bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2020‒08‒16
fifty-nine papers selected by
Christian Frezza
University of Cambridge, MRC Cancer Unit


  1. J Cell Sci. 2020 Aug 11. pii: jcs.248880. [Epub ahead of print]
    Zhou W, Hsu AY, Wang Y, Syahirah R, Wang T, Jeffries J, Wang X, Mohammad H, Seleem MN, Umulis D, Deng Q.
      Neutrophils rely on glycolysis for energy production. How mitochondria regulate neutrophil function is not fully understood. Here, we report that mitochondrial outer membrane protein Mitofusin 2 (Mfn2) regulates neutrophil homeostasis and chemotaxis in vivo. Mfn2-deficient neutrophils are released from the hematopoietic tissue, trapped in the vasculature in zebrafish embryos, and not capable of chemotaxis. Consistently, human neutrophil-like cells deficient with MFN2 fail to arrest on activated endothelium under sheer stress or perform chemotaxis on 2D surfaces. Deletion of Mfn2 results in a significant reduction of neutrophil infiltration to the inflamed peritoneal cavity in mice. Mechanistically, MFN2-deficient neutrophil-like cells display disrupted mitochondria-ER interaction, heightened intracellular calcium levels, and elevated Rac activation after chemokine stimulation. Restoring mitochondria-ER tether rescues the abnormal calcium levels, Rac hyperactivation, and chemotaxis defect resulted from MFN2 depletion. Finally, inhibition of Rac activation restores chemotaxis in MFN2-deficient neutrophils. Altogether, we identified that MFN2 regulates neutrophil migration via maintaining mitochondria-ER interaction to suppress Rac activation and uncovered a previously unrecognized role of MFN2 in regulating cell migration and the actin cytoskeleton.
    Keywords:  Actin; Chemotaxis; Leukocyte; Mitochondria; Rac; Zebrafish
    DOI:  https://doi.org/10.1242/jcs.248880
  2. Gastroenterology. 2020 Aug 03. pii: S0016-5085(20)35009-5. [Epub ahead of print]
    Tiwari A, Tashiro K, Dixit A, Soni A, Vogel K, Hall B, Shafqat I, Slaughter J, Param N, Le A, Saunders E, Paithane U, Garcia G, Campos AR, Zettervall J, Carlson M, Starr TK, Marahrens Y, Deshpande AJ, Commisso C, Provenzano PP, Bagchi A.
      BACKGROUND & AIMS: Pancreatic ductal adenocarcinomas (PDACs) are hypovascular, resulting in the upregulation of hypoxia inducible factor 1 alpha (HIF1A), which promotes survival of cells under low-oxygen conditions. We studied the roles of HIF1A in development of pancreatic tumors in mice.METHODS: We performed studies with KrasLSL-G12D/+;Trp53LSL-R172H/+; Pdx1-Cre (KPC) mice, KPC mice with labeled pancreatic epithelial cells (EKPC), and EKPC mice with pancreas-specific depletion of HIF1A. Pancreatic and other tissues were collected and analyzed by histology, and immunohistochemistry. Cancer cells were cultured from PDACs from mice and analyzed in cell migration and invasion assays and by immunoblots, real-time PCR, and liquid chromatography-mass spectrometry. We performed studies with the human pancreatic cancer cell lines PATU-8988T, BxPC-3, PANC-1 and MiaPACA-2, which have no or low metastatic activity, and PATU-8988S, AsPC-1, SUIT-2 and Capan-1, which have high-metastatic activity. Expression of genes was knocked down in primary cancer cells and pancreatic cancer cell lines using small hairpin RNAs; cells were injected intravenously into immune-competent and NOD/SCID mice and lung metastases were quantified. We compared levels of mRNAs in pancreatic tumors and normal pancreas in the Cancer Genome Atlas.
    RESULTS: EKPC mice with pancreas-specific deletion of HIF1A developed more advanced pancreatic neoplasias and PDACs with more invasion and metastasis, and had significantly shorter survival times, than EKPC mice. Pancreatic cancer cells from these tumors had higher invasive and metastatic activity in culture than cells from tumors of EKPC mice. HIF1A-knockout pancreatic cancer cells had increased expression of protein phosphatase 1 regulatory inhibitor subunit 1B (PPP1R1B). There was an inverse correlation between levels of HIF1A and PPP1R1B in human PDAC tumors; higher expression of PPP1R1B correlated with shorter survival times of patients. Metastatic human pancreatic cancer cell lines had increased levels of PPP1R1B and lower levels of HIF1A compared with non-metastatic cancer cell lines; knockdown of PPP1R1B significantly reduced the ability of pancreatic cancer cells to form lung metastases in mice. PPP1R1B promoted degradation of p53 by stabilizing phosphorylation of MDM2 at Ser166.
    CONCLUSIONS: HIF1A can act a tumor suppressor by preventing expression of PPP1R1B and subsequent degradation of the p53 protein in pancreatic cancer cells. Loss of HIF1A from pancreatic cancer cells increases their invasive and metastatic activity.
    Keywords:  Carcinogenesis; Cell Motility; Signal Transduction; Tumor Progression
    DOI:  https://doi.org/10.1053/j.gastro.2020.07.046
  3. Cancer Metab. 2020 ;8 7
    Panarsky R, Crooks DR, Lane AN, Yang Y, Cassel TA, Fan TW, Linehan WM, Moscow JA.
      Background: The loss-of-function mutation of fumarate hydratase (FH) is a driver of hereditary leiomyomatosis and renal cell carcinoma (HLRCC). Fumarate accumulation results in activation of stress-related mechanisms leading to upregulation of cell survival-related genes. To better understand how cells compensate for the loss of FH in HLRCC, we determined the amino acid nutrient requirements of the FH-deficient UOK262 cell line (UOK262) and its FH-repleted control (UOK262WT).Methods: We determined growth rates and survival of cell lines in response to amino acid depletion and supplementation. RNAseq was used to determine the transcription changes contingent on Asn and Gln supplementation, which was further followed with stable isotope resolved metabolomics (SIRM) using both [U- 13C,15N] Gln and Asn.
    Results: We found that Asn increased the growth rate of both cell lines in vitro. Gln, but not Asn, increased oxygen consumption rates and glycolytic reserve of both cell lines. Although Asn was taken up by the cells, there was little evidence of Asn-derived label in cellular metabolites, indicating that Asn was not catabolized. However, Asn strongly stimulated Gln labeling of uracil and precursors, uridine phosphates and hexosamine metabolites in the UOK262 cells and to a much lesser extent in the UOK262WT cells, indicating an activation of the hexosamine biosynthetic pathway (HBP) by Asn. Asn in combination with Gln, but not Asn or Gln alone, stimulated expression of genes associated with the endoplasmic reticulum (ER) stress and the unfolded protein response (UPR) in UOK262 to a greater extent than in FH-restored cells. The changes in expression of these genes were confirmed by RT-PCR, and the stimulation of the UPR was confirmed orthogonally by demonstration of an increase in spliced XBP1 (sXBP1) in UOK262 cells under these conditions. Asn exposure also increased both the RNA and protein expression of the HBP regulator GFPT2, which is a transcriptional target of sXBP1.
    Conclusions: Asn in the presence of Gln induces an ER stress response in FH-deficient UOK262 cells and stimulates increased synthesis of UDP-acetyl glycans indicative of HBP activity. These data demonstrate a novel effect of asparagine on cellular metabolism in FH-deficient cells that could be exploited therapeutically.
    Keywords:  Asparagine metabolism; Fumarate hydratase; Renal cell carcinoma; Unfolded protein response, SIRM
    DOI:  https://doi.org/10.1186/s40170-020-00214-9
  4. Cell Calcium. 2020 Jul 28. pii: S0143-4160(20)30099-3. [Epub ahead of print]91 102257
    Foskett JK.
      New cryo-electron microscopy structures of the mitochondrial Ca2+ uniporter ion channel complex in various conformations reveal channel gating regulation by Ca2+-dependent unblock of the channel pore by MICU1.
    Keywords:  Cryo-EM; EMRE; Ion channel; MCU; MICU1; Mitochondria; Structure
    DOI:  https://doi.org/10.1016/j.ceca.2020.102257
  5. Curr Opin Chem Biol. 2020 Aug 07. pii: S1367-5931(20)30095-8. [Epub ahead of print]57 122-134
    Liu S, Cadoux-Hudson T, Schofield CJ.
      Abnormal metabolism is common in cancer cells and often correlates with mutations in genes encoding for enzymes involved in small-molecule metabolism. Isocitrate dehydrogenase 1 (IDH1) is the most frequently mutated metabolic gene in cancer. Cancer-associated substitutions in IDH1 and IDH2 impair wild-type production of 2-oxoglutarate and reduced nicotinamide adenine dinucleotide phosphate (NADPH) from isocitrate and oxidised nicotinamide adenine dinucleotide phosphate (NADP+ ), and substantially promote the IDH variant catalysed conversion of 2-oxoglutarate to d-2-hydroxyglutarate (d-2HG). Elevated d-2HG is a biomarker for some cancers, and inhibition of IDH1 and IDH2 variants is being pursued as a medicinal chemistry target. We provide an overview of the types of cancer-associated IDH variants, discuss some of the proposed consequences of altered metabolism as a result of elevated d-2HG, summarise therapeutic efforts targeting IDH variants and identify areas for future research.
    Keywords:  2-Hydroxyglutarate; 2-oxoglutarate; Acute myeloid leukaemia; Alpha-ketoglutarate; Cancer metabolism; Epigenetics; Glioma; Hypoxia-inducible factor; Isocitrate dehydrogenase; JmjC demethylase
    DOI:  https://doi.org/10.1016/j.cbpa.2020.06.012
  6. Physiology (Bethesda). 2020 Sep 01. 35(5): 302-327
    Kunji ERS, King MS, Ruprecht JJ, Thangaratnarajah C.
      Members of the mitochondrial carrier family (SLC25) transport a variety of compounds across the inner membrane of mitochondria. These transport steps provide building blocks for the cell and link the pathways of the mitochondrial matrix and cytosol. An increasing number of diseases and pathologies has been associated with their dysfunction. In this review, the molecular basis of these diseases is explained based on our current understanding of their transport mechanism.
    Keywords:  bioenergetics; impaired transport mechanism; mitochondrial disease; mitochondrial physiology; pathological mutations
    DOI:  https://doi.org/10.1152/physiol.00009.2020
  7. Life Sci Alliance. 2020 Oct;pii: e202000718. [Epub ahead of print]3(10):
    MacEwen MJ, Markhard AL, Bozbeyoglu M, Bradford F, Goldberger O, Mootha VK, Sancak Y.
