bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2022–04–03
74 papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit
  1. Methylmalonic acid: an age-related metabolite that drives tumour aggressiveness.
  2. Starting the engine of the powerhouse: mitochondrial transcription and beyond.
  3. Altered propionate metabolism contributes to tumour progression and aggressiveness.
  4. Mitochondrial ROS signalling requires uninterrupted electron flow and is lost during ageing in flies.
  5. Partial inhibition of mitochondrial-linked pyrimidine synthesis increases tumorigenic potential and lysosome accumulation.
  6. Transsulfuration, minor player or crucial for cysteine homeostasis in cancer.
  7. Organelle transporters and inter-organelle communication as drivers of metabolic regulation and cellular homeostasis.
  8. Folliculin promotes substrate-selective mTORC1 activity by activating RagC to recruit TFE3.
  9. Quantitative metabolic fluxes regulated by trans-omic networks.
  10. Systemic Lactate Acts as a Metabolic Buffer in Humans and Prevents Nutrient Overflow in the Postprandial Phase.
  11. Sensitivity of VHL mutant kidney cancers to HIF2 inhibitors does not require an intact p53 pathway.
  12. Scinderin promotes fusion of electron transport chain dysfunctional muscle stem cells with myofibers.
  13. Transient changes to metabolic homeostasis initiate mitochondrial adaptation to endurance exercise.
  14. Cryo-EM structures of the human GATOR1-Rag-Ragulator complex reveal a spatial-constraint regulated GAP mechanism.
  15. Tumor-Derived Lactic Acid Modulates Activation and Metabolic Status of Draining Lymph Node Stroma.
  16. Proteomic profiling shows mitochondrial nucleoids are autophagy cargo in neurons: implications for neuron maintenance and neurodegenerative disease.
  17. Palmitoylation of MDH2 by ZDHHC18 activates mitochondrial respiration and accelerates ovarian cancer growth.
  18. Disruption of mitochondrial complex III in cap mesenchyme but not in ureteric progenitors results in defective nephrogenesis associated with amino acid deficiency.
  19. Heteroplasmic mitochondrial DNA variants in cardiovascular diseases.
  20. PTIP governs NAD+ metabolism by regulating CD38 expression to drive macrophage inflammation.
  21. YAP-deLIVERing the directions and the fuel.
  22. NFκB activation by hypoxic small extracellular vesicles drives oncogenic reprogramming in a breast cancer microenvironment.
  23. H3K9me3 represses G6PD expression to suppress the pentose phosphate pathway and ROS production to promote human mesothelioma growth.
  24. Mitochondrial Fission and Fusion in Tumor Progression to Metastasis.
  25. Pro-inflammatory polarization of macrophages is associated with reduced endoplasmic reticulum-mitochondria interaction.
  26. Redox Activation of Mitochondrial DAMPs and the Metabolic Consequences for Development of Autoimmunity.
  27. Mitochondrial DNA replication and repair defects: Clinical phenotypes and therapeutic interventions.
  28. ESCRT-I fuels lysosomal degradation to restrict TFEB/TFE3 signaling via the Rag-mTORC1 pathway.
  29. Immunometabolic crosstalk during bacterial infection.
  30. Simultaneous targeting of mitochondrial metabolism and immune checkpoints as a new strategy for renal cancer therapy.
  31. Lipid metabolic reprogramming by hypoxia-inducible factor-1 in the hypoxic tumour microenvironment.
  32. Multi-omics & pathway analysis identify potential roles for tumor N-acetyl aspartate accumulation in murine models of castration-resistant prostate cancer.
  33. Switching to the cyclic pentose phosphate pathway powers the oxidative burst in activated neutrophils.
  34. Macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution.
  35. Anatomic position determines oncogenic specificity in melanoma.
  36. Acetyl-CoA Carboxylases and Diseases.
  37. An In Vitro Approach to Study Mitochondrial Dysfunction: A Cybrid Model.
  38. Genome doubling causes double trouble.
  39. PGC-1α induced mitochondrial biogenesis in stromal cells underpins mitochondrial transfer to melanoma.
  40. Mitochondria and ferroptosis.
  41. The Interplay Between TGF-β Signaling and Cell Metabolism.
  42. Hypoxia Induces Saturated Fatty Acids Accumulation and Reduces Unsaturated Fatty Acids Independently of Reverse Tricarboxylic Acid Cycle in L6 Myotubes.
  43. BAX and BAK dynamics control mitochondrial DNA release during apoptosis.
  44. Assessing Changes in Human Natural Killer Cell Metabolism Using the Seahorse Extracellular Flux Analyzer.
  45. Inositol hexakisphosphate kinase-2 non-catalytically regulates mitophagy by attenuating PINK1 signaling.
  46. Deacetylation of MTHFD2 by SIRT4 senses stress signal to inhibit cancer cell growth by remodeling folate metabolism.
  47. Carbon sources and pathways for citrate secreted by human prostate cancer cells determined by NMR tracing and metabolic modeling.
  48. Perspective: a stirring role for metabolism in cells.
  49. Metabolic regulation of CD8+ T cells: from mechanism to therapy.
  50. Bladder cancer cells shift rapidly and spontaneously to cisplatin-resistant oxidative phosphorylation that is trackable in real time.
  51. Redox proteome analysis of auranofin exposed ovarian cancer cells (A2780).
  52. Roles of miR-124-3p/Scd1 in urolithin A-induced brown adipocyte differentiation and succinate-dependent regulation of mitochondrial complex II.
  53. Crucial role and mechanism of transcription-coupled DNA repair in bacteria.
  54. Long-chain ceramides are cell non-autonomous signals linking lipotoxicity to endoplasmic reticulum stress in skeletal muscle.
  55. Leveraging GPCR signaling in thermogenic fat to counteract metabolic diseases.
  56. Quantitative super-resolution microscopy reveals promoting mitochondrial interconnectivity protects against AKI.
  57. Dying cell-derived SAM switches off inflammation.
  58. Role and regulation of autophagy in cancer.
  59. T cell metabolism and possible therapeutic targets in systemic lupus erythematosus: a narrative review.
  60. Acetic acid triggers cytochrome c release in yeast heterologously expressing human Bax.
  61. Interplay between mechanics and signalling in regulating cell fate.
  62. Citrate transporter inhibitors: possible new anticancer agents.
  63. The synthesis and properties of mitochondrial targeted iron chelators.
  64. PI3Kγ stimulates a high molecular weight form of myosin light chain kinase to promote myeloid cell adhesion and tumor inflammation.
  65. Enhanced NCLX-dependent mitochondrial Ca2+ efflux attenuates pathological remodeling in heart failure.
  66. Oxygen sensing: Protein degradation meets retrograde signaling.
  67. Epithelial-mesenchymal plasticity in tumor immune evasion.
  68. Analysis of localized cAMP perturbations within a tissue reveal the effects of a local, dynamic gap junction state on ERK signaling.
  69. cGAS-STING mediates cytoplasmic mitochondrial-DNA-induced inflammatory signal transduction during accelerated senescence of pancreatic β-cells induced by metabolic stress.
  70. Protective role of chaperone-mediated autophagy against atherosclerosis.
  71. Glycolytic metabolism and activation of Na+ pumping contribute to extracellular acidification in the central clock of the suprachiasmatic nucleus: Differential glucose sensitivity and utilization between oxidative and non-oxidative glycolytic pathways.
  72. cGAS-STING signalings potentiate tumor progression via sustaining cancer stemness.
  73. Protein-Interaction Affinity Gradient Drives [4Fe-4S] Cluster Insertion in Human Lipoyl Synthase.
  74. The complete sequence of a human genome.
  1. Nat Metab. 2022 Mar 31.
    Methylmalonic acid: an age-related metabolite that drives tumour aggressiveness.
    Emily J Kay, Sara Zanivan.
      
    DOI:  https://doi.org/10.1038/s42255-022-00540-w
  2. Biol Chem. 2022 Mar 31.
    Starting the engine of the powerhouse: mitochondrial transcription and beyond.
    Maria Miranda, Nina A Bonekamp, Inge Kühl.
      Mitochondria are central hubs for cellular metabolism, coordinating a variety of metabolic reactions crucial for human health. Mitochondria provide most of the cellular energy via their oxidative phosphorylation (OXPHOS) system, which requires the coordinated expression of genes encoded by both the nuclear (nDNA) and mitochondrial genomes (mtDNA). Transcription of mtDNA is not only essential for the biogenesis of the OXPHOS system, but also generates RNA primers necessary to initiate mtDNA replication. Like the prokaryotic system, mitochondria have no membrane-based compartmentalization to separate the different steps of mtDNA maintenance and expression and depend entirely on nDNA-encoded factors imported into the organelle. Our understanding of mitochondrial transcription in mammalian cells has largely progressed, but the mechanisms regulating mtDNA gene expression are still poorly understood despite their profound importance for human disease. Here, we review mechanisms of mitochondrial gene expression with a focus on the recent findings in the field of mammalian mtDNA transcription and disease phenotypes caused by defects in proteins involved in this process.
    Keywords:   inhibitor of mitochondrial transcription; PPR proteins; mitochondria; mitochondrial disease; mitochondrial gene expression; mitochondrial transcription
    DOI:  https://doi.org/10.1515/hsz-2021-0416
  3. Nat Metab. 2022 Mar 31.
    Altered propionate metabolism contributes to tumour progression and aggressiveness.
    Ana P Gomes, Didem Ilter, Vivien Low, Stanislav Drapela, Tanya Schild, Edouard Mullarky, Julie Han, Ilaria Elia, Dorien Broekaert, Adam Rosenzweig, Michal Nagiec, Joana B Nunes, Bethany E Schaffer, Anders P Mutvei, John M Asara, Lewis C Cantley, Sarah-Maria Fendt, John Blenis.
      The alteration of metabolic pathways is a critical strategy for cancer cells to attain the traits necessary for metastasis in disease progression. Here, we find that dysregulation of propionate metabolism produces a pro-aggressive signature in breast and lung cancer cells, increasing their metastatic potential. This occurs through the downregulation of methylmalonyl coenzyme A epimerase (MCEE), mediated by an extracellular signal-regulated kinase 2-driven transcription factor Sp1/early growth response protein 1 transcriptional switch driven by metastatic signalling at its promoter level. The loss of MCEE results in reduced propionate-driven anaplerotic flux and intracellular and intratumoral accumulation of methylmalonic acid, a by-product of propionate metabolism that promotes cancer cell invasiveness. Altogether, we present a previously uncharacterized dysregulation of propionate metabolism as an important contributor to cancer and a valuable potential target in the therapeutic treatment of metastatic carcinomas.
    DOI:  https://doi.org/10.1038/s42255-022-00553-5
  4. Geroscience. 2022 Mar 30.
    Mitochondrial ROS signalling requires uninterrupted electron flow and is lost during ageing in flies.
    Charlotte Graham, Rhoda Stefanatos, Angeline E H Yek, Ruth V Spriggs, Samantha H Y Loh, Alejandro Huerta Uribe, Tong Zhang, L Miguel Martins, Oliver D K Maddocks, Filippo Scialo, Alberto Sanz.
      Mitochondrial reactive oxygen species (mtROS) are cellular messengers essential for cellular homeostasis. In response to stress, reverse electron transport (RET) through respiratory complex I generates high levels of mtROS. Suppression of ROS production via RET (ROS-RET) reduces survival under stress, while activation of ROS-RET extends lifespan in basal conditions. Here, we demonstrate that ROS-RET signalling requires increased electron entry and uninterrupted electron flow through the electron transport chain (ETC). We find that in old fruit flies, ROS-RET is abolished when electron flux is decreased and that their mitochondria produce consistently high levels of mtROS. Finally, we demonstrate that in young flies, limiting electron exit, but not entry, from the ETC phenocopies mtROS generation observed in old individuals. Our results elucidate the mechanism by which ROS signalling is lost during ageing.
    Keywords:  Ageing; Complex I; Complex IV; Drosophila; Mitochondria; Reactive oxygen species; Reverse electron transport
    DOI:  https://doi.org/10.1007/s11357-022-00555-x
  5. Mitochondrion. 2022 Mar 25. pii: S1567-7249(22)00025-3. [Epub ahead of print]64 73-81
    Partial inhibition of mitochondrial-linked pyrimidine synthesis increases tumorigenic potential and lysosome accumulation.
    Claus Desler, Jon Ambæk Durhuus, Thomas Lau-Lindestrand Hansen, Sharath Anugula, Nadia Thaulov Zelander, Sisse Bøggild, Lene Juel Rasmussen.
      The correlation between mitochondrial function and oncogenesis is complex and is not fully understood. Here we determine the importance of mitochondrial-linked pyrimidine synthesis for the aggressiveness of cancer cells. The enzyme dihydroorotate dehydrogenase (DHODH) links oxidative phosphorylation to de novo synthesis of pyrimidines. We demonstrate that an inhibition of DHODH results in a respiration-independent significant increase of anchorage-independent growth but does not affect DNA repair ability. Instead, we show an autophagy-independent increase of lysosomes. The results of this study suggest that inhibition of mitochondrial-linked pyrimidine synthesis in cancer cells results in a more aggressive tumor phenotype.
    Keywords:  DNA repair; Lysosome increase; Mitochondria; Mitochondrial-linked pyrimidine synthesis; Tumorigenesis
    DOI:  https://doi.org/10.1016/j.mito.2022.03.005
  6. Trends Cell Biol. 2022 Mar 29. pii: S0962-8924(22)00060-5. [Epub ahead of print]
    Transsulfuration, minor player or crucial for cysteine homeostasis in cancer.
    Hai-Feng Zhang, Ramon I Klein Geltink, Seth J Parker, Poul H Sorensen.
      Cysteine, a thiol-containing amino acid, is crucial for the synthesis of sulfur-containing biomolecules that control multiple essential cellular activities. Altered cysteine metabolism has been linked to numerous driver oncoproteins and tumor suppressors, as well as to malignant traits in cancer. Cysteine can be acquired from extracellular sources or synthesized de novo via the transsulfuration (TSS) pathway. Limited availability of cystine in tumor interstitial fluids raises the possible dependency on de novo cysteine synthesis via TSS. However, the contribution of TSS to cancer metabolism remains highly contentious. Based on recent findings, we provide new perspectives on this crucial but understudied metabolic pathway in cancer.
