle exercise metabolism, framing further advances and translation into practice.
    DOI:  https://doi.org/10.1038/s41580-023-00606-x
  24. Cancer Cell. 2023 May 18. pii: S1535-6108(23)00168-X. [Epub ahead of print]
    CDKN2A deletion remodels lipid metabolism to prime glioblastoma for ferroptosis.
    Jenna K Minami, Danielle Morrow, Nicholas A Bayley, Elizabeth G Fernandez, Jennifer J Salinas, Christopher Tse, Henan Zhu, Baolong Su, Rhea Plawat, Anthony Jones, Alessandro Sammarco, Linda M Liau, Thomas G Graeber, Kevin J Williams, Timothy F Cloughesy, Scott J Dixon, Steven J Bensinger, David A Nathanson.
      Malignant tumors exhibit heterogeneous metabolic reprogramming, hindering the identification of translatable vulnerabilities for metabolism-targeted therapy. How molecular alterations in tumors promote metabolic diversity and distinct targetable dependencies remains poorly defined. Here we create a resource consisting of lipidomic, transcriptomic, and genomic data from 156 molecularly diverse glioblastoma (GBM) tumors and derivative models. Through integrated analysis of the GBM lipidome with molecular datasets, we identify CDKN2A deletion remodels the GBM lipidome, notably redistributing oxidizable polyunsaturated fatty acids into distinct lipid compartments. Consequently, CDKN2A-deleted GBMs display higher lipid peroxidation, selectively priming tumors for ferroptosis. Together, this study presents a molecular and lipidomic resource of clinical and preclinical GBM specimens, which we leverage to detect a therapeutically exploitable link between a recurring molecular lesion and altered lipid metabolism in GBM.
    Keywords:  CDKN2A; GPX4; RNA sequencing; ferroptosis; glioblastoma; lipid droplet; lipid peroxidation; shotgun lipidomics; triacylglyceride
    DOI:  https://doi.org/10.1016/j.ccell.2023.05.001
  25. Redox Biol. 2023 May 15. pii: S2213-2317(23)00141-6. [Epub ahead of print]63 102740
    The metabolic state of the heart regulates mitochondrial supercomplex abundance in mice.
    Yuting Zheng, Andrew A Gibb, Hongkai Xu, Siqi Liu, Bradford G Hill.
      Mitochondrial supercomplexes are observed in mammalian tissues with high energy demand and may influence metabolism and redox signaling. Nevertheless, the mechanisms that regulate supercomplex abundance remain unclear. In this study, we examined the composition of supercomplexes derived from murine cardiac mitochondria and determined how their abundance changes with substrate provision or by genetically induced changes to the cardiac glucose-fatty acid cycle. Protein complexes from digitonin-solubilized cardiac mitochondria were resolved by blue-native polyacrylamide gel electrophoresis and were identified by mass spectrometry and immunoblotting to contain constituents of Complexes I, III, IV, and V as well as accessory proteins involved in supercomplex assembly and stability, cristae architecture, carbohydrate and fat oxidation, and oxidant detoxification. Respiratory analysis of high molecular mass supercomplexes confirmed the presence of intact respirasomes, capable of transferring electrons from NADH to O2. Provision of respiratory substrates to isolated mitochondria augmented supercomplex abundance, with fatty acyl substrate (octanoylcarnitine) promoting higher supercomplex abundance than carbohydrate-derived substrate (pyruvate). Mitochondria isolated from transgenic hearts that express kinase-deficient 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (GlycoLo), which decreases glucose utilization and increases reliance on fatty acid oxidation for energy, had higher mitochondrial supercomplex abundance and activity compared with mitochondria from wild-type or phosphatase-deficient 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-expressing hearts (GlycoHi), the latter of which encourages reliance on glucose catabolism for energy. These findings indicate that high energetic reliance on fatty acid catabolism bolsters levels of mitochondrial supercomplexes, supporting the idea that the energetic state of the heart is regulatory factor in supercomplex assembly or stability.
    Keywords:  Glycolysis; Heart; Metabolism; Mitochondria; Respirasome; Supercomplex
    DOI:  https://doi.org/10.1016/j.redox.2023.102740
  26. Nat Commun. 2023 May 20. 14(1): 2894
    Alanine supplementation exploits glutamine dependency induced by SMARCA4/2-loss.
    Xianbing Zhu, Zheng Fu, Shary Y Chen, Dionzie Ong, Giulio Aceto, Rebecca Ho, Jutta Steinberger, Anie Monast, Virginie Pilon, Eunice Li, Monica Ta, Kyle Ching, Bianca N Adams, Gian L Negri, Luc Choiniere, Lili Fu, Kitty Pavlakis, Patrick Pirrotte, Daina Z Avizonis, Jeffrey Trent, Bernard E Weissman, Ramon I Klein Geltink, Gregg B Morin, Morag Park, David G Huntsman, William D Foulkes, Yemin Wang, Sidong Huang.
      SMARCA4 (BRG1) and SMARCA2 (BRM) are the two paralogous ATPases of the SWI/SNF chromatin remodeling complexes frequently inactivated in cancers. Cells deficient in either ATPase have been shown to depend on the remaining counterpart for survival. Contrary to this paralog synthetic lethality, concomitant loss of SMARCA4/2 occurs in a subset of cancers associated with very poor outcomes. Here, we uncover that SMARCA4/2-loss represses expression of the glucose transporter GLUT1, causing reduced glucose uptake and glycolysis accompanied with increased dependency on oxidative phosphorylation (OXPHOS); adapting to this, these SMARCA4/2-deficient cells rely on elevated SLC38A2, an amino acid transporter, to increase glutamine import for fueling OXPHOS. Consequently, SMARCA4/2-deficient cells and tumors are highly sensitive to inhibitors targeting OXPHOS or glutamine metabolism. Furthermore, supplementation of alanine, also imported by SLC38A2, restricts glutamine uptake through competition and selectively induces death in SMARCA4/2-deficient cancer cells. At a clinically relevant dose, alanine supplementation synergizes with OXPHOS inhibition or conventional chemotherapy eliciting marked antitumor activity in patient-derived xenografts. Our findings reveal multiple druggable vulnerabilities of SMARCA4/2-loss exploiting a GLUT1/SLC38A2-mediated metabolic shift. Particularly, unlike dietary deprivation approaches, alanine supplementation can be readily applied to current regimens for better treatment of these aggressive cancers.
