bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2021–08–15
forty-two papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit
  1. GOT1 inhibition promotes pancreatic cancer cell death by ferroptosis.
  2. Sustained intracellular calcium rise mediates neuronal mitophagy in models of autosomal dominant optic atrophy.
  3. Metabolism and Innate Immunity Meet at the Mitochondria.
  4. Defining the molecular mechanisms of the mitochondrial permeability transition through genetic manipulation of F-ATP synthase.
  5. Spontaneous hydrolysis and spurious metabolic properties of α-ketoglutarate esters.
  6. Mitochondrial Oxidation of Ubiquinol Is Required for Tumorigenesis.
  7. The pathogenesis of mesothelioma is driven by a dysregulated translatome.
  8. Two parallel pathways connect glutamine metabolism and mTORC1 activity to regulate glutamoptosis.
  9. Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
  10. Cell competition in intratumoral and tumor microenvironment interactions.
  11. Metabolic orchestration of the wound healing response.
  12. Pharmacological inhibition of mitochondrial soluble adenylyl cyclase in astrocytes causes activation of AMP-activated protein kinase and induces breakdown of glycogen.
  13. A persistent look at how tumours evade therapy.
  14. Allostatic hypermetabolic response in PGC1α/β heterozygote mouse despite mitochondrial defects.
  15. Cycling cancer persister cells arise from lineages with distinct programs.
  16. Proline metabolism in cancer.
  17. The requirement for pyruvate dehydrogenase in leukemogenesis depends on cell lineage.
  18. The lysosome as a master regulator of iron metabolism.
  19. SLC15A4 mediates M1-prone metabolic shifts in macrophages and guards immune cells from metabolic stress.
  20. Targeting Aging: Lessons Learned From Immunometabolism and Cellular Senescence.
  21. A transepithelial pathway delivers succinate to macrophages, thus perpetuating their pro-inflammatory metabolic state.
  22. The tumor suppressor folliculin inhibits lactate dehydrogenase A and regulates the Warburg effect.
  23. YAP drives cell competition by activating choline metabolism.
  24. The conformational stability of pro-apoptotic BAX is dictated by discrete residues of the protein core.
  25. Targeting Pin1 renders pancreatic cancer eradicable by synergizing with immunochemotherapy.
  26. Mechanisms of cellular iron sensing, regulation of erythropoiesis and mitochondrial iron utilization.
  27. ATPAF1 deficiency impairs ATP synthase assembly and mitochondrial respiration.
  28. PERM1 interacts with the MICOS-MIB complex to connect the mitochondria and sarcolemma via ankyrin B.
  29. Glutathione peroxidase 4-regulated neutrophil ferroptosis induces systemic autoimmunity.
  30. Reduced Shmt2 Expression Impairs Mitochondrial Folate Accumulation and Respiration, and Leads to Uracil Accumulation in Mouse Mitochondrial DNA.
  31. Hexokinases inhibit death receptor-dependent apoptosis on the mitochondria.
  32. MicroRNA-mediated inhibition of AMPK coordinates tissue-specific downregulation of skeletal muscle metabolism in hypoxic naked mole-rats.
  33. GDF15 mediates the metabolic effects of PPARβ/δ by activating AMPK.
  34. Why meals during resting time cause fat accumulation in mammals? Mathematical modeling of circadian regulation on glucose metabolism.
  35. 3D neuronal mitochondrial morphology in axons, dendrites, and somata of the aging mouse hippocampus.
  36. A composite DNA element that functions as a maintainer required for epigenetic inheritance of heterochromatin.
  37. A DRP-1 dependent autophagy process facilitates rebuilding of the mitochondrial network and modulates adaptation capacity in response to acute heat stress during C. elegans development.
  38. NAD+ metabolism controls growth inhibition by HIF1 in normoxia and determines differential sensitivity of normal and cancer cells.
  39. Mutations in the transcription factor FOXO1 mimic positive selection signals to promote germinal center B cell expansion and lymphomagenesis.
  40. A feedback loop between the androgen receptor and 6-phosphogluoconate dehydrogenase (6PGD) drives prostate cancer growth.
  41. Putative homeostatic role of cancer driver mutations.
  42. The somatic molecular evolution of cancer: Mutation, selection, and epistasis.
  1. Nat Commun. 2021 08 11. 12(1): 4860
    GOT1 inhibition promotes pancreatic cancer cell death by ferroptosis.
    Daniel M Kremer, Barbara S Nelson, Lin Lin, Emily L Yarosz, Christopher J Halbrook, Samuel A Kerk, Peter Sajjakulnukit, Amy Myers, Galloway Thurston, Sean W Hou, Eileen S Carpenter, Anthony C Andren, Zeribe C Nwosu, Nicholas Cusmano, Stephanie Wisner, Nneka E Mbah, Mengrou Shan, Nupur K Das, Brian Magnuson, Andrew C Little, Milan R Savani, Johanna Ramos, Tina Gao, Stephen A Sastra, Carmine F Palermo, Michael A Badgley, Li Zhang, John M Asara, Samuel K McBrayer, Marina Pasca di Magliano, Howard C Crawford, Yatrik M Shah, Kenneth P Olive, Costas A Lyssiotis.
      Cancer metabolism is rewired to support cell survival in response to intrinsic and environmental stressors. Identification of strategies to target these adaptions is an area of active research. We previously described a cytosolic aspartate aminotransaminase (GOT1)-driven pathway in pancreatic cancer used to maintain redox balance. Here, we sought to identify metabolic dependencies following GOT1 inhibition to exploit this feature of pancreatic cancer and to provide additional insight into regulation of redox metabolism. Using pharmacological methods, we identify cysteine, glutathione, and lipid antioxidant function as metabolic vulnerabilities following GOT1 withdrawal. We demonstrate that targeting any of these pathways triggers ferroptosis, an oxidative, iron-dependent form of cell death, in GOT1 knockdown cells. Mechanistically, we reveal that GOT1 inhibition represses mitochondrial metabolism and promotes a catabolic state. Consequently, we find that this enhances labile iron availability through autophagy, which potentiates the activity of ferroptotic stimuli. Overall, our study identifies a biochemical connection between GOT1, iron regulation, and ferroptosis.
    DOI:  https://doi.org/10.1038/s41467-021-24859-2
  2. Cell Death Differ. 2021 Aug 13.
    Sustained intracellular calcium rise mediates neuronal mitophagy in models of autosomal dominant optic atrophy.
    Marta Zaninello, Konstantinos Palikaras, Aggeliki Sotiriou, Nektarios Tavernarakis, Luca Scorrano.
      Mitochondrial dysfunction and mitophagy are often hallmarks of neurodegenerative diseases such as autosomal dominant optic atrophy (ADOA) caused by mutations in the key mitochondrial dynamics protein optic atrophy 1 (Opa1). However, the second messengers linking mitochondrial dysfunction to initiation of mitophagy remain poorly characterized. Here, we show in mammalian and nematode neurons that Opa1 mutations trigger Ca2+-dependent mitophagy. Deletion or expression of mutated Opa1 in mouse retinal ganglion cells and Caenorhabditis elegans motor neurons lead to mitochondrial dysfunction, increased cytosolic Ca2+ levels, and decreased axonal mitochondrial density. Chelation of Ca2+ restores mitochondrial density in neuronal processes, neuronal function, and viability. Mechanistically, sustained Ca2+ levels activate calcineurin and AMPK, placed in the same genetic pathway regulating axonal mitochondrial density. Our data reveal that mitophagy in ADOA depends on Ca2+-calcineurin-AMPK signaling cascade.
    DOI:  https://doi.org/10.1038/s41418-021-00847-3
  3. Front Cell Dev Biol. 2021 ;9 720490
    Metabolism and Innate Immunity Meet at the Mitochondria.
    Amir Bahat, Thomas MacVicar, Thomas Langer.
      Mitochondria are master regulators of metabolism and have emerged as key signalling organelles of the innate immune system. Each mitochondrion harbours potent agonists of inflammation, including mitochondrial DNA (mtDNA), which are normally shielded from the rest of the cell and extracellular environment and therefore do not elicit detrimental inflammatory cascades. Mitochondrial damage and dysfunction can lead to the cytosolic and extracellular exposure of mtDNA, which triggers inflammation in a number of diseases including autoimmune neurodegenerative disorders. However, recent research has revealed that the extra-mitochondrial exposure of mtDNA is not solely a negative consequence of mitochondrial damage and pointed to an active role of mitochondria in innate immunity. Metabolic cues including nucleotide imbalance can stimulate the release of mtDNA from mitochondria in order to drive a type I interferon response. Moreover, important effectors of the innate immune response to pathogen infection, such as the mitochondrial antiviral signalling protein (MAVS), are located at the mitochondrial surface and modulated by the cellular metabolic status and mitochondrial dynamics. In this review, we explore how and why metabolism and innate immunity converge at the mitochondria and describe how mitochondria orchestrate innate immune signalling pathways in different metabolic scenarios. Understanding how cellular metabolism and metabolic programming of mitochondria are translated into innate immune responses bears relevance to a broad range of human diseases including cancer.
    Keywords:  CGAS; MAVS; STING; innate immunity; metabolism; mitochondria; mitochondrial DNA
    DOI:  https://doi.org/10.3389/fcell.2021.720490
  4. Nat Commun. 2021 08 10. 12(1): 4835
    Defining the molecular mechanisms of the mitochondrial permeability transition through genetic manipulation of F-ATP synthase.