      The mitochondrial calcium uniporter (MCU) is a calcium-activated calcium channel critical for signaling and bioenergetics. MCU, the pore-forming subunit of the uniporter, contains two transmembrane domains and is found in all major eukaryotic taxa. In amoeba and fungi, MCU homologs are sufficient to form a functional calcium channel, whereas human MCU exhibits a strict requirement for the metazoan protein essential MCU regulator (EMRE) for conductance. Here, we exploit this evolutionary divergence to decipher the molecular basis of human MCU's dependence on EMRE. By systematically generating chimeric proteins that consist of EMRE-independent Dictyostelium discoideum MCU and Homo sapiens MCU (HsMCU), we converged on a stretch of 10 amino acids in D. discoideum MCU that can be transplanted to HsMCU to render it EMRE independent. We call this region in human MCU the EMRE dependence domain (EDD). Crosslinking experiments show that EMRE directly interacts with HsMCU at its transmembrane domains as well as the EDD. Our results suggest that EMRE stabilizes the EDD of MCU, permitting both channel opening and calcium conductance, consistent with recently published structures of MCU-EMRE.
    DOI:  https://doi.org/10.26508/lsa.202000718
  8. Curr Opin Immunol. 2020 Aug 08. pii: S0952-7915(20)30071-6. [Epub ahead of print]67 10-17
    Galgani M, Bruzzaniti S, Matarese G.
      Over the last few years, immune cell metabolism has become one of the most stimulating areas of investigation in the field of immunology. Compelling evidence has revealed that metabolic pathways are closely associated to cell functions and immune cells adopt defined metabolic programs to sustain their activity and respond to micro-environmental demands. It is now clear that alterations in cell metabolism can favour dysregulation typical of autoreactive immune cells, thus sustaining loss of immunological self-tolerance. In this short review, we highlight the main metabolic alterations associated with both innate and adaptive immune cells in autoimmune conditions, such as multiple sclerosis (MS) and type 1 diabetes (T1D). We also summarize recent findings reporting the use of pharmacological agents, which modulate the immunometabolism to possibly control immune responses during autoimmune disorders.
    DOI:  https://doi.org/10.1016/j.coi.2020.07.002
  9. Cell Metab. 2020 Aug 10. pii: S1550-4131(20)30371-5. [Epub ahead of print]
    Hui S, Cowan AJ, Zeng X, Yang L, TeSlaa T, Li X, Bartman C, Zhang Z, Jang C, Wang L, Lu W, Rojas J, Baur J, Rabinowitz JD.
      Mammalian organs are nourished by nutrients carried by the blood circulation. These nutrients originate from diet and internal stores, and can undergo various interconversions before their eventual use as tissue fuel. Here we develop isotope tracing, mass spectrometry, and mathematical analysis methods to determine the direct sources of circulating nutrients, their interconversion rates, and eventual tissue-specific contributions to TCA cycle metabolism. Experiments with fifteen nutrient tracers enabled extensive accounting for both circulatory metabolic cycles and tissue TCA inputs, across fed and fasted mice on either high-carbohydrate or ketogenic diet. We find that a majority of circulating carbon flux is carried by two major cycles: glucose-lactate and triglyceride-glycerol-fatty acid. Futile cycling through these pathways is prominent when dietary content of the associated nutrients is low, rendering internal metabolic activity robust to food choice. The presented in vivo flux quantification methods are broadly applicable to different physiological and disease states.
    Keywords:  TCA cycle; circulating metabolites; energy metabolism; in vivo flux quantification; isotope tracing; ketogenic diet; metabolic cycling
    DOI:  https://doi.org/10.1016/j.cmet.2020.07.013
  10. EMBO Rep. 2020 Aug 11. e48260
    Xu R, Jones W, Wilcz-Villega E, Costa AS, Rajeeve V, Bentham RB, Bryson K, Nagano A, Yaman B, Olendo Barasa S, Wang Y, Chelala C, Cutillas P, Szabadkai G, Frezza C, Bianchi K.
      IκB kinase ε (IKKε) is a key molecule at the crossroads of inflammation and cancer. Known to regulate cytokine secretion via NFκB and IRF3, the kinase is also a breast cancer oncogene, overexpressed in a variety of tumours. However, to what extent IKKε remodels cellular metabolism is currently unknown. Here, we used metabolic tracer analysis to show that IKKε orchestrates a complex metabolic reprogramming that affects mitochondrial metabolism and consequently serine biosynthesis independently of its canonical signalling role. We found that IKKε upregulates the serine biosynthesis pathway (SBP) indirectly, by limiting glucose-derived pyruvate utilisation in the TCA cycle, inhibiting oxidative phosphorylation. Inhibition of mitochondrial function induces activating transcription factor 4 (ATF4), which in turn drives upregulation of the expression of SBP genes. Importantly, pharmacological reversal of the IKKε-induced metabolic phenotype reduces proliferation of breast cancer cells. Finally, we show that in a highly proliferative set of ER negative, basal breast tumours, IKKε and PSAT1 are both overexpressed, corroborating the link between IKKε and the SBP in the clinical context.
    Keywords:  ATF4; IKKε; breast cancer; mitochondrial metabolism; serine biosynthesis
    DOI:  https://doi.org/10.15252/embr.201948260
  11. EMBO J. 2020 Aug 13. e104285
    Wu W, Shen Q, Zhang R, Qiu Z, Wang Y, Zheng J, Jia Z.
      The MICU1-MICU2 heterodimer regulates the mitochondrial calcium uniporter (MCU) and mitochondrial calcium uptake. Herein, we present two crystal structures of the MICU1-MICU2 heterodimer, in which Ca2+ -free and Ca2+ -bound EF-hands are observed in both proteins, revealing both electrostatic and hydrophobic interfaces. Furthermore, we show that MICU1 interacts with EMRE, another regulator of MCU, through a Ca2+ -dependent alkaline groove. Ca2+ binding strengthens the MICU1-EMRE interaction, which in turn facilitates Ca2+ uptake. Conversely, the MICU1-MCU interaction is favored in the absence of Ca2+ , thus inhibiting the channel activity. This Ca2+ -dependent switch illuminates how calcium signals are transmitted from regulatory subunits to the calcium channel and the transition between gatekeeping and activation channel functions. Furthermore, competition with an EMRE peptide alters the uniporter threshold in resting conditions and elevates Ca2+ accumulation in stimulated mitochondria, confirming the gatekeeper role of the MICU1-MICU2 heterodimer. Taken together, these structural and functional data provide new insights into the regulation of mitochondrial calcium uptake.
    Keywords:   EMRE ; MICU1-MICU2; mitochondria; uniporter
    DOI:  https://doi.org/10.15252/embj.2019104285
  12. JCI Insight. 2020 Aug 11. pii: 133225. [Epub ahead of print]
    Sharma G, Ojha R, Noguera-Ortega E, Rebecca VW, Attanasio J, Liu S, Piao S, Lee JJ, Nicastri MC, Harper SL, Ronghe A, Jain V, Winkler JD, Speicher DW, Mastio J, Gimotty PA, Xu X, Wherry EJ, Gabrilovich DI, Amaravadi RK.
      New strategies are needed to enhance the efficacy of anti-programmed cell death protein (PD-1) antibody (Ab) in cancer. Here, we report that inhibiting palmitoyl-protein thioesterase 1 (PPT1), a target of CQ derivatives like hydroxychloroquine (HCQ), enhances the antitumor efficacy of anti-PD-1 Ab in melanoma. The combination resulted tumor growth impairment and improved survival in mouse models. Genetic suppression of core autophagy genes, but not Ppt1, in cancer cells reduced priming and cytotoxic capacity of primed T cells. Exposure of antigen primed T cells to macrophage conditioned medium derived from macrophages treated with PPT1 inhibitors enhanced melanoma specific killing. Genetic or chemical PPT1 inhibition resulted an M2 to M1 phenotype switching in macrophages. The combination was associated with a reduction in myeloid-derived suppressor cells (MDSCs) in the tumor. Ppt1 inhibition by HCQ, or DC661, induced cyclic GMP-AMP synthase (cGAS), stimulator of interferon genes (STING), tank-binding kinase 1 (TBK1) pathway activation and the secretion of interferon β (IFN-β) in macrophages which was a key component for augmented T cell-mediated cytotoxicity. Genetic Ppt1 inhibition produced similar findings. These data provide the rationale for a melanoma clinical trial testing this new immunotherapy combination and may also be effective in other cancers.
    Keywords:  Autophagy; Lysosomes; Melanoma; Oncology; Therapeutics
    DOI:  https://doi.org/10.1172/jci.insight.133225
  13. Mol Genet Metab. 2020 Jul 30. pii: S1096-7192(20)30179-7. [Epub ahead of print]
    Leandro J, Houten SM.
      Lysine degradation via formation of saccharopine is a pathway confined to the mitochondria. The second pathway for lysine degradation, the pipecolic acid pathway, is not yet fully elucidated and known enzymes are localized in the mitochondria, cytosol and peroxisome. The tissue-specific roles of these two pathways are still under investigation. The lysine degradation pathway is clinically relevant due to the occurrence of two severe neurometabolic disorders, pyridoxine-dependent epilepsy (PDE) and glutaric aciduria type 1 (GA1). The existence of three other disorders affecting lysine degradation without apparent clinical consequences opens up the possibility to find alternative therapeutic strategies for PDE and GA1 through pathway modulation. A better understanding of the mechanisms, compartmentalization and interplay between the different enzymes and metabolites involved in lysine degradation is of utmost importance.
    Keywords:  Inborn errors; Lysine degradation; Mitochondria; Pipecolic acid pathway; Saccharopine pathway; Substrate reduction therapy
    DOI:  https://doi.org/10.1016/j.ymgme.2020.07.010
  14. Cell Rep. 2020 Aug 11. pii: S2211-1247(20)31009-3. [Epub ahead of print]32(6): 108024
    Martínez-Montañés F, Casanovas A, Sprenger RR, Topolska M, Marshall DL, Moreno-Torres M, Poad BLJ, Blanksby SJ, Hermansson M, Jensen ON, Ejsing CS.
      The ability to remodel lipid metabolism under changing conditions is pivotal for cellular functionality and homeostasis. Here, we characterize the regulatory landscape of phosphorylation-based signaling events across the life cycle of Saccharomyces cerevisiae and determine its impact on the regulation of lipid metabolism. Our data show that 50 lipid metabolic proteins are differentially phosphorylated as cells transit between different physiological states. To identify functional phosphosites, we devised a strategy where multiple phosphosites are simultaneously mutated into phosphomimetic or phosphodeficient alleles and mutants are phenotyped by in-depth lipidomics flux analysis. This uncovers functional phosphosites in the phosphatidate cytidylyltransferase Cds1, the phosphatidylserine synthase Cho1, and Fas2, the α-subunit of the fatty acid synthase (FAS) complex. Furthermore, we show that the fatty acyl chain length produced by FAS is governed by phosphorylation. Overall, our work demonstrates a vital role for phosphoregulation of lipid metabolism and provides a resource to investigate its molecular underpinnings.