    DOI:  https://doi.org/10.1038/s41467-023-38594-3
  27. Antioxidants (Basel). 2023 Apr 25. pii: 992. [Epub ahead of print]12(5):
    Identifying Redox-Sensitive Cysteine Residues in Mitochondria.
    Eleni A Kisty, Emma C Saart, Eranthie Weerapana.
      The mitochondrion is the primary energy generator of a cell and is a central player in cellular redox regulation. Mitochondrial reactive oxygen species (mtROS) are the natural byproducts of cellular respiration that are critical for the redox signaling events that regulate a cell's metabolism. These redox signaling pathways primarily rely on the reversible oxidation of the cysteine residues on mitochondrial proteins. Several key sites of this cysteine oxidation on mitochondrial proteins have been identified and shown to modulate downstream signaling pathways. To further our understanding of mitochondrial cysteine oxidation and to identify uncharacterized redox-sensitive cysteines, we coupled mitochondrial enrichment with redox proteomics. Briefly, differential centrifugation methods were used to enrich for mitochondria. These purified mitochondria were subjected to both exogenous and endogenous ROS treatments and analyzed by two redox proteomics methods. A competitive cysteine-reactive profiling strategy, termed isoTOP-ABPP, enabled the ranking of the cysteines by their redox sensitivity, due to a loss of reactivity induced by cysteine oxidation. A modified OxICAT method enabled a quantification of the percentage of reversible cysteine oxidation. Initially, we assessed the cysteine oxidation upon treatment with a range of exogenous hydrogen peroxide concentrations, which allowed us to differentiate the mitochondrial cysteines by their susceptibility to oxidation. We then analyzed the cysteine oxidation upon inducing reactive oxygen species generation via the inhibition of the electron transport chain. Together, these methods identified the mitochondrial cysteines that were sensitive to endogenous and exogenous ROS, including several previously known redox-regulated cysteines and uncharacterized cysteines on diverse mitochondrial proteins.
    Keywords:  OxICAT; ROS; cysteine; isoTOP-ABPP; mass spectrometry; mitochondria; oxidation
    DOI:  https://doi.org/10.3390/antiox12050992
  28. Nature. 2023 May 24.
    γ-Linolenic acid in maternal milk drives cardiac metabolic maturation.
    Ana Paredes, Raquel Justo-Méndez, Daniel Jiménez-Blasco, Vanessa Núñez, Irene Calero, María Villalba-Orero, Andrea Alegre-Martí, Thierry Fischer, Ana Gradillas, Viviane Aparecida Rodrigues Sant'Anna, Felipe Were, Zhiqiang Huang, Pablo Hernansanz-Agustín, Carmen Contreras, Fernando Martínez, Emilio Camafeita, Jesús Vázquez, Jesús Ruiz-Cabello, Estela Area-Gómez, Fátima Sánchez-Cabo, Eckardt Treuter, Juan Pedro Bolaños, Eva Estébanez-Perpiñá, Francisco Javier Rupérez, Coral Barbas, José Antonio Enríquez, Mercedes Ricote.
      Birth presents a metabolic challenge to cardiomyocytes as they reshape fuel preference from glucose to fatty acids for postnatal energy production1,2. This adaptation is triggered in part by post-partum environmental changes3, but the molecules orchestrating cardiomyocyte maturation remain unknown. Here we show that this transition is coordinated by maternally supplied γ-linolenic acid (GLA), an 18:3 omega-6 fatty acid enriched in the maternal milk. GLA binds and activates retinoid X receptors4 (RXRs), ligand-regulated transcription factors that are expressed in cardiomyocytes from embryonic stages. Multifaceted genome-wide analysis revealed that the lack of RXR in embryonic cardiomyocytes caused an aberrant chromatin landscape that prevented the induction of an RXR-dependent gene expression signature controlling mitochondrial fatty acid homeostasis. The ensuing defective metabolic transition featured blunted mitochondrial lipid-derived energy production and enhanced glucose consumption, leading to perinatal cardiac dysfunction and death. Finally, GLA supplementation induced RXR-dependent expression of the mitochondrial fatty acid homeostasis signature in cardiomyocytes, both in vitro and in vivo. Thus, our study identifies the GLA-RXR axis as a key transcriptional regulatory mechanism underlying the maternal control of perinatal cardiac metabolism.
    DOI:  https://doi.org/10.1038/s41586-023-06068-7
  29. Nat Cell Biol. 2023 May 25.
    Divergent metabolic programmes control two populations of MAIT cells that protect the lung.
    Thomas Riffelmacher, Mallory Paynich Murray, Chantal Wientjens, Shilpi Chandra, Viankail Cedillo-Castelán, Ting-Fang Chou, Sara McArdle, Christopher Dillingham, Jordan Devereaux, Aaron Nilsen, Simon Brunel, David M Lewinsohn, Jeff Hasty, Gregory Seumois, Christopher A Benedict, Pandurangan Vijayanand, Mitchell Kronenberg.