    Keywords:  cancer; cysteine metabolism; ferroptosis; glutathione; redox homeostasis; transsulfuration
    DOI:  https://doi.org/10.1016/j.tcb.2022.02.009
  7. Mol Metab. 2022 Mar 25. pii: S2212-8778(22)00050-3. [Epub ahead of print] 101481
    Organelle transporters and inter-organelle communication as drivers of metabolic regulation and cellular homeostasis.
    Aakriti Jain, Roberto Zoncu.
      Spatial compartmentalization of metabolic pathways within membrane-separated organelles is key to the ability of eukaryotic cells to precisely regulate their biochemical functions. Membrane-bound organelles such as mitochondria, endoplasmic reticulum (ER) and lysosomes enable the concentration of metabolic precursors within optimized chemical environments, greatly accelerating the efficiency of both anabolic and catabolic reactions, enabling division of labor and optimal utilization of resources. However, metabolic compartmentalization also poses a challenge to cells because it creates spatial discontinuities that must be bridged for reaction cascades to be connected and completed. To do so, cells employ different methods to coordinate metabolic fluxes occurring in different organelles, such as membrane-localized transporters to facilitate regulated metabolite exchange between mitochondria and lysosomes, non-vesicular transport pathways via physical contact sites connecting the ER with both mitochondria and lysosomes, as well as localized regulatory signaling processes that coordinately regulate the activity of all these organelles. Effective communication among these systems is essential to cellular health and function, whereas disruption of inter-organelle communication is an emerging driver in a multitude of diseases, from cancer to neurodegeneration.
    Keywords:  Contact sites; Lysosome; Metabolism; Mitochondria; Transporters; mTORC1
    DOI:  https://doi.org/10.1016/j.molmet.2022.101481
  8. PLoS Biol. 2022 Mar 31. 20(3): e3001594
    Folliculin promotes substrate-selective mTORC1 activity by activating RagC to recruit TFE3.
    Kristina Li, Shogo Wada, Bridget S Gosis, Chelsea Thorsheim, Paige Loose, Zolt Arany.
      Mechanistic target of rapamycin complex I (mTORC1) is central to cellular metabolic regulation. mTORC1 phosphorylates a myriad of substrates, but how different substrate specificity is conferred on mTORC1 by different conditions remains poorly defined. Here, we show how loss of the mTORC1 regulator folliculin (FLCN) renders mTORC1 specifically incompetent to phosphorylate TFE3, a master regulator of lysosome biogenesis, without affecting phosphorylation of other canonical mTORC1 substrates, such as S6 kinase. FLCN is a GTPase-activating protein (GAP) for RagC, a component of the mTORC1 amino acid (AA) sensing pathway, and we show that active RagC is necessary and sufficient to recruit TFE3 onto the lysosomal surface, allowing subsequent phosphorylation of TFE3 by mTORC1. Active mutants of RagC, but not of RagA, rescue both phosphorylation and lysosomal recruitment of TFE3 in the absence of FLCN. These data thus advance the paradigm that mTORC1 substrate specificity is in part conferred by direct recruitment of substrates to the subcellular compartments where mTORC1 resides and identify potential targets for specific modulation of specific branches of the mTOR pathway.
    DOI:  https://doi.org/10.1371/journal.pbio.3001594
  9. Biochem J. 2022 Mar 31. 479(6): 787-804
    Quantitative metabolic fluxes regulated by trans-omic networks.
    Satoshi Ohno, Saori Uematsu, Shinya Kuroda.
      Cells change their metabolism in response to internal and external conditions by regulating the trans-omic network, which is a global biochemical network with multiple omic layers. Metabolic flux is a direct measure of the activity of a metabolic reaction that provides valuable information for understanding complex trans-omic networks. Over the past decades, techniques to determine metabolic fluxes, including 13C-metabolic flux analysis (13C-MFA), flux balance analysis (FBA), and kinetic modeling, have been developed. Recent studies that acquire quantitative metabolic flux and multi-omic data have greatly advanced the quantitative understanding and prediction of metabolism-centric trans-omic networks. In this review, we present an overview of 13C-MFA, FBA, and kinetic modeling as the main techniques to determine quantitative metabolic fluxes, and discuss their advantages and disadvantages. We also introduce case studies with the aim of understanding complex metabolism-centric trans-omic networks based on the determination of metabolic fluxes.
    Keywords:  computational models; metabolic flux; metabolism; trans-omics
    DOI:  https://doi.org/10.1042/BCJ20210596
  10. Front Nutr. 2022 ;9 785999
    Systemic Lactate Acts as a Metabolic Buffer in Humans and Prevents Nutrient Overflow in the Postprandial Phase.
    Lisa Schlicker, Gang Zhao, Christian-Alexander Dudek, Hanny M Boers, Michael Meyer-Hermann, Doris M Jacobs, Karsten Hiller.
      On an organismal level, metabolism needs to react in a well-orchestrated manner to metabolic challenges such as nutrient uptake. Key metabolic hubs in human blood are pyruvate and lactate, both of which are constantly interconverted by very fast exchange fluxes. The quantitative contribution of different food sources to these metabolite pools remains unclear. Here, we applied in vivo stable isotope labeling to determine postprandial metabolic fluxes in response to two carbohydrate sources of different complexity. Depending on the ingested carbohydrate source, glucose or wheat flour, the net direction of the lactate dehydrogenase, and the alanine amino transferase fluxes were adjusted in a way to ensure sufficient availability, while, at the same time, preventing an overflow in the respective metabolite pools. The systemic lactate pool acts as a metabolic buffer which is fueled in the early- and depleted in the late-postprandial phase and thus plays a key role for systemic metabolic homeostasis.
    Keywords:  glucose; lactate; metabolic flux; metabolic modeling; stable isotope labeling; wheat
    DOI:  https://doi.org/10.3389/fnut.2022.785999
  11. Proc Natl Acad Sci U S A. 2022 Apr 05. 119(14): e2120403119
    Sensitivity of VHL mutant kidney cancers to HIF2 inhibitors does not require an intact p53 pathway.
    Laura A Stransky, Sean M Vigeant, Bofu Huang, Destiny West, Thomas Denize, Emily Walton, Sabina Signoretti, William G Kaelin.
      SignificanceVHL tumor suppressor gene inactivation is a hallmark of clear cell renal cell carcinoma (ccRCC), the most common form of kidney cancer, and promotes tumor growth by stabilizing the hypoxia-inducible factor 2 (HIF2) transcription factor. HIF2 inhibitors appear to be helpful for some, but not all, ccRCC patients in clinical trials. Previous preclinical and clinical data suggested that only ccRCCs that can activate the p53 tumor suppressor in response to DNA damage would respond to HIF2 inhibitors. Here, we show that an intact p53 pathway is neither necessary nor sufficient for the sensitivity of ccRCCs to HIF2 inhibitors, suggesting that it would be premature to use p53 status to determine which ccRCC patients should be treated with a HIF2 inhibitor.
    Keywords:  HIF; TP53; VHL; belzutifan; ccRCC
    DOI:  https://doi.org/10.1073/pnas.2120403119
  12. Nat Aging. 2022 ;2(2): 155-169
    Scinderin promotes fusion of electron transport chain dysfunctional muscle stem cells with myofibers.
    Xun Wang, Spencer D Shelton, Bogdan Bordieanu, Anderson R Frank, Yating Yi, Siva Sai Krishna Venigalla, Zhimin Gu, Nicholas P Lenser, Michael Glogauer, Navdeep S Chandel, Hu Zhao, Zhiyu Zhao, David G McFadden, Prashant Mishra.
      Muscle stem cells (MuSCs) experience age-associated declines in number and function, accompanied by mitochondrial electron transport chain (ETC) dysfunction and increased reactive oxygen species (ROS). The source of these changes, and how MuSCs respond to mitochondrial dysfunction, is unknown. We report here that in response to mitochondrial ROS, murine MuSCs directly fuse with neighboring myofibers; this phenomenon removes ETC-dysfunctional MuSCs from the stem cell compartment. MuSC-myofiber fusion is dependent on the induction of Scinderin, which promotes formation of actin-dependent protrusions required for membrane fusion. During aging, we find that the declining MuSC population accumulates mutations in the mitochondrial genome, but selects against dysfunctional variants. In the absence of clearance by Scinderin, the decline in MuSC numbers during aging is repressed; however, ETC-dysfunctional MuSCs are retained and can regenerate dysfunctional myofibers. We propose a model in which ETC-dysfunctional MuSCs are removed from the stem cell compartment by fusing with differentiated tissue.
    DOI:  https://doi.org/10.1038/s43587-021-00164-x
  13. Semin Cell Dev Biol. 2022 Mar 26. pii: S1084-9521(22)00096-9. [Epub ahead of print]
    Transient changes to metabolic homeostasis initiate mitochondrial adaptation to endurance exercise.
    Jessica R Dent, Ben Stocks, Dean G Campelj, Andrew Philp.
      Endurance exercise is well established to increase mitochondrial content and function in skeletal muscle, a process termed mitochondrial biogenesis. Current understanding is that exercise initiates skeletal muscle mitochondrial remodeling via modulation of cellular nutrient, energetic and contractile stress pathways. These subtle changes in the cellular milieu are sensed by numerous transduction pathways that serve to initiate and coordinate an increase in mitochondrial gene transcription and translation. The result of these acute signaling events is the promotion of growth and assembly of mitochondria, coupled to a greater capacity for aerobic ATP provision in skeletal muscle. The aim of this review is to highlight the acute metabolic events induced by endurance exercise and the subsequent molecular pathways that sense this transient change in cellular homeostasis to drive mitochondrial adaptation and remodeling.
    Keywords:  Adaptation; Exercise; Metabolism; Mitochondria
    DOI:  https://doi.org/10.1016/j.semcdb.2022.03.022
  14. Mol Cell. 2022 Mar 21. pii: S1097-2765(22)00211-8. [Epub ahead of print]
    Cryo-EM structures of the human GATOR1-Rag-Ragulator complex reveal a spatial-constraint regulated GAP mechanism.
    Shawn B Egri, Christna Ouch, Hui-Ting Chou, Zhiheng Yu, Kangkang Song, Chen Xu, Kuang Shen.
      mTORC1 controls cellular metabolic processes in response to nutrient availability. Amino acid signals are transmitted to mTORC1 through the Rag GTPases, which are localized on the lysosomal surface by the Ragulator complex. The Rag GTPases receive amino acid signals from multiple upstream regulators. One negative regulator, GATOR1, is a GTPase activating protein (GAP) for RagA. GATOR1 binds to the Rag GTPases via two modes: an inhibitory mode and a GAP mode. How these two binding interactions coordinate to process amino acid signals is unknown. Here, we resolved three cryo-EM structural models of the GATOR1-Rag-Ragulator complex, with the Rag-Ragulator subcomplex occupying the inhibitory site, the GAP site, and both binding sites simultaneously. When the Rag GTPases bind to GATOR1 at the GAP site, both Rag subunits contact GATOR1 to coordinate their nucleotide loading states. These results reveal a potential GAP mechanism of GATOR1 during the mTORC1 inactivation process.
    Keywords:  GAP; GATOR1; Rag GTPase; enzyme mechanism; mTOR complex 1; mTORC1; nutrient sensing
    DOI:  https://doi.org/10.1016/j.molcel.2022.03.002
  15. Cancer Immunol Res. 2022 Apr 01. 10(4): 482-497
    Tumor-Derived Lactic Acid Modulates Activation and Metabolic Status of Draining Lymph Node Stroma.
    Angela Riedel, Moutaz Helal, Luisa Pedro, Jonathan J Swietlik, David Shorthouse, Werner Schmitz, Lisa Haas, Timothy Young, Ana S H da Costa, Sarah Davidson, Pranjali Bhandare, Elmar Wolf, Benjamin A Hall, Christian Frezza, Thordur Oskarsson, Jacqueline D Shields.
      Communication between tumors and the stroma of tumor-draining lymph nodes (TDLN) exists before metastasis arises, altering the structure and function of the TDLN niche. Transcriptional profiling of fibroblastic reticular cells (FRC), the dominant stromal population of lymph nodes, has revealed that FRCs in TDLNs are reprogrammed. However, the tumor-derived factors driving the changes in FRCs remain to be identified. Taking an unbiased approach, we have shown herein that lactic acid (LA), a metabolite released by cancer cells, was not only secreted by B16.F10 and 4T1 tumors in high amounts, but also that it was enriched in TDLNs. LA supported an upregulation of Podoplanin (Pdpn) and Thy1 and downregulation of IL7 in FRCs of TDLNs, making them akin to activated fibroblasts found at the primary tumor site. Furthermore, we found that tumor-derived LA altered mitochondrial function of FRCs in TDLNs. Thus, our results demonstrate a mechanism by which a tumor-derived metabolite connected with a low pH environment modulates the function of fibroblasts in TDLNs. How lymph node function is perturbed to support cancer metastases remains unclear. The authors show that tumor-derived LA drains to lymph nodes where it modulates the function of lymph node stromal cells, prior to metastatic colonization.
    DOI:  https://doi.org/10.1158/2326-6066.CIR-21-0778
  16. Autophagy. 2022 Mar 29. 1-3
    Proteomic profiling shows mitochondrial nucleoids are autophagy cargo in neurons: implications for neuron maintenance and neurodegenerative disease.
    Juliet Goldsmith, Erika L F Holzbaur.
      Neurons depend on macroautophagy/autophagy to maintain cellular homeostasis, and loss of autophagy leads to neurodegeneration. To better understand the role of basal autophagy in neurons, we enriched autophagic vesicles from healthy adult mouse brain and performed mass spectrometry to identify cargos cleared by autophagy. We found that synaptic and mitochondrial proteins comprise nearly half of the unique AV cargos identified in brain. Similarly, synaptic and mitochondrial proteins are major cargos for basal autophagy in neurons. Strikingly, we noted a specific enrichment of mitochondrial nucleoids within neuronal autophagosomes, which occurs through a mechanism distinct from damage-associated mitophagy. Here, we discuss the implications of these findings for our understanding of homeostatic mechanisms in neurons and how the age-dependent decline of autophagy in neurons may contribute to the onset or progression of neurodegenerative disease.
    Keywords:  DNM1L; SYN1; TFAM; macroautophagy; mitochondria; mitochondrial division; mitochondrial nucleoids; mitophagy; neurodegeneration; neuronal homeostasis
    DOI:  https://doi.org/10.1080/15548627.2022.2056865
  17. Sci China Life Sci. 2022 Mar 25.
    Palmitoylation of MDH2 by ZDHHC18 activates mitochondrial respiration and accelerates ovarian cancer growth.
