bims-meprid Biomed News
on Metabolic-dependent epigenetic reprogramming in differentiation and disease
Issue of 2021–08–29
nine papers selected by
Alessandro Carrer, Veneto Institute of Molecular Medicine
  1. A Single LC-MS/MS Analysis to Quantify CoA Biosynthetic Intermediates and Short-Chain Acyl CoAs.
  2. Metabolic Enzymes Function as Epigenetic Modulators: A Trojan Horse for Chromatin Regulation and Gene Expression.
  3. Histone Lysine Lactylation Regulates Gene Expression.
  4. Metabolic Controls on Epigenetic Reprogramming in Regulatory T Cells.
  5. Urinary 2-Hydroxyglutarate Enantiomers Are Markedly Elevated in a Murine Model of Type 2 Diabetic Kidney Disease.
  6. Pancreatic Cancer Cell Fate Is Mediated by a p53-α-Ketoglutarate Link.
  7. IDH1 mutant glioma is preferentially sensitive to the HDAC inhibitor panobinostat.
  8. Hexosamine Biosynthetic Pathway-Derived O-GlcNAcylation Is Critical for RANKL-Mediated Osteoclast Differentiation.
  9. Cell cycle induction in human cardiomyocytes is dependent on biosynthetic pathway activation.
  1. Metabolites. 2021 Jul 21. pii: 468. [Epub ahead of print]11(8):
    A Single LC-MS/MS Analysis to Quantify CoA Biosynthetic Intermediates and Short-Chain Acyl CoAs.
    Anthony E Jones, Nataly J Arias, Aracely Acevedo, Srinivasa T Reddy, Ajit S Divakaruni, David Meriwether.
      Coenzyme A (CoA) is an essential cofactor for dozens of reactions in intermediary metabolism. Dysregulation of CoA synthesis or acyl CoA metabolism can result in metabolic or neurodegenerative disease. Although several methods use liquid chromatography coupled with mass spectrometry/mass spectrometry (LC-MS/MS) to quantify acyl CoA levels in biological samples, few allow for simultaneous measurement of intermediates in the CoA biosynthetic pathway. Here we describe a simple sample preparation and LC-MS/MS method that can measure both short-chain acyl CoAs and biosynthetic precursors of CoA. The method does not require use of a solid phase extraction column during sample preparation and exhibits high sensitivity, precision, and accuracy. It reproduces expected changes from known effectors of cellular CoA homeostasis and helps clarify the mechanism by which excess concentrations of etomoxir reduce intracellular CoA levels.
    Keywords:  CoA biosynthesis; LC-MS/MS; etomoxir; mitochondria; short-chain acyl CoAs
    DOI:  https://doi.org/10.3390/metabo11080468
  2. Pharmacol Res. 2021 Aug 24. pii: S1043-6618(21)00418-7. [Epub ahead of print] 105834
    Metabolic Enzymes Function as Epigenetic Modulators: A Trojan Horse for Chromatin Regulation and Gene Expression.
    Xiaoyu Liao, Yifan Guo, Yumin He, Yanxuan Xiao, Jingyi Li, Rui Liu.
      Epigenetic modification is a fundamental biological process in living organisms, which has significant impact on health and behavior. Metabolism refers to a set of life-sustaining chemical reactions, including the uptake of nutrients, the subsequent conversion of nutrients into energy or building blocks for organism growth, and finally the clearance of redundant or toxic substances. It is well established that epigenetic modifications govern the metabolic profile of a cell by modulating the expression of metabolic enzymes. Strikingly, almost all the epigenetic modifications require substrates produced by cellular metabolism, and a large proportion of metabolic enzymes can transfer into nucleus to locally produce substrates for epigenetic modification, thereby providing an alternative link between metabolism, epigenetic modification and gene expression. Here, we summarize the recent literature pertinent to metabolic enzymes functioning as epigenetic modulators in the regulation of chromatin architecture and gene expression.
    Keywords:  RNA modification; epigenetic modification; gene expression; metabolic enzyme; metabolites
    DOI:  https://doi.org/10.1016/j.phrs.2021.105834
  3. Cancer Discov. 2019 Dec;9(12): 1643
    Histone Lysine Lactylation Regulates Gene Expression.
      A previously unknown histone modification, lysine lactylation, was found in mouse and human cells.
    DOI:  https://doi.org/10.1158/2159-8290.CD-RW2019-163
  4. Front Immunol. 2021 ;12 728783
    Metabolic Controls on Epigenetic Reprogramming in Regulatory T Cells.
    Jingli Lu, Yan Liang, Haiyang Meng, Ailing Zhang, Junjie Zhao, Chengliang Zhang.
