bims-meprid 2021-07-04 papers

bims-meprid

Biomed News

on Metabolic-dependent epigenetic reprogramming in differentiation and disease

Issue of 2021–07–04
nine papers selected by
Alessandro Carrer, Veneto Institute of Molecular Medicine

Transcriptional Profiling of Cardiac Cells Links Age-Dependent Changes in Acetyl-CoA Signaling to Chromatin Modifications.
The SESAME complex regulates cell senescence through the generation of acetyl-CoA.
Redirected nuclear glutamate dehydrogenase supplies Tet3 with α-ketoglutarate in neurons.
One carbon metabolism and early development: a diet-dependent destiny.
Metabolic Rewiring and the Characterization of Oncometabolites.
From the (Epi)Genome to Metabolism and Vice Versa; Examples from Hematologic Malignancy.
Comparative Analysis of Histone H3K4me3 Distribution in Mouse Liver in Different Diets Reveals the Epigenetic Efficacy of Cyanidin-3-O-glucoside Dietary Intake.
Chromatin Regulation in the Response of Ethylene: Nuclear Events in Ethylene Signaling.
Mitochondrial O-GlcNAc Transferase Interacts with and Modifies Many Proteins and Its Up-Regulation Affects Mitochondrial Function and Cellular Energy Homeostasis.

Int J Mol Sci. 2021 Jun 29. pii: 6987. [Epub ahead of print]22(13):

Transcriptional Profiling of Cardiac Cells Links Age-Dependent Changes in Acetyl-CoA Signaling to Chromatin Modifications.

Justin Kurian, Veronica Bohl, Michael Behanan, Sadia Mohsin, Mohsin Khan.

  Metabolism has emerged as a regulator of core stem cell properties such as proliferation, survival, self-renewal, and multilineage potential. Metabolites serve as secondary messengers, fine-tuning signaling pathways in response to microenvironment alterations. Studies show a role for central metabolite acetyl-CoA in the regulation of chromatin state through changes in histone acetylation. Nevertheless, metabolic regulators of chromatin remodeling in cardiac cells in response to increasing biological age remains unknown. Previously, we identified novel cardiac-derived stem-like cells (CTSCs) that exhibit increased functional properties in the neonatal heart (nCTSC). These cells are linked to a unique metabolism which is altered with CTSC aging (aCTSC). Here, we present an in-depth, RNA-sequencing-based (RNA-Seq) bioinformatic with cluster analysis that details a distinct epigenome present in nCTSCs but not in aCTSCs. Gene Ontology (GO) and pathway enrichment reveal biological processes, including metabolism, gene regulation enriched in nCTSCs, and STRING analysis that identifies a network of genes related to acetyl-CoA that can potentially influence chromatin remodeling. Additional validation by Western blot and qRT-PCR shows increased acetyl-CoA signaling and histone acetylation in nCTSCs compared to aCTSCs. In conclusion, our data reveal that the link between metabolism and histone acetylation in cardiac cells is altered with the aging of the cardiac tissue.

Keywords:  RNA sequencing; acetyl-CoA; bioinformatics; cardiac stem cells; chromatin remodeling; epigenetics; metabolism

DOI:  https://doi.org/10.3390/ijms22136987
Nat Metab. 2021 Jun 28.

The SESAME complex regulates cell senescence through the generation of acetyl-CoA.

Wanping Chen, Xilan Yu, Yinsheng Wu, Jie Tang, Qi Yu, Xiaodong Lv, Zitong Zha, Bicheng Hu, Xin Li, Jianguo Chen, Lixin Ma, Jerry L Workman, Shanshan Li.