    Andrea Carrer, Ludovica Tommasin, Justina Šileikytė, Francesco Ciscato, Riccardo Filadi, Andrea Urbani, Michael Forte, Andrea Rasola, Ildikò Szabò, Michela Carraro, Paolo Bernardi.
      F-ATP synthase is a leading candidate as the mitochondrial permeability transition pore (PTP) but the mechanism(s) leading to channel formation remain undefined. Here, to shed light on the structural requirements for PTP formation, we test cells ablated for g, OSCP and b subunits, and ρ0 cells lacking subunits a and A6L. Δg cells (that also lack subunit e) do not show PTP channel opening in intact cells or patch-clamped mitoplasts unless atractylate is added. Δb and ΔOSCP cells display currents insensitive to cyclosporin A but inhibited by bongkrekate, suggesting that the adenine nucleotide translocator (ANT) can contribute to channel formation in the absence of an assembled F-ATP synthase. Mitoplasts from ρ0 mitochondria display PTP currents indistinguishable from their wild-type counterparts. In this work, we show that peripheral stalk subunits are essential to turn the F-ATP synthase into the PTP and that the ANT provides mitochondria with a distinct permeability pathway.
    DOI:  https://doi.org/10.1038/s41467-021-25161-x
  5. Nat Commun. 2021 08 12. 12(1): 4905
    Spontaneous hydrolysis and spurious metabolic properties of α-ketoglutarate esters.
    Seth J Parker, Joel Encarnación-Rosado, Kate E R Hollinshead, David M Hollinshead, Leonard J Ash, Juan A K Rossi, Elaine Y Lin, Albert S W Sohn, Mark R Philips, Drew R Jones, Alec C Kimmelman.
      α-ketoglutarate (KG), also referred to as 2-oxoglutarate, is a key intermediate of cellular metabolism with pleiotropic functions. Cell-permeable esterified analogs are widely used to study how KG fuels bioenergetic and amino acid metabolism and DNA, RNA, and protein hydroxylation reactions, as cellular membranes are thought to be impermeable to KG. Here we show that esterified KG analogs rapidly hydrolyze in aqueous media, yielding KG that, in contrast to prevailing assumptions, imports into many cell lines. Esterified KG analogs exhibit spurious KG-independent effects on cellular metabolism, including extracellular acidification, arising from rapid hydrolysis and de-protonation of α-ketoesters, and significant analog-specific inhibitory effects on glycolysis or mitochondrial respiration. We observe that imported KG decarboxylates to succinate in the cytosol and contributes minimally to mitochondrial metabolism in many cell lines cultured in normal conditions. These findings demonstrate that nuclear and cytosolic KG-dependent reactions may derive KG from functionally distinct subcellular pools and sources.
    DOI:  https://doi.org/10.1038/s41467-021-25228-9
  6. Cancer Discov. 2020 Sep;10(9): 1250
    Mitochondrial Oxidation of Ubiquinol Is Required for Tumorigenesis.
      The ability of mitochondrial complex III to oxidize ubiquinol was essential to tumor growth in vivo.
    DOI:  https://doi.org/10.1158/2159-8290.CD-RW2020-107
  7. Nat Commun. 2021 Aug 13. 12(1): 4920
    The pathogenesis of mesothelioma is driven by a dysregulated translatome.
    Stefano Grosso, Alberto Marini, Katarina Gyuraszova, Johan Vande Voorde, Aristeidis Sfakianos, Gavin D Garland, Angela Rubio Tenor, Ryan Mordue, Tanya Chernova, Nobu Morone, Marco Sereno, Claire P Smith, Leah Officer, Pooyeh Farahmand, Claire Rooney, David Sumpton, Madhumita Das, Ana Teodósio, Catherine Ficken, Maria Guerra Martin, Ruth V Spriggs, Xiao-Ming Sun, Martin Bushell, Owen J Sansom, Daniel Murphy, Marion MacFarlane, John P C Le Quesne, Anne E Willis.
      Malignant mesothelioma (MpM) is an aggressive, invariably fatal tumour that is causally linked with asbestos exposure. The disease primarily results from loss of tumour suppressor gene function and there are no 'druggable' driver oncogenes associated with MpM. To identify opportunities for management of this disease we have carried out polysome profiling to define the MpM translatome. We show that in MpM there is a selective increase in the translation of mRNAs encoding proteins required for ribosome assembly and mitochondrial biogenesis. This results in an enhanced rate of mRNA translation, abnormal mitochondrial morphology and oxygen consumption, and a reprogramming of metabolic outputs. These alterations delimit the cellular capacity for protein biosynthesis, accelerate growth and drive disease progression. Importantly, we show that inhibition of mRNA translation, particularly through combined pharmacological targeting of mTORC1 and 2, reverses these changes and inhibits malignant cell growth in vitro and in ex-vivo tumour tissue from patients with end-stage disease. Critically, we show that these pharmacological interventions prolong survival in animal models of asbestos-induced mesothelioma, providing the basis for a targeted, viable therapeutic option for patients with this incurable disease.
    DOI:  https://doi.org/10.1038/s41467-021-25173-7
  8. Nat Commun. 2021 08 10. 12(1): 4814
    Two parallel pathways connect glutamine metabolism and mTORC1 activity to regulate glutamoptosis.
    Clément Bodineau, Mercedes Tomé, Sarah Courtois, Ana S H Costa, Marco Sciacovelli, Benoit Rousseau, Elodie Richard, Pierre Vacher, Carlos Parejo-Pérez, Emilie Bessede, Christine Varon, Pierre Soubeyran, Christian Frezza, Piedad Del Socorro Murdoch, Victor H Villar, Raúl V Durán.
      Glutamoptosis is the induction of apoptotic cell death as a consequence of the aberrant activation of glutaminolysis and mTORC1 signaling during nutritional imbalance in proliferating cells. The role of the bioenergetic sensor AMPK during glutamoptosis is not defined yet. Here, we show that AMPK reactivation blocks both the glutamine-dependent activation of mTORC1 and glutamoptosis in vitro and in vivo. We also show that glutamine is used for asparagine synthesis and the GABA shunt to produce ATP and to inhibit AMPK, independently of glutaminolysis. Overall, our results indicate that glutamine metabolism is connected with mTORC1 activation through two parallel pathways: an acute alpha-ketoglutarate-dependent pathway; and a secondary ATP/AMPK-dependent pathway. This dual metabolic connection between glutamine and mTORC1 must be considered for the future design of therapeutic strategies to prevent cell growth in diseases such as cancer.
    DOI:  https://doi.org/10.1038/s41467-021-25079-4
  9. Cell. 2021 Aug 03. pii: S0092-8674(21)00880-1. [Epub ahead of print]
    Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
    Simone Caielli, Jacob Cardenas, Adriana Almeida de Jesus, Jeanine Baisch, Lynnette Walters, Jean Philippe Blanck, Preetha Balasubramanian, Cristy Stagnar, Marina Ohouo, Seunghee Hong, Lorien Nassi, Katie Stewart, Julie Fuller, Jinghua Gu, Jacques F Banchereau, Tracey Wright, Raphaela Goldbach-Mansky, Virginia Pascual.
      Emerging evidence supports that mitochondrial dysfunction contributes to systemic lupus erythematosus (SLE) pathogenesis. Here we show that programmed mitochondrial removal, a hallmark of mammalian erythropoiesis, is defective in SLE. Specifically, we demonstrate that during human erythroid cell maturation, a hypoxia-inducible factor (HIF)-mediated metabolic switch is responsible for the activation of the ubiquitin-proteasome system (UPS), which precedes and is necessary for the autophagic removal of mitochondria. A defect in this pathway leads to accumulation of red blood cells (RBCs) carrying mitochondria (Mito+ RBCs) in SLE patients and in correlation with disease activity. Antibody-mediated internalization of Mito+ RBCs induces type I interferon (IFN) production through activation of cGAS in macrophages. Accordingly, SLE patients carrying both Mito+ RBCs and opsonizing antibodies display the highest levels of blood IFN-stimulated gene (ISG) signatures, a distinctive feature of SLE.
    Keywords:  CANDLE syndrome; HIF2a; autoimmunity; cGAS; human erythropoiesis; interferon; mitochondrial DNA; mitophagy; proteasome; systemic lupus erythematosus
    DOI:  https://doi.org/10.1016/j.cell.2021.07.021
  10. EMBO J. 2021 Aug 09. e107271
    Cell competition in intratumoral and tumor microenvironment interactions.
    Taylor M Parker, Kartik Gupta, António M Palma, Michail Yekelchyk, Paul B Fisher, Steven R Grossman, Kyoung Jae Won, Esha Madan, Eduardo Moreno, Rajan Gogna.
      Tumors are complex cellular and acellular environments within which cancer clones are under continuous selection pressures. Cancer cells are in a permanent mode of interaction and competition with each other as well as with the immediate microenvironment. In the course of these competitive interactions, cells share information regarding their general state of fitness, with less-fit cells being typically eliminated via apoptosis at the hands of those cells with greater cellular fitness. Competitive interactions involving exchange of cell fitness information have implications for tumor growth, metastasis, and therapy outcomes. Recent research has highlighted sophisticated pathways such as Flower, Hippo, Myc, and p53 signaling, which are employed by cancer cells and the surrounding microenvironment cells to achieve their evolutionary goals by means of cell competition mechanisms. In this review, we discuss these recent findings and explain their importance and role in evolution, growth, and treatment of cancer. We further consider potential physiological conditions, such as hypoxia and chemotherapy, that can function as selective pressures under which cell competition mechanisms may evolve differently or synergistically to confer oncogenic advantages to cancer.