      Forkhead box protein 3 (Foxp3+)-expressing regulatory T (Treg) cells are a unique CD4+T cell subset that suppresses excessive immune responses. The epigenetic plasticity and metabolic traits of Treg cells are crucial for the acquisition of their phenotypic and functional characteristics. Therefore, alterations to the epigenetics and metabolism affect Treg cell development and function. Recent evidence reveals that altering the metabolic pathways and generation of metabolites can regulate the epigenetics of Treg cells. Specifically, some intermediates of cell metabolism can directly act as substrates or cofactors of epigenetic-modifying enzymes. Here, we describe the metabolic and epigenetic features during Treg cell development, and discuss how metabolites can contribute to epigenetic alterations of Treg cells, which affects Treg cell activation, differentiation, and function.
    Keywords:  epigenetics; immune suppression; metabolism; metabolites; regulatory T cells
    DOI:  https://doi.org/10.3389/fimmu.2021.728783
  5. Metabolites. 2021 Jul 21. pii: 469. [Epub ahead of print]11(8):
    Urinary 2-Hydroxyglutarate Enantiomers Are Markedly Elevated in a Murine Model of Type 2 Diabetic Kidney Disease.
    Judy Baek, Subramaniam Pennathur.
      Metabolic reprogramming is a hallmark of diabetic kidney disease (DKD); nutrient overload leads to increased production of metabolic byproducts that may become toxic at high levels. One metabolic byproduct may be 2-hydroxyglutarate (2-HG), a metabolite with many regulatory functions that exists in both enantiomeric forms physiologically. We quantitatively determined the levels of L and D-2HG enantiomers in the urine, plasma, and kidney cortex of db/db mice, a pathophysiologically relevant murine model of type 2 diabetes and DKD. We found increased fractional excretion of both L and D-2HG enantiomers, suggesting increased tubular secretion and/or production of the two metabolites in DKD. Quantitation of TCA cycle metabolites in db/db cortex suggests that TCA cycle overload and an increase in 2-HG precursor substrate, α-ketoglutarate, drive the increased L and D-2HG production in DKD. In conclusion, we demonstrated increased 2-HG enantiomer production and urinary excretion in murine type 2 DKD, which may contribute to metabolic reprogramming and progression of diabetic kidney disease.
    Keywords:  2-hydroxyglutarate; TCA cycle; biomarker; diabetic kidney disease; mitochondria
    DOI:  https://doi.org/10.3390/metabo11080469
  6. Cancer Discov. 2019 Nov;9(11): 1480
    Pancreatic Cancer Cell Fate Is Mediated by a p53-α-Ketoglutarate Link.
      Restoration of p53 led to an accumulation of αKG in mouse pancreatic cancer cells.
    DOI:  https://doi.org/10.1158/2159-8290.CD-RW2019-148
  7. J Neurooncol. 2021 Aug 23.
    IDH1 mutant glioma is preferentially sensitive to the HDAC inhibitor panobinostat.
    Thomas K Sears, Craig M Horbinski, Kevin D Woolard.
       INTRODUCTION: A large subset of diffusely infiltrative gliomas contains a gain-of-function mutation in isocitrate dehydrogenase 1 or 2 (IDH1/2mut) which produces 2-hydroxglutarate, an inhibitor of α-ketoglutarate-dependent DNA demethylases, thereby inducing widespread DNA and histone methylation. Because histone deacetylase (HDAC) enzymes are localized to methylated chromatin via methyl-binding domain proteins, IDH1/2mut gliomas may be more dependent on HDAC activity, and therefore may be more sensitive to HDAC inhibitors.
    METHODS: Six cultured patient-derived glioma cell lines, IDH1wt (n = 3) and IDH1mut (n = 3), were treated with an FDA-approved HDAC inhibitor, panobinostat. Cellular cytotoxicity and proliferation assays were conducted by flow cytometry. Histone modifications and cell signaling pathways were assessed using immunoblot and/or ELISA.
    RESULTS: IDH1mut gliomas exhibited marked upregulation of genes associated with the HDAC activity. Glioma cell cultures bearing IDH1mut were significantly more sensitive to the cytotoxic and antiproliferative effects of panobinostat, compared to IDH1wt glioma cells. Panobinostat caused a greater increase in acetylation of the histone residues H3K14, H3K18, and H3K27 in IDH1mut glioma cells. Another HDAC inhibitor, valproic acid, was also more effective against IDH1mut glioma cells.
    CONCLUSION: These data suggest that IDH1mut gliomas may be preferentially sensitive to HDAC inhibitors. Further, IDH1mut glioma cultures showed enhanced accumulation of acetylated histone residues in response to panobinostat treatment, suggesting a direct epigenetic mechanism for this sensitivity. This provides a rationale for further exploration of HDAC inhibitors against IDH1mut gliomas.