    Keywords:  FAS; Saccharomyces cerevisiae; fatty acid synthase; fatty acyl chain-length control; flux analysis; lipid metabolism; lipidomics; phosphoproteomics; signaling pathways
    DOI:  https://doi.org/10.1016/j.celrep.2020.108024
  15. Proc Natl Acad Sci U S A. 2020 Aug 11. pii: 202009364. [Epub ahead of print]
    Pape JK, Stephan T, Balzarotti F, Büchner R, Lange F, Riedel D, Jakobs S, Hell SW.
      The mitochondrial contact site and cristae organizing system (MICOS) is a multisubunit protein complex that is essential for the proper architecture of the mitochondrial inner membrane. MICOS plays a key role in establishing and maintaining crista junctions, tubular or slit-like structures that connect the cristae membrane with the inner boundary membrane, thereby ensuring a contiguous inner membrane. MICOS is enriched at crista junctions, but the detailed distribution of its subunits around crista junctions is unclear because such small length scales are inaccessible with established fluorescence microscopy. By targeting individually activated fluorophores with an excitation beam featuring a central zero-intensity point, the nanoscopy method called MINFLUX delivers single-digit nanometer-scale three-dimensional (3D) resolution and localization precision. We employed MINFLUX nanoscopy to investigate the submitochondrial localization of the core MICOS subunit Mic60 in relation to two other MICOS proteins, Mic10 and Mic19. We demonstrate that dual-color 3D MINFLUX nanoscopy is applicable to the imaging of organellar substructures, yielding a 3D localization precision of ∼5 nm in human mitochondria. This isotropic precision facilitated the development of an analysis framework that assigns localization clouds to individual molecules, thus eliminating a source of bias when drawing quantitative conclusions from single-molecule localization microscopy data. MINFLUX recordings of Mic60 indicate ringlike arrangements of multiple molecules with a diameter of 40 to 50 nm, suggesting that Mic60 surrounds individual crista junctions. Statistical analysis of dual-color MINFLUX images demonstrates that Mic19 is generally in close proximity to Mic60, whereas the spatial coordination of Mic10 with Mic60 is less regular, suggesting structural heterogeneity of MICOS.
    Keywords:  MICOS; MINFLUX; cluster analysis; mitochondria; superresolution microscopy
    DOI:  https://doi.org/10.1073/pnas.2009364117
  16. Nat Cancer. 2020 Mar;1(3): 315-328
    Amgalan D, Garner TP, Pekson R, Jia XF, Yanamandala M, Paulino V, Liang FG, Corbalan JJ, Lee J, Chen Y, Karagiannis GS, Sanchez LR, Liang H, Narayanagari SR, Mitchell K, Lopez A, Margulets V, Scarlata M, Santulli G, Asnani A, Peterson RT, Hazan RB, Condeelis JS, Oktay MH, Steidl U, Kirshenbaum LA, Gavathiotis E, Kitsis RN.
      Doxorubicin remains an essential component of many cancer regimens, but its use is limited by lethal cardiomyopathy, which has been difficult to target, owing to pleiotropic mechanisms leading to apoptotic and necrotic cardiac cell death. Here we show that BAX is rate-limiting in doxorubicin-induced cardiomyopathy and identify a small-molecule BAX inhibitor that blocks both apoptosis and necrosis to prevent this syndrome. By allosterically inhibiting BAX conformational activation, this compound blocks BAX translocation to mitochondria, thereby abrogating both forms of cell death. When co-administered with doxorubicin, this BAX inhibitor prevents cardiomyopathy in zebrafish and mice. Notably, cardioprotection does not compromise the efficacy of doxorubicin in reducing leukemia or breast cancer burden in vivo, primarily due to increased priming of mitochondrial death mechanisms and higher BAX levels in cancer cells. This study identifies BAX as an actionable target for doxorubicin-induced cardiomyopathy and provides a prototype small-molecule therapeutic.
    DOI:  https://doi.org/10.1038/s43018-020-0039-1
  17. Elife. 2020 Aug 14. pii: e58573. [Epub ahead of print]9
    Kulkarni CA, Nadtochiy SM, Kennedy L, Zhang J, Chhim S, Alwaseem H, Murphy E, Fu D, Brookes PS.
      Alkb homolog 7 (ALKBH7) is a mitochondrial α-ketoglutarate dioxygenase required for DNA alkylation induced necrosis, but its function and substrates remain unclear. Herein we show ALKBH7 regulates dialdehyde metabolism, which impacts the cardiac response to ischemia-reperfusion (IR) injury. Using a multi-omics approach, we find no evidence ALKBH7 functions as a prolyl-hydroxylase, but we do find Alkbh7-/- mice have elevated glyoxalase I (GLO-1), a dialdehyde detoxifying enzyme. Metabolic pathways related to the glycolytic by-product methylglyoxal (MGO) are rewired in Alkbh7-/- mice, along with elevated levels of MGO protein adducts. Despite greater glycative stress, hearts from Alkbh7-/- mice are protected against IR injury, in a manner blocked by GLO-1 inhibition. Integrating these observations, we propose ALKBH7 regulates glyoxal metabolism, and that protection against necrosis and cardiac IR injury bought on by ALKBH7 deficiency originates from the signaling response to elevated MGO stress.
    Keywords:  cell biology; mouse
    DOI:  https://doi.org/10.7554/eLife.58573
  18. Cell Death Differ. 2020 Aug 07.
    Yang Z, Zhao X, Shang W, Liu Y, Ji JF, Liu JP, Tong C.
      Pyrroline-5-carboxylate synthase (P5CS) catalyzes the synthesis of pyrroline-5-carboxylate (P5C), a key precursor for the synthesis of proline and ornithine. P5CS malfunction leads to multiple human diseases; however, the molecular mechanism underlying these diseases is unknown. We found that P5CS localizes in mitochondria in rod- and ring-like patterns but diffuses inside the mitochondria upon cellular starvation or exposure to oxidizing agents. Some of the human disease-related mutant forms of P5CS also exhibit diffused distribution. Multimerization (but not the catalytic activity) of P5CS regulates its localization. P5CS mutant cells have a reduced proliferation rate and are sensitive to cellular stresses. Flies lacking P5CS have reduced eclosion rates. Lipid droplets accumulate in the eyes of the newly eclosed P5CS mutant flies, which degenerate with aging. The loss of P5CS in cells leads to abnormal purine metabolism and lipid-droplet accumulation. The reduced lipid-droplet consumption is likely due to decreased expression of the fatty acid transporter, CPT1, and few β-oxidation-related genes following P5CS knockdown. Surprisingly, we found that P5CS is required for mitochondrial respiratory complex organization and that the respiration defects in P5CS knockout cells likely contribute to the metabolic defects in purine synthesis and lipid consumption. This study links amino acid synthesis with mitochondrial respiration and other key metabolic processes, whose imbalance might contribute to P5CS-related disease conditions.
    DOI:  https://doi.org/10.1038/s41418-020-0601-5
  19. Cancer Cell. 2020 Jul 30. pii: S1535-6108(20)30369-X. [Epub ahead of print]
    Chung C, Sweha SR, Pratt D, Tamrazi B, Panwalkar P, Banda A, Bayliss J, Hawes D, Yang F, Lee HJ, Shan M, Cieslik M, Qin T, Werner CK, Wahl DR, Lyssiotis CA, Bian Z, Shotwell JB, Yadav VN, Koschmann C, Chinnaiyan AM, Blüml S, Judkins AR, Venneti S.
      H3K27M diffuse intrinsic pontine gliomas (DIPGs) are fatal and lack treatments. They mainly harbor H3.3K27M mutations resulting in H3K27me3 reduction. Integrated analysis in H3.3K27M cells, tumors, and in vivo imaging in patients showed enhanced glycolysis, glutaminolysis, and tricarboxylic acid cycle metabolism with high alpha-ketoglutarate (α-KG) production. Glucose and/or glutamine-derived α-KG maintained low H3K27me3 in H3.3K27M cells, and inhibition of key enzymes in glycolysis or glutaminolysis increased H3K27me3, altered chromatin accessibility, and prolonged survival in animal models. Previous studies have shown that mutant isocitrate-dehydrogenase (mIDH)1/2 glioma cells convert α-KG to D-2-hydroxyglutarate (D-2HG) to increase H3K27me3. Here, we show that H3K27M and IDH1 mutations are mutually exclusive and experimentally synthetic lethal. Overall, we demonstrate that H3.3K27M and mIDH1 hijack a conserved and critical metabolic pathway in opposing ways to maintain their preferred epigenetic state. Consequently, interruption of this metabolic/epigenetic pathway showed potent efficacy in preclinical models, suggesting key therapeutic targets for much needed treatments.
    Keywords:  D-2HG; DIPG; H3K27me3; IDH mutation; epigenetics; glutaminolysis; glycolysis; histone methylation; histone mutation; metabolism; α-KG
    DOI:  https://doi.org/10.1016/j.ccell.2020.07.008
  20. Mitochondrion. 2020 Aug 09. pii: S1567-7249(20)30170-7. [Epub ahead of print]
    Purushottam Dharaskar S, Paithankar K, Kanugovi Vijayavittal A, Shabbir Kara H, Amere Subbarao S.
      Mitochondria play a central role in regulating cellular energy metabolism. However, the present understanding of mitochondria has changed from its unipotent functions to pluripotent and insists on understanding the role of mitochondria not only in regulating the life and death of cells, but in pathological conditions such as cancer. Unlike other cellular organelles, subtle alterations in mitochondrial organization may significantly influence the balance between metabolic networks and cellular behavior. Therefore, the delicate balance between the fusion and fission dynamics of mitochondrion can indicate cell fate. Here, we present mitochondrial chaperone TRAP1 influence on mitochondrial architecture and its correlation with tumor growth and metastasis. We show that TRAP1 overexpression (TRAP1 OE) promotes mitochondrial fission, whereas, TRAP1 knockdown (TRAP1 KD) promotes mitochondrial fusion. Interestingly, TRAP1 OE or KD had a negligible effect on mitochondrial integrity. However, TRAP1 OE cells exhibited enhanced proliferative potential, while TRAP1 KD cells showing increased doubling time. Further, TRAP1 dependent mitochondrial dynamic alterations appeared to be unique since mitochondrial localization of TRAP1 is a mandate for dynamic changes. The expression patterns of fusion and fission genes have failed to correlate with TRAP1 expression, indicating a possibility that the dynamic changes can be independent of these genes. In agreement with enhanced proliferative potential, TRAP1 OE cells also exhibited enhanced migration in vitro and tumor metastasis in vivo. Further, TRAP1 OE cells showed altered homing properties, which may challenge site-specific anticancer treatments. Our findings unravel the TRAP1 role in tumor metastasis, which is in addition to altered energy metabolism.