    Keywords:  cancer; cell competition; chemotherapy; clonal selection; tumor heterogeneity
    DOI:  https://doi.org/10.15252/embj.2020107271
  11. Cell Metab. 2021 Aug 09. pii: S1550-4131(21)00362-4. [Epub ahead of print]
    Metabolic orchestration of the wound healing response.
    Sabine A Eming, Peter J Murray, Edward J Pearce.
      Wound healing requires cooperation between different cell types, among which macrophages play a central role. In particular, inflammatory macrophages are engaged in the initial response to wounding, and alternatively activated macrophages are essential for wound closure and the resolution of tissue repair. The links between temporal activation-induced changes in the metabolism of such macrophages and the influence this has on their functional states, along with the realization that metabolites play both intrinsic and extrinsic roles in the cells that produce them, has focused attention on the metabolism of wound healing. Here, we discuss macrophage metabolism during distinct stages of normal healing and its related pathologic processes, such as during cancer and fibrosis. Further, we frame these insights in a broader context of the current understanding of macrophage metabolic reprogramming linked to cellular activation and function. Finally, we discuss parallels between the metabolism of macrophages and fibroblasts, the latter being a key stromal cell type in wound healing, and consider the importance of the metabolic interplay between different cell types in the wound microenvironment.
    DOI:  https://doi.org/10.1016/j.cmet.2021.07.017
  12. Glia. 2021 Aug 11.
    Pharmacological inhibition of mitochondrial soluble adenylyl cyclase in astrocytes causes activation of AMP-activated protein kinase and induces breakdown of glycogen.
    Emil Jakobsen, Jens V Andersen, Sofie K Christensen, Olga Siamka, Martin R Larsen, Helle S Waagepetersen, Blanca I Aldana, Lasse K Bak.
      Mobilization of astrocyte glycogen is key for processes such as synaptic plasticity and memory formation but the link between neuronal activity and glycogen breakdown is not fully known. Activation of cytosolic soluble adenylyl cyclase (sAC) in astrocytes has been suggested to link neuronal depolarization and glycogen breakdown partly based on experiments employing pharmacological inhibition of sAC. However, several studies have revealed that sAC located within mitochondria is a central regulator of respiration and oxidative phosphorylation. Thus, pharmacological sAC inhibition is likely to affect both cytosolic and mitochondrial sAC and if bioenergetic readouts are studied, the observed effects are likely to stem from inhibition of mitochondrial rather than cytosolic sAC. Here, we report that a pharmacologically induced inhibition of sAC activity lowers mitochondrial respiration, induces phosphorylation of the metabolic master switch AMP-activated protein kinase (AMPK), and decreases glycogen stores in cultured primary murine astrocytes. From these data and our discussion of the literature, mitochondrial sAC emerges as a key regulator of astrocyte bioenergetics. Lastly, we discuss the challenges of investigating the functional and metabolic roles of cytosolic versus mitochondrial sAC in astrocytes employing the currently available pharmacological tool compounds.
    Keywords:  AMPK; astrocytes; cAMP; glycogen; mitochondria; soluble adenylyl cyclase (sAC)
    DOI:  https://doi.org/10.1002/glia.24072
  13. Nature. 2021 Aug 11.
    A persistent look at how tumours evade therapy.
    Karen Gomez, Raul Rabadan.
      
    Keywords:  Cancer; Medical research; Metabolism
    DOI:  https://doi.org/10.1038/d41586-021-02117-1
  14. FASEB J. 2021 Sep;35(9): e21752
    Allostatic hypermetabolic response in PGC1α/β heterozygote mouse despite mitochondrial defects.
    Sergio Rodriguez-Cuenca, Christopher J Lelliot, Mark Campbell, Gopal Peddinti, Maite Martinez-Uña, Camilla Ingvorsen, Ana Rita Dias, Joana Relat, Silvia Mora, Tuulia Hyötyläinen, Antonio Zorzano, Matej Orešič, Mikael Bjursell, Mohammad Bohlooly-Y, Daniel Lindén, Antonio Vidal-Puig.
      Aging, obesity, and insulin resistance are associated with low levels of PGC1α and PGC1β coactivators and defective mitochondrial function. We studied mice deficient for PGC1α and PGC1β [double heterozygous (DH)] to investigate their combined pathogenic contribution. Contrary to our hypothesis, DH mice were leaner, had increased energy dissipation, a pro-thermogenic profile in BAT and WAT, and improved carbohydrate metabolism compared to wild types. WAT showed upregulation of mitochondriogenesis/oxphos machinery upon allelic compensation of PGC1α4 from the remaining allele. However, DH mice had decreased mitochondrial OXPHOS and biogenesis transcriptomes in mitochondria-rich organs. Despite being metabolically healthy, mitochondrial defects in DH mice impaired muscle fiber remodeling and caused qualitative changes in the hepatic lipidome. Our data evidence first the existence of organ-specific compensatory allostatic mechanisms are robust enough to drive an unexpected phenotype. Second, optimization of adipose tissue bioenergetics is sufficient to maintain a healthy metabolic phenotype despite a broad severe mitochondrial dysfunction in other relevant metabolic organs. Third, the decrease in PGC1s in adipose tissue of obese and diabetic patients is in contrast with the robustness of the compensatory upregulation in the adipose of the DH mice.
    Keywords:  PGC-1alpha; adipose tissue; hepatic lipidome; lipotoxicity; mitochondrial dysfunction
    DOI:  https://doi.org/10.1096/fj.202100262RR
  15. Nature. 2021 Aug 11.
    Cycling cancer persister cells arise from lineages with distinct programs.
    Yaara Oren, Michael Tsabar, Michael S Cuoco, Liat Amir-Zilberstein, Heidie F Cabanos, Jan-Christian Hütter, Bomiao Hu, Pratiksha I Thakore, Marcin Tabaka, Charles P Fulco, William Colgan, Brandon M Cuevas, Sara A Hurvitz, Dennis J Slamon, Amy Deik, Kerry A Pierce, Clary Clish, Aaron N Hata, Elma Zaganjor, Galit Lahav, Katerina Politi, Joan S Brugge, Aviv Regev.
      Non-genetic mechanisms have recently emerged as important drivers of cancer therapy failure1, where some cancer cells can enter a reversible drug-tolerant persister state in response to treatment2. Although most cancer persisters remain arrested in the presence of the drug, a rare subset can re-enter the cell cycle under constitutive drug treatment. Little is known about the non-genetic mechanisms that enable cancer persisters to maintain proliferative capacity in the presence of drugs. To study this rare, transiently resistant, proliferative persister population, we developed Watermelon, a high-complexity expressed barcode lentiviral library for simultaneous tracing of each cell's clonal origin and proliferative and transcriptional states. Here we show that cycling and non-cycling persisters arise from different cell lineages with distinct transcriptional and metabolic programs. Upregulation of antioxidant gene programs and a metabolic shift to fatty acid oxidation are associated with persister proliferative capacity across multiple cancer types. Impeding oxidative stress or metabolic reprogramming alters the fraction of cycling persisters. In human tumours, programs associated with cycling persisters are induced in minimal residual disease in response to multiple targeted therapies. The Watermelon system enabled the identification of rare persister lineages that are preferentially poised to proliferate under drug pressure, thus exposing new vulnerabilities that can be targeted to delay or even prevent disease recurrence.
    DOI:  https://doi.org/10.1038/s41586-021-03796-6
  16. Amino Acids. 2021 Aug 14.
    Proline metabolism in cancer.
    Pengyu Geng, Wangshu Qin, Guowang Xu.
      Cancer cells often change their metabolism to support uncontrolled proliferation. Proline is the only proteogenic secondary amino acid that is abundant in the body. Recent studies have shown that proline metabolism plays an important role in metabolic reprogramming and affects the occurrence and development of cancer. Proline metabolism is related to ATP production, protein and nucleotide synthesis, and redox homeostasis in tumor cells. Proline can be synthesized by aldehyde dehydrogenase family 18 member A1 (ALDH18A1) and delta1-pyrroline-5-carboxylate reductase (PYCR), up-regulating ALDH18A1 and PYCR can promote the proliferation and invasion of cancer cells. As the main storage of proline, collagen can influence cancer cells proliferation, invasion, and metastasis. Its synthesis depends on the hydroxylation of proline catalyzed by prolyl 4-hydroxylases (P4Hs), which will affect the plasticity and metastasis of cancer cells. The degradation of proline occurs in the mitochondria and involves an oxidation step catalyzed by proline dehydrogenase/proline oxidase (PRODH/POX). Proline catabolism has a dual role in cancer, linking apoptosis with the survival and metastasis of cancer cells. In addition, it has been demonstrated that the regulation of proline metabolic enzymes at the genetic and post-translational levels is related to cancer. This article reviews the role of proline metabolic enzymes in cancer proliferation, apoptosis, metastasis, and development. Research on proline metabolism may provide a new strategy for cancer treatment.
