bims-medhac Biomed News
on Metabolism dependent histone acetylation
Issue of 2020–07–12
seven papers selected by
Alessandro Carrer, Veneto Institute of Molecular Medicine
  1. Sustained Activation of AMPK Enhances Differentiation of Human iPSC-Derived Cardiomyocytes via Sirtuin Activation.
  2. Linking epigenetic dysregulation, mitochondrial impairment, and metabolic dysfunction in SBMA motor neurons.
  3. Inhalation exposure to cigarette smoke and inflammatory agents induces epigenetic changes in the lung.
  4. Oxidized ATM promotes breast cancer stem cell enrichment through energy metabolism reprogram-mediated acetyl-CoA accumulation.
  5. Nutrient Sensing by Histone Marks: Reading the Metabolic Histone Code Using Tracing, Omics, and Modeling.
  6. Metabolite sensing and signaling in Cancer.
  7. Cellular metabolism and homeostasis in pluripotency regulation.
  1. Stem Cell Reports. 2020 Jun 28. pii: S2213-6711(20)30233-2. [Epub ahead of print]
    Sustained Activation of AMPK Enhances Differentiation of Human iPSC-Derived Cardiomyocytes via Sirtuin Activation.
    Mohsen Sarikhani, Jessica C Garbern, Sai Ma, Rebecca Sereda, Jeffrey Conde, Guido Krähenbühl, Gabriela O Escalante, Aishah Ahmed, Jason D Buenrostro, Richard T Lee.
      Recent studies suggest that metabolic regulation may improve differentiation of cardiomyocytes derived from induced pluripotent stem cells (iPSCs). AMP-activated protein kinase (AMPK) is a master regulator of metabolic activities. We investigated whether AMPK participates in iPSC-derived cardiomyocyte differentiation. We observed that AMPK phosphorylation at Thr172 increased at day 9 but then decreased after day 11 of differentiation to cardiomyocytes. Inhibition of AMPK with compound C significantly reduced mRNA and protein expression of cardiac troponins TNNT2 and TNNI3. Moreover, sustained AMPK activation using AICAR from days 9 to 14 of differentiation increased mRNA and protein expression of both TNNT2 and TNNI3. AICAR decreased acetylation of histone 3 at Lys9 and 56 and histone 4 at Lys16 (known target sites for nuclear-localized sirtuins [SIRT1, SIRT6]), suggesting that AMPK activation enhances sirtuin activity. Sustained AMPK activation during days 9-14 of differentiation induces sirtuin-mediated histone deacetylation and may enhance cardiomyocyte differentiation from iPSCs.
    Keywords:  AMPK; histone acetylation; iPSC-derived cardiomyocytes; sirtuin
    DOI:  https://doi.org/10.1016/j.stemcr.2020.06.012
  2. JCI Insight. 2020 Jul 09. pii: 136539. [Epub ahead of print]5(13):
    Linking epigenetic dysregulation, mitochondrial impairment, and metabolic dysfunction in SBMA motor neurons.
    Naemeh Pourshafie, Ester Masati, Eric Bunker, Alec R Nickolls, Parisorn Thepmankorn, Kory Johnson, Xia Feng, Tyler Ekins, Christopher Grunseich, Kenneth H Fischbeck.
      Spinal and bulbar muscular atrophy (SBMA) is a neuromuscular disorder caused by a polyglutamine expansion in the androgen receptor (AR). Using gene expression analysis and ChIP sequencing, we mapped transcriptional changes in genetically engineered patient stem cell-derived motor neurons. We found that transcriptional dysregulation in SBMA can occur through AR-mediated histone modification. We detected reduced histone acetylation, along with decreased expression of genes encoding compensatory metabolic proteins and reduced substrate availability for mitochondrial function. Furthermore, we found that pyruvate supplementation corrected this deficiency and improved mitochondrial function and SBMA motor neuron viability. We propose that epigenetic dysregulation of metabolic genes contributes to reduced mitochondrial ATP production. Our results show a molecular link between altered epigenetic regulation and mitochondrial metabolism that contributes to neurodegeneration.