Acetyl-CoA is a central node in carbon metabolism and plays critical roles in regulatory and biosynthetic processes. The acetyl-CoA synthetase Acs2, which catalyses acetyl-CoA production from acetate, is an integral subunit of the serine-responsive SAM-containing metabolic enzyme (SESAME) complex, but the precise function of Acs2 within the SESAME complex remains unclear. Here, using budding yeast, we show that Acs2 within the SESAME complex is required for the regulation of telomere silencing and cellular senescence. Mechanistically, the SESAME complex interacts with the histone acetyltransferase SAS protein complex to promote histone H4K16 acetylation (H4K16ac) enrichment and the occupancy of bromodomain-containing protein, Bdf1, at subtelomeric regions. This interaction maintains telomere silencing by antagonizing the spreading of Sir2 along the telomeres, which is enhanced by acetate. Consequently, dissociation of Sir2 from telomeres by acetate leads to compromised telomere silencing and accelerated chronological ageing. In human endothelial cells, ACSS2, the ortholog of yeast Acs2, also interacts with H4K16 acetyltransferase hMOF and are required for acetate to increase H4K16ac, reduce telomere silencing and induce cell senescence. Altogether, our results reveal a conserved mechanism to connect cell metabolism with telomere silencing and cellular senescence.

DOI: https://doi.org/10.1038/s42255-021-00412-9
Nat Commun. 2021 Jul 02. 12(1): 4100

Redirected nuclear glutamate dehydrogenase supplies Tet3 with α-ketoglutarate in neurons.

Franziska R Traube, Dilara Özdemir, Hanife Sahin, Constanze Scheel, Andrea F Glück, Anna S Geserich, Sabine Oganesian, Sarantos Kostidis, Katharina Iwan, René Rahimoff, Grazia Giorgio, Markus Müller, Fabio Spada, Martin Biel, Jürgen Cox, Martin Giera, Stylianos Michalakis, Thomas Carell.

Tet3 is the main α-ketoglutarate (αKG)-dependent dioxygenase in neurons that converts 5-methyl-dC into 5-hydroxymethyl-dC and further on to 5-formyl- and 5-carboxy-dC. Neurons possess high levels of 5-hydroxymethyl-dC that further increase during neural activity to establish transcriptional plasticity required for learning and memory functions. How αKG, which is mainly generated in mitochondria as an intermediate of the tricarboxylic acid cycle, is made available in the nucleus has remained an unresolved question in the connection between metabolism and epigenetics. We show that in neurons the mitochondrial enzyme glutamate dehydrogenase, which converts glutamate into αKG in an NAD+-dependent manner, is redirected to the nucleus by the αKG-consumer protein Tet3, suggesting on-site production of αKG. Further, glutamate dehydrogenase has a stimulatory effect on Tet3 demethylation activity in neurons, and neuronal activation increases the levels of αKG. Overall, the glutamate dehydrogenase-Tet3 interaction might have a role in epigenetic changes during neural plasticity.

DOI: https://doi.org/10.1038/s41467-021-24353-9
Trends Endocrinol Metab. 2021 Jun 28. pii: S1043-2760(21)00128-4. [Epub ahead of print]

One carbon metabolism and early development: a diet-dependent destiny.

Hunter W Korsmo, Xinyin Jiang.

  One carbon metabolism (OCM) is critical for early development, as it provides one carbon (1C) units for the biosynthesis of DNA, proteins, and lipids and epigenetic modification of the genome. Epigenetic marks established early in life can be maintained and exert lasting impacts on gene expression and functions later in life. Animal and human studies have increasingly demonstrated that prenatal 1C nutrient deficiencies impair fetal growth, neurodevelopment, and cardiometabolic parameters in childhood, while sufficient maternal 1C nutrient intake is protective against these detrimental outcomes. However, recent studies also highlight the potential risk of maternal 1C nutrient excess or imbalance in disrupting early development. Further studies are needed to delineate the dose-response relationship among prenatal 1C nutrient exposure, epigenetic modifications, and developmental outcomes.

Keywords:  early development; epigenetics; fetal programming; methyl donor; one carbon metabolism

DOI:  https://doi.org/10.1016/j.tem.2021.05.011
Cancers (Basel). 2021 Jun 10. pii: 2900. [Epub ahead of print]13(12):

Metabolic Rewiring and the Characterization of Oncometabolites.

Diren Beyoğlu, Jeffrey R Idle.