    DOI:  https://doi.org/10.1016/j.mito.2020.08.001
  21. Elife. 2020 Aug 14. pii: e52558. [Epub ahead of print]9
    Panic V, Pearson S, Banks J, Tippetts TS, Velasco-Silva JN, Lee S, Simcox J, Geoghegan G, Bensard CL, van Ry T, Holland WL, Summers SA, Cox J, Ducker GS, Rutter J, Villanueva CJ.
      Brown adipose tissue (BAT) is composed of thermogenic cells that convert chemical energy into heat to help maintain a constant body temperature and counteract metabolic disease in mammals. The metabolic adaptations required for thermogenesis are not fully understood. Here we explore how steady state levels of metabolic intermediates are altered in brown adipose tissue in response to cold exposure. Transcriptome and metabolome analysis revealed changes in pathways involved in amino acid, glucose, and TCA cycle metabolism. Using isotopic labeling experiments, we found that activated brown adipocytes increased labeling of pyruvate and TCA cycle intermediates from U13C-glucose. Although glucose oxidation has been implicated as being essential for thermogenesis, its requirement for efficient thermogenesis has not been directly tested. Here we show that mitochondrial pyruvate uptake is essential for optimal thermogenesis, as conditional deletion of Mpc1 in brown adipocytes leads to impaired cold adaptation. Isotopic labeling experiments using U13C-glucose showed that loss of MPC1 led to impaired labeling of TCA cycle intermediates, while labeling of glycolytic intermediates was unchanged. Loss of MPC1 in BAT increased 3-hydroxybutyrate levels in blood and BAT in response to the cold, suggesting that ketogenesis provides an alternative fuel source to compensate for impaired mitochondrial oxidation of cytosolic pyruvate. Collectively, these studies highlight that complete glucose oxidation is essential for optimal brown fat thermogenesis.
    Keywords:  biochemistry; chemical biology; mouse
    DOI:  https://doi.org/10.7554/eLife.52558
  22. Redox Biol. 2020 Jul 27. pii: S2213-2317(20)30866-1. [Epub ahead of print]36 101661
    Wu H, Wei H, Zhang D, Sehgal SA, Zhang D, Wang X, Qin Y, Liu L, Chen Q.
      Both iron metabolism and mitophagy, a selective mitochondrial degradation process via autolysosomal pathway, are fundamental for the cellular well-being. Mitochondria are the major site for iron metabolism, especially the biogenesis of iron-sulfur clusters (ISCs) via the mitochondria-localized ISCs assembly machinery. Here we report that mitochondrial ISCs biogenesis is coupled with receptor-mediated mitophagy in mammalian cells. Perturbation of mitochondrial ISCs biogenesis, either by depleting iron with the iron chelator or by knocking down the core components of the mitochondrial ISCs assembly machinery, triggers FUNDC1-dependent mitophagy. IRP1, one of the cellular iron sensors to maintain iron homeostasis, is crucial for iron stresses induced mitophagy. Knockdown of IRP1 disturbed iron stresses induced mitophagy. Furthermore, IRP1 could bind to a newly characterized IRE in the 5' untranslated region of the Bcl-xL mRNA and suppress its translation. Bcl-xL is an intrinsic inhibitory protein of the mitochondrial phosphatase PGAM5, which catalyzes the dephosphorylation of FUNDC1 for mitophagy activation. Alterations of the IRP1/Bcl-xL axis navigate iron stresses induced mitophagy. We conclude that ISCs serve as physiological signals for mitophagy activation, thus coupling mitophagy with iron metabolism.
    Keywords:  Bcl-xL; FUNDC1; ISCs; Mitophagy
    DOI:  https://doi.org/10.1016/j.redox.2020.101661
  23. Acta Biochim Biophys Sin (Shanghai). 2020 Aug 12. pii: gmaa081. [Epub ahead of print]
    Qing J, Zhang Z, Novák P, Zhao G, Yin K.
      As a major type of immune cells with heterogeneity and plasticity, macrophages are classically divided into inflammatory (M1) and alternative/anti-inflammatory (M2) types and play a crucial role in the progress of the inflammatory diseases. Recent studies have shown that metabolism is an important determinant of macrophage phenotype. Mitochondria, one of the most important compartments involving cell metabolism, are closely associated with the regulation of cell functions. In most types of cell, mitochondrial oxidative phosphorylation (OXPHOS) is the primary mode of cellular energy production. However, mitochondrial OXPHOS is inhibited in activated M1 macrophages, rendering them unable to be converted into M2 phenotype. Thus, mitochondrial metabolism is a crucial regulator in macrophage functions. This review summarizes the roles of mitochondria in macrophage polarization and analyzes the molecular mechanisms underlying mitochondrial metabolism and function, which may provide new approaches for the treatment of metabolic inflammatory diseases.
    Keywords:  inflammation; macrophage polarization; metabolism; mitochondria
    DOI:  https://doi.org/10.1093/abbs/gmaa081
  24. Ann Transl Med. 2020 Jul;8(14): 904
    Yu D, Liu C, Guo L.
      Metastasis is regarded as the most important cause of cancer-related deaths around the world. During the complicated metastatic cascade, altered mitochondrial metabolism adapts to serve distinct conditions and microenvironments. In this review, we discuss how cells regulate their mitochondria metabolism to adapt to environmental cues during the metastasis, as well as how cancer cells and their tumor micro-environment (TME) are metabolically coupled during the metastatic cascade. We place a strong emphasis on how mitochondrial proline metabolism and extracellular matrix (ECM) are coupled.
    Keywords:  Metastasis; extracellular matrix (ECM); mitochondrial metabolism; proline metabolism; tumor micro-environment (TME)
    DOI:  https://doi.org/10.21037/atm.2020.03.42
  25. Biol Chem. 2020 Aug 01. pii: /j/bchm.just-accepted/hsz-2020-0157/hsz-2020-0157.xml. [Epub ahead of print]
    Galber C, Acosta MJ, Minervini G, Giorgio V.
      The mitochondrial ATP synthase is a multi-subunit enzyme complex located in the inner mitochondrial membrane which is essential for oxidative phosphorylation under physiological conditions. In this review, we analyse the enzyme functions involved in cancer progression by dissecting specific conditions in which ATP synthase contributes to cancer development or metastasis. Moreover, we propose the role of ATP synthase in the formation of the permeability transition pore (PTP) as an additional mechanism which controls tumour cell death. We further describe transcriptional and translational modifications of the enzyme subunits and of the inhibitor protein IF1that may promote adaptations leading to cancer metabolism. Finally, we outline ATP synthase gene mutations and epigenetic modifications associated with cancer development or drug resistance, with the aim of highlighting this enzyme complex as a potential novel target for future anti-cancer therapy.
    Keywords:  ATP synthase; cancer; mitochondria; permeability transition
    DOI:  https://doi.org/10.1515/hsz-2020-0157
  26. Cancer Discov. 2020 Aug 12. pii: CD-20-0442. [Epub ahead of print]
    Zafra MP, Parsons MJ, Kim J, Alonso-Curbelo D, Goswami S, Schatoff EM, Han T, Katti A, Calvo Fernandez MT, Wilkinson JE, Piskounova E, Dow LE.
      KRAS is the most frequently mutated oncogene in cancer, yet there is little understanding of how specific KRAS amino acid changes impact tumor initiation, progression, or therapy response. Using high-fidelity CRISPR-based engineering, we created an allelic series of new LSL-Kras mutant mice, reflecting codon 12 and 13 mutations that are highly prevalent in lung (KRASG12C), pancreas (KRASG12R) and colon (KRASG13D) cancers. Induction of each allele in either the murine colon or pancreas revealed striking quantitative and qualitative differences between KRAS mutants in driving the early stages of transformation. Further, using pancreatic organoid models we show that KRASG13D mutants are sensitive to EGFR inhibition, while KRASG12C mutant organoids are selectively responsive to covalent G12C inhibitors only when EGFR is suppressed. Together, these new mouse strains provide an ideal platform for investigating KRAS biology in vivo and for developing pre-clinical precision oncology models of KRAS-mutant pancreas, colon, and lung cancers.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-0442
  27. Dev Cell. 2020 Aug 04. pii: S1534-5807(20)30588-8. [Epub ahead of print]
    Bertolini I, Ghosh JC, Kossenkov AV, Mulugu S, Krishn SR, Vaira V, Qin J, Plow EF, Languino LR, Altieri DC.
      The crosstalk between tumor cells and the adjacent normal epithelium contributes to cancer progression, but its regulators have remained elusive. Here, we show that breast cancer cells maintained in hypoxia release small extracellular vesicles (sEVs) that activate mitochondrial dynamics, stimulate mitochondrial movements, and promote organelle accumulation at the cortical cytoskeleton in normal mammary epithelial cells. This results in AKT serine/threonine kinase (Akt) activation, membrane focal adhesion turnover, and increased epithelial cell migration. RNA sequencing profiling identified integrin-linked kinase (ILK) as the most upregulated pathway in sEV-treated epithelial cells, and genetic or pharmacologic targeting of ILK reversed mitochondrial reprogramming and suppressed sEV-induced cell movements. In a three-dimensional (3D) model of mammary gland morphogenesis, sEV treatment induced hallmarks of malignant transformation, with deregulated cell death and/or cell proliferation, loss of apical-basal polarity, and appearance of epithelial-to-mesenchymal transition (EMT) markers. Therefore, sEVs released by hypoxic breast cancer cells reprogram mitochondrial dynamics and induce oncogenic changes in a normal mammary epithelium.
    Keywords:  breast cancer; extracellular vesicles; hypoxia; mitochondria; morphogenesis; normal mammary epithelium; transformation
    DOI:  https://doi.org/10.1016/j.devcel.2020.07.014
  28. Nat Commun. 2020 Aug 13. 11(1): 4055
    Bechard ME, Smalling R, Hayashi A, Zhong Y, Word AE, Campbell SL, Tran AV, Weiss VL, Iacobuzio-Donahue C, Wellen KE, McDonald OG.
      Although metastasis is the most common cause of cancer deaths, metastasis-intrinsic dependencies remain largely uncharacterized. We previously reported that metastatic pancreatic cancers were dependent on the glucose-metabolizing enzyme phosphogluconate dehydrogenase (PGD). Surprisingly, PGD catalysis was constitutively elevated without activating mutations, suggesting a non-genetic basis for enhanced activity. Here we report a metabolic adaptation that stably activates PGD to reprogram metastatic chromatin. High PGD catalysis prevents transcriptional up-regulation of thioredoxin-interacting protein (TXNIP), a gene that negatively regulates glucose import. This allows glucose consumption rates to rise in support of PGD, while simultaneously facilitating epigenetic reprogramming through a glucose-fueled histone hyperacetylation pathway. Restoring TXNIP normalizes glucose consumption, lowers PGD catalysis, reverses hyperacetylation, represses malignant transcripts, and impairs metastatic tumorigenesis. We propose that PGD-driven suppression of TXNIP allows pancreatic cancers to avidly consume glucose. This renders PGD constitutively activated and enables metaboloepigenetic selection of additional traits that increase fitness along glucose-replete metastatic routes.