    Xuan Pei, Kai-Yue Li, Yuan Shen, Jin-Tao Li, Ming-Zhu Lei, Cai-Yun Fang, Hao-Jie Lu, Hui-Juan Yang, Wenyu Wen, Miao Yin, Jia Qu, Qun-Ying Lei.
      Epithelial ovarian cancer (EOC) exhibits strong dependency on the tricarboxylic acid (TCA) cycle and oxidative phosphorylation to fuel anabolic process. Here, we show that malate dehydrogenase 2 (MDH2), a key enzyme of the TCA cycle, is palmitoylated at cysteine 138 (C138) residue, resulting in increased activity of MDH2. We next identify that ZDHHC18 acts as a palmitoyltransferase of MDH2. Glutamine deprivation enhances MDH2 palmitoylation by increasing the binding between ZDHHC18 and MDH2. MDH2 silencing represses mitochondrial respiration as well as ovarian cancer cell proliferation both in vitro and in vivo. Intriguingly, re-expression of wild-type MDH2, but not its palmitoylation-deficient C138S mutant, sustains mitochondrial respiration and restores the growth as well as clonogenic capability of ovarian cancer cells. Notably, MDH2 palmitoylation level is elevated in clinical cancer samples from patients with high-grade serous ovarian cancer. These observations suggest that MDH2 palmitoylation catalyzed by ZDHHC18 sustains mitochondrial respiration and promotes the malignancy of ovarian cancer, yielding possibilities of targeting ZDHHC18-mediated MDH2 palmitoylation in the treatment of EOC.
    Keywords:  EOC; MDH2; ZDHHC18; cysteine palmitoylation; glutamine
    DOI:  https://doi.org/10.1007/s11427-021-2048-2
  18. Kidney Int. 2022 Mar 24. pii: S0085-2538(22)00212-5. [Epub ahead of print]
    Disruption of mitochondrial complex III in cap mesenchyme but not in ureteric progenitors results in defective nephrogenesis associated with amino acid deficiency.
    Nan Guan, Hanako Kobayashi, Ken Ishii, Olena Davidoff, Feng Sha, Talat A Ikizler, Chuan-Ming Hao, Navdeep S Chandel, Volker H Haase.
      Oxidative metabolism in mitochondria regulates cellular differentiation and gene expression through intermediary metabolites and reactive oxygen species. Its role in kidney development and pathogenesis is not completely understood. Here we inactivated ubiquinone-binding protein QPC, a subunit of mitochondrial complex III, in two types of kidney progenitor cells to investigate the role of mitochondrial electron transport in kidney homeostasis. Inactivation of QPC in sine oculis-related homeobox 2 (SIX2)-expressing cap mesenchyme progenitors, which give rise to podocytes and all nephron segments except collecting ducts, resulted in perinatal death from severe kidney dysplasia. This was characterized by decreased proliferation of SIX2 progenitors and their failure to differentiate into kidney epithelium. QPC inactivation in cap mesenchyme progenitors induced activating transcription factor 4-mediated nutritional stress responses and was associated with a reduction in kidney tricarboxylic acid cycle metabolites and amino acid levels, which negatively impacted purine and pyrimidine synthesis. In contrast, QPC inactivation in ureteric tree epithelial cells, which give rise to the kidney collecting system, did not inhibit ureteric differentiation, and resulted in the development of functional kidneys that were smaller in size. Thus, our data demonstrate that mitochondrial oxidative metabolism is critical for the formation of cap mesenchyme-derived nephron segments but dispensable for formation of the kidney collecting system. Hence, our studies reveal compartment-specific needs for metabolic reprogramming during kidney development.
    Keywords:  TCA cycle; amino acids; kidney development; mitochondria; mitochondrial complex III; mitochondrial electron transport chain
    DOI:  https://doi.org/10.1016/j.kint.2022.02.030
  19. PLoS Genet. 2022 Apr 01. 18(4): e1010068
    Heteroplasmic mitochondrial DNA variants in cardiovascular diseases.
    Claudia Calabrese, Angela Pyle, Helen Griffin, Jonathan Coxhead, Rafiqul Hussain, Peter S Braund, Linxin Li, Annette Burgess, Patricia B Munroe, Louis Little, Helen R Warren, Claudia Cabrera, Alistair Hall, Mark J Caulfield, Peter M Rothwell, Nilesh J Samani, Gavin Hudson, Patrick F Chinnery.
      Mitochondria are implicated in the pathogenesis of cardiovascular diseases (CVDs) but the reasons for this are not well understood. Maternally-inherited population variants of mitochondrial DNA (mtDNA) which affect all mtDNA molecules (homoplasmic) are associated with cardiometabolic traits and the risk of developing cardiovascular disease. However, it is not known whether mtDNA mutations only affecting a proportion of mtDNA molecules (heteroplasmic) also play a role. To address this question, we performed a high-depth (~1000-fold) mtDNA sequencing of blood DNA in 1,399 individuals with hypertension (HTN), 1,946 with ischemic heart disease (IHD), 2,146 with ischemic stroke (IS), and 723 healthy controls. We show that the per individual burden of heteroplasmic single nucleotide variants (mtSNVs) increases with age. The age-effect was stronger for low-level heteroplasmies (heteroplasmic fraction, HF, 5-10%), likely reflecting acquired somatic events based on trinucleotide mutational signatures. After correcting for age and other confounders, intermediate heteroplasmies (HF 10-95%) were more common in hypertension, particularly involving non-synonymous variants altering the amino acid sequence of essential respiratory chain proteins. These findings raise the possibility that heteroplasmic mtSNVs in the pathophysiology of hypertension.
    DOI:  https://doi.org/10.1371/journal.pgen.1010068
  20. Cell Rep. 2022 Mar 29. pii: S2211-1247(22)00351-5. [Epub ahead of print]38(13): 110603
    PTIP governs NAD+ metabolism by regulating CD38 expression to drive macrophage inflammation.
    Qifan Wang, Jin Hu, Guoqiang Han, Peipei Wang, Sha Li, Jiwei Chang, Kexin Gao, Rong Yin, Yashu Li, Tong Zhang, Jihua Chai, Zhuying Gao, Tiantian Zhang, Ying Cheng, Chengli Guo, Jing Wang, Weidong Liu, Manman Cui, Yu Xu, Jinxuan Hou, Quan-Fei Zhu, Yu-Qi Feng, Haojian Zhang.
      NAD+ metabolism is involved in many biological processes. However, the underlying mechanism of how NAD+ metabolism is regulated remains elusive. Here, we find that PTIP governs NAD+ metabolism in macrophages by regulating CD38 expression and is required for macrophage inflammation. Through integrating histone modifications with NAD+ metabolic gene expression profiling, we identify PTIP as a key factor in regulating CD38 expression, the primary NAD+-consuming enzyme in macrophages. Interestingly, we find that PTIP deletion impairs the proinflammatory response of primary murine and human macrophages, promotes their metabolic switch from glycolysis to oxidative phosphorylation, and alters NAD+ metabolism via downregulating CD38 expression. Mechanistically, an intronic enhancer of CD38 is identified. PTIP regulates CD38 expression by cooperating with acetyltransferase p300 in establishing the CD38 active enhancer with enriched H3K27ac. Overall, our findings reveal a critical role for PTIP in fine-tuning the inflammatory responses of macrophages via regulating NAD+ metabolism.
    Keywords:  CD38; CP: Immunology; CP: Metabolism; NAD(+); PTIP; inflammation; macrophage
    DOI:  https://doi.org/10.1016/j.celrep.2022.110603
  21. Dev Cell. 2022 Mar 28. pii: S1534-5807(22)00151-4. [Epub ahead of print]57(6): 687-689
    YAP-deLIVERing the directions and the fuel.
    Scott H Freeburg, Wolfram Goessling.
      Tissues and cells require fuel and cellular building blocks to respond to proliferative cues. In this issue of Developmental Cell, Vaidyanathan and colleagues modulate yes-associated protein (YAP) signaling and its downstream targets, together with phenotyping and metabolic tracing, to determine the central role of YAP in lipogenesis and associated liver growth.
    DOI:  https://doi.org/10.1016/j.devcel.2022.03.003
  22. Oncogene. 2022 Mar 30.
    NFκB activation by hypoxic small extracellular vesicles drives oncogenic reprogramming in a breast cancer microenvironment.
    Irene Bertolini, Michela Perego, Jagadish C Ghosh, Andrew V Kossenkov, Dario C Altieri.
      Small extracellular vesicles (sEV) contribute to the crosstalk between tumor cells and stroma, but the underlying signals are elusive. Here, we show that sEV generated by breast cancer cells in hypoxic (sEVHYP), but not normoxic (sEVNORM) conditions activate NFκB in recipient normal mammary epithelial cells. This increases the production and release of inflammatory cytokines, promotes mitochondrial dynamics leading to heightened cell motility and disrupts 3D mammary acini architecture with aberrant cell proliferation, reduced apoptosis and EMT. Mechanistically, Integrin-Linked Kinase packaged in sEVHYP via HIF1α is sufficient to activate NFκB in the normal mammary epithelium, in vivo. Therefore, sEVHYP activation of NFκB drives multiple oncogenic steps of inflammation, mitochondrial dynamics, and mammary gland morphogenesis in a breast cancer microenvironment.
    DOI:  https://doi.org/10.1038/s41388-022-02280-3
  23. Oncogene. 2022 Mar 30.
    H3K9me3 represses G6PD expression to suppress the pentose phosphate pathway and ROS production to promote human mesothelioma growth.
    Chunwan Lu, Dafeng Yang, John D Klement, Yolonda L Colson, Nicholas H Oberlies, Cedric J Pearce, Aaron H Colby, Mark W Grinstaff, Zhuoqi Liu, Huidong Shi, Han-Fei Ding, Kebin Liu.
      The role of glucose-6-phosphate dehydrogenase (G6PD) in human cancer is incompletely understood. In a metabolite screening, we observed that inhibition of H3K9 methylation suppressed aerobic glycolysis and enhances the PPP in human mesothelioma cells. Genome-wide screening identified G6PD as an H3K9me3 target gene whose expression is correlated with increased tumor cell apoptosis. Inhibition of aerobic glycolysis enzyme LDHA and G6PD had no significant effects on tumor cell survival. Ablation of G6PD had no significant effect on human mesothelioma and colon carcinoma xenograft growth in athymic mice. However, activation of G6PD with the G6PD-selective activator AG1 induced tumor cell death. AG1 increased tumor cell ROS production and the resultant extrinsic and intrinsic death pathways, mitochondrial processes, and unfolded protein response in tumor cells. Consistent with increased tumor cell death in vitro, AG1 suppressed human mesothelioma xenograft growth in a dose-dependent manner in vivo. Furthermore, AG1 treatment significantly increased tumor-bearing mouse survival in an intra-peritoneum xenograft athymic mouse model. Therefore, in human mesothelioma and colon carcinoma, G6PD is not essential for tumor growth. G6PD acts as a metabolic checkpoint to control metabolic flux towards the PPP to promote tumor cell apoptosis, and its expression is repressed by its promotor H3K9me3 deposition.
    DOI:  https://doi.org/10.1038/s41388-022-02283-0
  24. Front Cell Dev Biol. 2022 ;10 849962
    Mitochondrial Fission and Fusion in Tumor Progression to Metastasis.
    Dillon P Boulton, M Cecilia Caino.
      Mitochondria are highly dynamic organelles which can change their shape, via processes termed fission and fusion, in order to adapt to different environmental and developmental contexts. Due to the importance of these processes in maintaining a physiologically healthy pool of mitochondria, aberrant cycles of fission/fusion are often seen in pathological contexts. In this review we will discuss how dysregulated fission and fusion promote tumor progression. We focus on the molecular mechanisms involved in fission and fusion, discussing how altered mitochondrial fission and fusion change tumor cell growth, metabolism, motility, and invasion and, finally how changes to these tumor-cell intrinsic phenotypes directly and indirectly impact tumor progression to metastasis. Although this is an emerging field of investigation, the current consensus is that mitochondrial fission positively influences metastatic potential in a broad variety of tumor types. As mitochondria are now being investigated as vulnerable targets in a variety of cancer types, we underscore the importance of their dynamic nature in potentiating tumor progression.
    Keywords:  cancer; fission; fusion; metastasis; mitochondria; mitochondrial dynamics
    DOI:  https://doi.org/10.3389/fcell.2022.849962
  25. Biochem Biophys Res Commun. 2022 Mar 17. pii: S0006-291X(22)00419-3. [Epub ahead of print]606 61-67
    Pro-inflammatory polarization of macrophages is associated with reduced endoplasmic reticulum-mitochondria interaction.
    Leandro Henrique de Paula Assis, Gabriel de Gabriel Dorighello, Helena Coutinho Franco de Oliveira.
      Macrophages play a role in host defense, tissue remodeling and inflammation. Different inflammatory stimuli drive macrophage phenotypes and responses. In this study we investigated the relationship between macrophages immune phenotype and mitochondrial bioenergetics, cell redox state and endoplasmic reticulum (ER)-mitochondria interaction. Bacterial lipopolysaccharide (LPS) and interferon-γ (IFNγ) pro-inflammatory stimuli decreased oxidative metabolism (basal, phosphorylating and maximal conditions) and increased baseline glycolysis (117%) and glycolytic capacity (43%) in THP-1 macrophages. In contrast, interleukin-4 (IL4) and interleukin-13 (IL13) anti-inflammatory stimuli increased the oxygen consumption rates in baseline conditions (21%) and associated with ATP production (19%). LPS + IFNγ stimuli reduced superoxide anion levels by accelerating its conversion into hydrogen peroxide (H2O2) while IL4+IL13 decreased H2O2 release rates. The source of these oxidants was extra-mitochondrial and associated with increased NOX2 and SOD1 gene expression. LPS + IFNγ stimuli decreased ER-mitochondria contact sites as measured by IP3R1-VDAC1 interaction (34%) and markedly upregulated genes involved in mitochondrial fusion (9-10 fold, MFN1 and 2) and fission (∼7 fold, DRP1 and FIS1). Conversely, IL4+IL13 stimuli did not altered ER-mitochondria interactions nor MFN1 and 2 expression. Together, these results unveil ER-mitochondria interaction pattern as a novel feature of macrophage immunological, metabolic and redox profiles.
