bims-meprid Biomed News
on Metabolic-dependent epigenetic reprogramming in differentiation and disease
Issue of 2020‒12‒13
six papers selected by
Alessandro Carrer
Veneto Institute of Molecular Medicine


  1. Front Physiol. 2020 ;11 580167
    Moffett JR, Puthillathu N, Vengilote R, Jaworski DM, Namboodiri AM.
      Acetate is a major end product of bacterial fermentation of fiber in the gut. Acetate, whether derived from the diet or from fermentation in the colon, has been implicated in a range of health benefits. Acetate is also generated in and released from various tissues including the intestine and liver, and is generated within all cells by deacetylation reactions. To be utilized, all acetate, regardless of the source, must be converted to acetyl coenzyme A (acetyl-CoA), which is carried out by enzymes known as acyl-CoA short-chain synthetases. Acyl-CoA short-chain synthetase-2 (ACSS2) is present in the cytosol and nuclei of many cell types, whereas ACSS1 is mitochondrial, with greatest expression in heart, skeletal muscle, and brown adipose tissue. In addition to acting to redistribute carbon systemically like a ketone body, acetate is becoming recognized as a cellular regulatory molecule with diverse functions beyond the formation of acetyl-CoA for energy derivation and lipogenesis. Acetate acts, in part, as a metabolic sensor linking nutrient balance and cellular stress responses with gene transcription and the regulation of protein function. ACSS2 is an important task-switching component of this sensory system wherein nutrient deprivation, hypoxia and other stressors shift ACSS2 from a lipogenic role in the cytoplasm to a regulatory role in the cell nucleus. Protein acetylation is a critical post-translational modification involved in regulating cell behavior, and alterations in protein acetylation status have been linked to multiple disease states, including cancer. Improving our fundamental understanding of the "acetylome" and how acetate is generated and utilized at the subcellular level in different cell types will provide much needed insight into normal and neoplastic cellular metabolism and the epigenetic regulation of phenotypic expression under different physiological stressors. This article is Part 1 of 2 - for Part 2 see doi: 10.3389/fphys.2020.580171.
    Keywords:  ACSS1; ACSS2; N-acetylaspartate; NAT8L; acetylation; aspartoacylase; deacetylation; transcription factor
    DOI:  https://doi.org/10.3389/fphys.2020.580167
  2. Front Physiol. 2020 ;11 580171
    Moffett JR, Puthillathu N, Vengilote R, Jaworski DM, Namboodiri AM.
      Acetate, the shortest chain fatty acid, has been implicated in providing health benefits whether it is derived from the diet or is generated from microbial fermentation of fiber in the gut. These health benefits range widely from improved cardiac function to enhanced red blood cell generation and memory formation. Understanding how acetate could influence so many disparate biological functions is now an area of intensive research. Protein acetylation is one of the most common post-translational modifications and increased systemic acetate strongly drives protein acetylation. By virtue of acetylation impacting the activity of virtually every class of protein, acetate driven alterations in signaling and gene transcription have been associated with several common human diseases, including cancer. In part 2 of this review, we will focus on some of the roles that acetate plays in health and human disease. The acetate-activating enzyme acyl-CoA short-chain synthetase family member 2 (ACSS2) will be a major part of that focus due to its role in targeted protein acetylation reactions that can regulate central metabolism and stress responses. ACSS2 is the only known enzyme that can recycle acetate derived from deacetylation reactions in the cytoplasm and nucleus of cells, including both protein and metabolite deacetylation reactions. As such, ACSS2 can recycle acetate derived from histone deacetylase reactions as well as protein deacetylation reactions mediated by sirtuins, among many others. Notably, ACSS2 can activate acetate released from acetylated metabolites including N-acetylaspartate (NAA), the most concentrated acetylated metabolite in the human brain. NAA has been associated with the metabolic reprograming of cancer cells, where ACSS2 also plays a role. Here, we discuss the context-specific roles that acetate can play in health and disease.
    Keywords:  N-acetylaspartate; NAT8L; acetyl coenzyme A; acetyl-CoA synthetase; acyl-CoA short-chain synthetase; aspartoacylase; glyceryl triacetate; microbiome
    DOI:  https://doi.org/10.3389/fphys.2020.580171
  3. Front Mol Biosci. 2020 ;7 593866
    Petillo A, Abruzzese V, Koshal P, Ostuni A, Bisaccia F.
      The first intermediate in the mitochondrial tricarboxylic acid (TCA) cycle is citrate, which is essential and acts as a metabolic regulator for glycolysis, TCA cycle, gluconeogenesis, and fatty acid synthesis. Within the cytosol, citrate is cleaved by ATP citrate lyase (ACLY) into oxaloacetate (OAA) and acetyl-CoA; OAA can be used for neoglucogenesis or in the TCA cycle, while acetyl-CoA is the precursor of some biosynthetic processes, including the synthesis of fatty acids. Accumulating evidence suggests that citrate is involved in numerous physiological and pathophysiological processes such as inflammation, insulin secretion, neurological disorders, and cancer. Considering the crucial role of citrate to supply the acetyl-CoA pool for fatty acid synthesis and histone acetylation in tumors, in this study we evaluated the effect of citrate added to the growth medium on lipid deposition and histone H4 acetylation in hepatoma cells (HepG2). At low concentration, citrate increased both histone H4 acetylation and lipid deposition; at high concentration, citrate inhibited both, thus suggesting a crucial role of acetyl-CoA availability, which prompted us to investigate the effect of citrate on ACLY. In HepG2 cells, the expression of ACLY is correlated with histone acetylation, which, in turn, depends on citrate concentration. A decrease in H4 acetylation was also observed when citrate was added at a high concentration to immortalized human hepatic cells, whereas ACLY expression was unaffected, indicating a lack of control by histone acetylation. Considering the strong demand for acetyl-CoA but not for OAA in tumor cells, the exogenous citrate would behave like a trojan horse that carries OAA inside the cells and reduces ACLY expression and cellular metabolism. In addition, this study confirmed the already reported dual role of citrate both as a promoter of cell proliferation (at lower concentrations) and as an anticancer agent (at higher concentrations), providing useful tips on the use of citrate for the treatment of tumors.