    Keywords:  ALDH18A1; Cancer; P4Hs; PRODH/POX; PYCR; Proline metabolism
    DOI:  https://doi.org/10.1007/s00726-021-03060-1
  17. Cell Metab. 2021 Aug 03. pii: S1550-4131(21)00332-6. [Epub ahead of print]
    The requirement for pyruvate dehydrogenase in leukemogenesis depends on cell lineage.
    Sojeong Jun, Swetha Mahesula, Thomas P Mathews, Misty S Martin-Sandoval, Zhiyu Zhao, Elena Piskounova, Michalis Agathocleous.
      Cancer cells are metabolically similar to their corresponding normal tissues. Differences between cancers and normal tissues may reflect reprogramming during transformation or maintenance of the metabolism of the specific normal cell type that originated the cancer. Here, we compare glucose metabolism in hematopoiesis and leukemia. Thymus T cell progenitors were glucose avid and oxidized more glucose in the tricarboxylic acid cycle through pyruvate dehydrogenase (PDH) as compared with other hematopoietic cells. PDH deletion decreased double-positive T cell progenitor cells but had no effect on hematopoietic stem cells, myeloid progenitors, or other hematopoietic cells. PDH deletion blocked the development of Pten-deficient T cell leukemia, but not the development of a Pten-deficient myeloid neoplasm. Therefore, the requirement for PDH in leukemia reflected the metabolism of the normal cell of origin independently of the driver genetic lesion. PDH was required to prevent pyruvate accumulation and maintain glutathione levels and redox homeostasis.
    Keywords:  T cell leukemia; double-positive thymocytes; glycolysis; hematopoietic stem cells; metabolism; pyruvate dehydrogenase; thymus
    DOI:  https://doi.org/10.1016/j.cmet.2021.07.016
  18. Trends Biochem Sci. 2021 Aug 09. pii: S0968-0004(21)00159-6. [Epub ahead of print]
    The lysosome as a master regulator of iron metabolism.
    Francesca Rizzollo, Sanket More, Peter Vangheluwe, Patrizia Agostinis.
      Intracellular iron fulfills crucial cellular processes, including DNA synthesis and mitochondrial metabolism, but also mediates ferroptosis, a regulated form of cell death driven by lipid-based reactive oxygen species (ROS). Beyond their established role in degradation and recycling, lysosomes occupy a central position in iron homeostasis and integrate metabolic and cell death signals emanating from different subcellular sites. We discuss the central role of the lysosome in preserving iron homeostasis and provide an integrated outlook of the regulatory circuits coupling the lysosomal system to the control of iron trafficking, interorganellar crosstalk, and ferroptosis induction. We also discuss novel studies unraveling how deregulated lysosomal iron-handling functions contribute to cancer, neurodegeneration, and viral infection, and can be harnessed for therapeutic interventions.
    Keywords:  cancer; ferroptosis; iron homeostasis; iron trafficking; neurodegenerative diseases; viruses
    DOI:  https://doi.org/10.1016/j.tibs.2021.07.003
  19. Proc Natl Acad Sci U S A. 2021 Aug 17. pii: e2100295118. [Epub ahead of print]118(33):
    SLC15A4 mediates M1-prone metabolic shifts in macrophages and guards immune cells from metabolic stress.
    Toshihiko Kobayashi, Dat Nguyen-Tien, Yuriko Sorimachi, Yuki Sugiura, Takehiro Suzuki, Hitomi Karyu, Shiho Shimabukuro-Demoto, Tatsuki Uemura, Tadashi Okamura, Tomohiko Taguchi, Kohjiro Ueki, Norihiro Kato, Nobuhito Goda, Naoshi Dohmae, Keiyo Takubo, Makoto Suematsu, Noriko Toyama-Sorimachi.
      The amino acid and oligopeptide transporter Solute carrier family 15 member A4 (SLC15A4), which resides in lysosomes and is preferentially expressed in immune cells, plays critical roles in the pathogenesis of lupus and colitis in murine models. Toll-like receptor (TLR)7/9- and nucleotide-binding oligomerization domain-containing protein 1 (NOD1)-mediated inflammatory responses require SLC15A4 function for regulating the mechanistic target of rapamycin complex 1 (mTORC1) or transporting L-Ala-γ-D-Glu-meso-diaminopimelic acid, IL-12: interleukin-12 (Tri-DAP), respectively. Here, we further investigated the mechanism of how SLC15A4 directs inflammatory responses. Proximity-dependent biotin identification revealed glycolysis as highly enriched gene ontology terms. Fluxome analyses in macrophages indicated that SLC15A4 loss causes insufficient biotransformation of pyruvate to the tricarboxylic acid cycle, while increasing glutaminolysis to the cycle. Furthermore, SLC15A4 was required for M1-prone metabolic change and inflammatory IL-12 cytokine productions after TLR9 stimulation. SLC15A4 could be in close proximity to AMP-activated protein kinase (AMPK) and mTOR, and SLC15A4 deficiency impaired TLR-mediated AMPK activation. Interestingly, SLC15A4-intact but not SLC15A4-deficient macrophages became resistant to fluctuations in environmental nutrient levels by limiting the use of the glutamine source; thus, SLC15A4 was critical for macrophage's respiratory homeostasis. Our findings reveal a mechanism of metabolic regulation in which an amino acid transporter acts as a gatekeeper that protects immune cells' ability to acquire an M1-prone metabolic phenotype in inflammatory tissues by mitigating metabolic stress.
    Keywords:  amino acid transporter; cytokine; immunometabolism; innate immune cell; macrophage
    DOI:  https://doi.org/10.1073/pnas.2100295118
  20. Front Immunol. 2021 ;12 714742
    Targeting Aging: Lessons Learned From Immunometabolism and Cellular Senescence.
    Dominique E Martin, Blake L Torrance, Laura Haynes, Jenna M Bartley.
      It is well known that aging is associated with dysregulated metabolism. This is seen both in terms of systemic metabolism, as well as at the cellular level with clear mitochondrial dysfunction. More recently, the importance of cellular metabolism in immune cells, or immunometabolism, has been highlighted as a major modifier of immune cell function. Indeed, T cell activation, differentiation, and effector function partly depend on alterations in metabolic pathways with different cell types and functionality favoring either glycolysis or oxidative phosphorylation. While immune system dysfunction with aging is well described, what remains less elucidated is how the integral networks that control immune cell metabolism are specifically affected by age. In recent years, this significant gap has been identified and work has begun to investigate the various ways immunometabolism could be impacted by both chronological age and age-associated symptoms, such as the systemic accumulation of senescent cells. Here, in this mini-review, we will examine immunometabolism with a focus on T cells, aging, and interventions, such as mTOR modulators and senolytics. This review also covers a timely perspective on how immunometabolism may be an ideal target for immunomodulation with aging.
    Keywords:  T cell; aging; geroscience; immunometabolism; senescence
    DOI:  https://doi.org/10.3389/fimmu.2021.714742
  21. Cell Rep. 2021 Aug 10. pii: S2211-1247(21)00952-9. [Epub ahead of print]36(6): 109521
    A transepithelial pathway delivers succinate to macrophages, thus perpetuating their pro-inflammatory metabolic state.
    Moran Fremder, Seung Won Kim, Ahlam Khamaysi, Liana Shimshilashvili, Hadar Eini-Rider, I Seul Park, Uzi Hadad, Jae Hee Cheon, Ehud Ohana.
      The gut metabolite composition determined by the microbiota has paramount impact on gastrointestinal physiology. However, the role that bacterial metabolites play in communicating with host cells during inflammatory diseases is poorly understood. Here, we aim to identify the microbiota-determined output of the pro-inflammatory metabolite, succinate, and to elucidate the pathways that control transepithelial succinate absorption and subsequent succinate delivery to macrophages. We show a significant increase of succinate uptake into pro-inflammatory macrophages, which is controlled by Na+-dependent succinate transporters in macrophages and epithelial cells. Furthermore, we find that fecal and serum succinate concentrations were markedly augmented in inflammatory bowel diseases (IBDs) and corresponded to changes in succinate-metabolizing gut bacteria. Together, our results describe a succinate production and transport pathway that controls the absorption of succinate generated by distinct gut bacteria and its delivery into macrophages. In IBD, this mechanism fails to protect against the succinate surge, which may result in chronic inflammation.
    Keywords:  citrate; epithelia; inflammation; ion transport; macrophages; metabolism; microbiota; succinate
    DOI:  https://doi.org/10.1016/j.celrep.2021.109521
  22. Nat Struct Mol Biol. 2021 Aug;28(8): 662-670
    The tumor suppressor folliculin inhibits lactate dehydrogenase A and regulates the Warburg effect.
    Mark R Woodford, Alexander J Baker-Williams, Rebecca A Sager, Sarah J Backe, Adam R Blanden, Fiza Hashmi, Priyanka Kancherla, Alessandro Gori, David R Loiselle, Matteo Castelli, Stefano A Serapian, Giorgio Colombo, Timothy A Haystead, Sandra M Jensen, William G Stetler-Stevenson, Stewart N Loh, Laura S Schmidt, W Marston Linehan, Alaji Bah, Dimitra Bourboulia, Gennady Bratslavsky, Mehdi Mollapour.