    DOI:  https://doi.org/10.1038/s41467-020-17839-5
  29. Nat Immunol. 2020 Aug 10.
    Zhou H, Wang H, Yu M, Schugar RC, Qian W, Tang F, Liu W, Yang H, McDowell RE, Zhao J, Gao J, Dongre A, Carman JA, Yin M, Drazba JA, Dent R, Hine C, Chen YR, Smith JD, Fox PL, Brown JM, Li X.
      Chronic inflammation is a common feature of obesity, with elevated cytokines such as interleukin-1 (IL-1) in the circulation and tissues. Here, we report an unconventional IL-1R-MyD88-IRAK2-PHB/OPA1 signaling axis that reprograms mitochondrial metabolism in adipocytes to exacerbate obesity. IL-1 induced recruitment of IRAK2 Myddosome to mitochondria outer membranes via recognition by TOM20, followed by TIMM50-guided translocation of IRAK2 into mitochondria inner membranes, to suppress oxidative phosphorylation and fatty acid oxidation, thereby attenuating energy expenditure. Adipocyte-specific MyD88 or IRAK2 deficiency reduced high-fat-diet-induced weight gain, increased energy expenditure and ameliorated insulin resistance, associated with a smaller adipocyte size and increased cristae formation. IRAK2 kinase inactivation also reduced high-fat diet-induced metabolic diseases. Mechanistically, IRAK2 suppressed respiratory super-complex formation via interaction with PHB1 and OPA1 upon stimulation of IL-1. Taken together, our results suggest that the IRAK2 Myddosome functions as a critical link between inflammation and metabolism, representing a novel therapeutic target for patients with obesity.
    DOI:  https://doi.org/10.1038/s41590-020-0750-1
  30. Nat Commun. 2020 Aug 12. 11(1): 4031
    Pittis AA, Goh V, Cebrian-Serrano A, Wettmarshausen J, Perocchi F, Gabaldón T.
      Calcium (Ca2+) influx into mitochondria occurs through a Ca2+-selective uniporter channel, which regulates essential cellular processes in eukaryotic organisms. Previous evolutionary analyses of its pore-forming subunits MCU and EMRE, and gatekeeper MICU1, pinpointed an evolutionary paradox: the presence of MCU homologs in fungal species devoid of any other uniporter components and of mt-Ca2+ uptake. Here, we trace the mt-Ca2+ uniporter evolution across 1,156 fully-sequenced eukaryotes and show that animal and fungal MCUs represent two distinct paralogous subfamilies originating from an ancestral duplication. Accordingly, we find EMRE orthologs outside Holoza and uncover the existence of an animal-like uniporter within chytrid fungi, which enables mt-Ca2+ uptake when reconstituted in vivo in the yeast Saccharomyces cerevisiae. Our study represents the most comprehensive phylogenomic analysis of the mt-Ca2+ uptake system and demonstrates that MCU, EMRE, and MICU formed the core of the ancestral opisthokont uniporter, with major implications for comparative structural and functional studies.
    DOI:  https://doi.org/10.1038/s41467-020-17705-4
  31. Cancer Metab. 2020 ;8 9
    Oizel K, Yang C, Renoult O, Gautier F, Do QN, Joalland N, Gao X, Ko B, Vallette F, Ge WP, Paris F, DeBerardinis RJ, Pecqueur C.
      Background: Glioblastoma (GBM) are highly heterogeneous on the cellular and molecular basis. It has been proposed that glutamine metabolism of primary cells established from human tumors discriminates aggressive mesenchymal GBM subtype to other subtypes.Methods: To study glutamine metabolism in vivo, we used a human orthotopic mouse model for GBM. Tumors evolving from the implanted primary GBM cells expressing different molecular signatures were analyzed using mass spectrometry for their metabolite pools and enrichment in carbon 13 (13C) after 13C-glutamine infusion.
    Results: Our results showed that mesenchymal GBM tumors displayed increased glutamine uptake and utilization compared to both control brain tissue and other GBM subtypes. Furthermore, both glutamine synthetase and transglutaminase-2 were expressed accordingly to GBM metabolic phenotypes.
    Conclusion: Thus, our results outline the specific enhanced glutamine flux in vivo of the aggressive mesenchymal GBM subtype.
    Keywords:  Glioblastoma; Glutamine; Human primary cells; Mesenchymal; Metabolism; Molecular subtype; Orthotopic model
    DOI:  https://doi.org/10.1186/s40170-020-00215-8
  32. Am J Transl Res. 2020 ;12(7): 3412-3428
    Madungwe NB, Feng Y, Imam Aliagan A, Tombo N, Kaya F, Bopassa JC.
      MPV17 is an inner mitochondrial membrane protein whose mutation results in mitochondrial DNA (mtDNA) depletion diseases such as neurohepatopathy. MPV17 is expressed in several organs including the liver and kidneys. Here, we investigated its role and mechanism of action in cardiac ischemia/reperfusion (I/R) injury. Using isolated hearts from wild type and Mpv17 mutant (Mpv17mut) mice, we found that mtDNA levels and normal cardiac function were similar between the groups. Furthermore, reactive oxygen species (ROS) generation, mitochondrial morphology, and calcium levels required to trigger mitochondrial permeability transition pore (mPTP) opening were all similar in normal/non-ischemic animals. However, following I/R, we found that mutant mice had poorer cardiac functional recovery and exhibited more mitochondrial structural damage. We also found that after I/R, Mpv17mut heart mitochondria did not produce more ROS than wild type hearts but that calcium retention capacity was gravely compromised. Using immunoprecipitation and mass spectrometry, we identified ATP synthase, Cyclophilin D, MIC60 and GRP75 as proteins critical to mitochondrial cristae organization and calcium handling that interact with MPV17, and this interaction is reduced by I/R. Together our results suggest that MPV17 has a protective function in the heart and is necessary for recovery following insults to the heart.
    Keywords:  MPV17; ischemia/reperfusion; mPTP opening; mitochondrial DNA; mitochondrial calcium retention capacity; mitochondrial inner membrane proteins; reactive oxygen species
  33. Nat Chem Biol. 2020 Aug 10.
    Spada F, Schiffers S, Kirchner A, Zhang Y, Arista G, Kosmatchev O, Korytiakova E, Rahimoff R, Ebert C, Carell T.
      Epigenetic plasticity underpins cell potency, but the extent to which active turnover of DNA methylation contributes to such plasticity is not known, and the underlying pathways are poorly understood. Here we use metabolic labeling with stable isotopes and mass spectrometry to quantitatively address the global turnover of genomic 5-methyl-2'-deoxycytidine (mdC), 5-hydroxymethyl-2'-deoxycytidine (hmdC) and 5-formyl-2'-deoxycytidine (fdC) across mouse pluripotent cell states. High rates of mdC/hmdC oxidation and fdC turnover characterize a formative-like pluripotent state. In primed pluripotent cells, the global mdC turnover rate is about 3-6% faster than can be explained by passive dilution through DNA synthesis. While this active component is largely dependent on ten-eleven translocation (Tet)-mediated mdC oxidation, we unveil additional oxidation-independent mdC turnover, possibly through DNA repair. This process accelerates upon acquisition of primed pluripotency and returns to low levels in lineage-committed cells. Thus, in pluripotent cells, active mdC turnover involves both mdC oxidation-dependent and oxidation-independent processes.
    DOI:  https://doi.org/10.1038/s41589-020-0621-y
  34. Cell Metab. 2020 Aug 01. pii: S1550-4131(20)30370-3. [Epub ahead of print]
    Koh A, Mannerås-Holm L, Yunn NO, Nilsson PM, Ryu SH, Molinaro A, Perkins R, Smith JG, Bäckhed F.
      Metformin is the first-line therapy for type 2 diabetes, but there are large inter-individual variations in responses to this drug. Its mechanism of action is not fully understood, but activation of AMP-activated protein kinase (AMPK) and changes in the gut microbiota appear to be important. The inhibitory role of microbial metabolites on metformin action has not previously been investigated. Here, we show that concentrations of the microbial metabolite imidazole propionate are higher in subjects with type 2 diabetes taking metformin who have high blood glucose. We also show that metformin-induced glucose lowering is not observed in mice pretreated with imidazole propionate. Furthermore, we demonstrate that imidazole propionate inhibits AMPK activity by inducing inhibitory AMPK phosphorylation, which is dependent on imidazole propionate-induced basal Akt activation. Finally, we identify imidazole propionate-activated p38γ as a novel kinase for Akt and demonstrate that p38γ kinase activity mediates the inhibitory action of imidazole propionate on metformin.
    Keywords:  AMPK; diabetes; imidazole propionate; individual variations; metformin; microbial metabolites; microbiota; p38γ
    DOI:  https://doi.org/10.1016/j.cmet.2020.07.012
  35. Am J Physiol Endocrinol Metab. 2020 Aug 10.
    Merry TL, Chan A, Woodhead JST, Reynolds JC, Kumaga H, Kim SJ, Lee C.
      Mitochondrial-derived peptides (MDPs) are small bioactive peptides encoded by short open reading frames (sORF) in mitochondrial DNA that do not necessarily have traditional hallmarks of protein-coding genes. To date, eight MDPs have been identified, all of which have been shown to have various cyto- or metabolo-protective properties. The 12S ribosomal RNA (MT-RNR1) gene harbors the sequence for MOTS-c, while the other seven MDPs, [humanin and small humanin-like peptides (SHLP) 1-6] are encoded by the 16S ribosomal RNA gene. Here we review the evidence that endogenous MDPs are sensitive to changes in metabolism, showing that metabolic conditions like obesity, diabetes and aging are associated with lower circulating MDPs. Whereas, in humans, muscle MDP expression is upregulated in response to stress that perturbs the mitochondria like exercise, some mtDNA mutation-associated diseases, and healthy aging, which potentially suggests a tissue-specific response aimed at restoring cellular or mitochondrial homeostasis. Consistent with this, treatment of rodents with humanin, MOTS-c and SHLP2 can enhance insulin sensitivity and offer protection against a range of age-associated metabolic disorders. Further, assessing how mtDNA variants alter the functions of MDPs is beginning to provide evidence that MDPs are metabolic signal transducers in humans. Taken together, MDPs appear to form an important aspect of a retrograde signaling network that communicates mitochondrial status with the wider cell, and to distal tissues, to modulate adaptative responses to metabolic stress. It remains to be fully determined whether the metabolo-protective properties of MDPs can be harnessed into therapies for metabolic disease.