    Keywords:  Endoplasmic reticulum-mitochondria interaction; Macrophage; Mitochondrial respiration; Oxidants production
    DOI:  https://doi.org/10.1016/j.bbrc.2022.03.086
  26. Antioxid Redox Signal. 2022 Mar;36(7-9): 441-461
    Redox Activation of Mitochondrial DAMPs and the Metabolic Consequences for Development of Autoimmunity.
    Andreas Koenig, Iwona A Buskiewicz-Koenig.
      Significance: Reactive oxygen species (ROS) are well known to promote innate immune responses during and in the absence of microbial infections. However, excessive or prolonged exposure to ROS provokes innate immune signaling dysfunction and contributes to the pathogenesis of many autoimmune diseases. The relatively high basal expression of pattern recognition receptors (PRRs) in innate immune cells renders them prone to activation in response to minor intrinsic or extrinsic ROS misbalances in the absence of pathogens. Critical Issues: A prominent source of ROS are mitochondria, which are also major inter-organelle hubs for innate immunity activation, since most PRRs and downstream receptor molecules are directly located either at mitochondria or at mitochondria-associated membranes. Due to their ancestral bacterial origin, mitochondria can also act as quasi-intrinsic self-microbes that mimic a pathogen invasion and become a source of danger-associated molecular patterns (DAMPs) that triggers innate immunity from within. Recent Advances: The release of mitochondrial DAMPs correlates with mitochondrial metabolism changes and increased generation of ROS, which can lead to the oxidative modification of DAMPs. Recent studies suggest that ROS-modified mitochondrial DAMPs possess increased, persistent immunogenicity. Future Directions: Herein, we discuss how mitochondrial DAMP release and oxidation activates PRRs, changes cellular metabolism, and causes innate immune response dysfunction by promoting systemic inflammation, thereby contributing to the onset or progression of autoimmune diseases. The future goal is to understand what the tipping point for DAMPs is to become oxidized, and whether this is a road without return. Antioxid. Redox Signal. 36, 441-461.
    Keywords:  ATP; Carbamoyl phosphate synthetase-1 (CPS1); MAVS oligomerization; N-formyl peptides (NFPs); autoimmunity; cardiolipin (CL); cyclic GMP-AMP synthase (cGAS); cytochrome C; damage-associated molecular pattern (DAMP); innate immunity; metabolism; mitochondria; mitochondrial ROS (mtROS); mitochondrial TFAM; mitochondrial antiviral signaling (MAVS) protein; neutrophil extracellular trap (NET); oxidized ATP; oxidized cardiolipin; oxidized mitochondrial DNA (mtDNA); oxidized mitochondrial RNA (mtRNA); reactive oxygen species (ROS); redox; stimulator of interferon genes (STING); succinate; systemic lupus erythematosus (SLE); transcription factor A
    DOI:  https://doi.org/10.1089/ars.2021.0073
  27. Biochim Biophys Acta Bioenerg. 2022 Mar 24. pii: S0005-2728(22)00023-8. [Epub ahead of print]1863(5): 148554
    Mitochondrial DNA replication and repair defects: Clinical phenotypes and therapeutic interventions.
    Abhipsa Roy, Amoolya Kandettu, Swagat Ray, Sanjiban Chakrabarty.
      Mitochondria is a unique cellular organelle involved in multiple cellular processes and is critical for maintaining cellular homeostasis. This semi-autonomous organelle contains its circular genome - mtDNA (mitochondrial DNA), that undergoes continuous cycles of replication and repair to maintain the mitochondrial genome integrity. The majority of the mitochondrial genes, including mitochondrial replisome and repair genes, are nuclear-encoded. Although the repair machinery of mitochondria is quite efficient, the mitochondrial genome is highly susceptible to oxidative damage and other types of exogenous and endogenous agent-induced DNA damage, due to the absence of protective histones and their proximity to the main ROS production sites. Mutations in replication and repair genes of mitochondria can result in mtDNA depletion and deletions subsequently leading to mitochondrial genome instability. The combined action of mutations and deletions can result in compromised mitochondrial genome maintenance and lead to various mitochondrial disorders. Here, we review the mechanism of mitochondrial DNA replication and repair process, key proteins involved, and their altered function in mitochondrial disorders. The focus of this review will be on the key genes of mitochondrial DNA replication and repair machinery and the clinical phenotypes associated with mutations in these genes.
    Keywords:  Base-excision repair; CPEO; LIG3; POLG; mtDNA replication
    DOI:  https://doi.org/10.1016/j.bbabio.2022.148554
  28. Life Sci Alliance. 2022 Jul;pii: e202101239. [Epub ahead of print]5(7):
    ESCRT-I fuels lysosomal degradation to restrict TFEB/TFE3 signaling via the Rag-mTORC1 pathway.
    Marta Wróbel, Jarosław Cendrowski, Ewelina Szymańska, Malwina Grębowicz-Maciukiewicz, Noga Budick-Harmelin, Matylda Macias, Aleksandra Szybińska, Michał Mazur, Krzysztof Kolmus, Krzysztof Goryca, Michalina Dąbrowska, Agnieszka Paziewska, Michał Mikula, Marta Miączyńska.
      Within the endolysosomal pathway in mammalian cells, ESCRT complexes facilitate degradation of proteins residing in endosomal membranes. Here, we show that mammalian ESCRT-I restricts the size of lysosomes and promotes degradation of proteins from lysosomal membranes, including MCOLN1, a Ca2+ channel protein. The altered lysosome morphology upon ESCRT-I depletion coincided with elevated expression of genes annotated to biogenesis of lysosomes due to prolonged activation of TFEB/TFE3 transcription factors. Lack of ESCRT-I also induced transcription of cholesterol biosynthesis genes, in response to inefficient delivery of cholesterol from endolysosomal compartments. Among factors that could possibly activate TFEB/TFE3 signaling upon ESCRT-I deficiency, we excluded lysosomal cholesterol accumulation and Ca2+-mediated dephosphorylation of TFEB/TFE3. However, we discovered that this activation occurs due to the inhibition of Rag GTPase-dependent mTORC1 pathway that specifically reduced phosphorylation of TFEB at S112. Constitutive activation of the Rag GTPase complex in cells lacking ESCRT-I restored S112 phosphorylation and prevented TFEB/TFE3 activation. Our results indicate that ESCRT-I deficiency evokes a homeostatic response to counteract lysosomal nutrient starvation, that is, improper supply of nutrients derived from lysosomal degradation.
    DOI:  https://doi.org/10.26508/lsa.202101239
  29. Nat Microbiol. 2022 Apr;7(4): 497-507
    Immunometabolic crosstalk during bacterial infection.
    Gili Rosenberg, Sebastian Riquelme, Alice Prince, Roi Avraham.
      Following detection of bacteria, macrophages switch their metabolism from oxidative respiration through the tricarboxylic acid cycle to high-rate aerobic glycolysis. This immunometabolic shift enables pro-inflammatory and antimicrobial responses and is facilitated by the accumulation of fatty acids, tricarboxylic acid-derived metabolites and catabolism of amino acids. Recent studies have shown that these immunometabolites are co-opted by pathogens as environmental cues for expression of virulence genes. We review mechanisms by which host immunometabolites regulate bacterial pathogenicity and discuss opportunities for the development of therapeutics targeting metabolic host-pathogen crosstalk.
    DOI:  https://doi.org/10.1038/s41564-022-01080-5
  30. Clin Transl Med. 2022 Mar;12(3): e645
    Simultaneous targeting of mitochondrial metabolism and immune checkpoints as a new strategy for renal cancer therapy.
    Sona Stemberkova-Hubackova, Renata Zobalova, Maria Dubisova, Jana Smigova, Sarka Dvorakova, Klara Korinkova, Zuzana Ezrova, Berwini Endaya, Kristyna Blazkova, Erik Vlcak, Petra Brisudova, Dan-Diem Thi Le, Stefan Juhas, Daniel Rosel, Cristina Daniela Kelemen, Dana Sovilj, Eliska Vacurova, Tomas Cajka, Vlada Filimonenko, Lanfeng Dong, Ladislav Andera, Pavel Hozak, Jan Brabek, Zuzana Bielcikova, Jan Stursa, Lukas Werner, Jiri Neuzil.
      
    DOI:  https://doi.org/10.1002/ctm2.645
  31. Pflugers Arch. 2022 Mar 28.
    Lipid metabolic reprogramming by hypoxia-inducible factor-1 in the hypoxic tumour microenvironment.
    Jieun Seo, Jeong-Eun Yun, Sung Joon Kim, Yang-Sook Chun.
      Cancer cells rewire metabolic processes to adapt to the nutrient- and oxygen-deprived tumour microenvironment, thereby promoting their proliferation and metastasis. Previous research has shown that modifying glucose metabolism, the Warburg effect, makes glycolytic cancer cells more invasive and aggressive. Lipid metabolism has also been receiving attention because lipids function as energy sources and signalling molecules. Because obesity is a risk factor for various cancer types, targeting lipid metabolism may be a promising cancer therapy. Here, we review the lipid metabolic reprogramming in cancer cells mediated by hypoxia-inducible factor-1 (HIF-1). HIF-1 is the master transcription factor for tumour growth and metastasis by transactivating genes related to proliferation, survival, angiogenesis, invasion, and metabolism. The glucose metabolic shift (the Warburg effect) is mediated by HIF-1. Recent research on HIF-1-related lipid metabolic reprogramming in cancer has confirmed that HIF-1 also modifies lipid accumulation, β-oxidation, and lipolysis in cancer, triggering its progression. Therefore, targeting lipid metabolic alterations by HIF-1 has therapeutic potential for cancer. We summarize the role of the lipid metabolic shift mediated by HIF-1 in cancer and its putative applications for cancer therapy.
    Keywords:  Cancer therapy; Hypoxia-inducible factor-1; Lipid metabolism; Tumour microenvironment
    DOI:  https://doi.org/10.1007/s00424-022-02683-x
  32. iScience. 2022 Apr 15. 25(4): 104056
    Multi-omics & pathway analysis identify potential roles for tumor N-acetyl aspartate accumulation in murine models of castration-resistant prostate cancer.
    Mark J Salji, Arnaud Blomme, J Henry M Däbritz, Peter Repiscak, Sergio Lilla, Rachana Patel, David Sumpton, Niels J F van den Broek, Ronan Daly, Sara Zanivan, Hing Y Leung.
      Castration-resistant prostate cancer (CRPC) is incurable and remains a significant worldwide challenge (Oakes and Papa, 2015). Matched untargeted multi-level omic datasets may reveal biological changes driving CRPC, identifying novel biomarkers and/or therapeutic targets. Untargeted RNA sequencing, proteomics, and metabolomics were performed on xenografts derived from three independent sets of hormone naive and matched CRPC human cell line models of local, lymph node, and bone metastasis grown as murine orthografts. Collectively, we tested the feasibility of muti-omics analysis on models of CRPC in revealing pathways of interest for future validation investigation. Untargeted metabolomics revealed NAA and NAAG commonly accumulating in CRPC across three independent models and proteomics showed upregulation of related enzymes, namely N-acetylated alpha-linked acidic dipeptidases (FOLH1/NAALADL2). Based on pathway analysis integrating multiple omic levels, we hypothesize that increased NAA in CRPC may be due to upregulation of NAAG hydrolysis via NAALADLases providing a pool of acetyl Co-A for upregulated sphingolipid metabolism and a pool of glutamate and aspartate for nucleotide synthesis during tumor growth.
    Keywords:  Cell biology; Metabolomics; Proteomics
    DOI:  https://doi.org/10.1016/j.isci.2022.104056
  33. Nat Metab. 2022 Mar;4(3): 389-403
    Switching to the cyclic pentose phosphate pathway powers the oxidative burst in activated neutrophils.
    Emily C Britt, Jorgo Lika, Morgan A Giese, Taylor J Schoen, Gretchen L Seim, Zhengping Huang, Pui Y Lee, Anna Huttenlocher, Jing Fan.
      Neutrophils are cells at the frontline of innate immunity that can quickly activate effector functions to eliminate pathogens upon stimulation. However, little is known about the metabolic adaptations that power these functions. Here we show rapid metabolic alterations in neutrophils upon activation, particularly drastic reconfiguration around the pentose phosphate pathway, which is specifically and quantitatively coupled to an oxidative burst. During this oxidative burst, neutrophils switch from glycolysis-dominant metabolism to a unique metabolic mode termed 'pentose cycle', where all glucose-6-phosphate is diverted into oxidative pentose phosphate pathway and net flux through upper glycolysis is reversed to allow substantial recycling of pentose phosphates. This reconfiguration maximizes NADPH yield to fuel superoxide production via NADPH oxidase. Disruptions of pentose cycle greatly suppress oxidative burst, the release of neutrophil extracellular traps and pathogen killing by neutrophils. Together, these results demonstrate the remarkable metabolic flexibility of neutrophils, which is essential for their functions as the first responders in innate immunity.
    DOI:  https://doi.org/10.1038/s42255-022-00550-8
  34. Nat Metab. 2022 Mar 31.
    Macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution.
    Patrick B Ampomah, Bishuang Cai, Santosh R Sukka, Brennan D Gerlach, Arif Yurdagul, Xiaobo Wang, George Kuriakose, Lancia N F Darville, Yan Sun, Simone Sidoli, John M Koomen, Alan R Tall, Ira Tabas.
      Efferocytosis, the clearance of apoptotic cells (ACs) by macrophages, is critical for tissue resolution, with defects driving many diseases. Mechanisms of efferocytosis-mediated resolution are incompletely understood. Here, we show that AC-derived methionine regulates resolution through epigenetic repression of the extracellular signal-regulated kinase 1/2 (ERK1/2) phosphatase Dusp4. We focus on two key efferocytosis-induced pro-resolving mediators, prostaglandin E2 (PGE2) and transforming growth factor beta 1 (TGF-β1), and show that efferocytosis induces prostaglandin-endoperoxide synthase 2/cyclooxygenase 2 (Ptgs2/COX2), leading to PGE2 synthesis and PGE2-mediated induction of TGF-β1. ERK1/2 phosphorylation/activation by AC-activated CD36 is necessary for Ptgs2 induction, but this is insufficient owing to an ERK-DUSP4 negative feedback pathway that lowers phospho-ERK. However, subsequent AC engulfment and phagolysosomal degradation lead to Dusp4 repression, enabling enhanced p-ERK and induction of the Ptgs2-PGE2-TGF-β1 pathway. Mechanistically, AC-derived methionine is converted to S-adenosylmethionine, which is used by DNA methyltransferase-3A (DNMT3A) to methylate Dusp4. Bone-marrow DNMT3A deletion in mice blocks COX2/PGE2, TGF-β1, and resolution in sterile peritonitis, apoptosis-induced thymus injury and atherosclerosis. Knowledge of how macrophages use AC-cargo and epigenetics to induce resolution provides mechanistic insight and therapeutic options for diseases driven by impaired resolution.