      Aerobic glycolysis in cancer cells, also known as the 'Warburg effect', is driven by hyperactivity of lactate dehydrogenase A (LDHA). LDHA is thought to be a substrate-regulated enzyme, but it is unclear whether a dedicated intracellular protein also regulates its activity. Here, we identify the human tumor suppressor folliculin (FLCN) as a binding partner and uncompetitive inhibitor of LDHA. A flexible loop within the amino terminus of FLCN controls movement of the LDHA active-site loop, tightly regulating its enzyme activity and, consequently, metabolic homeostasis in normal cells. Cancer cells that experience the Warburg effect show FLCN dissociation from LDHA. Treatment of these cells with a decapeptide derived from the FLCN loop region causes cell death. Our data suggest that the glycolytic shift of cancer cells is the result of FLCN inactivation or dissociation from LDHA. Together, FLCN-mediated inhibition of LDHA provides a new paradigm for the regulation of glycolysis.
    DOI:  https://doi.org/10.1038/s41594-021-00633-2
  23. Biochem Biophys Res Commun. 2021 Aug 04. pii: S0006-291X(21)01140-2. [Epub ahead of print]572 178-184
    YAP drives cell competition by activating choline metabolism.
    Sachi Sunaga, Satoshi Kofuji, Hiroshi Nishina.
      Cell competition is a phenomenon that eliminates unfit cells from cell society, a function vital for maintaining cellular and organismal homeostasis. We previously showed that Madin-Darby canine kidney (MDCK) epithelial cells expressing the active form of the transcriptional coactivator Yes-associated protein (YAP) are apically extruded when surrounded by normal MDCK cells. Although we demonstrated that the arachidonic acid (AA) cascade is involved in YAP-dependent apical extrusion, the metabolic events leading to this outcome remained unclear. Here, we present the results of metabolomic analysis that identified phosphatidylcholine (PC) biosynthesis as the most significant player in this process. Removal of the PC biosynthetic components choline and methionine from culture medium inhibited YAP-dependent apical extrusion. Inhibition of either choline uptake or metabolic cycles involving choline or methionine also decreased YAP-dependent apical extrusion. At the molecular level, active YAP induced expression of the genes encoding glycerophosphocholine phosphodiesterase 1 (GPCPD1) and lecithin-cholesterol acyltransferase (LCAT), which are involved in choline metabolism. Our results indicate that YAP-dependent cell competition depends on YAP-mediated activation of the choline metabolic cycle.
    Keywords:  Apical extrusion; Cell competition; Choline; MDCK; Methionine; YAP
    DOI:  https://doi.org/10.1016/j.bbrc.2021.07.101
  24. Nat Commun. 2021 Aug 13. 12(1): 4932
    The conformational stability of pro-apoptotic BAX is dictated by discrete residues of the protein core.
    Noah B Bloch, Thomas E Wales, Michelle S Prew, Hannah R Levy, John R Engen, Loren D Walensky.
      BAX is a pro-apoptotic member of the BCL-2 family, which regulates the balance between cellular life and death. During homeostasis, BAX predominantly resides in the cytosol as a latent monomer but, in response to stress, transforms into an oligomeric protein that permeabilizes the mitochondria, leading to apoptosis. Because renegade BAX activation poses a grave risk to the cell, the architecture of BAX must ensure monomeric stability yet enable conformational change upon stress signaling. The specific structural features that afford both stability and dynamic flexibility remain ill-defined and represent a critical control point of BAX regulation. We identify a nexus of interactions involving four residues of the BAX core α5 helix that are individually essential to maintaining the structure and latency of monomeric BAX and are collectively required for dimeric assembly. The dual yet distinct roles of these residues reveals the intricacy of BAX conformational regulation and opportunities for therapeutic modulation.
    DOI:  https://doi.org/10.1038/s41467-021-25200-7
  25. Cell. 2021 Aug 06. pii: S0092-8674(21)00879-5. [Epub ahead of print]
    Targeting Pin1 renders pancreatic cancer eradicable by synergizing with immunochemotherapy.
    Kazuhiro Koikawa, Shin Kibe, Futoshi Suizu, Nobufumi Sekino, Nami Kim, Theresa D Manz, Benika J Pinch, Dipikaa Akshinthala, Ana Verma, Giorgio Gaglia, Yutaka Nezu, Shizhong Ke, Chenxi Qiu, Kenoki Ohuchida, Yoshinao Oda, Tae Ho Lee, Babara Wegiel, John G Clohessy, Nir London, Sandro Santagata, Gerburg M Wulf, Manuel Hidalgo, Senthil K Muthuswamy, Masafumi Nakamura, Nathanael S Gray, Xiao Zhen Zhou, Kun Ping Lu.
      Pancreatic ductal adenocarcinoma (PDAC) is characterized by notorious resistance to current therapies attributed to inherent tumor heterogeneity and highly desmoplastic and immunosuppressive tumor microenvironment (TME). Unique proline isomerase Pin1 regulates multiple cancer pathways, but its role in the TME and cancer immunotherapy is unknown. Here, we find that Pin1 is overexpressed both in cancer cells and cancer-associated fibroblasts (CAFs) and correlates with poor survival in PDAC patients. Targeting Pin1 using clinically available drugs induces complete elimination or sustained remissions of aggressive PDAC by synergizing with anti-PD-1 and gemcitabine in diverse model systems. Mechanistically, Pin1 drives the desmoplastic and immunosuppressive TME by acting on CAFs and induces lysosomal degradation of the PD-1 ligand PD-L1 and the gemcitabine transporter ENT1 in cancer cells, besides activating multiple cancer pathways. Thus, Pin1 inhibition simultaneously blocks multiple cancer pathways, disrupts the desmoplastic and immunosuppressive TME, and upregulates PD-L1 and ENT1, rendering PDAC eradicable by immunochemotherapy.
    Keywords:  Pin1; cancer immune evasion; cancer-associated fibroblasts; chemotherapy; combination therapy; immuni checkpoint therapy; pancreatic cancer; targeted therapy; tumor immune microenvironment; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.cell.2021.07.020
  26. Semin Hematol. 2021 Jul;pii: S0037-1963(21)00033-0. [Epub ahead of print]58(3): 161-174
    Mechanisms of cellular iron sensing, regulation of erythropoiesis and mitochondrial iron utilization.
    Nunziata Maio, De-Liang Zhang, Manik C Ghosh, Anshika Jain, Anna M SantaMaria, Tracey A Rouault.
      To maintain an adequate iron supply for hemoglobin synthesis and essential metabolic functions while counteracting iron toxicity, humans and other vertebrates have evolved effective mechanisms to conserve and finely regulate iron concentration, storage, and distribution to tissues. At the systemic level, the iron-regulatory hormone hepcidin is secreted by the liver in response to serum iron levels and inflammation. Hepcidin regulates the expression of the sole known mammalian iron exporter, ferroportin, to control dietary absorption, storage and tissue distribution of iron. At the cellular level, iron regulatory proteins 1 and 2 (IRP1 and IRP2) register cytosolic iron concentrations and post-transcriptionally regulate the expression of iron metabolism genes to optimize iron availability for essential cellular processes, including heme biosynthesis and iron-sulfur cluster biogenesis. Genetic malfunctions affecting the iron sensing mechanisms or the main pathways that utilize iron in the cell cause a broad range of human diseases, some of which are characterized by mitochondrial iron accumulation. This review will discuss the mechanisms of systemic and cellular iron sensing with a focus on the main iron utilization pathways in the cell, and on human conditions that arise from compromised function of the regulatory axes that control iron homeostasis.
    Keywords:  Ferroportin; Heme biosynthesis; IRP1; IRP2; Iron metabolism; Iron-sulfur clusters
    DOI:  https://doi.org/10.1053/j.seminhematol.2021.06.001
  27. Mitochondrion. 2021 Aug 07. pii: S1567-7249(21)00106-9. [Epub ahead of print]
    ATPAF1 deficiency impairs ATP synthase assembly and mitochondrial respiration.
    Zhou Zhou, Kailiang Zhang, Zhiheng Liu, Xu Gao, Kai Huang, Chen Chen, Wang Daowen, Qinglin Yang, Qinqiang Long.
      ATP11p and ATP12p are two nuclear-encoded mitochondrial chaperone proteins required for assembling the F1Fo-ATP synthase F1 sector. ATPAF1 and ATPAF2 are the mammalian homologs of ATP11p and ATP12p. However, the biochemical and physiological relevance of ATPAF1 and ATPAF2 in animal tissues with high energy-dependence remains unclear. To explore the in vivo role of ATP assembly and the effects of ATP synthase deficiency in animals, we have generated knockout (KO) mouse models of these assembly factors using CRISPR/Cas9 technology. While the Atpaf2-KO mice were embryonically lethal, Atpaf1-KO mice grew to adulthood but with smaller body sizes and elevated blood lactate later in life. We specifically investigated how ATPAF1 deficiency may affect ATP synthase biogenesis and mitochondrial respiration in the mouse heart, an organ highly energy-dependent. Western blots and Blue-Native electrophoresis (BN-PAGE) demonstrated a decreased F1 content and ATP synthase dimers in the Atpaf1-KO heart. Mitochondria from ATPAF1-deficient hearts showed ultrastructural abnormalities with condensed degenerated mitochondria, loss of cristae, and impaired respiratory capacity. ATP synthase deficiency also leads to impaired autophagy and mitochondrial dynamic. Consequently, decreased cardiac function was exhibited in adult Atpaf1-KO mice. The results provide strong support that ATPAF1 is essential for ATP synthase assembly and mitochondrial oxidative phosphorylation, thus playing a crucial role in maintaining cardiac structure and function in animals.