    Keywords:  MOTS-c; Mitokine; ageing; mitochondria; mitochondrial derived peptides
    DOI:  https://doi.org/10.1152/ajpendo.00249.2020
  36. Sci Adv. 2020 Jul;6(31): eabb2529
    Zhu D, Wu X, Zhou J, Li X, Huang X, Li J, Wu J, Bian Q, Wang Y, Tian Y.
      Mild mitochondrial stress experienced early in life can have beneficial effects on the life span of organisms through epigenetic regulations. Here, we report that acetyl-coenzyme A (CoA) represents a critical mitochondrial signal to regulate aging through the chromatin remodeling and histone deacetylase complex (NuRD) in Caenorhabditis elegans. Upon mitochondrial stress, the impaired tricarboxylic acid cycle results in a decreased level of citrate, which accounts for reduced production of acetyl-CoA and consequently induces nuclear accumulation of the NuRD and a homeodomain-containing transcription factor DVE-1, thereby enabling decreased histone acetylation and chromatin reorganization. The metabolic stress response is thus established during early life and propagated into adulthood to allow transcriptional regulation for life-span extension. Furthermore, adding nutrients to restore acetyl-CoA production is sufficient to counteract the chromatin changes and diminish the longevity upon mitochondrial stress. Our findings uncover the molecular mechanism of the metabolite-mediated epigenome for the regulation of organismal aging.
    DOI:  https://doi.org/10.1126/sciadv.abb2529
  37. Nat Chem Biol. 2020 Aug 10.
    Bazhin AA, Sinisi R, De Marchi U, Hermant A, Sambiagio N, Maric T, Budin G, Goun EA.
      Mitochondrial membrane potential (ΔΨm) is a universal selective indicator of mitochondrial function and is known to play a central role in many human pathologies, such as diabetes mellitus, cancer and Alzheimer's and Parkinson's diseases. Here, we report the design, synthesis and several applications of mitochondria-activatable luciferin (MAL), a bioluminescent probe sensitive to ΔΨm, and partially to plasma membrane potential (ΔΨp), for non-invasive, longitudinal monitoring of ΔΨm in vitro and in vivo. We applied this new technology to evaluate the aging-related change of ΔΨm in mice and showed that nicotinamide riboside (NR) reverts aging-related mitochondrial depolarization, revealing another important aspect of the mechanism of action of this potent biomolecule. In addition, we demonstrated application of the MAL probe for studies of brown adipose tissue (BAT) activation and non-invasive in vivo assessment of ΔΨm in animal cancer models, opening exciting opportunities for understanding the underlying mechanisms and for discovery of effective treatments for many human pathologies.
    DOI:  https://doi.org/10.1038/s41589-020-0602-1
  38. Cell Metab. 2020 Jul 31. pii: S1550-4131(20)30366-1. [Epub ahead of print]
    Hamaidi I, Zhang L, Kim N, Wang MH, Iclozan C, Fang B, Liu M, Koomen JM, Berglund AE, Yoder SJ, Yao J, Engelman RW, Creelan BC, Conejo-Garcia JR, Antonia SJ, Mulé JJ, Kim S.
      Dysregulated metabolism is a key driver of maladaptive tumor-reactive T lymphocytes within the tumor microenvironment. Actionable targets that rescue the effector activity of antitumor T cells remain elusive. Here, we report that the Sirtuin-2 (Sirt2) NAD+-dependent deacetylase inhibits T cell metabolism and impairs T cell effector functions. Remarkably, upregulation of Sirt2 in human tumor-infiltrating lymphocytes (TILs) negatively correlates with response to TIL therapy in advanced non-small-cell lung cancer. Mechanistically, Sirt2 suppresses T cell metabolism by targeting key enzymes involved in glycolysis, tricarboxylic acid-cycle, fatty acid oxidation, and glutaminolysis. Accordingly, Sirt2-deficient murine T cells exhibit increased glycolysis and oxidative phosphorylation, resulting in enhanced proliferation and effector functions and subsequently exhibiting superior antitumor activity. Importantly, pharmacologic inhibition of Sirt2 endows human TILs with these superior metabolic fitness and effector functions. Our findings unveil Sirt2 as an unexpected actionable target for reprogramming T cell metabolism to augment a broad spectrum of cancer immunotherapies.
    Keywords:  FAO; OxPhos; Sirt2; T cells; antitumor immunity; deacetylase; dysregulated metabolism; glutaminolysis; glycolysis; metabolic checkpoint
    DOI:  https://doi.org/10.1016/j.cmet.2020.07.008
  39. N Engl J Med. 2020 Aug 12.
    Walker MA, Lareau CA, Ludwig LS, Karaa A, Sankaran VG, Regev A, Mootha VK.
      Many mitochondrial diseases are caused by mutations in mitochondrial DNA (mtDNA). Patients' cells contain a mixture of mutant and nonmutant mtDNA (a phenomenon called heteroplasmy). The proportion of mutant mtDNA varies across patients and among tissues within a patient. We simultaneously assayed single-cell heteroplasmy and cell state in thousands of blood cells obtained from three unrelated patients who had A3243G-associated mitochondrial encephalomyopathy, lactic acidosis, and strokelike episodes. We observed a broad range of heteroplasmy across all cell types but also found markedly reduced heteroplasmy in T cells, a finding consistent with purifying selection within this lineage. We observed this pattern in six additional patients who had heteroplasmic A3243G without strokelike episodes. (Funded by the Marriott Foundation and others.).
    DOI:  https://doi.org/10.1056/NEJMoa2001265
  40. Cell Death Dis. 2020 Aug 13. 11(8): 616
    Roca-Portoles A, Rodriguez-Blanco G, Sumpton D, Cloix C, Mullin M, Mackay GM, O'Neill K, Lemgruber L, Luo X, Tait SWG.
      BH3-mimetics are a new class of anti-cancer drugs that inhibit anti-apoptotic Bcl-2 proteins. In doing so, BH3-mimetics sensitise to cell death. Venetoclax is a potent, BCL-2 selective BH3-mimetic that is clinically approved for use in chronic lymphocytic leukaemia. Venetoclax has also been shown to inhibit mitochondrial metabolism, this is consistent with a proposed role for BCL-2 in metabolic regulation. We used venetoclax to understand BCL-2 metabolic function. Similar to others, we found that venetoclax inhibited mitochondrial respiration. In addition, we also found that venetoclax impairs TCA cycle activity leading to activation of reductive carboxylation. Importantly, the metabolic effects of venetoclax were independent of cell death because they were also observed in apoptosis-resistant BAX/BAK-deficient cells. However, unlike venetoclax treatment, inhibiting BCL-2 expression had no effect on mitochondrial respiration. Unexpectedly, we found that venetoclax also inhibited mitochondrial respiration and the TCA cycle in BCL-2 deficient cells and in cells lacking all anti-apoptotic BCL-2 family members. Investigating the basis of this off-target effect, we found that venetoclax-induced metabolic reprogramming was dependent upon the integrated stress response and ATF4 transcription factor. These data demonstrate that venetoclax affects cellular metabolism independent of BCL-2 inhibition. This off-target metabolic effect has potential to modulate venetoclax cytotoxicity.
    DOI:  https://doi.org/10.1038/s41419-020-02867-2
  41. Cell. 2020 Aug 04. pii: S0092-8674(20)30873-4. [Epub ahead of print]
    Licznerski P, Park HA, Rolyan H, Chen R, Mnatsakanyan N, Miranda P, Graham M, Wu J, Cruz-Reyes N, Mehta N, Sohail S, Salcedo J, Song E, Effman C, Effman S, Brandao L, Xu GN, Braker A, Gribkoff VK, Levy RJ, Jonas EA.
      Loss of the gene (Fmr1) encoding Fragile X mental retardation protein (FMRP) causes increased mRNA translation and aberrant synaptic development. We find neurons of the Fmr1-/y mouse have a mitochondrial inner membrane leak contributing to a "leak metabolism." In human Fragile X syndrome (FXS) fibroblasts and in Fmr1-/y mouse neurons, closure of the ATP synthase leak channel by mild depletion of its c-subunit or pharmacological inhibition normalizes stimulus-induced and constitutive mRNA translation rate, decreases lactate and key glycolytic and tricarboxylic acid (TCA) cycle enzyme levels, and triggers synapse maturation. FMRP regulates leak closure in wild-type (WT), but not FX synapses, by stimulus-dependent ATP synthase β subunit translation; this increases the ratio of ATP synthase enzyme to its c-subunit, enhancing ATP production efficiency and synaptic growth. In contrast, in FXS, inability to close developmental c-subunit leak prevents stimulus-dependent synaptic maturation. Therefore, ATP synthase c-subunit leak closure encourages development and attenuates autistic behaviors.
    Keywords:  Fragile X syndrome; autism; autism syndrome; glycolysis; mitochondria; oxidative phosphorylation; permeability transition pore; protein synthesis; repetitive mouse behavior; synaptic development; synaptic plasticity
    DOI:  https://doi.org/10.1016/j.cell.2020.07.008
  42. Nat Commun. 2020 Aug 12. 11(1): 4029
    Zaninello M, Palikaras K, Naon D, Iwata K, Herkenne S, Quintana-Cabrera R, Semenzato M, Grespi F, Ross-Cisneros FN, Carelli V, Sadun AA, Tavernarakis N, Scorrano L.
      In autosomal dominant optic atrophy (ADOA), caused by mutations in the mitochondrial cristae biogenesis and fusion protein optic atrophy 1 (Opa1), retinal ganglion cell (RGC) dysfunction and visual loss occur by unknown mechanisms. Here, we show a role for autophagy in ADOA pathogenesis. In RGCs expressing mutated Opa1, active 5' AMP-activated protein kinase (AMPK) and its autophagy effector ULK1 accumulate at axonal hillocks. This AMPK activation triggers localized hillock autophagosome accumulation and mitophagy, ultimately resulting in reduced axonal mitochondrial content that is restored by genetic inhibition of AMPK and autophagy. In C. elegans, deletion of AMPK or of key autophagy and mitophagy genes normalizes the axonal mitochondrial content that is reduced upon mitochondrial dysfunction. In conditional, RGC specific Opa1-deficient mice, depletion of the essential autophagy gene Atg7 normalizes the excess autophagy and corrects the visual defects caused by Opa1 ablation. Thus, our data identify AMPK and autophagy as targetable components of ADOA pathogenesis.
    DOI:  https://doi.org/10.1038/s41467-020-17821-1
  43. Front Oncol. 2020 ;10 1197
    Jiang Z, Hsu JL, Li Y, Hortobagyi GN, Hung MC.