    DOI:  https://doi.org/10.1038/s42255-022-00551-7
  35. Nature. 2022 Mar 30.
    Anatomic position determines oncogenic specificity in melanoma.
    Joshua M Weiss, Miranda V Hunter, Nelly M Cruz, Arianna Baggiolini, Mohita Tagore, Yilun Ma, Sandra Misale, Michelangelo Marasco, Theresa Simon-Vermot, Nathaniel R Campbell, Felicity Newell, James S Wilmott, Peter A Johansson, John F Thompson, Georgina V Long, John V Pearson, Graham J Mann, Richard A Scolyer, Nicola Waddell, Emily D Montal, Ting-Hsiang Huang, Philip Jonsson, Mark T A Donoghue, Christopher C Harris, Barry S Taylor, Tianhao Xu, Ronan Chaligné, Pavel V Shliaha, Ronald Hendrickson, Achim A Jungbluth, Cecilia Lezcano, Richard Koche, Lorenz Studer, Charlotte E Ariyan, David B Solit, Jedd D Wolchok, Taha Merghoub, Neal Rosen, Nicholas K Hayward, Richard M White.
      Oncogenic alterations to DNA are not transforming in all cellular contexts1,2. This may be due to pre-existing transcriptional programmes in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body, whereas the acral subtype arises on the palms of the hands, soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma and enrichment for CRKL amplifications in acral melanoma. We modelled these changes in transgenic zebrafish models and found that CRKL-driven tumours formed predominantly in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs, indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin and limb melanocytes, when compared with body melanocytes, revealed a positional identity gene programme typified by posterior HOX13 genes. This positional gene programme synergized with CRKL to amplify insulin-like growth factor (IGF) signalling and drive tumours at acral sites. Abrogation of this CRKL-driven programme eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults.
    DOI:  https://doi.org/10.1038/s41586-022-04584-6
  36. Front Oncol. 2022 ;12 836058
    Acetyl-CoA Carboxylases and Diseases.
    Yu Wang, Weixing Yu, Sha Li, Dingyuan Guo, Jie He, Yugang Wang.
      Acetyl-CoA carboxylases (ACCs) are enzymes that catalyze the carboxylation of acetyl-CoA to produce malonyl-CoA. In mammals, ACC1 and ACC2 are two members of ACCs. ACC1 localizes in the cytosol and acts as the first and rate-limiting enzyme in the de novo fatty acid synthesis pathway. ACC2 localizes on the outer membrane of mitochondria and produces malonyl-CoA to regulate the activity of carnitine palmitoyltransferase 1 (CPT1) that involves in the β-oxidation of fatty acid. Fatty acid synthesis is central in a myriad of physiological and pathological conditions. ACC1 is the major member of ACCs in mammalian, mountains of documents record the roles of ACC1 in various diseases, such as cancer, diabetes, obesity. Besides, acetyl-CoA and malonyl-CoA are cofactors in protein acetylation and malonylation, respectively, so that the manipulation of acetyl-CoA and malonyl-CoA by ACC1 can also markedly influence the profile of protein post-translational modifications, resulting in alternated biological processes in mammalian cells. In the review, we summarize our understandings of ACCs, including their structural features, regulatory mechanisms, and roles in diseases. ACC1 has emerged as a promising target for diseases treatment, so that the specific inhibitors of ACC1 for diseases treatment are also discussed.
    Keywords:  acetyl-CoA carboxylase; cancer metabolism; lipogenesis; metabolic diseases; tumorigenesis
    DOI:  https://doi.org/10.3389/fonc.2022.836058
  37. J Vis Exp. 2022 Mar 09.
    An In Vitro Approach to Study Mitochondrial Dysfunction: A Cybrid Model.
    Andrea Cavaliere, Silvia Marchet, Ivano Di Meo, Valeria Tiranti.
      Deficiency of the mitochondrial respiratory chain complexes that carry out oxidative phosphorylation (OXPHOS) is the biochemical marker of human mitochondrial disorders. From a genetic point of view, the OXPHOS represents a unique example because it results from the complementation of two distinct genetic systems: nuclear DNA (nDNA) and mitochondrial DNA (mtDNA). Therefore, OXPHOS defects can be due to mutations affecting nuclear and mitochondrial encoded genes. The groundbreaking work by King and Attardi, published in 1989, showed that human cell lines depleted of mtDNA (named rho0) could be repopulated by exogenous mitochondria to obtain the so-called "transmitochondrial cybrids." Thanks to these cybrids containing mitochondria derived from patients with mitochondrial disorders (MDs) and nuclei from rho0 cells, it is possible to verify whether a defect is mtDNA- or nDNA-related. These cybrids are also a powerful tool to validate the pathogenicity of a mutation and study its impact at a biochemical level. This paper presents a detailed protocol describing cybrid generation, selection, and characterization.
    DOI:  https://doi.org/10.3791/63452
  38. Nature. 2022 Mar 30.
    Genome doubling causes double trouble.
    Yonatan Eliezer, Uri Ben-David.
      
    Keywords:  Cancer; Cell biology; Medical research
    DOI:  https://doi.org/10.1038/d41586-022-00849-2
  39. Br J Cancer. 2022 Mar 26.
    PGC-1α induced mitochondrial biogenesis in stromal cells underpins mitochondrial transfer to melanoma.
    Prakrit R Kumar, Mona Saad, Charlotte Hellmich, Jayna J Mistry, Jamie A Moore, Shannon Conway, Christopher J Morris, Kristian M Bowles, Marc D Moncrieff, Stuart A Rushworth.
       INTRODUCTION: Progress in the knowledge of metabolic interactions between cancer and its microenvironment is ongoing and may lead to novel therapeutic approaches. Until recently, melanoma was considered a glycolytic tumour due to mutations in mitochondrial-DNA, however, these malignant cells can regain OXPHOS capacity via the transfer of mitochondrial-DNA, a process that supports their proliferation in-vitro and in-vivo. Here we study how melanoma cells acquire mitochondria and how this process is facilitated from the tumour microenvironment.
    METHODS: Primary melanoma cells, and MSCs derived from patients were obtained. Genes' expression and DNA quantification was analysed using Real-time PCR. MSC migration, melanoma proliferation and tumour volume, in a xenograft subcutaneous mouse model, were monitored through bioluminescent live animal imaging.
    RESULTS: Human melanoma cells attract bone marrow-derived stromal cells (MSCs) to the primary tumour site where they stimulate mitochondrial biogenesis in the MSCs through upregulation of PGC1a. Mitochondria are transferred to the melanoma cells via direct contact with the MSCs. Moreover, inhibition of MSC-derived PGC1a was able to prevent mitochondrial transfer and improve NSG melanoma mouse tumour burden.
    CONCLUSION: MSC mitochondrial biogenesis stimulated by melanoma cells is prerequisite for mitochondrial transfer and subsequent tumour growth, where targeting this pathway may provide an effective novel therapeutic approach in melanoma.
    DOI:  https://doi.org/10.1038/s41416-022-01783-w
  40. Curr Opin Physiol. 2022 Feb;pii: 100483. [Epub ahead of print]25
    Mitochondria and ferroptosis.
    Sabzali Javadov.
      Ferroptosis is a regulated iron-dependent cell death mechanism accompanied by the accumulation of peroxidized phospholipids, particularly phosphatidylethanolamine, in the cell. It occurs due to the disbalance between production and elimination of oxidized phospholipids in response to ferroptotic stimuli. A growing body of recent studies indicates that ferroptosis is involved in the pathogenesis of various human diseases leading to organ/tissue abnormalities. Due to their central role in ATP synthesis, ROS production, iron homeostasis, and redox status, mitochondria have been proposed to mediate ferroptotic signaling pathways. However, precise mechanisms underlying the potential role of mitochondria in ferroptosis remain unrevealed. This review summarizes and discusses previous studies on the contribution of mitochondria to ferroptotic cell death and highlights future directions elucidating the mitochondria as a promising target to prevent cell death through blocking ferroptosis.
    Keywords:  cell death; ferroptosis; iron metabolism; mitochondria; oxidized phospholipids; reactive oxygen species
    DOI:  https://doi.org/10.1016/j.cophys.2022.100483
  41. Front Cell Dev Biol. 2022 ;10 846723
    The Interplay Between TGF-β Signaling and Cell Metabolism.
    Huidong Liu, Ye-Guang Chen.
      The transforming growth factor-β (TGF-β) signaling plays a critical role in the development and tissue homeostasis in metazoans, and deregulation of TGF-β signaling leads to many pathological conditions. Mounting evidence suggests that TGF-β signaling can actively alter metabolism in diverse cell types. Furthermore, metabolic pathways, beyond simply regarded as biochemical reactions, are closely intertwined with signal transduction. Here, we discuss the role of TGF-β in glucose, lipid, amino acid, redox and polyamine metabolism with an emphasis on how TGF-β can act as a metabolic modulator and how metabolic changes can influence TGF-β signaling. We also describe how interplay between TGF-β signaling and cell metabolism regulates cellular homeostasis as well as the progression of multiple diseases, including cancer.
    Keywords:  Smad; TGF-β signaling; amino acid metabolism; glucose metabolism; lipid metabolism
    DOI:  https://doi.org/10.3389/fcell.2022.846723
  42. Front Endocrinol (Lausanne). 2022 ;13 663625
    Hypoxia Induces Saturated Fatty Acids Accumulation and Reduces Unsaturated Fatty Acids Independently of Reverse Tricarboxylic Acid Cycle in L6 Myotubes.
    Lukas Vacek, Ales Dvorak, Kamila Bechynska, Vit Kosek, Moustafa Elkalaf, Minh Duc Trinh, Ivana Fiserova, Katerina Pospisilova, Lucie Slovakova, Libor Vitek, Jana Hajslova, Jan Polak.
      Obstructive sleep apnea syndrome, characterized by repetitive episodes of tissue hypoxia, is associated with several metabolic impairments. Role of fatty acids and lipids attracts attention in its pathogenesis for their metabolic effects. Parallelly, hypoxia-induced activation of reverse tricarboxylic acid cycle (rTCA) with reductive glutamine metabolism provides precursor molecules for de novo lipogenesis. Gas-permeable cultureware was used to culture L6-myotubes in chronic hypoxia (12%, 4% and 1% O2) with 13C labelled glutamine and inhibitors of glutamine uptake or rTCA-mediated lipogenesis. We investigated changes in lipidomic profile, 13C appearance in rTCA-related metabolites, gene and protein expression of rTCA-related proteins and glutamine transporters, glucose uptake and lactate production. Lipid content increased by 308% at 1% O2, predominantly composed of saturated fatty acids, while triacylglyceroles containing unsaturated fatty acids and membrane lipids (phosphatidylcholines, phosphatidylethanolamines, phosphatidylinositol) decreased by 20-70%. rTCA labelling of malate, citrate and 2-hydroxyglutarate increased by 4.7-fold, 2.2-fold and 1.9-fold in 1% O2, respectively. ATP-dependent citrate lyase inhibition in 1% O2 decreased lipid amount by 23% and increased intensity of triacylglyceroles containing unsaturated fatty acids by 56-80%. Lactate production increased with hypoxia. Glucose uptake dropped by 75% with progression of hypoxia from 4% to 1% O2. Protein expression remained unchanged. Altogether, hypoxia modified cell metabolism leading to lipid composition alteration and rTCA activation.
    Keywords:  L6 myotubes; glutamin; hypoxia; lipids; obstructive sleep apnea ; reverse TCA
    DOI:  https://doi.org/10.3389/fendo.2022.663625
  43. Cell Death Differ. 2022 Mar 26.
    BAX and BAK dynamics control mitochondrial DNA release during apoptosis.
    Takahiro Yamazaki, Lorenzo Galluzzi.
      
    DOI:  https://doi.org/10.1038/s41418-022-00985-2
  44. Methods Mol Biol. 2022 ;2463 165-180
    Assessing Changes in Human Natural Killer Cell Metabolism Using the Seahorse Extracellular Flux Analyzer.
    Javier Traba, Olga M Antón.
      Natural killer (NK) cells are cytotoxic cells that mediate anti-tumor and anti-viral immunity. The response of NK cells to different cytokines and stimuli may involve cell survival, proliferation, and changes in their cytotoxic function. These responses will be supported by changes in cellular metabolism. Therefore, changes in NK metabolic parameters could somehow predict changes in NK cell function and cytotoxicity. In this chapter, we describe a protocol to measure NK cell metabolism in primary human NK cells by using an extracellular flux analyzer. This machine measures pH and oxygen changes in the medium and allows the study of NK cell glycolysis and mitochondrial respiration in real time with a small number of cells.
    Keywords:  Electron transporter chain; Extracellular flux analyzer; Glycolysis; Mitochondrial respiration; Natural killer cell
    DOI:  https://doi.org/10.1007/978-1-0716-2160-8_12
  45. Proc Natl Acad Sci U S A. 2022 Apr 05. 119(14): e2121946119
    Inositol hexakisphosphate kinase-2 non-catalytically regulates mitophagy by attenuating PINK1 signaling.
    Latika Nagpal, Michael D Kornberg, Solomon H Snyder.
      SignificanceInositol pyrophosphates are versatile messenger molecules containing the energetic pyrophosphate bond. One of the principal enzymes generating the inositol pyrophosphate IP7 (5-diphosphoinositolpentakisphosphate) is inositol hexakisphosphate kinase 2 (IP6K2). Previous work has shown that IP6K2 is neuroprotective and maintains mitochondrial respiration. We now report that loss of IP6K2 leads to increased mitochondrial fission and mitophagy. Regulation of mitochondrial dynamics by IP6K2 depends on the protein PINK1 and, interestingly, is independent of IP6K2 enzymatic activity. These findings provide mechanistic insight into the regulation of mitochondrial function by IP6K2, which has implications for neuroprotection and mitochondrial physiology more generally.