    Keywords:  ATP synthase assembly; mitochondria; mitochondrial dysfunction; oxidative phosphorylation (OXPHOS)
    DOI:  https://doi.org/10.1016/j.mito.2021.08.005
  28. Nat Commun. 2021 08 12. 12(1): 4900
    PERM1 interacts with the MICOS-MIB complex to connect the mitochondria and sarcolemma via ankyrin B.
    Theresa Bock, Clara Türk, Sriram Aravamudhan, Lena Keufgens, Wilhelm Bloch, Dieu Hien Rozsivalova, Vanina Romanello, Leonardo Nogara, Bert Blaauw, Aleksandra Trifunovic, Thomas Braun, Marcus Krüger.
      Skeletal muscle subsarcolemmal mitochondria (SSM) and intermyofibrillar mitochondria subpopulations have distinct metabolic activity and sensitivity, though the mechanisms that localize SSM to peripheral areas of muscle fibers are poorly understood. A protein interaction study and complexome profiling identifies PERM1 interacts with the MICOS-MIB complex. Ablation of Perm1 in mice reduces muscle force, decreases mitochondrial membrane potential and complex I activity, and reduces the numbers of SSM in skeletal muscle. We demonstrate PERM1 interacts with the intracellular adaptor protein ankyrin B (ANKB) that connects the cytoskeleton to the plasma membrane. Moreover, we identify a C-terminal transmembrane helix that anchors PERM1 into the outer mitochondrial membrane. We conclude PERM1 functions in the MICOS-MIB complex and acts as an adapter to connect the mitochondria with the sarcolemma via ANKB.
    DOI:  https://doi.org/10.1038/s41467-021-25185-3
  29. Nat Immunol. 2021 Aug 12.
    Glutathione peroxidase 4-regulated neutrophil ferroptosis induces systemic autoimmunity.
    Pengchong Li, Mengdi Jiang, Ketian Li, Hao Li, Yangzhong Zhou, Xinyue Xiao, Yue Xu, Suzanne Krishfield, Peter E Lipsky, George C Tsokos, Xuan Zhang.
      The linkage between neutrophil death and the development of autoimmunity has not been thoroughly explored. Here, we show that neutrophils from either lupus-prone mice or patients with systemic lupus erythematosus (SLE) undergo ferroptosis. Mechanistically, autoantibodies and interferon-α present in the serum induce neutrophil ferroptosis through enhanced binding of the transcriptional repressor CREMα to the glutathione peroxidase 4 (Gpx4, the key ferroptosis regulator) promoter, which leads to suppressed expression of Gpx4 and subsequent elevation of lipid-reactive oxygen species. Moreover, the findings that mice with neutrophil-specific Gpx4 haploinsufficiency recapitulate key clinical features of human SLE, including autoantibodies, neutropenia, skin lesions and proteinuria, and that the treatment with a specific ferroptosis inhibitor significantly ameliorates disease severity in lupus-prone mice reveal the role of neutrophil ferroptosis in lupus pathogenesis. Together, our data demonstrate that neutrophil ferroptosis is an important driver of neutropenia in SLE and heavily contributes to disease manifestations.
    DOI:  https://doi.org/10.1038/s41590-021-00993-3
  30. J Nutr. 2021 Aug 12. pii: nxab211. [Epub ahead of print]
    Reduced Shmt2 Expression Impairs Mitochondrial Folate Accumulation and Respiration, and Leads to Uracil Accumulation in Mouse Mitochondrial DNA.
    Joanna L Fiddler, Yuwen Xiu, Jamie E Blum, Simon G Lamarre, Whitney N Phinney, Sally P Stabler, Margaret E Brosnan, John T Brosnan, Anna E Thalacker-Mercer, Martha S Field.
       BACKGROUND: Adequate cellular thymidylate (dTMP) pools are essential for preservation of nuclear and mitochondrial genome stability. Previous studies have indicated that disruption in nuclear dTMP synthesis leads to increased uracil misincorporation into DNA, affecting genome stability. To date, the effects of impaired mitochondrial dTMP synthesis in nontransformed tissues have been understudied.
    OBJECTIVES: This study aimed to determine the effects of decreased serine hydroxymethyltransferase 2 (Shmt2) expression and dietary folate deficiency on mitochondrial DNA (mtDNA) integrity and mitochondrial function in mouse tissues.
    METHODS: Liver mtDNA content, and uracil content in liver mtDNA, were measured in Shmt2+/- and Shmt2+/+ mice weaned onto either a folate-sufficient control diet (2 mg/kg folic acid; C) or a modified diet lacking folic acid (0 mg/kg folic acid) for 7 wk. Shmt2+/- and Shmt2+/+ mouse embryonic fibroblast (MEF) cells were cultured in defined culture medium containing either 0 or 25 nM folate (6S-5-formyl-tetrahydrofolate, folinate) to assess proliferative capacity and mitochondrial function. Chi-square tests, linear mixed models, and 2-factor ANOVA with Tukey post hoc analyses were used to analyze data.
    RESULTS: Shmt2 +/- mice exhibited a 48%-67% reduction in SHMT2 protein concentrations in tissues. Interestingly, Shmt2+/- mice consuming the folate-sufficient C diet exhibited a 25% reduction in total folate in liver mitochondria. There was also a >20-fold increase in uracil in liver mtDNA in Shmt2+/- mice consuming the C diet, and dietary folate deficiency also increased uracil content in mouse liver mtDNA from both Shmt2+/+ and Shmt2+/- mice. Furthermore, decreased Shmt2 expression in MEF cells reduced cell proliferation, mitochondrial membrane potential, and oxygen consumption rate.
    CONCLUSIONS: This study demonstrates that Shmt2 heterozygosity and dietary folate deficiency impair mitochondrial dTMP synthesis in mice, as evidenced by the increased uracil in mtDNA. In addition, Shmt2 heterozygosity impairs mitochondrial function in MEF cells. These findings suggest that elevated uracil in mtDNA may impair mitochondrial function.
    Keywords:  SHMT2; folate; one-carbon metabolism; oxygen consumption rate; thymidylate; uracil
    DOI:  https://doi.org/10.1093/jn/nxab211
  31. Proc Natl Acad Sci U S A. 2021 Aug 17. pii: e2021175118. [Epub ahead of print]118(33):
    Hexokinases inhibit death receptor-dependent apoptosis on the mitochondria.
    Joachim Lauterwasser, Franziska Fimm-Todt, Aline Oelgeklaus, Annabell Schreiner, Kathrin Funk, Hugo Falquez-Medina, Ramona Klesse, Günther Jahreis, Ralf M Zerbes, Katelyn O'Neill, Martin van der Laan, Xu Luo, Frank Edlich.
      Death receptor-mediated apoptosis requires the mitochondrial apoptosis pathway in many mammalian cells. In response to death receptor signaling, the truncated BH3-only protein BID can activate the proapoptotic BCL-2 proteins BAX and BAK and trigger the permeabilization of the mitochondria. BAX and BAK are inhibited by prosurvival BCL-2 proteins through retrotranslocation from the mitochondria into the cytosol, but a specific resistance mechanism to truncated BID-dependent apoptosis is unknown. Here, we report that hexokinase 1 and hexokinase 2 inhibit the apoptosis activator truncated BID as well as the effectors BAX and BAK by retrotranslocation from the mitochondria into the cytosol. BCL-2 protein shuttling and protection from TRAIL- and FasL-induced cell death requires mitochondrial hexokinase localization and interactions with the BH3 motifs of BCL-2 proteins but not glucose phosphorylation. Together, our work establishes hexokinase-dependent retrotranslocation of truncated BID as a selective protective mechanism against death receptor-induced apoptosis on the mitochondria.
    Keywords:  BCL-2 proteins; BH3-only proteins; apoptosis
    DOI:  https://doi.org/10.1073/pnas.2021175118
  32. J Exp Biol. 2021 Aug 01. pii: jeb242968. [Epub ahead of print]224(15):
    MicroRNA-mediated inhibition of AMPK coordinates tissue-specific downregulation of skeletal muscle metabolism in hypoxic naked mole-rats.
    Hanane Hadj-Moussa, Sarah Chiasson, Hang Cheng, Liam Eaton, Kenneth B Storey, Matthew E Pamenter.