      Although mucosal-associated invariant T (MAIT) cells provide rapid, innate-like responses, they are not pre-set, and memory-like responses have been described for MAIT cells following infections. The importance of metabolism for controlling these responses, however, is unknown. Here, following pulmonary immunization with a Salmonella vaccine strain, mouse MAIT cells expanded as separate CD127-Klrg1+ and CD127+Klrg1- antigen-adapted populations that differed in terms of their transcriptome, function and localization in lung tissue. These populations remained altered from steady state for months as stable, separate MAIT cell lineages with enhanced effector programmes and divergent metabolism. CD127+ MAIT cells engaged in an energetic, mitochondrial metabolic programme, which was critical for their maintenance and IL-17A synthesis. This programme was supported by high fatty acid uptake and mitochondrial oxidation and relied on highly polarized mitochondria and autophagy. After vaccination, CD127+ MAIT cells protected mice against Streptococcus pneumoniae infection. In contrast, Klrg1+ MAIT cells had dormant but ready-to-respond mitochondria and depended instead on Hif1a-driven glycolysis to survive and produce IFN-γ. They responded antigen independently and participated in protection from influenza virus. These metabolic dependencies may enable tuning of memory-like MAIT cell responses for vaccination and immunotherapies.
    DOI:  https://doi.org/10.1038/s41556-023-01152-6
  30. bioRxiv. 2023 May 08. pii: 2023.05.08.539795. [Epub ahead of print]
    Crucial neuroprotective roles of the metabolite BH4 in dopaminergic neurons.
    Shane J F Cronin, Weonjin Yu, Ashley Hale, Simon Licht-Mayer, Mark J Crabtree, Joanna A Korecka, Evgenii O Tretiakov, Marco Sealey-Cardona, Mate Somlyay, Masahiro Onji, Meilin An, Jesse D Fox, Bruna Lenfers Turnes, Carlos Gomez-Diaz, Débora da Luz Scheffer, Domagoj Cikes, Vanja Nagy, Adelheid Weidinger, Alexandra Wolf, Harald Reither, Antoine Chabloz, Anoop Kavirayani, Shuan Rao, Nick Andrews, Alban Latremoliere, Michael Costigan, Gillian Douglas, Fernando Cini Freitas, Christian Pifl, Roger Walz, Robert Konrat, Don J Mahad, Andrey V Koslov, Alexandra Latini, Ole Isacson, Tibor Harkany, Penelope J Hallett, Stefan Bagby, Clifford J Woolf, Keith M Channon, Hyunsoo Shawn Je, Josef M Penninger.
      Dopa-responsive dystonia (DRD) and Parkinson's disease (PD) are movement disorders caused by the dysfunction of nigrostriatal dopaminergic neurons. Identifying druggable pathways and biomarkers for guiding therapies is crucial due to the debilitating nature of these disorders. Recent genetic studies have identified variants of GTP cyclohydrolase-1 (GCH1), the rate-limiting enzyme in tetrahydrobiopterin (BH4) synthesis, as causative for these movement disorders. Here, we show that genetic and pharmacological inhibition of BH4 synthesis in mice and human midbrain-like organoids accurately recapitulates motor, behavioral and biochemical characteristics of these human diseases, with severity of the phenotype correlating with extent of BH4 deficiency. We also show that BH4 deficiency increases sensitivities to several PD-related stressors in mice and PD human cells, resulting in worse behavioral and physiological outcomes. Conversely, genetic and pharmacological augmentation of BH4 protects mice from genetically- and chemically induced PD-related stressors. Importantly, increasing BH4 levels also protects primary cells from PD-affected individuals and human midbrain-like organoids (hMLOs) from these stressors. Mechanistically, BH4 not only serves as an essential cofactor for dopamine synthesis, but also independently regulates tyrosine hydroxylase levels, protects against ferroptosis, scavenges mitochondrial ROS, maintains neuronal excitability and promotes mitochondrial ATP production, thereby enhancing mitochondrial fitness and cellular respiration in multiple preclinical PD animal models, human dopaminergic midbrain-like organoids and primary cells from PD-affected individuals. Our findings pinpoint the BH4 pathway as a key metabolic program at the intersection of multiple protective mechanisms for the health and function of midbrain dopaminergic neurons, identifying it as a potential therapeutic target for PD.
    DOI:  https://doi.org/10.1101/2023.05.08.539795
  31. Biomolecules. 2023 Apr 28. pii: 765. [Epub ahead of print]13(5):
    Real-Time Assessment of Intracellular Metabolites in Single Cells through RNA-Based Sensors.
    Alvaro Darío Ortega.
      Quantification of the concentration of particular cellular metabolites reports on the actual utilization of metabolic pathways in physiological and pathological conditions. Metabolite concentration also constitutes the readout for screening cell factories in metabolic engineering. However, there are no direct approaches that allow for real-time assessment of the levels of intracellular metabolites in single cells. In recent years, the modular architecture of natural bacterial RNA riboswitches has inspired the design of genetically encoded synthetic RNA devices that convert the intracellular concentration of a metabolite into a quantitative fluorescent signal. These so-called RNA-based sensors are composed of a metabolite-binding RNA aptamer as the sensor domain, connected through an actuator segment to a signal-generating reporter domain. However, at present, the variety of available RNA-based sensors for intracellular metabolites is still very limited. Here, we go through natural mechanisms for metabolite sensing and regulation in cells across all kingdoms, focusing on those mediated by riboswitches. We review the design principles underlying currently developed RNA-based sensors and discuss the challenges that hindered the development of novel sensors and recent strategies to address them. We finish by introducing the current and potential applicability of synthetic RNA-based sensors for intracellular metabolites.
    Keywords:  RNA-based sensor; aptamer; biosensor; fructose-1,6-bisphosphate; metabolic flux; metabolism; metabolite; riboswitch; ribozyme; spinach
    DOI:  https://doi.org/10.3390/biom13050765
  32. Cell Metab. 2023 May 17. pii: S1550-4131(23)00178-X. [Epub ahead of print]
    Canagliflozin impairs T cell effector function via metabolic suppression in autoimmunity.
    Benjamin J Jenkins, Julianna Blagih, Fernando M Ponce-Garcia, Mary Canavan, Nancy Gudgeon, Simon Eastham, David Hill, Megan M Hanlon, Eric H Ma, Emma L Bishop, April Rees, James G Cronin, Elizabeth C Jury, Sarah K Dimeloe, Douglas J Veale, Catherine A Thornton, Karen H Vousden, David K Finlay, Ursula Fearon, Gareth W Jones, Linda V Sinclair, Emma E Vincent, Nicholas Jones.