      Immune checkpoint inhibitors (ICIs) targeting immune checkpoint proteins, such as CTLA-4 and PD-1/PD-L1, have demonstrated remarkable and durable clinical responses in various cancer types. However, a considerable number of patients receiving ICIs eventually experience a relapse due to diverse resistance mechanisms. As a result, there have been increasing research efforts to elucidate the molecular mechanisms behind resistance to ICIs and improve patient outcomes. There is growing evidence that the dysregulated metabolic activity of tumor cells generates an immunosuppressive tumor microenvironment (TME) that orchestrates an impaired anti-tumor immune response. Notably, the immunosuppressive TME is characterized by nutrient shortage, hypoxia, an acidic extracellular milieu, and abundant immunosuppressive molecules. A detailed understanding of the TME remains a major challenge in mounting a more effective anti-tumor immune response. Herein, we discuss how tumor cells reprogram metabolism to modulate a pro-tumor TME, driving disease progression and immune evasion; in particular, we highlight potential approaches to target metabolic vulnerabilities in the context of anti-tumor immunotherapy.
    Keywords:  cancer cell metabolite; cancer metabolism; immune checkpoint inhibitors; immune evasion; tumor microenvironment
    DOI:  https://doi.org/10.3389/fonc.2020.01197
  44. Cancer Lett. 2020 Aug 05. pii: S0304-3835(20)30388-8. [Epub ahead of print]
    Teoh ST, Ogrodzinski MP, Lunt SY.
      Dysregulated metabolism is a hallmark of cancer that supports tumor growth and metastasis. One understudied aspect of cancer metabolism is altered nucleotide sugar biosynthesis, which drives aberrant cell surface glycosylation known to support various aspects of cancer cell behavior including migration and signaling. We examined clinical association of nucleotide sugar pathway gene expression and found that UGDH, encoding UDP-glucose 6-dehydrogenase which catalyzes production of UDP-glucuronate, is associated with worse breast cancer patient survival. Knocking out the mouse homolog Ugdh in highly-metastatic 6DT1 breast cancer cells impaired migration ability without affecting in vitro proliferation. Further, Ugdh-KO resulted in significantly decreased metastatic capacity in vivo when the cells were orthotopically injected in syngeneic mice. Our experiments show that UDP-glucuronate biosynthesis is critical for metastasis in a mouse model of breast cancer.
    DOI:  https://doi.org/10.1016/j.canlet.2020.07.031
  45. Cell Metab. 2020 Aug 04. pii: S1550-4131(20)30411-3. [Epub ahead of print]
    Hooftman A, Angiari S, Hester S, Corcoran SE, Runtsch MC, Ling C, Ruzek MC, Slivka PF, McGettrick AF, Banahan K, Hughes MM, Irvine AD, Fischer R, O'Neill LAJ.
      The Krebs cycle-derived metabolite itaconate is highly upregulated in inflammatory macrophages and exerts immunomodulatory effects through cysteine modifications on target proteins. The NLRP3 inflammasome, which cleaves IL-1β, IL-18, and gasdermin D, must be tightly regulated to avoid excessive inflammation. Here we provide evidence that itaconate modifies NLRP3 and inhibits inflammasome activation. Itaconate and its derivative, 4-octyl itaconate (4-OI), inhibited NLRP3 inflammasome activation, but not AIM2 or NLRC4. Conversely, NLRP3 activation was increased in itaconate-depleted Irg1-/- macrophages. 4-OI inhibited the interaction between NLRP3 and NEK7, a key step in the activation process, and "dicarboxypropylated" C548 on NLRP3. Furthermore, 4-OI inhibited NLRP3-dependent IL-1β release from PBMCs isolated from cryopyrin-associated periodic syndrome (CAPS) patients, and reduced inflammation in an in vivo model of urate-induced peritonitis. Our results identify itaconate as an endogenous metabolic regulator of the NLRP3 inflammasome and describe a process that may be exploited therapeutically to alleviate inflammation in NLRP3-driven disorders.
    Keywords:  IL-1β; NEK7; NLRP3; cysteine modification; immunometabolism; inflammasome; itaconate; macrophage; metabolite; pyroptosis
    DOI:  https://doi.org/10.1016/j.cmet.2020.07.016
  46. Nat Commun. 2020 Aug 13. 11(1): 4046
    Bailey PSJ, Ortmann BM, Martinelli AW, Houghton JW, Costa ASH, Burr SP, Antrobus R, Frezza C, Nathan JA.
      2-oxoglutarate (2-OG or α-ketoglutarate) relates mitochondrial metabolism to cell function by modulating the activity of 2-OG dependent dioxygenases involved in the hypoxia response and DNA/histone modifications. However, metabolic pathways that regulate these oxygen and 2-OG sensitive enzymes remain poorly understood. Here, using CRISPR Cas9 genome-wide mutagenesis to screen for genetic determinants of 2-OG levels, we uncover a redox sensitive mitochondrial lipoylation pathway, dependent on the mitochondrial hydrolase ABHD11, that signals changes in mitochondrial 2-OG metabolism to 2-OG dependent dioxygenase function. ABHD11 loss or inhibition drives a rapid increase in 2-OG levels by impairing lipoylation of the 2-OG dehydrogenase complex (OGDHc)-the rate limiting step for mitochondrial 2-OG metabolism. Rather than facilitating lipoate conjugation, ABHD11 associates with the OGDHc and maintains catalytic activity of lipoyl domain by preventing the formation of lipoyl adducts, highlighting ABHD11 as a regulator of functional lipoylation and 2-OG metabolism.
    DOI:  https://doi.org/10.1038/s41467-020-17862-6
  47. Nat Chem Biol. 2020 Aug 10.
    Soula M, Weber RA, Zilka O, Alwaseem H, La K, Yen F, Molina H, Garcia-Bermudez J, Pratt DA, Birsoy K.
      Cancer cells rewire their metabolism and rely on endogenous antioxidants to mitigate lethal oxidative damage to lipids. However, the metabolic processes that modulate the response to lipid peroxidation are poorly defined. Using genetic screens, we compared metabolic genes essential for proliferation upon inhibition of cystine uptake or glutathione peroxidase-4 (GPX4). Interestingly, very few genes were commonly required under both conditions, suggesting that cystine limitation and GPX4 inhibition may impair proliferation via distinct mechanisms. Our screens also identify tetrahydrobiopterin (BH4) biosynthesis as an essential metabolic pathway upon GPX4 inhibition. Mechanistically, BH4 is a potent radical-trapping antioxidant that protects lipid membranes from autoxidation, alone and in synergy with vitamin E. Dihydrofolate reductase catalyzes the regeneration of BH4, and its inhibition by methotrexate synergizes with GPX4 inhibition. Altogether, our work identifies the mechanism by which BH4 acts as an endogenous antioxidant and provides a compendium of metabolic modifiers of lipid peroxidation.
    DOI:  https://doi.org/10.1038/s41589-020-0613-y
  48. Nat Rev Cancer. 2020 Aug 11.
    Nacev BA, Jones KB, Intlekofer AM, Yu JSE, Allis CD, Tap WD, Ladanyi M, Nielsen TO.
      Epigenetic regulation is critical to physiological control of development, cell fate, cell proliferation, genomic integrity and, fundamentally, transcriptional regulation. This epigenetic control occurs at multiple levels including through DNA methylation, histone modification, nucleosome remodelling and modulation of the 3D chromatin structure. Alterations in genes that encode chromatin regulators are common among mesenchymal neoplasms, a collection of more than 160 tumour types including over 60 malignant variants (sarcomas) that have unique and varied genetic, biological and clinical characteristics. Herein, we review those sarcomas in which chromatin pathway alterations drive disease biology. Specifically, we emphasize examples of dysregulation of each level of epigenetic control though mechanisms that include alterations in metabolic enzymes that regulate DNA methylation and histone post-translational modifications, mutations in histone genes, subunit loss or fusions in chromatin remodelling and modifying complexes, and disruption of higher-order chromatin structure. Epigenetic mechanisms of tumorigenesis have been implicated in mesenchymal tumours ranging from chondroblastoma and giant cell tumour of bone to chondrosarcoma, malignant peripheral nerve sheath tumour, synovial sarcoma, epithelioid sarcoma and Ewing sarcoma - all diseases that present in a younger patient population than most cancers. Finally, we review current and potential future approaches for the development of sarcoma therapies based on this emerging understanding of chromatin dysregulation.
    DOI:  https://doi.org/10.1038/s41568-020-0288-4
  49. J Clin Invest. 2020 Aug 13. pii: 138538. [Epub ahead of print]
    Zhou B, Wang DD, Qiu Y, Airhart S, Liu Y, Stempien-Otero A, O'Brien KD, Tian R.
      BACKGROUND: While mitochondria play an important role in innate immunity, the relationship between mitochondrial dysfunction and inflammation in heart failure (HF) is poorly understood. In this study we aimed to investigate the mechanistic link between mitochondrial dysfunction and inflammatory activation in peripheral blood mononuclear cells (PBMCs), and the potential anti-inflammatory effect of boosting NAD level.METHODS: We compared the PBMC mitochondrial respiration of 19 hospitalized Stage D HF patients with 19 healthy participants. We then created an in vitro model of sterile inflammation by treating healthy PBMC with MitoDAMP (Mitochondrial Damage-Associated Molecular Patterns) isolated from human heart tissue. Lastly, we enrolled Stage D HF patients and sampled their blood before and after taking 5-9 days of oral nicotinamide riboside, an NAD precursor.
    RESULTS: We demonstrated that HF is associated with both reduced respiratory capacity and elevated proinflammatory cytokine gene expressions. In our in vitro model, MitoDAMP-treated PBMCs secreted IL-6 that impaired mitochondrial respiration by reducing Complex I activity. Last, oral NR administration enhanced PBMC respiration and reduced proinflammatory cytokine gene expression in 4 HF subjects.
    CONCLUSION: These findings suggest that systemic inflammation in HF patients is causally linked to mitochondrial function of the PBMC. Increasing NAD levels may have the potential to improve mitochondrial respiration and attenuate proinflammatory activation of PBMC in HF. FundingThis study is funded by NIH R21 HL126209 (to RT and KO), NIH R01 HL144937 (to KO and RT) and University of Washington ITHS Catalyst Award (to DDW). Both BZ (18POST33990352) and DDW (18POST34030098) are funded by the AHA Postdoctoral Fellowships.
    Keywords:  Cardiology; Cardiovascular disease; Drug therapy; Inflammation; Mitochondria
    DOI:  https://doi.org/10.1172/JCI138538
  50. Nat Med. 2020 Aug 10.
    Adhikari AN, Gallagher RC, Wang Y, Currier RJ, Amatuni G, Bassaganyas L, Chen F, Kundu K, Kvale M, Mooney SD, Nussbaum RL, Randi SS, Sanford J, Shieh JT, Srinivasan R, Sunderam U, Tang H, Vaka D, Zou Y, Koenig BA, Kwok PY, Risch N, Puck JM, Brenner SE.