    Keywords:  Epigenetics; Genetics; Mitochondria; Neurological disorders; Neuroscience
    DOI:  https://doi.org/10.1172/jci.insight.136539
  3. Sci Rep. 2020 Jul 09. 10(1): 11290
    Inhalation exposure to cigarette smoke and inflammatory agents induces epigenetic changes in the lung.
    Christopher L Seiler, J Ung Min Song, Delshanee Kotandeniya, Jianji Chen, Thomas J Y Kono, Qiyuan Han, Mathia Colwell, Benjamin Auch, Aaron L Sarver, Pramod Upadhyaya, Yanan Ren, Christopher Faulk, Silvio De Flora, Sebastiano La Maestra, Yue Chen, Fekadu Kassie, Natalia Y Tretyakova.
      Smoking-related lung tumors are characterized by profound epigenetic changes including scrambled patterns of DNA methylation, deregulated histone acetylation, altered gene expression levels, distorted microRNA profiles, and a global loss of cytosine hydroxymethylation marks. Here, we employed an enhanced version of bisulfite sequencing (RRBS/oxRRBS) followed by next generation sequencing to separately map DNA epigenetic marks 5-methyl-dC and 5-hydroxymethyl-dC in genomic DNA isolated from lungs of A/J mice exposed whole-body to environmental cigarette smoke for 10 weeks. Exposure to cigarette smoke significantly affected the patterns of cytosine methylation and hydroxymethylation in the lungs. Differentially hydroxymethylated regions were associated with inflammatory response/disease, organismal injury, and respiratory diseases and were involved in regulation of cellular development, function, growth, and proliferation. To identify epigenetic changes in the lung associated with exposure to tobacco carcinogens and inflammation, A/J mice were intranasally treated with the tobacco carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), the inflammatory agent lipopolysaccharide (LPS), or both. NNK alone caused minimal epigenetic alterations, while exposure either to LPS or NNK/LPS in combination led to increased levels of global cytosine methylation and formylation, reduced cytosine hydroxymethylation, decreased histone acetylation, and altered expression levels of multiple genes. Our results suggest that inflammatory processes are responsible for epigenetic changes contributing to lung cancer development.
    DOI:  https://doi.org/10.1038/s41598-020-67502-8
  4. Cell Death Dis. 2020 Jul 03. 11(7): 508
    Oxidized ATM promotes breast cancer stem cell enrichment through energy metabolism reprogram-mediated acetyl-CoA accumulation.
    Dan Yang, Meixi Peng, Yixuan Hou, Yilu Qin, Xueying Wan, Pengpeng Zhu, Shuiqing Liu, Liping Yang, Huan Zeng, Ting Jin, Yuxiang Qiu, Qiao Li, Manran Liu.
      Cancer stem cell (CSC) is a challenge in the therapy of triple-negative breast cancer (TNBC). Intratumoral hypoxia is a common feature of solid tumor. Hypoxia may contribute to the maintenance of CSC, resulting in a poor efficacy of traditional treatment and recurrence of TNBC cases. However, the underlying molecular mechanism involved in hypoxia-induced CSC stemness maintenance remains unclear. Here, we report that hypoxia stimulated DNA double-strand breaks independent of ATM kinase activation (called oxidized ATM in this paper) play a crucial role in TNBC mammosphere formation and stemness maintenance by governing a specific energy metabolism reprogramming (EMR). Oxidized ATM up-regulates GLUT1, PKM2, and PDHa expressions to enhance the uptake of glucose and production of pyruvate rather than lactate products, which facilitates glycolytic flux to mitochondrial pyruvate and citrate, thus resulting in accumulation of cytoplasmic acetyl-CoA instead of the tricarboxylic acid (TCA) cycle by regulating ATP-citrate lyase (ACLY) activity. Our findings unravel a novel model of TNBC-CSC glucose metabolism and its functional role in maintenance of hypoxic TNBC-CSC stemness. This work may help us to develop new therapeutic strategies for TNBC treatment.