      Augmented T cell function leading to host damage in autoimmunity is supported by metabolic dysregulation, making targeting immunometabolism an attractive therapeutic avenue. Canagliflozin, a type 2 diabetes drug, is a sodium glucose co-transporter 2 (SGLT2) inhibitor with known off-target effects on glutamate dehydrogenase and complex I. However, the effects of SGLT2 inhibitors on human T cell function have not been extensively explored. Here, we show that canagliflozin-treated T cells are compromised in their ability to activate, proliferate, and initiate effector functions. Canagliflozin inhibits T cell receptor signaling, impacting on ERK and mTORC1 activity, concomitantly associated with reduced c-Myc. Compromised c-Myc levels were encapsulated by a failure to engage translational machinery resulting in impaired metabolic protein and solute carrier production among others. Importantly, canagliflozin-treated T cells derived from patients with autoimmune disorders impaired their effector function. Taken together, our work highlights a potential therapeutic avenue for repurposing canagliflozin as an intervention for T cell-mediated autoimmunity.
    Keywords:  CD4 T cell; T cell; autoimmunity; canagliflozin; gliflozins; human; immunometabolism
    DOI:  https://doi.org/10.1016/j.cmet.2023.05.001
  33. Science. 2023 May 26. 380(6647): 796-798
    Emerging frontiers in regenerative medicine.
    Kara L McKinley, Michael T Longaker, Shruti Naik.
      Bridging knowledge gaps could enable regenerative therapy.
    DOI:  https://doi.org/10.1126/science.add6492
  34. Sci Adv. 2023 May 24. 9(21): eadg8156
    Mitophagy restricts BAX/BAK-independent, Parkin-mediated apoptosis.
    Giovanni Quarato, Luigi Mari, Nicholas J Barrows, Mao Yang, Sebastian Ruehl, Mark J Chen, Cliff S Guy, Jonathan Low, Taosheng Chen, Douglas R Green.
      Degradation of defective mitochondria is an essential process to maintain cellular homeostasis and it is strictly regulated by the ubiquitin-proteasome system (UPS) and lysosomal activities. Here, using genome-wide CRISPR and small interference RNA screens, we identified a critical contribution of the lysosomal system in controlling aberrant induction of apoptosis following mitochondrial damage. After treatment with mitochondrial toxins, activation of the PINK1-Parkin axis triggered a BAX- and BAK-independent process of cytochrome c release from mitochondria followed by APAF1 and caspase 9-dependent apoptosis. This phenomenon was mediated by UPS-dependent outer mitochondrial membrane (OMM) degradation and was reversed using proteasome inhibitors. We found that the subsequent recruitment of the autophagy machinery to the OMM protected cells from apoptosis, mediating the lysosomal degradation of dysfunctional mitochondria. Our results underscore a major role of the autophagy machinery in counteracting aberrant noncanonical apoptosis and identified autophagy receptors as key elements in the regulation of this process.
    DOI:  https://doi.org/10.1126/sciadv.adg8156
  35. Geroscience. 2023 May 23.
    Cystine rather than cysteine is the preferred substrate for β-elimination by cystathionine γ-lyase: implications for dietary methionine restriction.
    Thomas M Jeitner, Juan A Azcona, Gene P Ables, Diana Cooke, Mark C Horowitz, Pradeep Singh, James M Kelly, Arthur J L Cooper.
      Dietary methionine restriction (MR) increases longevity by improving health. In experimental models, MR is accompanied by decreased cystathionine β-synthase activity and increased cystathionine γ-lyase activity. These enzymes are parts of the transsulfuration pathway which produces cysteine and 2-oxobutanoate. Thus, the decrease in cystathionine β-synthase activity is likely to account for the loss of tissue cysteine observed in MR animals. Despite this decrease in cysteine levels, these tissues exhibit increased H2S production which is thought to be generated by β-elimination of the thiol moiety of cysteine, as catalyzed by cystathionine β-synthase or cystathionine γ-lyase. Another possibility for this H2S production is the cystathionine γ-lyase-catalyzed β-elimination of cysteine persulfide from cystine, which upon reduction yields H2S and cysteine. Here, we demonstrate that MR increases cystathionine γ-lyase production and activities in the liver and kidneys, and that cystine is a superior substrate for cystathionine γ-lyase catalyzed β-elimination as compared to cysteine. Moreover, cystine and cystathionine exhibit comparable Kcat/Km values (6000 M-1 s-1) as substrates for cystathionine γ-lyase-catalyzed β-elimination. By contrast, cysteine inhibits cystathionine γ-lyase in a non-competitive manner (Ki ~ 0.5 mM), which limits its ability to function as a substrate for β-elimination by this enzyme. Cysteine inhibits the enzyme by reacting with its pyridoxal 5'-phosphate cofactor to form a thiazolidine and in so doing prevents further catalysis. These enzymological observations are consistent with the notion that during MR cystathionine γ-lyase is repurposed to catabolize cystine and thereby form cysteine persulfide, which upon reduction produces cysteine.
    Keywords:  Cystathionine beta-synthase; Cystathionine gamma-lyase; Cysteine; Cystine; Methionine restriction; Transsulfuration
    DOI:  https://doi.org/10.1007/s11357-023-00788-4
  36. Cell Rep. 2023 May 17. pii: S2211-1247(23)00530-2. [Epub ahead of print] 112519
    PROX1 induction by autolysosomal activity stabilizes persister-like state of colon cancer via feedback repression of the NOX1-mTORC1 pathway.
    Hirokazu Ohata, Daisuke Shiokawa, Hiroaki Sakai, Yusuke Kanda, Yoshie Okimoto, Syuzo Kaneko, Ryuji Hamamoto, Hitoshi Nakagama, Koji Okamoto.