    Keywords:  PINK1; inositol phosphate; mitochondrial biogenesis; mitophagy; neuroprotection
    DOI:  https://doi.org/10.1073/pnas.2121946119
  46. J Mol Cell Biol. 2022 Mar 29. pii: mjac020. [Epub ahead of print]
    Deacetylation of MTHFD2 by SIRT4 senses stress signal to inhibit cancer cell growth by remodeling folate metabolism.
    Fan Zhang, Di Wang, Jintao Li, Ying Su, Suling Liu, Qun-Ying Lei, Miao Yin.
      Folate metabolism plays an essential role in tumor development. Various cancers display therapeutic response to reagents targeting key enzymes of folate cycle, but obtaining chemo-resistance later. Therefore, novel targets in folate metabolism are highly demanded. Methylenetetrahydrofolate dehydrogenase/methylenetetrahydrofolate cyclohydrolase 2 (MTHFD2) is one of the key enzymes in folate metabolism and its expression is highly increased in multiple human cancers. However, the underlying mechanism that regulates MTHFD2 expression remains unknown. Here, we elucidate that SIRT4 deacetylates the conserved lysine residue at 50 (K50) in MTHFD2. K50 de-acetylation destabilizes MTHFD2 by elevating Cullin 3 (CUL3) E3 ligase-mediated proteasomal degradation in response to stressful stimuli of folate deprivation, leading to suppression of nicotinamide adenine dinucleotide phosphate (NADPH) production in tumor cells and accumulation of intracellular reactive oxygen species (ROS), which in turn inhibits the growth of breast cancer cells. Collectively, our study reveals that SIRT4 senses folate availability to control MTHFD2 K50 acetylation and its protein stability, bridging nutrient/folate stress and cellular redox to act on cancer cell growth.
    Keywords:  CUL3; MTHFD2; SIRT4; acetylation; breast cancer; folate metabolism
    DOI:  https://doi.org/10.1093/jmcb/mjac020
  47. Proc Natl Acad Sci U S A. 2022 Apr 05. 119(14): e2024357119
    Carbon sources and pathways for citrate secreted by human prostate cancer cells determined by NMR tracing and metabolic modeling.
    Frits H A van Heijster, Vincent Breukels, Kees C F J Jansen, Jack A Schalken, Arend Heerschap.
      SignificanceThe human prostate accumulates high luminal citrate levels to serve sperm viability. There is only indirect qualitative evidence about metabolic pathways and carbon sources maintaining these levels. Human citrate-secreting prostate cancer cells were supplied with 13C-labeled substrates, and NMR spectra of extracellular fluid were recorded. We report absolute citrate production rates of prostate cells and direct evidence that glucose is the main carbon source for secreted citrate. Pyruvate carboxylase provides sufficient anaplerotic carbons to support citrate secretion. Glutamine carbons exchange with carbons for secreted citrate but are likely not involved in its net synthesis. Moreover, we developed metabolic models employing the 13C distribution in extracellular citrate as input to assess intracellular pathways followed by carbons toward citrate.
    Keywords:  Krebs cycle; cancer; carbon-13; citrate; prostate
    DOI:  https://doi.org/10.1073/pnas.2024357119
  48. Mol Syst Biol. 2022 Apr;18(4): e10822
    Perspective: a stirring role for metabolism in cells.
    José Losa, Simeon Leupold, Diego Alonso-Martinez, Petteri Vainikka, Sebastian Thallmair, Katarzyna M Tych, Siewert J Marrink, Matthias Heinemann.
      Based on recent findings indicating that metabolism might be governed by a limit on the rate at which cells can dissipate Gibbs energy, in this Perspective, we propose a new mechanism of how metabolic activity could globally regulate biomolecular processes in a cell. Specifically, we postulate that Gibbs energy released in metabolic reactions is used to perform work, allowing enzymes to self-propel or to break free from supramolecular structures. This catalysis-induced enzyme movement will result in increased intracellular motion, which in turn can compromise biomolecular functions. Once the increased intracellular motion has a detrimental effect on regulatory mechanisms, this will establish a feedback mechanism on metabolic activity, and result in the observed thermodynamic limit. While this proposed explanation for the identified upper rate limit on cellular Gibbs energy dissipation rate awaits experimental validation, it offers an intriguing perspective of how metabolic activity can globally affect biomolecular functions and will hopefully spark new research.
    Keywords:  Gibbs energy; active matter; enhanced diffusion; metabolism; regulation
    DOI:  https://doi.org/10.15252/msb.202110822
  49. Antioxid Redox Signal. 2022 Mar 29.
    Metabolic regulation of CD8+ T cells: from mechanism to therapy.
    Ying Zheng, Xiaomin Wang, Min Huang.
       SIGNIFICANCE: Cancer immunotherapy has yielded striking anti-tumor effects in many cancers, yet the proportion of benefited patients are still limited. As key mediators of tumor suppression, CD8+ T cells are crucial for cancer immunotherapy. It has been widely appreciated that modulation of CD8+ T cell immunity could be an effective way to further improve the therapeutic benefit of immunotherapy.
    RECENT ADVANCES: Emerging evidence has underlined a close link between metabolism and immune functions, providing a metabolism-immune axis that is increasingly investigated for understanding CD8+ T cells regulation. On the other hand, growing findings have reported that tumors adopt multiple approaches to induce metabolic reprogramming of CD8+ T cells, leading to the compromised immunotherapy.
    CRITICAL ISSUES: CD8+ T cell metabolism in the tumor microenvironment (TME) is often adapted to diminish anti-tumor immune responses and thereby evade from immune surveillance. A better understanding of metabolic regulation of CD8+ T cells in the TME is believed to hold promise for opening a new therapeutic window to further improve the benefit of immunotherapy. We herein review the mechanistic understanding of how CD8+ T cell metabolism is reprogrammed in the TME, mainly focusing on the impact of nutrient availability and bioactive molecules secreted by surrounding cells.
    FUTURE DIRECTIONS: Future research should pay attention to tumor heterogeneity in the metabolic microenvironment and associated immune responses. It is also important to include the trending opinion of "precision medicine" in cancer immunotherapies to tailor metabolic interventions for individual patients in combination with immunotherapy treatments.
    DOI:  https://doi.org/10.1089/ars.2022.0040
  50. Sci Rep. 2022 Apr 01. 12(1): 5518
    Bladder cancer cells shift rapidly and spontaneously to cisplatin-resistant oxidative phosphorylation that is trackable in real time.
    Tong Xu, Jason A Junge, Alireza Delfarah, Yi-Tsung Lu, Cosimo Arnesano, Maheen Iqbal, Kevin Delijani, Tien-Chan Hsieh, Emmanuelle Hodara, Hemal H Mehta, Pinchas Cohen, Nicholas A Graham, Scott E Fraser, Amir Goldkorn.
      Genetic mutations have long been recognized as drivers of cancer drug resistance, but recent work has defined additional non-genetic mechanisms of plasticity, wherein cancer cells assume a drug resistant phenotype marked by altered epigenetic and transcriptional states. Currently, little is known about the real-time, dynamic nature of this phenotypic shift. Using a bladder cancer model of nongenetic plasticity, we discovered that rapid transition to drug resistance entails upregulation of mitochondrial gene expression and a corresponding metabolic shift towards the tricarboxylic acid cycle and oxidative phosphorylation. Based on this distinction, we were able to track cancer cell metabolic profiles in real time using fluorescence lifetime microscopy (FLIM). We observed single cells transitioning spontaneously to an oxidative phosphorylation state over hours to days, a trend that intensified with exposure to cisplatin chemotherapy. Conversely, pharmacological inhibition of oxidative phosphorylation significantly reversed the FLIM metabolic signature and reduced cisplatin resistance. These rapid, spontaneous metabolic shifts offer a new means of tracking nongenetic cancer plasticity and forestalling the emergence of drug resistance.
    DOI:  https://doi.org/10.1038/s41598-022-09438-9
  51. Redox Biol. 2022 Mar 22. pii: S2213-2317(22)00066-0. [Epub ahead of print]52 102294
    Redox proteome analysis of auranofin exposed ovarian cancer cells (A2780).
    Giovanni Chiappetta, Tania Gamberi, Fiorella Faienza, Xhesika Limaj, Salvatore Rizza, Luigi Messori, Giuseppe Filomeni, Alessandra Modesti, Joelle Vinh.
      The effects of Auranofin (AF) on protein expression and protein oxidation in A2780 cancer cells were investigated through a strategy based on simultaneous expression proteomics and redox proteomics determinations. Bioinformatics analysis of the proteomics data supports the view that the most critical cellular changes elicited by AF treatment consist of thioredoxin reductase inhibition, alteration of the cell redox state, impairment of the mitochondrial functions, metabolic changes associated with conversion to a glycolytic phenotype, induction of ER stress. The occurrence of the above cellular changes was extensively validated by performing direct biochemical assays. Our data are consistent with the concept that AF produces its effects through a multitarget mechanism that mainly affects the redox metabolism and the mitochondrial functions and results into severe ER stress. Results are discussed in the context of the current mechanistic knowledge existing on AF.
    Keywords:  Auranofin; Cysteine; Gold drugs; Ovarian cancer; Redox proteomics
    DOI:  https://doi.org/10.1016/j.redox.2022.102294
  52. Biochem Biophys Res Commun. 2022 Mar 24. pii: S0006-291X(22)00457-0. [Epub ahead of print]
    Roles of miR-124-3p/Scd1 in urolithin A-induced brown adipocyte differentiation and succinate-dependent regulation of mitochondrial complex II.
    Qian Li, Lina Wang, Huan Liu, Weiyuan Ren, Zhiying Zhang, Bo Xia.
      Brown adipocytes have been linked to managing human obesity and related metabolic diseases. A large number of natural products have emerged that can activate brown adipocytes tissue (BAT) to active thermogenesis, but the epigenetic mechanisms have not been fully resolved. In this study, we identified the induction of miR-124-3p by urolithin A (UA) as a means to increase the thermogenic activity of brown adipocytes. Overexpression of miR-124-3p enhances thermogenesis by increasing mitochondrial content in brown adipocytes. Mechanistically, to clarify that miR-124-3p affects fatty acid synthesis using bioinformatics methods, it is clear that miR-124 affects the synthesis of fatty acids through the enrichment analysis of the KEGG pathway, and using dual luci. ferase to determine the target gene as stearoyl-CoA desaturase 1 (SCD1) while controlling rates of fatty acids synthesis and de novo brown fat biogenesis. Finally, in the overexpression of miR-124-3p and UA-treated BAT, succinate accumulation was enhanced in cells and fueled mitochondrial complex II activities. This study highlights a miR-124-3p/SCD1/succinate pathway that stimulates thermogenesis of BAT via the modulatory roles of UA.
    Keywords:  Mitochondrial complex II; SCD1; Succinate; Urolithin A; miR-124-3p
    DOI:  https://doi.org/10.1016/j.bbrc.2022.03.112
  53. Nature. 2022 Mar 30.
    Crucial role and mechanism of transcription-coupled DNA repair in bacteria.
    Binod K Bharati, Manjunath Gowder, Fangfang Zheng, Khaled Alzoubi, Vladimir Svetlov, Venu Kamarthapu, Jacob W Weaver, Vitaly Epshtein, Nikita Vasilyev, Liqiang Shen, Yu Zhang, Evgeny Nudler.
      Transcription-coupled DNA repair (TCR) is presumed to be a minor sub-pathway of nucleotide excision repair (NER) in bacteria. Global genomic repair is thought to perform the bulk of repair independently of transcription. TCR is also believed to be mediated exclusively by Mfd-a DNA translocase of a marginal NER phenotype1-3. Here we combined in cellulo cross-linking mass spectrometry with structural, biochemical and genetic approaches to map the interactions within the TCR complex (TCRC) and to determine the actual sequence of events that leads to NER in vivo. We show that RNA polymerase (RNAP) serves as the primary sensor of DNA damage and acts as a platform for the recruitment of NER enzymes. UvrA and UvrD associate with RNAP continuously, forming a surveillance pre-TCRC. In response to DNA damage, pre-TCRC recruits a second UvrD monomer to form a helicase-competent UvrD dimer that promotes backtracking of the TCRC. The weakening of UvrD-RNAP interactions renders cells sensitive to genotoxic stress. TCRC then recruits a second UvrA molecule and UvrB to initiate the repair process. Contrary to the conventional view, we show that TCR accounts for the vast majority of chromosomal repair events; that is, TCR thoroughly dominates over global genomic repair. We also show that TCR is largely independent of Mfd. We propose that Mfd has an indirect role in this process: it participates in removing obstructive RNAPs in front of TCRCs and also in recovering TCRCs from backtracking after repair has been completed.
    DOI:  https://doi.org/10.1038/s41586-022-04530-6
  54. Nat Commun. 2022 Apr 01. 13(1): 1748
    Long-chain ceramides are cell non-autonomous signals linking lipotoxicity to endoplasmic reticulum stress in skeletal muscle.
    Ben D McNally, Dean F Ashley, Lea Hänschke, Hélène N Daou, Nicole T Watt, Steven A Murfitt, Amanda D V MacCannell, Anna Whitehead, T Scott Bowen, Francis W B Sanders, Michele Vacca, Klaus K Witte, Graeme R Davies, Reinhard Bauer, Julian L Griffin, Lee D Roberts.
      The endoplasmic reticulum (ER) regulates cellular protein and lipid biosynthesis. ER dysfunction leads to protein misfolding and the unfolded protein response (UPR), which limits protein synthesis to prevent cytotoxicity. Chronic ER stress in skeletal muscle is a unifying mechanism linking lipotoxicity to metabolic disease. Unidentified signals from cells undergoing ER stress propagate paracrine and systemic UPR activation. Here, we induce ER stress and lipotoxicity in myotubes. We observe ER stress-inducing lipid cell non-autonomous signal(s). Lipidomics identifies that palmitate-induced cell stress induces long-chain ceramide 40:1 and 42:1 secretion. Ceramide synthesis through the ceramide synthase 2 de novo pathway is regulated by UPR kinase Perk. Inactivation of CerS2 in mice reduces systemic and muscle ceramide signals and muscle UPR activation. The ceramides are packaged into extracellular vesicles, secreted and induce UPR activation in naïve myotubes through dihydroceramide accumulation. This study furthers our understanding of ER stress by identifying UPR-inducing cell non-autonomous signals.