      Naked mole-rats reduce their metabolic requirements to tolerate severe hypoxia. However, the regulatory mechanisms that underpin this metabolic suppression have yet to be elucidated. 5'-AMP-activated protein kinase (AMPK) is the cellular 'master' energy effector and we hypothesized that alterations in the AMPK pathway contribute to metabolic reorganization in hypoxic naked mole-rat skeletal muscle. To test this hypothesis, we exposed naked mole-rats to 4 h of normoxia (21% O2) or severe hypoxia (3% O2), while indirectly measuring whole-animal metabolic rate and fuel preference. We then isolated skeletal muscle and assessed protein expression and post-translational modification of AMPK, and downstream changes in key glucose and fatty acid metabolic proteins mediated by AMPK, including acetyl-CoA carboxylase (ACC1), glycogen synthase (GS) and glucose transporters (GLUTs) 1 and 4. We found that in hypoxic naked mole-rats (1) metabolic rate decreased ∼80% and fuel use switched to carbohydrates, and that (2) levels of activated phosphorylated AMPK and GS, and GLUT4 expression were downregulated in skeletal muscle, while ACC1 was unchanged. To explore the regulatory mechanism underlying this hypometabolic state, we used RT-qPCR to examine 55 AMPK-associated microRNAs (miRNAs), which are short non-coding RNA post-transcriptional silencers. We identified changes in 10 miRNAs (three upregulated and seven downregulated) implicated in AMPK downregulation. Our results suggest that miRNAs and post-translational mechanisms coordinately reduce AMPK activity and downregulate metabolism in naked mole-rat skeletal muscle during severe hypoxia. This novel mechanism may support tissue-specific prioritization of energy for more essential organs in hypoxia.
    Keywords:   Heterocephalus glaber ; GLUT4; Glycogen synthase; Glycolysis; Hypometabolism; Hypoxic metabolic response; miRNA
    DOI:  https://doi.org/10.1242/jeb.242968
  33. Cell Rep. 2021 Aug 10. pii: S2211-1247(21)00929-3. [Epub ahead of print]36(6): 109501
    GDF15 mediates the metabolic effects of PPARβ/δ by activating AMPK.
    David Aguilar-Recarte, Emma Barroso, Anna Gumà, Javier Pizarro-Delgado, Lucía Peña, Maria Ruart, Xavier Palomer, Walter Wahli, Manuel Vázquez-Carrera.
      Peroxisome proliferator-activated receptor β/δ (PPARβ/δ) activates AMP-activated protein kinase (AMPK) and plays a crucial role in glucose and lipid metabolism. Here, we examine whether PPARβ/δ activation effects depend on growth differentiation factor 15 (GDF15), a stress response cytokine that regulates energy metabolism. Pharmacological PPARβ/δ activation increases GDF15 levels and ameliorates glucose intolerance, fatty acid oxidation, endoplasmic reticulum stress, and inflammation, and activates AMPK in HFD-fed mice, whereas these effects are abrogated by the injection of a GDF15 neutralizing antibody and in Gdf15-/- mice. The AMPK-p53 pathway is involved in the PPARβ/δ-mediated increase in GDF15, which in turn activates again AMPK. Consistently, Gdf15-/- mice show reduced AMPK activation in skeletal muscle, whereas GDF15 administration results in AMPK activation in this organ. Collectively, these data reveal a mechanism by which PPARβ/δ activation increases GDF15 levels via AMPK and p53, which in turn mediates the metabolic effects of PPARβ/δ by sustaining AMPK activation.
    Keywords:  AMPK; GDF15; PPARβ/δ; glucose tolerance; p53
    DOI:  https://doi.org/10.1016/j.celrep.2021.109501
  34. J Math Biol. 2021 Aug 09. 83(3): 26
    Why meals during resting time cause fat accumulation in mammals? Mathematical modeling of circadian regulation on glucose metabolism.
    Akane Hara, Akiko Satake.
      Synchronization of metabolic rhythms regulated by circadian clock and meal timing is essential for maintaining nutrient homeostasis in response to fluctuating food intake in animals. Despite numerous experimental findings on the involvement of circadian regulation of glucose and lipid metabolism, the optimal regulatory strategy for the maintenance of energy homeostasis remains poorly defined. A mathematical framework is useful to assess the circadian regulation of glycogen production/breakdown and de novo lipogenesis/lipolysis by evaluating the contribution of time of the day-dependent activation or the repression of each metabolic process in the maintenance of energy homeostasis. Here, we present a mathematical model that describes the dynamics of glycogen and triglyceride contents, two major forms of energy storage in the body that provide the fuel needed during different phases of food deprivation. By changing peak phases of glycogenesis and fat synthesis, we searched for the optimal phase set that minimizes the risks of two types of possible metabolic dysfunctions: (1) high blood glucose and (2) energy exhaustion. Based on the optimal phase set, we compared the level of fat accumulation between meal timing in the active and resting periods. Our results showed that an increased fat accumulation by food intake in the resting period can be the byproduct of minimizing energy homeostasis risks in the synchronized feeding schedule that animals adopt in nature. Our finding will be useful to schedule an optimal meal timing to prevent metabolic diseases caused by misalignment of biological and social time in modern society.
    Keywords:  Chrononutrition; Circadian rhythm; Nutrient metabolism; Obesity
    DOI:  https://doi.org/10.1007/s00285-021-01645-8
  35. Cell Rep. 2021 Aug 10. pii: S2211-1247(21)00939-6. [Epub ahead of print]36(6): 109509
    3D neuronal mitochondrial morphology in axons, dendrites, and somata of the aging mouse hippocampus.
    Julie Faitg, Clay Lacefield, Tracey Davey, Kathryn White, Ross Laws, Stylianos Kosmidis, Amy K Reeve, Eric R Kandel, Amy E Vincent, Martin Picard.
      The brain's ability to process complex information relies on the constant supply of energy through aerobic respiration by mitochondria. Neurons contain three anatomically distinct compartments-the soma, dendrites, and projecting axons-which have different energetic and biochemical requirements, as well as different mitochondrial morphologies in cultured systems. In this study, we apply quantitative three-dimensional electron microscopy to map mitochondrial network morphology and complexity in the mouse brain. We examine somatic, dendritic, and axonal mitochondria in the dentate gyrus and cornu ammonis 1 (CA1) of the mouse hippocampus, two subregions with distinct principal cell types and functions. We also establish compartment-specific differences in mitochondrial morphology across these cell types between young and old mice, highlighting differences in age-related morphological recalibrations. Overall, these data define the nature of the neuronal mitochondrial network in the mouse hippocampus, providing a foundation to examine the role of mitochondrial morpho-function in the aging brain.
    Keywords:  3D reconstruction; SBF-SEM; aging; hippocampus; microscopy; mitochondria; morphology; morphometry; three-dimensional; topology
    DOI:  https://doi.org/10.1016/j.celrep.2021.109509
  36. Mol Cell. 2021 Aug 03. pii: S1097-2765(21)00586-4. [Epub ahead of print]
    A composite DNA element that functions as a maintainer required for epigenetic inheritance of heterochromatin.
    Xiaoyi Wang, Joao A Paulo, Xue Li, Haining Zhou, Juntao Yu, Steven P Gygi, Danesh Moazed.
      Epigenetic inheritance of heterochromatin requires DNA-sequence-independent propagation mechanisms, coupling to RNAi, or input from DNA sequence, but how DNA contributes to inheritance is not understood. Here, we identify a DNA element (termed "maintainer") that is sufficient for epigenetic inheritance of pre-existing histone H3 lysine 9 methylation (H3K9me) and heterochromatin in Schizosaccharomyces pombe but cannot establish de novo gene silencing in wild-type cells. This maintainer is a composite DNA element with binding sites for the Atf1/Pcr1 and Deb1 transcription factors and the origin recognition complex (ORC), located within a 130-bp region, and can be converted to a silencer in cells with lower rates of H3K9me turnover, suggesting that it participates in recruiting the H3K9 methyltransferase Clr4/Suv39h. These results suggest that, in the absence of RNAi, histone H3K9me is only heritable when it can collaborate with maintainer-associated DNA-binding proteins that help recruit the enzyme responsible for its epigenetic deposition.
    Keywords:  Atf1; Clr4; Deb1; H3K9me; ORC; Pcr1; Suv39h; epigenetic inheritance; heterochromatin; maintainer
    DOI:  https://doi.org/10.1016/j.molcel.2021.07.017
  37. Autophagy. 2021 Aug 12. 1-2
    A DRP-1 dependent autophagy process facilitates rebuilding of the mitochondrial network and modulates adaptation capacity in response to acute heat stress during C. elegans development.
    Yanfang Chen, Emmanuel Culetto, Renaud Legouis.
      Temperature variations induce stressful conditions that challenge the ability of organisms to maintain cell homeostasis. The intensity and duration of heat stress affect cell response very differently, ranging from a beneficial effect - hormesis - to necrotic cell death. There is a strong interplay between the cell response to heat shock and macroautophagy/autophagy, which is induced to cope with stress. Using Caenorhabditis elegans, we developed a new paradigm to study adaptation to acute non-lethal heat-stress (aHS) during development. We found that aHS results in transient fragmentation of mitochondria, decreased cellular respiration, and delayed development. Moreover, an active autophagy flux associated with mitophagy events is triggered in many tissues, enables the rebuilding of the mitochondrial network and modulates the adaptive plasticity of the development, showing that the autophagic response is protective for C. elegans. Using genetic and cellular approaches, we showed that mitochondria are a major site for autophagosome biogenesis in the epidermis, under both standard and heat-stress conditions. We determined that DRP-1 (Dynamin-Related Protein 1) involved in mitochondrial fission, is an important player for the autophagy process and the adaptation to aHS. Our study suggests that DRP-1 is involved in coordinating mitochondrial fission and autophagosome biogenesis during stress.