      Cancer chemoresistance is often attributed to slow-cycling persister populations with cancer stem cell (CSC)-like features. However, how persister populations emerge and prevail in cancer remains obscure. We previously demonstrated that while the NOX1-mTORC1 pathway is responsible for proliferation of a fast-cycling CSC population, PROX1 expression is required for chemoresistant persisters in colon cancer. Here, we show that enhanced autolysosomal activity mediated by mTORC1 inhibition induces PROX1 expression and that PROX1 induction in turn inhibits NOX1-mTORC1 activation. CDX2, identified as a transcriptional activator of NOX1, mediates PROX1-dependent NOX1 inhibition. PROX1-positive and CDX2-positive cells are present in distinct populations, and mTOR inhibition triggers conversion of the CDX2-positive population to the PROX1-positive population. Inhibition of autophagy synergizes with mTOR inhibition to block cancer proliferation. Thus, mTORC1 inhibition-mediated induction of PROX1 stabilizes a persister-like state with high autolysosomal activity via a feedback regulation that involves a key cascade of proliferating CSCs.
    Keywords:  CP: Cancer; NOX1; PROX1; autophagy; colon cancer; mTORC1; persister cells
    DOI:  https://doi.org/10.1016/j.celrep.2023.112519
  37. Nat Cell Biol. 2023 May 22.
    Proteolytic rewiring of mitochondria by LONP1 directs cell identity switching of adipocytes.
    Tingting Fu, Wanping Sun, Jiachen Xue, Zheng Zhou, Wen Wang, Qiqi Guo, Xinyi Chen, Danxia Zhou, Zhisheng Xu, Lin Liu, Liwei Xiao, Yan Mao, Likun Yang, Yujing Yin, Xue-Na Zhang, Qiangyou Wan, Bin Lu, Yuncong Chen, Min-Sheng Zhu, Philipp E Scherer, Lei Fang, Hai-Long Piao, Mengle Shao, Zhenji Gan.
      Mitochondrial proteases are emerging as key regulators of mitochondrial plasticity and acting as both protein quality surveillance and regulatory enzymes by performing highly regulated proteolytic reactions. However, it remains unclear whether the regulated mitochondrial proteolysis is mechanistically linked to cell identity switching. Here we report that cold-responsive mitochondrial proteolysis is a prerequisite for white-to-beige adipocyte cell fate programming during adipocyte thermogenic remodelling. Thermogenic stimulation selectively promotes mitochondrial proteostasis in mature white adipocytes via the mitochondrial protease LONP1. Disruption of LONP1-dependent proteolysis substantially impairs cold- or β3 adrenergic agonist-induced white-to-beige identity switching of mature adipocytes. Mechanistically, LONP1 selectively degrades succinate dehydrogenase complex iron sulfur subunit B and ensures adequate intracellular succinate levels. This alters the histone methylation status on thermogenic genes and thereby enables adipocyte cell fate programming. Finally, augmented LONP1 expression raises succinate levels and corrects ageing-related impairments in white-to-beige adipocyte conversion and adipocyte thermogenic capacity. Together, these findings reveal that LONP1 links proteolytic surveillance to mitochondrial metabolic rewiring and directs cell identity conversion during adipocyte thermogenic remodelling.
    DOI:  https://doi.org/10.1038/s41556-023-01155-3
  38. EMBO Rep. 2023 May 22. e56574
    mTORC1 activity negatively regulates human hair follicle growth and pigmentation.
    Takahiro Suzuki, Jérémy Chéret, Fernanda Dinelli Scala, Aysun Akhundlu, Jennifer Gherardini, Dana-Lee Demetrius, James D B O'Sullivan, Gorana Kuka Epstein, Alan J Bauman, Constantinos Demetriades, Ralf Paus.
      Dysregulation of the activity of the mechanistic target of rapamycin complex 1 (mTORC1) is commonly linked to aging, cancer, and genetic disorders such as tuberous sclerosis (TS), a rare neurodevelopmental multisystemic disease characterized by benign tumors, seizures, and intellectual disability. Although patches of white hair on the scalp (poliosis) are considered as early signs of TS, the underlying molecular mechanisms and potential involvement of mTORC1 in hair depigmentation remain unclear. Here, we have used healthy, organ-cultured human scalp hair follicles (HFs) to interrogate the role of mTORC1 in a prototypic human (mini-)organ. Gray/white HFs exhibit high mTORC1 activity, while mTORC1 inhibition by rapamycin stimulated HF growth and pigmentation, even in gray/white HFs that still contained some surviving melanocytes. Mechanistically, this occurred via increased intrafollicular production of the melanotropic hormone, α-MSH. In contrast, knockdown of intrafollicular TSC2, a negative regulator of mTORC1, significantly reduced HF pigmentation. Our findings introduce mTORC1 activity as an important negative regulator of human HF growth and pigmentation and suggest that pharmacological mTORC1 inhibition could become a novel strategy in the management of hair loss and depigmentation disorders.
    Keywords:  alpha-MSH/MC1R; mTORC1; melanocyte; rapamycin; tuberous sclerosis
    DOI:  https://doi.org/10.15252/embr.202256574
  39. bioRxiv. 2023 May 08. pii: 2023.05.07.539780. [Epub ahead of print]
    IL-10 constrains sphingolipid metabolism via fatty acid desaturation to limit inflammation.
    Autumn G York, Mathias H Skadow, Rihao Qu, Joonseok Oh, Walter K Mowel, J Richard Brewer, Eleanna Kaffe, Kevin J Williams, Yuval Kluger, Jason M Crawford, Stephen T Smale, Steven J Bensinger, Richard A Flavell.