    DOI:  https://doi.org/10.1038/s41467-022-29363-9
  55. Mol Metab. 2022 Mar 23. pii: S2212-8778(22)00043-6. [Epub ahead of print] 101474
    Leveraging GPCR signaling in thermogenic fat to counteract metabolic diseases.
    Olivia Sveidahl Johansen, Tao Ma, Zachary Gerhart-Hines.
      
    DOI:  https://doi.org/10.1016/j.molmet.2022.101474
  56. Kidney360. 2021 Dec;2(12): 1892-1907
    Quantitative super-resolution microscopy reveals promoting mitochondrial interconnectivity protects against AKI.
    Kensei Taguchi, Bertha C Elias, Evan Krystofiak, Subo Qian, Snehal Sant, Haichun Yang, Agnes B Fogo, Craig R Brooks.
       Background: The root of many kidney diseases in humans can be traced to alterations or damage to subcellular organelles. Mitochondrial fragmentation, endoplasmic reticulum (ER) stress, and lysosomal inhibition, among others, ultimately contribute to kidney injury and are the target of therapeutics in development. Although recent technological advancements allow for the understanding of disease states at the cellular level, investigating changes in subcellular organelles from kidney tissue remains challenging.
    Methods: Using structured illumination microscopy, we imaged mitochondria and other organelles from paraffin sections of mouse tissue and human kidney biopsy specimens. The resulting images were 3D rendered to quantify mitochondrial size, content, and morphology. Results were compared with those from transmission electron microscopy and segmentation.
    Results: Super-resolution imaging reveals kidney tubular epithelial cell mitochondria in rodent and human kidney tissue form large, interconnected networks under basal conditions, which are fragmented with injury. This approach can be expanded to other organelles and cellular structures including autophagosomes, ER, brush border, and cell morphology. We find that, during unilateral ischemia, mitochondrial fragmentation occurs in most tubule cells, and they remain fragmented for >96 hours. Promoting mitochondrial fusion with the fusion promotor M1 preserves mitochondrial morphology and interconnectivity and protects against cisplatin-induced kidney injury.
    Conclusions: We provide, for the first time, a nonbiased, semiautomated approach for quantification of the 3D morphology of mitochondria in kidney tissue. Maintaining mitochondrial interconnectivity and morphology protects against kidney injury. Super-resolution imaging has the potential to both drive discovery of novel pathobiologic mechanisms in kidney tissue and broaden the diagnoses that can be made on human biopsy specimens.
    DOI:  https://doi.org/10.34067/kid.0001602021
  57. Nat Metab. 2022 Mar 31.
    Dying cell-derived SAM switches off inflammation.
    Roel P H De Maeyer, Derek W Gilroy.
      
    DOI:  https://doi.org/10.1038/s42255-022-00556-2
  58. Biochim Biophys Acta Mol Basis Dis. 2022 Mar 25. pii: S0925-4439(22)00070-9. [Epub ahead of print]1868(7): 166400
    Role and regulation of autophagy in cancer.
    Ravichandran Rakesh, Loganathan Chandramani PriyaDharshini, Kunnathur Murugesan Sakthivel, Rajan Radha Rasmi.
      Autophagy is an intracellular self-degradative mechanism which responds to cellular conditions like stress or starvation and plays a key role in regulating cell metabolism, energy homeostasis, starvation adaptation, development and cell death. Numerous studies have stipulated the participation of autophagy in cancer, but the role of autophagy either as tumor suppressor or tumor promoter is not clearly understood. However, mechanisms by which autophagy promotes cancer involves a diverse range of modifications of autophagy associated proteins such as ATGs, Beclin-1, mTOR, p53, KRAS etc. and autophagy pathways like mTOR, PI3K, MAPK, EGFR, HIF and NFκB. Furthermore, several researches have highlighted a context-dependent, cell type and stage-dependent regulation of autophagy in cancer. Alongside this, the interaction between tumor cells and their microenvironment including hypoxia has a great potential in modulating autophagy response in favour to substantiate cancer cell metabolism, self-proliferation and metastasis. In this review article, we highlight the mechanism of autophagy and their contribution to cancer cell proliferation and development. In addition, we discuss about tumor microenvironment interaction and their consequence on selective autophagy pathways and the involvement of autophagy in various tumor types and their therapeutic interventions concentrated on exploiting autophagy as a potential target to improve cancer therapy.
    Keywords:  Autophagy; Cancer; Homeostasis; Hypoxia
    DOI:  https://doi.org/10.1016/j.bbadis.2022.166400
  59. Immunopharmacol Immunotoxicol. 2022 Mar 30. 1-14
    T cell metabolism and possible therapeutic targets in systemic lupus erythematosus: a narrative review.
    Marcela Muñoz-Urbano, Diana C Quintero-González, Gloria Vasquez.
      In the immunopathogenesis of systemic lupus erythematosus (SLE), there is a dysregulation of specific immune cells, including T cells. The metabolic reprogramming in T cells causes different effects. Metabolic programs are critical checkpoints in immune responses and are involved in the etiology of autoimmune disease. For instance, resting lymphocytes generate energy through oxidative phosphorylation (OXPHOS) and fatty acid oxidation (FAO), whereas activated lymphocytes rapidly shift to the glycolytic pathway. Specifically, mitochondrial dysfunction, oxidative stress, abnormal metabolism (including glucose, lipid, and amino acid metabolism), and mTOR signaling are hallmarks of T lymphocyte metabolic dysfunction in SLE. Herein it is summarized how metabolic defects contribute to T cell responses in SLE, and some epigenetic alterations involved in the disease. Finally, it is shown how metabolic defects could be modified therapeutically.
    Keywords:  SLE; T cell metabolism; fatty acid oxidation; glycolysis; mTOR pathway; mitochondrial dysfunction
    DOI:  https://doi.org/10.1080/08923973.2022.2055568
  60. Apoptosis. 2022 Apr 01.
    Acetic acid triggers cytochrome c release in yeast heterologously expressing human Bax.
    Joana P Guedes, Vitória Baptista, Cátia Santos-Pereira, Maria João Sousa, Stéphen Manon, Susana R Chaves, Manuela Côrte-Real.
      Proteins of the Bcl-2 protein family, including pro-apoptotic Bax and anti-apoptotic Bcl-xL, are critical for mitochondrial-mediated apoptosis regulation. Since yeast lacks obvious orthologs of Bcl-2 family members, heterologous expression of these proteins has been used to investigate their molecular and functional aspects. Active Bax is involved in the formation of mitochondrial outer membrane pores, through which cytochrome c (cyt c) is released, triggering a cascade of downstream apoptotic events. However, when in its inactive form, Bax is largely cytosolic or weakly bound to mitochondria. Given the central role of Bax in apoptosis, studies aiming to understand its regulation are of paramount importance towards its exploitation as a therapeutic target. So far, studies taking advantage of heterologous expression of human Bax in yeast to unveil regulation of Bax activation have relied on the use of artificial mutated or mitochondrial tagged Bax for its activation, rather than the wild type Bax (Bax α). Here, we found that cell death could be triggered in yeast cells heterologoulsy expressing Bax α with concentrations of acetic acid that are not lethal to wild type cells. This was associated with Bax mitochondrial translocation and cyt c release, closely resembling the natural Bax function in the cellular context. This regulated cell death process was reverted by co-expression with Bcl-xL, but not with Bcl-xLΔC, and in the absence of Rim11p, the yeast ortholog of mammalian GSK3β. This novel system mimics human Bax α regulation by GSK3β and can therefore be used as a platform to uncover novel Bax regulators and explore its therapeutic modulation.
    Keywords:  Acetic acid; Apoptosis; Bax; Bcl-2 family proteins; Heterologous expression; Yeast
    DOI:  https://doi.org/10.1007/s10495-022-01717-0
  61. Nat Rev Mol Cell Biol. 2022 Apr 01.
    Interplay between mechanics and signalling in regulating cell fate.
    Henry De Belly, Ewa K Paluch, Kevin J Chalut.
      Mechanical signalling affects multiple biological processes during development and in adult organisms, including cell fate transitions, cell migration, morphogenesis and immune responses. Here, we review recent insights into the mechanisms and functions of two main routes of mechanical signalling: outside-in mechanical signalling, such as mechanosensing of substrate properties or shear stresses; and mechanical signalling regulated by the physical properties of the cell surface itself. We discuss examples of how these two classes of mechanical signalling regulate stem cell function, as well as developmental processes in vivo. We also discuss how cell surface mechanics affects intracellular signalling and, in turn, how intracellular signalling controls cell surface mechanics, generating feedback into the regulation of mechanosensing. The cooperation between mechanosensing, intracellular signalling and cell surface mechanics has a profound impact on biological processes. We discuss here our understanding of how these three elements interact to regulate stem cell fate and development.
    DOI:  https://doi.org/10.1038/s41580-022-00472-z
  62. Future Med Chem. 2022 Mar 31.
    Citrate transporter inhibitors: possible new anticancer agents.
    Shivaputra A Patil, June A Mayor, Ronald S Kaplan.
      The culmination of 80+ years of cancer research implicates the aberrant metabolism in tumor cells as a root cause of pathogenesis. Citrate is an essential molecule in intermediary metabolism, and its amplified availability to critical pathways in cancer cells via citrate transporters confers a high rate of cancer cell growth and proliferation. Inhibiting the plasma membrane and mitochondrial citrate transporters - whether individually, in combination, or partnered with complementary metabolic targets - in order to combat cancer may prove to be a consequential chemotherapeutic strategy. This review aims to summarize the use of different classes of citrate transporter inhibitors for anticancer activity, either individually or as part of a cocktail.
    Keywords:  anticancer; citrate; drug discovery; mitochondrial citrate transporter (CTP); plasma membrane citrate transporter (PMCT)
    DOI:  https://doi.org/10.4155/fmc-2021-0341
  63. Biometals. 2022 Apr 02.
    The synthesis and properties of mitochondrial targeted iron chelators.
    Agostino Cilibrizzi, Charareh Pourzand, Vincenzo Abbate, Olivier Reelfs, Laura Versari, Giuseppe Floresta, Robert Hider.
      Iron levels in mitochondria are critically important for the normal functioning of the organelle. Abnormal levels of iron and the associated formation of toxic oxygen radicals have been linked to a wide range of diseases and consequently it is important to be able to both monitor and control levels of the mitochondrial labile iron pool. To this end a series of iron chelators which are targeted to mitochondria have been designed. This overview describes the synthesis of some of these molecules and their application in monitoring mitochondrial labile iron pools and in selectively removing excess iron from mitochondria.
    Keywords:  Chelator synthesis; Iron chelation; Iron-probe; Mitochondria
    DOI:  https://doi.org/10.1007/s10534-022-00383-8
  64. Nat Commun. 2022 Apr 01. 13(1): 1768
    PI3Kγ stimulates a high molecular weight form of myosin light chain kinase to promote myeloid cell adhesion and tumor inflammation.
    Michael C Schmid, Sang Won Kang, Hui Chen, Marc Paradise, Anghesom Ghebremedhin, Megan M Kaneda, Shao-Ming Chin, Anh Do, D Martin Watterson, Judith A Varner.
      Myeloid cells play key roles in cancer immune suppression and tumor progression. In response to tumor derived factors, circulating monocytes and granulocytes extravasate into the tumor parenchyma where they stimulate angiogenesis, immune suppression and tumor progression. Chemokines, cytokines and interleukins stimulate PI3Kγ-mediated Rap1 activation, leading to conformational changes in integrin α4β1 that promote myeloid cell extravasation and tumor inflammation Here we show that PI3Kγ activates a high molecular weight form of myosin light chain kinase, MLCK210, that promotes myosin-dependent Rap1 GTP loading, leading to integrin α4β1 activation. Genetic or pharmacological inhibition of MLCK210 suppresses integrin α4β1 activation, as well as tumor inflammation and progression. These results demonstrate a critical role for myeloid cell MLCK210 in tumor inflammation and serve as basis for the development of alternative approaches to develop immune oncology therapeutics.
    DOI:  https://doi.org/10.1038/s41467-022-29471-6
  65. J Mol Cell Cardiol. 2022 Mar 28. pii: S0022-2828(22)00037-2. [Epub ahead of print]167 52-66
    Enhanced NCLX-dependent mitochondrial Ca2+ efflux attenuates pathological remodeling in heart failure.
    Joanne F Garbincius, Timothy S Luongo, Pooja Jadiya, Alycia N Hildebrand, Devin W Kolmetzky, Adam S Mangold, Rajika Roy, Jessica Ibetti, Mary Nwokedi, Walter J Koch, John W Elrod.
      Mitochondrial calcium (mCa2+) uptake couples changes in cardiomyocyte energetic demand to mitochondrial ATP production. However, excessive mCa2+ uptake triggers permeability transition and necrosis. Despite these established roles during acute stress, the involvement of mCa2+ signaling in cardiac adaptations to chronic stress remains poorly defined. Changes in NCLX expression are reported in heart failure (HF) patients and models of cardiac hypertrophy. Therefore, we hypothesized that altered mCa2+ homeostasis contributes to the hypertrophic remodeling of the myocardium that occurs upon a sustained increase in cardiac workload. The impact of mCa2+ flux on cardiac function and remodeling was examined by subjecting mice with cardiomyocyte-specific overexpression (OE) of the mitochondrial Na+/Ca2+ exchanger (NCLX), the primary mediator of mCa2+ efflux, to several well-established models of hypertrophic and non-ischemic HF. Cardiomyocyte NCLX-OE preserved contractile function, prevented hypertrophy and fibrosis, and attenuated maladaptive gene programs in mice subjected to chronic pressure overload. Hypertrophy was attenuated in NCLX-OE mice, prior to any decline in cardiac contractility. NCLX-OE similarly attenuated deleterious cardiac remodeling in mice subjected to chronic neurohormonal stimulation. However, cardiomyocyte NCLX-OE unexpectedly reduced overall survival in mice subjected to severe neurohormonal stress with angiotensin II + phenylephrine. Adenoviral NCLX expression limited mCa2+ accumulation, oxidative metabolism, and de novo protein synthesis during hypertrophic stimulation of cardiomyocytes in vitro. Our findings provide genetic evidence for the contribution of mCa2+ to early pathological remodeling in non-ischemic heart disease, but also highlight a deleterious consequence of increasing mCa2+ efflux when the heart is subjected to extreme, sustained neurohormonal stress.