  The study of low-molecular-weight metabolites that exist in cells and organisms is known as metabolomics and is often conducted using mass spectrometry laboratory platforms. Definition of oncometabolites in the context of the metabolic phenotype of cancer cells has been accomplished through metabolomics. Oncometabolites result from mutations in cancer cell genes or from hypoxia-driven enzyme promiscuity. As a result, normal metabolites accumulate in cancer cells to unusually high concentrations or, alternatively, unusual metabolites are produced. The typical oncometabolites fumarate, succinate, (2R)-hydroxyglutarate and (2S)-hydroxyglutarate inhibit 2-oxoglutarate-dependent dioxygenases, such as histone demethylases and HIF prolyl-4-hydroxylases, together with DNA cytosine demethylases. As a result of the cancer cell acquiring this new metabolic phenotype, major changes in gene transcription occur and the modification of the epigenetic landscape of the cell promotes proliferation and progression of cancers. Stabilization of HIF1α through inhibition of HIF prolyl-4-hydroxylases by oncometabolites such as fumarate and succinate leads to a pseudohypoxic state that promotes inflammation, angiogenesis and metastasis. Metabolomics has additionally been employed to define the metabolic phenotype of cancer cells and patient biofluids in the search for cancer biomarkers. These efforts have led to the uncovering of the putative oncometabolites sarcosine, glycine, lactate, kynurenine, methylglyoxal, hypotaurine and (2R,3S)-dihydroxybutanoate, for which further research is required.

Keywords:  (2R)-hydroxyglutarate; (2S)-hydroxyglutarate; DNA demethylation; fumarate; histone demethylation; hypoxia; metabolomics; oncometabolite; succinate

DOI:  https://doi.org/10.3390/cancers13122900
Int J Mol Sci. 2021 Jun 12. pii: 6321. [Epub ahead of print]22(12):

From the (Epi)Genome to Metabolism and Vice Versa; Examples from Hematologic Malignancy.

Panagiota Karagianni, Stavroula Giannouli, Michael Voulgarelis.

  Hematologic malignancies comprise a heterogeneous group of neoplasms arising from hematopoietic cells or their precursors and most commonly presenting as leukemias, lymphomas, and myelomas. Genetic analyses have uncovered recurrent mutations which initiate or accumulate in the course of malignant transformation, as they provide selective growth advantage to the cell. These include mutations in genes encoding transcription factors and epigenetic regulators of metabolic genes, as well as genes encoding key metabolic enzymes. The resulting alterations contribute to the extensive metabolic reprogramming characterizing the transformed cell, supporting its increased biosynthetic needs and allowing it to withstand the metabolic stress that arises as a consequence of increased metabolic rates and changes in its microenvironment. Interestingly, this cross-talk is bidirectional, as metabolites also signal back to the nucleus and, via their widespread effects on modulating epigenetic modifications, shape the chromatin landscape and the transcriptional programs of the cell. In this article, we provide an overview of the main metabolic changes and relevant genetic alterations that characterize malignant hematopoiesis and discuss how, in turn, metabolites regulate epigenetic events during this process. The aim is to illustrate the intricate interrelationship between the genome (and epigenome) and metabolism and its relevance to hematologic malignancy.

Keywords:  epigenetic; genetic; hematologic malignancy; leukemia; lymphoma; metabolic; myelodysplastic syndrome; myeloma

DOI:  https://doi.org/10.3390/ijms22126321
Int J Mol Sci. 2021 Jun 17. pii: 6503. [Epub ahead of print]22(12):

Comparative Analysis of Histone H3K4me3 Distribution in Mouse Liver in Different Diets Reveals the Epigenetic Efficacy of Cyanidin-3-O-glucoside Dietary Intake.

Giuseppe Persico, Francesca Casciaro, Alessandra Marinelli, Chiara Tonelli, Katia Petroni, Marco Giorgio.