      Unchecked chronic inflammation is the underlying cause of many diseases, ranging from inflammatory bowel disease to obesity and neurodegeneration. Given the deleterious nature of unregulated inflammation, it is not surprising that cells have acquired a diverse arsenal of tactics to limit inflammation. IL-10 is a key anti-inflammatory cytokine that can limit immune cell activation and cytokine production in innate immune cell types; however, the exact mechanism by which IL-10 signaling subdues inflammation remains unclear. Here, we find that IL-10 signaling constrains sphingolipid metabolism. Specifically, we find increased saturated very long chain (VLC) ceramides are critical for the heightened inflammatory gene expression that is a hallmark of IL-10-deficient macrophages. Genetic deletion of CerS2, the enzyme responsible for VLC ceramide production, limited exacerbated inflammatory gene expression associated with IL-10 deficiency both in vitro and in vivo , indicating that "metabolic correction" is able to reduce inflammation in the absence of IL-10. Surprisingly, accumulation of saturated VLC ceramides was regulated by flux through the de novo mono-unsaturated fatty acid (MUFA) synthesis pathway, where addition of exogenous MUFAs could limit both saturated VLC ceramide production and inflammatory gene expression in the absence of IL-10 signaling. Together, these studies mechanistically define how IL-10 signaling manipulates fatty acid metabolism as part of its molecular anti-inflammatory strategy and could lead to novel and inexpensive approaches to regulate aberrant inflammation.
    DOI:  https://doi.org/10.1101/2023.05.07.539780
  40. Trends Cell Biol. 2023 May 23. pii: S0962-8924(23)00079-X. [Epub ahead of print]
    Ferroptosis: mechanisms and implications for cancer development and therapy response.
    Ancély Ferreira Dos Santos, Gholamreza Fazeli, Thamara Nishida Xavier da Silva, José Pedro Friedmann Angeli.
      As cancer cells develop resistance to apoptosis, non-apoptotic cell death modalities, such as ferroptosis, have emerged as promising strategies to combat therapy-resistant cancers. Cells that develop resistance to conventional therapies or metastatic cancer cells have been shown to have increased sensitivity to ferroptosis. Therefore, targeting the regulatory elements of ferroptosis in cancer could offer novel therapeutic opportunities. In this review, we first provide an overview of the known ferroptosis regulatory networks and discuss recent findings on how they contribute to cancer plasticity. We then expand into the critical role of selenium metabolism in regulating ferroptosis. Finally, we highlight specific cases where induction of ferroptosis could be used to sensitize cancer cells to this form of cell death.
    Keywords:  Ferroptosis; glutathione peroxidase 4 (GPX4); lipid peroxidation; radical trapping antioxidants (RTA); selenoproteins
    DOI:  https://doi.org/10.1016/j.tcb.2023.04.005
  41. PLoS Biol. 2023 May;21(5): e3002117
    Hypoxia extends lifespan and neurological function in a mouse model of aging.
    Robert S Rogers, Hong Wang, Timothy J Durham, Jonathan A Stefely, Norah A Owiti, Andrew L Markhard, Lev Sandler, Tsz-Leung To, Vamsi K Mootha.
      There is widespread interest in identifying interventions that extend healthy lifespan. Chronic continuous hypoxia delays the onset of replicative senescence in cultured cells and extends lifespan in yeast, nematodes, and fruit flies. Here, we asked whether chronic continuous hypoxia is beneficial in mammalian aging. We utilized the Ercc1 Δ/- mouse model of accelerated aging given that these mice are born developmentally normal but exhibit anatomic, physiological, and biochemical features of aging across multiple organs. Importantly, they exhibit a shortened lifespan that is extended by dietary restriction, the most potent aging intervention across many organisms. We report that chronic continuous 11% oxygen commenced at 4 weeks of age extends lifespan by 50% and delays the onset of neurological debility in Ercc1 Δ/- mice. Chronic continuous hypoxia did not impact food intake and did not significantly affect markers of DNA damage or senescence, suggesting that hypoxia did not simply alleviate the proximal effects of the Ercc1 mutation, but rather acted downstream via unknown mechanisms. To the best of our knowledge, this is the first study to demonstrate that "oxygen restriction" can extend lifespan in a mammalian model of aging.
    DOI:  https://doi.org/10.1371/journal.pbio.3002117
  42. Trends Cell Biol. 2023 May 24. pii: S0962-8924(23)00084-3. [Epub ahead of print]
    Mechanobiology of organelles: illuminating their roles in mechanosensing and mechanotransduction.
    Santosh Phuyal, Patrizia Romani, Sirio Dupont, Hesso Farhan.
      Mechanobiology studies the mechanisms by which cells sense and respond to physical forces, and the role of these forces in shaping cells and tissues themselves. Mechanosensing can occur at the plasma membrane, which is directly exposed to external forces, but also in the cell's interior, for example, through deformation of the nucleus. Less is known on how the function and morphology of organelles are influenced by alterations in their own mechanical properties, or by external forces. Here, we discuss recent advances on the mechanosensing and mechanotransduction of organelles, including the endoplasmic reticulum (ER), the Golgi apparatus, the endo-lysosmal system, and the mitochondria. We highlight open questions that need to be addressed to gain a broader understanding of the role of organelle mechanobiology.
    Keywords:  Golgi apparatus; endoplasmic reticulum; endosomes; mechanosensing; mechanotransduction; mitochondria
    DOI:  https://doi.org/10.1016/j.tcb.2023.05.001
  43. Cancer Cell. 2023 May 12. pii: S1535-6108(23)00162-9. [Epub ahead of print]
    Context-dependent activation of STING-interferon signaling by CD11b agonists enhances anti-tumor immunity.
    Xiuting Liu, Graham D Hogg, Chong Zuo, Nicholas C Borcherding, John M Baer, Varintra E Lander, Liang-I Kang, Brett L Knolhoff, Faiz Ahmad, Robin E Osterhout, Anna V Galkin, Jean-Marie Bruey, Laura L Carter, Cedric Mpoy, Kiran R Vij, Ryan C Fields, Julie K Schwarz, Haeseong Park, Vineet Gupta, David G DeNardo.