    Keywords:  Calcium; Mitochondria; NCLX; anabolism; heart failure; hypertrophy
    DOI:  https://doi.org/10.1016/j.yjmcc.2022.03.001
  66. Curr Biol. 2022 Mar 28. pii: S0960-9822(22)00280-9. [Epub ahead of print]32(6): R281-R284
    Oxygen sensing: Protein degradation meets retrograde signaling.
    Nico Dissmeyer.
      A new study shows that mitochondrial retrograde signaling relies on strongly compartmentalized individual pathways previously not taken into account. This involves a link between mitochondrial oxygen consumption and cytosolic oxygen sensing via the N-degron pathway.
    DOI:  https://doi.org/10.1016/j.cub.2022.02.047
  67. Cancer Res. 2022 Apr 01. pii: canres.4370.2021. [Epub ahead of print]
    Epithelial-mesenchymal plasticity in tumor immune evasion.
    Riley Mullins, Ananya Pal, Thomas F Barrett, Molly E Heft Neal, Sidharth V Puram.
      Epithelial-mesenchymal transition (EMT) is a fundamental process that occurs during embryogenesis and tissue repair. However, EMT can be hijacked by malignant cells, where it may promote immune evasion and metastasis. Classically considered a dichotomous transition, EMT in cancer has recently been considered a plastic process whereby malignant cells display and interconvert among hybrid epithelial/mesenchymal (E/M) states. Epithelial-mesenchymal plasticity (EMP) and associated hybrid E/M states are divergent from classical EMT with unique immunomodulatory effects. Here, we review recent insights into the EMP-immune crosstalk, highlighting possible mechanisms of immune evasion conferred by hybrid E/M states and roles of immune cells in EMP.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-4370
  68. PLoS Comput Biol. 2022 Mar 30. 18(3): e1009873
    Analysis of localized cAMP perturbations within a tissue reveal the effects of a local, dynamic gap junction state on ERK signaling.
    João Pedro Fonseca, Elham Aslankoohi, Andrew H Ng, Michael Chevalier.
      Beyond natural stimuli such as growth factors and stresses, the ability to experimentally modulate at will the levels or activity of specific intracellular signaling molecule(s) in specified cells within a tissue can be a powerful tool for uncovering new regulation and tissue behaviors. Here we perturb the levels of cAMP within specific cells of an epithelial monolayer to probe the time-dynamic behavior of cell-cell communication protocols implemented by the cAMP/PKA pathway and its coupling to the ERK pathway. The time-dependent ERK responses we observe in the perturbed cells for spatially uniform cAMP perturbations (all cells) can be very different from those due to spatially localized perturbations (a few cells). Through a combination of pharmacological and genetic perturbations, signal analysis, and computational modeling, we infer how intracellular regulation and regulated cell-cell coupling each impact the intracellular ERK response in single cells. Our approach reveals how a dynamic gap junction state helps sculpt the intracellular ERK response over time in locally perturbed cells.
    DOI:  https://doi.org/10.1371/journal.pcbi.1009873
  69. FASEB J. 2022 May;36(5): e22266
    cGAS-STING mediates cytoplasmic mitochondrial-DNA-induced inflammatory signal transduction during accelerated senescence of pancreatic β-cells induced by metabolic stress.
    Huiqing Hu, Ruxing Zhao, Qin He, Chen Cui, Jia Song, Xinghong Guo, Nan Zang, Mengmeng Yang, Ying Zou, Jingwen Yang, Jinquan Li, Liming Wang, Longqing Xia, Lingshu Wang, Falian He, Xinguo Hou, Fei Yan, Li Chen.
      Type 2 diabetes mellitus (T2DM) is an age-related disease characterized by impaired pancreatic β cell function and insulin resistance. Recent studies have shown that the accumulation of senescent β cells under metabolic stress conditions leads to the progression of T2DM, while senolysis can improve the prognosis. However, the specific mechanism of β cell senescence is still unclear. In this study, we found that the increased load of senescence pancreatic β cells in both older mice and obese mice induced by high-fat diet (HFD) (DIO mice) was accompanied by activation of the Cyclic GMP-AMP synthase (cGAS) - stimulator of interferon genes (STING) pathway and using cGAS or STING small interfering RNA or STING inhibitor C176 to downregulate this pathway reduced the senescence-associated secretion profile (SASP) and senescence of Min6 cells treated with palmitic acid or hydrogen peroxide. C176 intervention in DIO mice also significantly reduced the inflammation and senescence of the islets, thereby protecting the function of pancreatic β cell and glucose metabolism. Our study further revealed that mitochondrial DNA (mtDNA) leakage under metabolic stress conditions was critical for the activation of the cGAS-STING pathway, which can be reversed by the mtDNA depleting agent ethidium bromide. Consistently, mtDNA leakage was more severe in older mice and was accelerated by a chronic HFD. In conclusion, we demonstrate that cytoplasmic mtDNA activates the cGAS-STING pathway to mediate SASP during the accelerated senescence of pancreatic β-cells induced by metabolic stress, and this process can be downregulated by the STING inhibitor C176.
    Keywords:  SASP; cGAS-STING pathway; pancreatic β cell function; senescence; type 2 diabetes mellitus
    DOI:  https://doi.org/10.1096/fj.202101988R
  70. Proc Natl Acad Sci U S A. 2022 Apr 05. 119(14): e2121133119
    Protective role of chaperone-mediated autophagy against atherosclerosis.
    Julio Madrigal-Matute, Jenny de Bruijn, Kim van Kuijk, Dario F Riascos-Bernal, Antonio Diaz, Inmaculada Tasset, Adrián Martín-Segura, Marion J J Gijbels, Bianca Sander, Susmita Kaushik, Erik A L Biessen, Simoni Tiano, Mathieu Bourdenx, Gregory J Krause, Ian McCracken, Andrew H Baker, Han Jin, Nicholas E S Sibinga, Jose Javier Bravo-Cordero, Fernando Macian, Rajat Singh, Patrick C N Rensen, Jimmy F P Berbée, Gerard Pasterkamp, Judith C Sluimer, Ana Maria Cuervo.
      Significance Cardiovascular diseases remain the leading cause of death worldwide, with atherosclerosis being the most common source of clinical events. Metabolic changes with aging associate with concurrent increased risk of both type 2 diabetes and cardiovascular disease, with the former further raising the risk of the latter. The activity of a selective type of autophagy, chaperone-mediated autophagy (CMA), decreases with age or upon dietary excesses. Here we study whether reduced CMA activity increases risk of atherosclerosis in mouse models. We have identified that CMA is up-regulated early in response to proatherogenic challenges and demonstrate that reduced systemic CMA aggravates vascular pathology in these conditions. We also provide proof-of-concept support that CMA up-regulation is an effective intervention to reduce atherosclerosis severity and progression.
    Keywords:  atherosclerotic plaques; lipid challenge; lysosomes; proteolysis; vascular disease
    DOI:  https://doi.org/10.1073/pnas.2121133119
  71. Biomed J. 2021 Feb 12. pii: S2319-4170(21)00010-X. [Epub ahead of print]
    Glycolytic metabolism and activation of Na+ pumping contribute to extracellular acidification in the central clock of the suprachiasmatic nucleus: Differential glucose sensitivity and utilization between oxidative and non-oxidative glycolytic pathways.
    Hsin-Yi Lin, Rong-Chi Huang.
       BACKGROUND: The central clock of the suprachiasmatic nucleus (SCN) controls the metabolism of glucose and is sensitive to glucose shortage. However, it is only beginning to be understood how metabolic signals such as glucose availability regulate the SCN physiology. We previously showed that the ATP-sensitive K+ channel plays a glucose-sensing role in regulating SCN neuronal firing at times of glucose shortage. Nevertheless, it is unknown whether the energy-demanding Na+/K+-ATPase (NKA) is also sensitive to glucose availability. Furthermore, we recently showed that the metabolically active SCN constantly extrudes H+ to acidify extracellular pH (pHe). This study investigated whether the standing acidification is associated with Na+ pumping activity, energy metabolism, and glucose utilization, and whether glycolysis- and mitochondria-fueled NKAs may be differentially sensitive to glucose shortage.
    METHODS: Double-barreled pH-selective microelectrodes were used to determine the pHe in the SCN in hypothalamic slices.
    RESULTS: NKA inhibition with K+-free (0-K+) solution rapidly and reversibly alkalinized the pHe, an effect abolished by ouabain. Mitochondrial inhibition with cyanide acidified the pHe but did not inhibit 0-K+-induced alkalinization. Glycolytic inhibition with iodoacetate alkalinized the pHe, completely blocked cyanide-induced acidification, and nearly completely blocked 0-K+-induced alkalinization. The results indicate that glycolytic metabolism and activation of Na+ pumping contribute to the standing acidification. Glucoprivation also alkalinized the pHe, nearly completely eliminated cyanide-induced acidification, but only partially reduced 0-K+-induced alkalinization. In contrast, hypoglycemia preferentially and partially blocked cyanide-induced acidification. The result indicates sensitivity to glucose shortage for the mitochondria-associated oxidative glycolytic pathway.
    CONCLUSION: Glycolytic metabolism and activation of glycolysis-fueled NKA Na+ pumping activity contribute to the standing acidification in the SCN. Furthermore, the oxidative and non-oxidative glycolytic pathways differ in their glucose sensitivity and utilization, with the oxidative glycolytic pathway susceptible to glucose shortage, and the non-oxidative glycolytic pathway able to maintain Na+ pumping even in glucoprivation.
    Keywords:  Glycolysis; Metabolism; Na(+)/K(+)-ATPase; Suprachiasmatic nucleus; pH
    DOI:  https://doi.org/10.1016/j.bj.2021.02.004
  72. Transl Oncol. 2022 Mar 29. pii: S1936-5233(22)00066-3. [Epub ahead of print]20 101404
    cGAS-STING signalings potentiate tumor progression via sustaining cancer stemness.
    Fu-Rao Liu, Ming-Jie Jiang, Zhu Mei, Chen-Jing Lin, Ling Tian.
      The cytosolic DNA-sensing cGAS-STING pathway has been proved to be involved in tumor progression and influence the effect of cancer immunotherapy. However, little attentions have been paid to the role of cGAS-STING pathway on cancer stemness. Herein, we found that the cGAS-STING pathway was activated in different tumor cells. cGAS- or STING-knockout impaired the capability of tumor formation in vivo and tumorsphere formation in vitro. In addition, loss of cGAS-STING cascade promoted tumor apoptosis, but inhibited tumor growth and metastasis. We further demonstrated that cGAS-STING pathway potentiated tumor formation by sustaining cancer stemness. Moreover, analysis of RNA-seq showed that cGAS-STING pathway maintained cancer stemness probably by activating STAT3. Our findings highlight the role of intrinsic activation of cGAS-STING pathway in tumorigenesis, and reveal a new mechanism of its regulation of tumor progression via sustaining cancer stemness through STAT3 activation.
    Keywords:  Cancer stemness; STAT3; Tumor progression; Tumorigenesis; cGAS-STING pathway
    DOI:  https://doi.org/10.1016/j.tranon.2022.101404
  73. J Am Chem Soc. 2022 Mar 28.
    Protein-Interaction Affinity Gradient Drives [4Fe-4S] Cluster Insertion in Human Lipoyl Synthase.
    Giovanni Saudino, Simone Ciofi-Baffoni, Lucia Banci.
      Human lipoyl synthase (LIAS) is an enzyme containing two [4Fe-4S] clusters (named FeSRS and FeSaux) involved in the biosynthesis of the lipoyl cofactor. The mechanism by which a [4Fe-4S] cluster is inserted into LIAS has thus far remained elusive. Here we show that NFU1 and ISCA1 of the mitochondrial iron-sulfur cluster assembly machinery, via forming a heterodimeric complex, are the key factors for the insertion of a [4Fe-4S] cluster into the FeSRS site of LIAS. In this process, the crucial actor is the C-domain of NFU1, which, by exploiting a protein-interaction affinity gradient increasing from ISCA1 to LIAS, drives the cluster to its final destination.
    DOI:  https://doi.org/10.1021/jacs.1c13626
  74. Science. 2022 Apr;376(6588): 44-53
    The complete sequence of a human genome.
    Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V Bzikadze, Alla Mikheenko, Mitchell R Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman, Sergey Aganezov, Savannah J Hoyt, Mark Diekhans, Glennis A Logsdon, Michael Alonge, Stylianos E Antonarakis, Matthew Borchers, Gerard G Bouffard, Shelise Y Brooks, Gina V Caldas, Nae-Chyun Chen, Haoyu Cheng, Chen-Shan Chin, William Chow, Leonardo G de Lima, Philip C Dishuck, Richard Durbin, Tatiana Dvorkina, Ian T Fiddes, Giulio Formenti, Robert S Fulton, Arkarachai Fungtammasan, Erik Garrison, Patrick G S Grady, Tina A Graves-Lindsay, Ira M Hall, Nancy F Hansen, Gabrielle A Hartley, Marina Haukness, Kerstin Howe, Michael W Hunkapiller, Chirag Jain, Miten Jain, Erich D Jarvis, Peter Kerpedjiev, Melanie Kirsche, Mikhail Kolmogorov, Jonas Korlach, Milinn Kremitzki, Heng Li, Valerie V Maduro, Tobias Marschall, Ann M McCartney, Jennifer McDaniel, Danny E Miller, James C Mullikin, Eugene W Myers, Nathan D Olson, Benedict Paten, Paul Peluso, Pavel A Pevzner, David Porubsky, Tamara Potapova, Evgeny I Rogaev, Jeffrey A Rosenfeld, Steven L Salzberg, Valerie A Schneider, Fritz J Sedlazeck, Kishwar Shafin, Colin J Shew, Alaina Shumate, Ying Sims, Arian F A Smit, Daniela C Soto, Ivan Sović, Jessica M Storer, Aaron Streets, Beth A Sullivan, Françoise Thibaud-Nissen, James Torrance, Justin Wagner, Brian P Walenz, Aaron Wenger, Jonathan M D Wood, Chunlin Xiao, Stephanie M Yan, Alice C Young, Samantha Zarate, Urvashi Surti, Rajiv C McCoy, Megan Y Dennis, Ivan A Alexandrov, Jennifer L Gerton, Rachel J O'Neill, Winston Timp, Justin M Zook, Michael C Schatz, Evan E Eichler, Karen H Miga, Adam M Phillippy.
      Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion-base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.
    DOI:  https://doi.org/10.1126/science.abj6987
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