    DOI:  https://doi.org/10.1038/s41419-020-2714-7
  5. Bioessays. 2020 Jul 08. e2000083
    Nutrient Sensing by Histone Marks: Reading the Metabolic Histone Code Using Tracing, Omics, and Modeling.
    Scott E Campit, Alia Meliki, Neil A Youngson, Sriram Chandrasekaran.
      Several metabolites serve as substrates for histone modifications and communicate changes in the metabolic environment to the epigenome. Technologies such as metabolomics and proteomics have allowed us to reconstruct the interactions between metabolic pathways and histones. These technologies have shed light on how nutrient availability can have a dramatic effect on various histone modifications. This metabolism-epigenome cross talk plays a fundamental role in development, immune function, and diseases like cancer. Yet, major challenges remain in understanding the interactions between cellular metabolism and the epigenome. How the levels and fluxes of various metabolites impact epigenetic marks is still unclear. Discussed herein are recent applications and the potential of systems biology methods such as flux tracing and metabolic modeling to address these challenges and to uncover new metabolic-epigenetic interactions. These systems approaches can ultimately help elucidate how nutrients shape the epigenome of microbes and mammalian cells.
    DOI:  https://doi.org/10.1002/bies.202000083
  6. J Biol Chem. 2020 Jul 07. pii: jbc.REV119.007624. [Epub ahead of print]
    Metabolite sensing and signaling in Cancer.
    Yi-Ping Wang, Jin-Tao Li, Jia Qu, Miao Yin, Qun-Ying Lei.
      Metabolites are not only substrates in metabolic reactions, but also signaling molecules controlling a wide range of cellular processes. Discovery of the oncometabolite 2-hydroxyglutarate (2HG) provides an important link between metabolic dysfunction and cancer, unveiling the signaling function of metabolites in regulating epigenetic and epitranscriptomic modifications, genome integrity, and signal transduction. It is now known that cancer cells sense and remodel their metabolic network to support biogenesis, caused by or resulting in the dysregulation of various metabolites. Cancer cells can sense alterations in metabolic intermediates to better coordinate multiple biological processes and enhance cell metabolism. Recent studies have demonstrated that metabolite signaling is involved in the regulation of malignant transformation, cell proliferation, epithelial-to-mesenchymal transition (EMT), differentiation blockade, and cancer stemness. Additionally, intercellular metabolite signaling modulates inflammatory response and immunosurveillance in the tumor microenvironment. Here, we review recent advances in cancer-associated metabolite signaling. An in-depth understanding of metabolite signaling will provide new opportunities for the development of therapeutic interventions that target cancer.
    Keywords:  Metabolite; Sensing; Signaling; cancer; metabolic disease; metabolic regulation; metabolomics; oncometabolite; signaling
    DOI:  https://doi.org/10.1074/jbc.REV119.007624
  7. Protein Cell. 2020 Jul 08.
    Cellular metabolism and homeostasis in pluripotency regulation.
    Kun Liu, Jiani Cao, Xingxing Shi, Liang Wang, Tongbiao Zhao.
      Pluripotent stem cells (PSCs) can immortally self-renew in culture with a high proliferation rate, and they possess unique metabolic characteristics that facilitate pluripotency regulation. Here, we review recent progress in understanding the mechanisms that link cellular metabolism and homeostasis to pluripotency regulation, with particular emphasis on pathways involving amino acid metabolism, lipid metabolism, the ubiquitin-proteasome system and autophagy. Metabolism of amino acids and lipids is tightly coupled to epigenetic modification, organelle remodeling and cell signaling pathways for pluripotency regulation. PSCs harness enhanced proteasome and autophagy activity to meet the material and energy requirements for cellular homeostasis. These regulatory events reflect a fine balance between the intrinsic cellular requirements and the extrinsic environment. A more complete understanding of this balance will pave new ways to manipulate PSC fate.
    Keywords:  amino acid metabolism; autophagy; lipid metabolism; pluripotent stem cell (PSC); ubiquitin-proteasome system (UPS)
    DOI:  https://doi.org/10.1007/s13238-020-00755-1
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