      Public health newborn screening (NBS) programs provide population-scale ascertainment of rare, treatable conditions that require urgent intervention. Tandem mass spectrometry (MS/MS) is currently used to screen newborns for a panel of rare inborn errors of metabolism (IEMs)1-4. The NBSeq project evaluated whole-exome sequencing (WES) as an innovative methodology for NBS. We obtained archived residual dried blood spots and data for nearly all IEM cases from the 4.5 million infants born in California between mid-2005 and 2013 and from some infants who screened positive by MS/MS, but were unaffected upon follow-up testing. WES had an overall sensitivity of 88% and specificity of 98.4%, compared to 99.0% and 99.8%, respectively for MS/MS, although effectiveness varied among individual IEMs. Thus, WES alone was insufficiently sensitive or specific to be a primary screen for most NBS IEMs. However, as a secondary test for infants with abnormal MS/MS screens, WES could reduce false-positive results, facilitate timely case resolution and in some instances even suggest more appropriate or specific diagnosis than that initially obtained. This study represents the largest, to date, sequencing effort of an entire population of IEM-affected cases, allowing unbiased assessment of current capabilities of WES as a tool for population screening.
    DOI:  https://doi.org/10.1038/s41591-020-0966-5
  51. Nat Commun. 2020 Aug 13. 11(1): 4056
    Bosc C, Broin N, Fanjul M, Saland E, Farge T, Courdy C, Batut A, Masoud R, Larrue C, Skuli S, Espagnolle N, Pagès JC, Carrier A, Bost F, Bertrand-Michel J, Tamburini J, Récher C, Bertoli S, Mansat-De Mas V, Manenti S, Sarry JE, Joffre C.
      Autophagy has been associated with oncogenesis with one of its emerging key functions being its contribution to the metabolism of tumors. Therefore, deciphering the mechanisms of how autophagy supports tumor cell metabolism is essential. Here, we demonstrate that the inhibition of autophagy induces an accumulation of lipid droplets (LD) due to a decrease in fatty acid β-oxidation, that leads to a reduction of oxidative phosphorylation (OxPHOS) in acute myeloid leukemia (AML), but not in normal cells. Thus, the autophagic process participates in lipid catabolism that supports OxPHOS in AML cells. Interestingly, the inhibition of OxPHOS leads to LD accumulation with the concomitant inhibition of autophagy. Mechanistically, we show that the disruption of mitochondria-endoplasmic reticulum (ER) contact sites (MERCs) phenocopies OxPHOS inhibition. Altogether, our data establish that mitochondria, through the regulation of MERCs, controls autophagy that, in turn finely tunes lipid degradation to fuel OxPHOS supporting proliferation and growth in leukemia.
    DOI:  https://doi.org/10.1038/s41467-020-17882-2
  52. Clin Nutr. 2020 Jul 31. pii: S0261-5614(20)30380-0. [Epub ahead of print]
    Moinard C, Fontaine E.
      Muscle protein synthesis (MPS) is a complex and finely-regulated mechanism that plays a key role in muscle homeostasis. Amino acid bioavailability is widely considered a major driver of MPS regulation via mTOR pathway activation. However, recent results suggest that amino acid bioavailability affects cellular energy status. Whatever the tool used to modulate energy status (amino acid depletion or mild mitochondrial uncoupling), a decrease in cellular energy status decreases MPS, without necessarily involving the mTOR pathway. Here we propose that energy status directly regulates one or several energy-consuming step(s) during MPS. This new paradigm modifies our vision of protein metabolism and raises prospects for new advances in therapeutics.
    Keywords:  ATP; Amino acids; Energy status; Malnutrition; Muscle protein synthesis
    DOI:  https://doi.org/10.1016/j.clnu.2020.07.015
  53. Nat Commun. 2020 Aug 07. 11(1): 3978
    Xu Q, Li Y, Gao X, Kang K, Williams JG, Tong L, Liu J, Ji M, Deterding LJ, Tong X, Locasale JW, Li L, Shats I, Li X.
      Methionine restriction, a dietary regimen that protects against metabolic diseases and aging, represses cancer growth and improves cancer therapy. However, the response of different cancer cells to this nutritional manipulation is highly variable, and the molecular determinants of this heterogeneity remain poorly understood. Here we report that hepatocyte nuclear factor 4α (HNF4α) dictates the sensitivity of liver cancer to methionine restriction. We show that hepatic sulfur amino acid (SAA) metabolism is under transcriptional control of HNF4α. Knocking down HNF4α or SAA enzymes in HNF4α-positive epithelial liver cancer lines impairs SAA metabolism, increases resistance to methionine restriction or sorafenib, promotes epithelial-mesenchymal transition, and induces cell migration. Conversely, genetic or metabolic restoration of the transsulfuration pathway in SAA metabolism significantly alleviates the outcomes induced by HNF4α deficiency in liver cancer cells. Our study identifies HNF4α as a regulator of hepatic SAA metabolism that regulates the sensitivity of liver cancer to methionine restriction.
    DOI:  https://doi.org/10.1038/s41467-020-17818-w
  54. Science. 2020 Aug 14. 369(6505): 858-862
    Iwata R, Casimir P, Vanderhaeghen P.
      The conversion of neural stem cells into neurons is associated with the remodeling of organelles, but whether and how this is causally linked to fate change is poorly understood. We examined and manipulated mitochondrial dynamics during mouse and human cortical neurogenesis. We reveal that shortly after cortical stem cells have divided, daughter cells destined to self-renew undergo mitochondrial fusion, whereas those that retain high levels of mitochondria fission become neurons. Increased mitochondria fission promotes neuronal fate, whereas induction of mitochondria fusion after mitosis redirects daughter cells toward self-renewal. This occurs during a restricted time window that is doubled in human cells, in line with their increased self-renewal capacity. Our data reveal a postmitotic period of fate plasticity in which mitochondrial dynamics are linked with cell fate.
    DOI:  https://doi.org/10.1126/science.aba9760
  55. Nat Biotechnol. 2020 Aug 12.
    Lareau CA, Ludwig LS, Muus C, Gohil SH, Zhao T, Chiang Z, Pelka K, Verboon JM, Luo W, Christian E, Rosebrock D, Getz G, Boland GM, Chen F, Buenrostro JD, Hacohen N, Wu CJ, Aryee MJ, Regev A, Sankaran VG.
      Natural mitochondrial DNA (mtDNA) mutations enable the inference of clonal relationships among cells. mtDNA can be profiled along with measures of cell state, but has not yet been combined with the massively parallel approaches needed to tackle the complexity of human tissue. Here, we introduce a high-throughput, droplet-based mitochondrial single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq), a method that combines high-confidence mtDNA mutation calling in thousands of single cells with their concomitant high-quality accessible chromatin profile. This enables the inference of mtDNA heteroplasmy, clonal relationships, cell state and accessible chromatin variation in individual cells. We reveal single-cell variation in heteroplasmy of a pathologic mtDNA variant, which we associate with intra-individual chromatin variability and clonal evolution. We clonally trace thousands of cells from cancers, linking epigenomic variability to subclonal evolution, and infer cellular dynamics of differentiating hematopoietic cells in vitro and in vivo. Taken together, our approach enables the study of cellular population dynamics and clonal properties in vivo.
    DOI:  https://doi.org/10.1038/s41587-020-0645-6
  56. Rev Physiol Biochem Pharmacol. 2020 Aug 14.
    Danese A, Marchi S, Vitto VAM, Modesti L, Leo S, Wieckowski MR, Giorgi C, Pinton P.
      Endoplasmic reticulum (ER)-mitochondria regions are specialized subdomains called also mitochondria-associated membranes (MAMs). MAMs allow regulation of lipid synthesis and represent hubs for ion and metabolite signaling. As these two organelles can module both the amplitude and the spatiotemporal patterns of calcium (Ca2+) signals, this particular interaction controls several Ca2+-dependent pathways well known for their contribution to tumorigenesis, such as metabolism, survival, sensitivity to cell death, and metastasis. Mitochondria-mediated apoptosis arises from mitochondrial Ca2+ overload, permeabilization of the mitochondrial outer membrane, and the release of mitochondrial apoptotic factors into the cytosol. Decreases in Ca2+ signaling at the ER-mitochondria interface are being studied in depth as failure of apoptotic-dependent cell death is one of the predominant characteristics of cancer cells. However, some recent papers that linked MAMs Ca2+ crosstalk-related upregulation to tumor onset and progression have aroused the interest of the scientific community.In this review, we will describe how different MAMs-localized proteins modulate the effectiveness of Ca2+-dependent apoptotic stimuli by causing both increases and decreases in the ER-mitochondria interplay and, specifically, by modulating Ca2+ signaling.
    Keywords:  Calcium; Calcium signaling; Cancer; Downregulation; MAMs; Upregulation
    DOI:  https://doi.org/10.1007/112_2020_43
  57. Nature. 2020 Aug 12.
    Muthusamy T, Cordes T, Handzlik MK, You L, Lim EW, Gengatharan J, Pinto AFM, Badur MG, Kolar MJ, Wallace M, Saghatelian A, Metallo CM.
      Serine, glycine and other nonessential amino acids are critical for tumour progression, and strategies to limit their availability are emerging as potential therapies for cancer1-3. However, the molecular mechanisms driving this response remain unclear and the effects on lipid metabolism are relatively unexplored. Serine palmitoyltransferase (SPT) catalyses the de novo biosynthesis of sphingolipids but also produces noncanonical 1-deoxysphingolipids when using alanine as a substrate4,5. Deoxysphingolipids accumulate in the context of mutations in SPTLC1 or SPTLC26,7-or in conditions of low serine availability8,9-to drive neuropathy, and deoxysphinganine has previously been investigated as an anti-cancer agent10. Here we exploit amino acid metabolism and the promiscuity of SPT to modulate the endogenous synthesis of toxic deoxysphingolipids and slow tumour progression. Anchorage-independent growth reprogrammes a metabolic network involving serine, alanine and pyruvate that drives the endogenous synthesis and accumulation of deoxysphingolipids. Targeting the mitochondrial pyruvate carrier promotes alanine oxidation to mitigate deoxysphingolipid synthesis and improve spheroid growth, similar to phenotypes observed with the direct inhibition of SPT or ceramide synthesis. Restriction of dietary serine and glycine potently induces the accumulation of deoxysphingolipids while decreasing tumour growth in xenograft models in mice. Pharmacological inhibition of SPT rescues xenograft growth in mice fed diets restricted in serine and glycine, and the reduction of circulating serine by inhibition of phosphoglycerate dehydrogenase (PHGDH) leads to the accumulation of deoxysphingolipids and mitigates tumour growth. The promiscuity of SPT therefore links serine and mitochondrial alanine metabolism to membrane lipid diversity, which further sensitizes tumours to metabolic stress.
    DOI:  https://doi.org/10.1038/s41586-020-2609-x