    Keywords:  Autophagy; C. elegans; DRP-1; development plasticity; heat shock; mitochondria
    DOI:  https://doi.org/10.1080/15548627.2021.1953821
  38. Cell Cycle. 2021 Aug 12. 1-16
    NAD+ metabolism controls growth inhibition by HIF1 in normoxia and determines differential sensitivity of normal and cancer cells.
    Michal W Luczak, Casey Krawic, Anatoly Zhitkovich.
      The hypoxia-induced transcription factor HIF1 inhibits cell growth in normoxia through poorly understood mechanisms. A constitutive upregulation of hypoxia response is associated with increased malignancy, indicating a loss of antiproliferative effects of HIF1 in cancer cells. To understand these differences, we examined a control of cell cycle in primary human cells with activated hypoxia response in normoxia. Activated HIF1 caused a global slowdown of cell cycle progression through G1, S and G2 phases leading to the loss of mitotic cells. Cell cycle inhibition required a prolonged HIF1 activation and was not associated with upregulation of p53 or the CDK inhibitors p16, p21 or p27. Growth inhibition by HIF1 was independent of its Asn803 hydroxylation or the presence of HIF2. Antiproliferative effects of hypoxia response were alleviated by inhibition of lactate dehydrogenase and more effectively, by boosting cellular production of NAD+, which was decreased by HIF1 activation. In comparison to normal cells, various cancer lines showed several fold-higher expression of NAMPT which is a rate-limiting enzyme in the main biosynthetic pathway for NAD+. Inhibition of NAMPT activity in overexpressor cancer cells sensitized them to antigrowth effects of HIF1. Thus, metabolic changes in cancer cells, such as enhanced NAD+ production, create resistance to growth-inhibitory activity of HIF1 permitting manifestation of its tumor-promoting properties.AbbreviationsDMOG: dimethyloxalylglycine, DM-NOFD: dimethyl N-oxalyl-D-phenylalanine, NMN: β-nicotinamide mononucleotide.
    Keywords:  HIF1A; NAD+; NAMPT; cell cycle; hypoxia
    DOI:  https://doi.org/10.1080/15384101.2021.1959988
  39. Immunity. 2021 Aug 10. pii: S1074-7613(21)00295-8. [Epub ahead of print]54(8): 1807-1824.e14
    Mutations in the transcription factor FOXO1 mimic positive selection signals to promote germinal center B cell expansion and lymphomagenesis.
    Mark P Roberto, Gabriele Varano, Rosa Vinas-Castells, Antony B Holmes, Rahul Kumar, Laura Pasqualucci, Pedro Farinha, David W Scott, David Dominguez-Sola.
      The transcription factor forkhead box O1 (FOXO1), which instructs the dark zone program to direct germinal center (GC) polarity, is typically inactivated by phosphatidylinositol 3-kinase (PI3K) signals. Here, we investigated how FOXO1 mutations targeting this regulatory axis in GC-derived B cell non-Hodgkin lymphomas (B-NHLs) contribute to lymphomagenesis. Examination of primary B-NHL tissues revealed that FOXO1 mutations and PI3K pathway activity were not directly correlated. Human B cell lines bearing FOXO1 mutations exhibited hyperactivation of PI3K and Stress-activated protein kinase (SAPK)/Jun amino-terminal kinase (JNK) signaling, and increased cell survival under stress conditions as a result of alterations in FOXO1 transcriptional affinities and activation of transcriptional programs characteristic of GC-positive selection. When modeled in mice, FOXO1 mutations conferred competitive advantage to B cells in response to key T-dependent immune signals, disrupting GC homeostasis. FOXO1 mutant transcriptional signatures were prevalent in human B-NHL and predicted poor clinical outcomes. Thus, rather than enforcing FOXO1 constitutive activity, FOXO1 mutations enable co-option of GC-positive selection programs during the pathogenesis of GC-derived lymphomas.
    Keywords:  B cell; CD40; FOXO1; JNK; PI3K; germinal center; mouse model; mutation; non-Hodgkin lymphoma; positive selection
    DOI:  https://doi.org/10.1016/j.immuni.2021.07.009
  40. Elife. 2021 Aug 12. pii: e62592. [Epub ahead of print]10
    A feedback loop between the androgen receptor and 6-phosphogluoconate dehydrogenase (6PGD) drives prostate cancer growth.
    Joanna L Gillis, Josephine A Hinneh, Natalie K Ryan, Swati Irani, Max Moldovan, Lake-Ee Quek, Raj K Shrestha, Adrienne R Hanson, Jianling Xie, Andrew J Hoy, Jeff Holst, Margaret M Centenera, Ian G Mills, David J Lynn, Luke A Selth, Lisa M Butler.
      Alterations to the androgen receptor (AR) signalling axis and cellular metabolism are hallmarks of prostate cancer. This study provides insight into both hallmarks by uncovering a novel link between AR and the pentose phosphate pathway (PPP). Specifically, we identify 6-phosphogluoconate dehydrogenase (6PGD) as an androgen-regulated gene that is upregulated in prostate cancer. AR increased the expression of 6PGD indirectly via activation of sterol regulatory element binding protein 1 (SREBP1). Accordingly, loss of 6PGD, AR or SREBP1 resulted in suppression of PPP activity, as revealed by 1,2-13C2 glucose metabolic flux analysis. Knockdown of 6PGD also impaired growth and elicited death of prostate cancer cells, at least in part due to increased oxidative stress. We investigated the therapeutic potential of targeting 6PGD using two specific inhibitors, physcion and S3, and observed substantial anti-cancer activity in multiple models of prostate cancer, including aggressive, therapy-resistant models of castration-resistant disease as well as prospectively-collected patient-derived tumour explants. Targeting of 6PGD was associated with two important tumour-suppressive mechanisms: first, increased activity of the AMP-activated protein kinase (AMPK), which repressed anabolic growth-promoting pathways regulated by ACC1 and mTOR; and second, enhanced AR ubiquitylation, associated with a reduction in AR protein levels and activity. Supporting the biological relevance of positive feedback between AR and PGD, pharmacological co-targeting of both factors was more effective in suppressing the growth of prostate cancer cells than single agent therapies. Collectively, this work provides new insight into the dysregulated metabolism of prostate cancer and provides impetus for further investigation of co-targeting AR and the PPP as a novel therapeutic strategy.
    Keywords:  cancer biology; human
    DOI:  https://doi.org/10.7554/eLife.62592
  41. Trends Cell Biol. 2021 Aug 06. pii: S0962-8924(21)00142-2. [Epub ahead of print]
    Putative homeostatic role of cancer driver mutations.
    Avanthika Venkatachalam, Eli Pikarsky, Yinon Ben-Neriah.
      Somatic mutations have traditionally been associated with cancer, yet more recently, it was realized that they also appear in nontransformed cells beginning in early life. Remarkably, some of these mutations, commonly viewed as cancer driver mutations, are widely spread among cells of noncancerous tissues, sometimes affecting the majority of the tissue cells. This spreading process intensifies upon aging or exposure to extrinsic insults, such as UV irradiation, inhaling smoke, and inflammatory cues. Whereas classic driver mutations in normal cells are mostly viewed as a first step in the carcinogenesis process, here, we speculate that in certain states, they can play beneficial homeostatic roles while confronting stress and aging tissue repair.
    Keywords:  Tp53 hotspot mutations; beneficial mutations; clonal expansion; clonal fitness; clonal hematopoiesis
    DOI:  https://doi.org/10.1016/j.tcb.2021.07.002
  42. Prog Biophys Mol Biol. 2021 Aug 05. pii: S0079-6107(21)00096-1. [Epub ahead of print]
    The somatic molecular evolution of cancer: Mutation, selection, and epistasis.
    Krishna Dasari, Jason A Somarelli, Sudhir Kumar, Jeffrey P Townsend.
      Cancer progression has been attributed to somatic changes in single-nucleotide variants, copy-number aberrations, loss of heterozygosity, chromosomal instability, epistatic interactions, and the tumor microenvironment. It is not entirely clear which of these changes are essential and which are ancillary to cancer. The dynamic nature of cancer evolution in a patient can be illuminated using several concepts and tools from classical evolutionary biology. Neutral mutation rates in cancer cells are calculable from genomic data such as synonymous mutations, and selective pressures are calculable from rates of fixation occurring beyond the expectation by neutral mutation and drift. However, these cancer effect sizes of mutations are complicated by epistatic interactions that can determine the likely sequence of gene mutations. In turn, longitudinal phylogenetic analyses of somatic cancer progression offer an opportunity to identify key moments in cancer evolution, relating the timing of driver mutations to corresponding landmarks in the clinical timeline. These analyses reveal temporal aspects of genetic and phenotypic change during tumorigenesis and across clinical timescales. Using a related framework, clonal deconvolution, physical locations of clones, and their phylogenetic relations can be used to infer tumor migration histories. Additionally, genetic interactions with the tumor microenvironment can be analyzed with longstanding approaches applied to organismal genotype-by-environment interactions. Fitness landscapes for cancer evolution relating to genotype, phenotype, and environment could enable more accurate, personalized therapeutic strategies. An understanding of the trajectories underlying the evolution of neoplasms, primary, and metastatic tumors promises fundamental advances toward accurate and personalized predictions of therapeutic response.
    Keywords:  Cancer; Epistasis; Fitness landscapes; Metastasis; Molecular evolution; Tumor microenvironment
    DOI:  https://doi.org/10.1016/j.pbiomolbio.2021.08.003
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