      Chronic activation of inflammatory pathways and suppressed interferon are hallmarks of immunosuppressive tumors. Previous studies have shown that CD11b integrin agonists could enhance anti-tumor immunity through myeloid reprograming, but the underlying mechanisms remain unclear. Herein we find that CD11b agonists alter tumor-associated macrophage (TAM) phenotypes by repressing NF-κB signaling and activating interferon gene expression simultaneously. Repression of NF-κB signaling involves degradation of p65 protein and is context independent. In contrast, CD11b agonism induces STING/STAT1 pathway-mediated interferon gene expression through FAK-mediated mitochondrial dysfunction, with the magnitude of induction dependent on the tumor microenvironment and amplified by cytotoxic therapies. Using tissues from phase I clinical studies, we demonstrate that GB1275 treatment activates STING and STAT1 signaling in TAMs in human tumors. These findings suggest potential mechanism-based therapeutic strategies for CD11b agonists and identify patient populations more likely to benefit.
    Keywords:  CD11b; NF-κB; STING; immunotherapy; pancreatic cancer; tumor-associated macrophages
    DOI:  https://doi.org/10.1016/j.ccell.2023.04.018
  44. Nat Commun. 2023 May 23. 14(1): 2978
    Genetically encoded photocatalytic protein labeling enables spatially-resolved profiling of intracellular proteome.
    Fu Zheng, Xinyue Zhou, Peng Zou, Chenxin Yu.
      Mapping the subcellular organization of proteins is crucial for understanding their biological functions. Herein, we report a reactive oxygen species induced protein labeling and identification (RinID) method for profiling subcellular proteome in the context of living cells. Our method capitalizes on a genetically encoded photocatalyst, miniSOG, to locally generate singlet oxygen that reacts with proximal proteins. Labeled proteins are conjugated in situ with an exogenously supplied nucleophilic probe, which serves as a functional handle for subsequent affinity enrichment and mass spectrometry-based protein identification. From a panel of nucleophilic compounds, we identify biotin-conjugated aniline and propargyl amine as highly reactive probes. As a demonstration of the spatial specificity and depth of coverage in mammalian cells, we apply RinID in the mitochondrial matrix, capturing 477 mitochondrial proteins with 94% specificity. We further demonstrate the broad applicability of RinID in various subcellular compartments, including the nucleus and the endoplasmic reticulum (ER). The temporal control of RinID enables pulse-chase labeling of ER proteome in HeLa cells, which reveals substantially higher clearance rate for secreted proteins than ER resident proteins.
    DOI:  https://doi.org/10.1038/s41467-023-38565-8
  45. Antioxidants (Basel). 2023 May 03. pii: 1037. [Epub ahead of print]12(5):
    Tetrahydrobiopterin: Beyond Its Traditional Role as a Cofactor.
    Tuany Eichwald, Lucila de Bortoli da Silva, Ananda Christina Staats Pires, Laís Niero, Erick Schnorrenberger, Clovis Colpani Filho, Gisele Espíndola, Wei-Lin Huang, Gilles J Guillemin, José E Abdenur, Alexandra Latini.
      Tetrahydrobiopterin (BH4) is an endogenous cofactor for some enzymatic conversions of essential biomolecules, including nitric oxide, and monoamine neurotransmitters, and for the metabolism of phenylalanine and lipid esters. Over the last decade, BH4 metabolism has emerged as a promising metabolic target for negatively modulating toxic pathways that may result in cell death. Strong preclinical evidence has shown that BH4 metabolism has multiple biological roles beyond its traditional cofactor activity. We have shown that BH4 supports essential pathways, e.g., to generate energy, to enhance the antioxidant resistance of cells against stressful conditions, and to protect from sustained inflammation, among others. Therefore, BH4 should not be understood solely as an enzyme cofactor, but should instead be depicted as a cytoprotective pathway that is finely regulated by the interaction of three different metabolic pathways, thus assuring specific intracellular concentrations. Here, we bring state-of-the-art information about the dependency of mitochondrial activity upon the availability of BH4, as well as the cytoprotective pathways that are enhanced after BH4 exposure. We also bring evidence about the potential use of BH4 as a new pharmacological option for diseases in which mitochondrial disfunction has been implicated, including chronic metabolic disorders, neurodegenerative diseases, and primary mitochondriopathies.
    Keywords:  antioxidant; inflammation; memory; mitochondrial enhancer; neopterin; oxidative stress; sepiapterin
    DOI:  https://doi.org/10.3390/antiox12051037
  46. Nat Commun. 2023 May 25. 14(1): 3025
    Establishment of gastrointestinal assembloids to study the interplay between epithelial crypts and their mesenchymal niche.
    Manqiang Lin, Kimberly Hartl, Julian Heuberger, Giulia Beccaceci, Hilmar Berger, Hao Li, Lichao Liu, Stefanie Müllerke, Thomas Conrad, Felix Heymann, Andrew Woehler, Frank Tacke, Nikolaus Rajewsky, Michael Sigal.
      The cellular organization of gastrointestinal crypts is orchestrated by different cells of the stromal niche but available in vitro models fail to fully recapitulate the interplay between epithelium and stroma. Here, we establish a colon assembloid system comprising the epithelium and diverse stromal cell subtypes. These assembloids recapitulate the development of mature crypts resembling in vivo cellular diversity and organization, including maintenance of a stem/progenitor cell compartment in the base and their maturation into secretory/absorptive cell types. This process is supported by self-organizing stromal cells around the crypts that resemble in vivo organization, with cell types that support stem cell turnover adjacent to the stem cell compartment. Assembloids that lack BMP receptors either in epithelial or stromal cells fail to undergo proper crypt formation. Our data highlight the crucial role of bidirectional signaling between epithelium and stroma, with BMP as a central determinant of compartmentalization along the crypt axis.
    DOI:  https://doi.org/10.1038/s41467-023-38780-3
  47. Curr Opin Plant Biol. 2023 May 19. pii: S1369-5266(23)00047-X. [Epub ahead of print]74 102382
    Non-canonical and developmental roles of the TCA cycle in plants.
    Tao Zhang, Jesus T Peng, Amman Klair, Alexandra J Dickinson.