   BACKGROUND: Different diets result in significantly different phenotypes through metabolic and genomic reprogramming. Epigenetic marks, identified in humans and mouse models through caloric restriction, a high-fat diet or the intake of specific bioactives, suggest that genomic reprogramming drives this metabolic reprogramming and mediates the effect of nutrition on health. Histone modifications encode the epigenetic signal, which adapts genome functions to environmental conditions, including diets, by tuning the structure and properties of chromatin. To date, the effect of different diets on the genome-wide distribution of critical histone marks has not been determined.
METHODS: Using chromatin immunoprecipitation sequencing, we investigated the distribution of the trimethylation of lysine 4 of histone H3 in the liver of mice fed for one year with five different diets, including: chow containing yellow corn powder as an extra source of plant bioactives or specifically enriched with cyanidin-3-O-Glucoside, high-fat-enriched obesogenic diets, and caloric-restricted pro-longevity diets.
CONCLUSIONS: Comparison of the resulting histone mark profiles revealed that functional food containing cyanidin determines a broad effect.

Keywords:  anthocyanins; diets; epigenetics; functional food; histone modifications; mouse liver

DOI:  https://doi.org/10.3390/ijms22126503
Small Methods. 2020 Aug 14. pii: 1900288. [Epub ahead of print]4(8):

Chromatin Regulation in the Response of Ethylene: Nuclear Events in Ethylene Signaling.

Likai Wang, Fan Zhang, Hong Qiao.

  Plant hormones, produced in response to environmental stimuli, regulate almost all aspects of plant growth and development. Ethylene is a gaseous plant hormone that plays pleotropic roles in plant growth, plant development, fruit ripening, stress responses, and pathogen defenses. After decades of research, the key components of ethylene signaling have been identified and characterized. Although the molecular mechanisms of the sensing of ethylene signal and the transduction of ethylene signaling have been studied extensively, how chromatin influences ethylene signaling and ethylene response is a new area of research. This review describes the current understanding of how chromatin modifications, specifically histone acetylation, regulate ethylene signaling and the ethylene response.

Keywords:  chromatin; ethylene response; ethylene signaling; histone acetylation; transcription

DOI:  https://doi.org/10.1002/smtd.201900288
Cancers (Basel). 2021 Jun 12. pii: 2956. [Epub ahead of print]13(12):

Mitochondrial O-GlcNAc Transferase Interacts with and Modifies Many Proteins and Its Up-Regulation Affects Mitochondrial Function and Cellular Energy Homeostasis.

Paweł Jóźwiak, Piotr Ciesielski, Piotr K Zakrzewski, Karolina Kozal, Joanna Oracz, Grażyna Budryn, Dorota Żyżelewicz, Stéphanie Flament, Anne-Sophie Vercoutter-Edouart, Fabrice Bray, Tony Lefebvre, Anna Krześlak.

  O-GlcNAcylation is a cell glucose sensor. The addition of O-GlcNAc moieties to target protein is catalyzed by the O-Linked N-acetylglucosamine transferase (OGT). OGT is encoded by a single gene that yields differentially spliced OGT isoforms. One of them is targeted to mitochondria (mOGT). Although the impact of O-GlcNAcylation on cancer cells biology is well documented, mOGT's role remains poorly investigated. We performed studies using breast cancer cells with up-regulated mOGT or its catalytic inactive mutant to identify proteins specifically modified by mOGT. Proteomic approaches included isolation of mOGT protein partners and O-GlcNAcylated proteins from mitochondria-enriched fraction followed by their analysis by mass spectrometry. Moreover, we analyzed the impact of mOGT dysregulation on mitochondrial activity and cellular metabolism using a variety of biochemical assays. We found that mitochondrial OGT expression is glucose-dependent. Elevated mOGT expression affected the mitochondrial transmembrane potential and increased intramitochondrial ROS generation. Moreover, mOGT up-regulation caused a decrease in cellular ATP level. We identified many mitochondrial proteins as mOGT substrates. Most of these proteins are localized in the mitochondrial matrix and the inner mitochondrial membrane and participate in mitochondrial respiration, fatty acid metabolism, transport, translation, apoptosis, and mtDNA processes. Our findings suggest that mOGT interacts with and modifies many mitochondrial proteins, and its dysregulation affects cellular bioenergetics and mitochondria function.

Keywords:  O-GlcNAc; breast cancer; energy metabolism; glucose; mOGT; mitochondria

DOI:  https://doi.org/10.3390/cancers13122956