    Keywords:  Histone deacetylase (HDAC) inhibition; Isocitrate dehydrogenase (IDH) mutant glioma; Panobinostat; Valproic acid
    DOI:  https://doi.org/10.1007/s11060-021-03829-0
  8. Int J Mol Sci. 2021 Aug 18. pii: 8888. [Epub ahead of print]22(16):
    Hexosamine Biosynthetic Pathway-Derived O-GlcNAcylation Is Critical for RANKL-Mediated Osteoclast Differentiation.
    Myoung Jun Kim, Hyuk Soon Kim, Sangyong Lee, Keun Young Min, Wahn Soo Choi, Jueng Soo You.
      O-linked-N-acetylglucosaminylation (O-GlcNAcylation) performed by O-GlcNAc transferase (OGT) is a nutrient-responsive post-translational modification (PTM) via the hexosamine biosynthetic pathway (HBP). Various transcription factors (TFs) are O-GlcNAcylated, affecting their activities and significantly contributing to cellular processes ranging from survival to cellular differentiation. Given the pleiotropic functions of O-GlcNAc modification, it has been studied in various fields; however, the role of O-GlcNAcylation during osteoclast differentiation remains to be explored. Kinetic transcriptome analysis during receptor activator of nuclear factor-kappaB (NF-κB) ligand (RANKL)-mediated osteoclast differentiation revealed that the nexus of major nutrient metabolism, HBP was critical for this process. We observed that the critical genes related to HBP activation, including Nagk, Gfpt1, and Ogt, were upregulated, while the global O-GlcNAcylation was increased concomitantly during osteoclast differentiation. The O-GlcNAcylation inhibition by the small-molecule inhibitor OSMI-1 reduced osteoclast differentiation in vitro and in vivo by disrupting the translocation of NF-κB p65 and nuclear factor of activated T cells c1 (NFATc1) into the nucleus by controlling their PTM O-GlcNAcylation. Furthermore, OSMI-1 had a synergistic effect with bone target therapy on osteoclastogenesis. Lastly, knocking down Ogt with shRNA (shOgt) mimicked OSMI-1's effect on osteoclastogenesis. Targeting O-GlcNAcylation during osteoclast differentiation may be a valuable therapeutic approach for osteoclast-activated bone diseases.
    Keywords:  NFATc1; O-GlcNAc transferase; O-GlcNAcylation; osteoclast; osteoclastogenesis; p65
    DOI:  https://doi.org/10.3390/ijms22168888
  9. Redox Biol. 2021 Aug 05. pii: S2213-2317(21)00253-6. [Epub ahead of print]46 102094
    Cell cycle induction in human cardiomyocytes is dependent on biosynthetic pathway activation.
    Riham R E Abouleisa, Lindsey McNally, Abou Bakr M Salama, Sally K Hammad, Qinghui Ou, Collin Wells, Pawel K Lorkiewicz, Roberto Bolli, Tamer M A Mohamed, Bradford G Hill.
       AIMS: The coordinated gene and metabolic programs that facilitate cardiomyocyte entry and progression in the cell cycle are poorly understood. The purpose of this study was to identify the metabolic changes that influence myocyte proliferation.
    METHODS AND RESULTS: In adult mouse cardiomyocytes and human induced pluripotent stem cell cardiomyocytes (hiPS-CMs), cell cycle initiation by ectopic expression of Cyclin B1, Cyclin D1, CDK1, and CDK4 (termed 4F) downregulated oxidative phosphorylation genes and upregulated genes that regulate ancillary biosynthetic pathways of glucose metabolism. Results from metabolic analyses and stable isotope tracing experiments indicate that 4F-mediated cell cycle induction in hiPS-CMs decreases glucose oxidation and oxidative phosphorylation and augments NAD+, glycogen, hexosamine, phospholipid, and serine biosynthetic pathway activity. Interventions that diminish NAD+ synthesis, serine synthesis, or protein O-GlcNAcylation decreased 4F-mediated cell cycle entry. In a gain of function approach, we overexpressed phosphoenolpyruvate carboxykinase 2 (PCK2), which can drive carbon from the Krebs cycle to the glycolytic intermediate pool, and found that PCK2 augments 4F-mediated cell cycle entry.
    CONCLUSIONS: These findings suggest that a metabolic shift from catabolic to anabolic activity is a critical step for cardiomyocyte cell cycle entry and is required to facilitate proliferation.
    DOI:  https://doi.org/10.1016/j.redox.2021.102094
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