      Over recent years, our understanding of the tricarboxylic acid cycle (TCAC) in living organisms has expanded beyond its canonical role in cellular energy production. In plants, TCAC metabolites and related enzymes have important roles in physiology, including vacuolar function, chelation of metals and nutrients, photorespiration, and redox regulation. Research in other organisms, including animals, has demonstrated unexpected functions of the TCAC metabolites in a number of biological processes, including signaling, epigenetic regulation, and cell differentiation. Here, we review the recent progress in discovery of non-canonical roles of the TCAC. We then discuss research on these metabolites in the context of plant development, with a focus on research related to tissue-specific functions of the TCAC. Additionally, we review research describing connections between TCAC metabolites and phytohormone signaling pathways. Overall, we discuss the opportunities and challenges in discovering new functions of TCAC metabolites in plants.
    Keywords:  Phytohormones; Plant development; Primary metabolism; Tricarboxylic acid cycle
    DOI:  https://doi.org/10.1016/j.pbi.2023.102382
  48. Nat Biotechnol. 2023 May 22.
    Strand-selective base editing of human mitochondrial DNA using mitoBEs.
    Zongyi Yi, Xiaoxue Zhang, Wei Tang, Ying Yu, Xiaoxu Wei, Xue Zhang, Wensheng Wei.
      A number of mitochondrial diseases in humans are caused by point mutations that could be corrected by base editors, but delivery of CRISPR guide RNAs into the mitochondria is difficult. In this study, we present mitochondrial DNA base editors (mitoBEs), which combine a transcription activator-like effector (TALE)-fused nickase and a deaminase for precise base editing in mitochondrial DNA. Combining mitochondria-localized, programmable TALE binding proteins with the nickase MutH or Nt.BspD6I(C) and either the single-stranded DNA-specific adenine deaminase TadA8e or the cytosine deaminase ABOBEC1 and UGI, we achieve A-to-G or C-to-T base editing with up to 77% efficiency and high specificity. We find that mitoBEs are DNA strand-selective mitochondrial base editors, with editing results more likely to be retained on the nonnicked DNA strand. Furthermore, we correct pathogenic mitochondrial DNA mutations in patient-derived cells by delivering mitoBEs encoded in circular RNAs. mitoBEs offer a precise, efficient DNA editing tool with broad applicability for therapy in mitochondrial genetic diseases.
    DOI:  https://doi.org/10.1038/s41587-023-01791-y
  49. Nat Cancer. 2023 May;4(5): 754-773
    Genome-scale functional genomics identify genes preferentially essential for multiple myeloma cells compared to other neoplasias.
    Ricardo de Matos Simoes, Ryosuke Shirasaki, Sondra L Downey-Kopyscinski, Geoffrey M Matthews, Benjamin G Barwick, Vikas A Gupta, Daphné Dupéré-Richer, Shizuka Yamano, Yiguo Hu, Michal Sheffer, Eugen Dhimolea, Olga Dashevsky, Sara Gandolfi, Kazuya Ishiguro, Robin M Meyers, Jordan G Bryan, Neekesh V Dharia, Paul J Hengeveld, Johanna B Brüggenthies, Huihui Tang, Andrew J Aguirre, Quinlan L Sievers, Benjamin L Ebert, Brian J Glassner, Christopher J Ott, James E Bradner, Nicholas P Kwiatkowski, Daniel Auclair, Joan Levy, Jonathan J Keats, Richard W J Groen, Nathanael S Gray, Aedin C Culhane, James M McFarland, Joshua M Dempster, Jonathan D Licht, Lawrence H Boise, William C Hahn, Francisca Vazquez, Aviad Tsherniak, Constantine S Mitsiades.
      Clinical progress in multiple myeloma (MM), an incurable plasma cell (PC) neoplasia, has been driven by therapies that have limited applications beyond MM/PC neoplasias and do not target specific oncogenic mutations in MM. Instead, these agents target pathways critical for PC biology yet largely dispensable for malignant or normal cells of most other lineages. Here we systematically characterized the lineage-preferential molecular dependencies of MM through genome-scale clustered regularly interspaced short palindromic repeats (CRISPR) studies in 19 MM versus hundreds of non-MM lines and identified 116 genes whose disruption more significantly affects MM cell fitness compared with other malignancies. These genes, some known, others not previously linked to MM, encode transcription factors, chromatin modifiers, endoplasmic reticulum components, metabolic regulators or signaling molecules. Most of these genes are not among the top amplified, overexpressed or mutated in MM. Functional genomics approaches thus define new therapeutic targets in MM not readily identifiable by standard genomic, transcriptional or epigenetic profiling analyses.
    DOI:  https://doi.org/10.1038/s43018-023-00550-x
  50. Antioxidants (Basel). 2023 May 10. pii: 1075. [Epub ahead of print]12(5):
    PGC-1α Is a Master Regulator of Mitochondrial Lifecycle and ROS Stress Response.
    Othman Abu Shelbayeh, Tasnim Arroum, Silke Morris, Karin B Busch.
      Mitochondria play a major role in ROS production and defense during their life cycle. The transcriptional activator PGC-1α is a key player in the homeostasis of energy metabolism and is therefore closely linked to mitochondrial function. PGC-1α responds to environmental and intracellular conditions and is regulated by SIRT1/3, TFAM, and AMPK, which are also important regulators of mitochondrial biogenesis and function. In this review, we highlight the functions and regulatory mechanisms of PGC-1α within this framework, with a focus on its involvement in the mitochondrial lifecycle and ROS metabolism. As an example, we show the role of PGC-1α in ROS scavenging under inflammatory conditions. Interestingly, PGC-1α and the stress response factor NF-κB, which regulates the immune response, are reciprocally regulated. During inflammation, NF-κB reduces PGC-1α expression and activity. Low PGC-1α activity leads to the downregulation of antioxidant target genes resulting in oxidative stress. Additionally, low PGC-1α levels and concomitant oxidative stress promote NF-κB activity, which exacerbates the inflammatory response.
    Keywords:  PGC-1α; ROS defense; mitochondrial life cycle; mitonuclear communication
    DOI:  https://doi.org/10.3390/antiox12051075
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