    Keywords:  ATP citrate lyase; HepG2; IHH; cancer; citrate; epigenetics; histone acetylation
    DOI:  https://doi.org/10.3389/fmolb.2020.593866
  4. Free Radic Biol Med. 2020 Dec 08. pii: S0891-5849(20)31665-8. [Epub ahead of print]
    Coppedè F.
      One-carbon metabolism provides the methyl groups for both DNA and histone tail methylation reactions, two of the main epigenetic processes that tightly regulate the chromatin structure and gene expression levels. Several enzymes involved in one-carbon metabolism, as well as several epigenetic enzymes, are regulated by intracellular metabolites and redox cofactors, but their expression levels are in turn regulated by epigenetic modifications, in such a way that metabolism and gene expression reciprocally regulate each other to maintain homeostasis and regulate cell growth, survival, differentiation and response to environmental stimuli. Increasing evidence highlights the contribution of impaired one-carbon metabolism and epigenetic modifications in neurodegeneration. This article provides an overview of DNA and histone tail methylation changes in major neurodegenerative disorders, namely Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis, discussing the contribution of oxidative stress and impaired one-carbon and redox metabolism to their onset and progression.
    Keywords:  Alzheimer’s disease; Parkinson’s disease; amyotrophic lateral sclerosis; epigenetics; methylation; neurodegeneration; one-carbon metabolism; redox biology
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2020.12.002
  5. J Affect Disord. 2020 Nov 30. pii: S0165-0327(20)33055-X. [Epub ahead of print]281 51-60
    Huang W, Hu W, Cai L, Zeng G, Fang W, Dai X, Ye Q, Chen X, Zhang J.
      BACKGROUND: Abnormal energy metabolism is often documented in the brain of patients and rodents with depression. In metabolic stress, acetate serves as an important source of acetyl coenzyme A (Ac-CoA). However, its exact role and underlying mechanism remain to be investigated.METHOD: We used chronic social failure stress (CSDS) to induce depression-like phenotype of C57BL/6J mice. The drugs were administered by gavage. We evaluated the depressive symptoms by sucrose preference test, social interaction, tail suspension test and forced swimming test. The dendritic branches and spine density were detected by Golgi staining, mRNA level was analyzed by real-time quantitative RT-PCR, protein expression level was detected by western blot, and the content of Ac-CoA was detected by ELISA kit.
    RESULT: The present study found that acetate supplementation significantly improved the depression-like behaviors of mice either in acute forced swimming test (FST) or in CSDS model and that acetate administration enhanced the dendritic branches and spine density of the CA1 pyramidal neurons. Moreover, the down-regulated levels of BDNF and TrkB were rescued in the acetate-treated mice. Of note, chronic acetate treatment obviously lowered the transcription level of HDAC2, HDAC5, HDAC7, HDAC8, increased the transcription level of HAT and P300, and boosted the content of Ac-CoA in the nucleus, which facilitated the acetylation levels of histone H3 and H4.
    LIMITATIONS: The effect of acetate supplementation on other brain regions is not further elucidated.
    CONCLUSION: These findings indicate that acetate supplementation can produce antidepressant-like effects by increasing histone acetylation and improving synaptic plasticity in hippocampus.
    Keywords:  Acetate; Acetyl coenzyme A/Histone acetylation; Major depressive disorder; Social defeat stress; Synaptic plasticity
    DOI:  https://doi.org/10.1016/j.jad.2020.11.121
  6. JCI Insight. 2020 Dec 07. pii: 145027. [Epub ahead of print]
    Li S, Ma F, Yokota T, Garcia G, Palermo A, Wang Y, Farrell C, Wang YC, Wu R, Zhou Z, Pan C, Morselli M, Teitell MA, Ryazantsev S, Fishbein GA, Ten Hoeve J, Arboleda VA, Bloom J, Dillon BJ, Pellegrini M, Lusis AJ, Graeber TG, Arumugaswami V, Deb A.
      Extra-pulmonary manifestations of COVID-19 are associated with a much higher mortality rate. Yet, little is known about the pathogenesis of systemic complications of COVID-19. Here, we create a murine model of SARS-CoV-2 induced severe systemic toxicity and multi-organ involvement by expressing the human ACE2 transgene in multiple tissues via viral delivery followed by systemic administration of SARS-CoV-2. The animals develop a profound phenotype within 7 days with severe weight loss, morbidity and failure to thrive. We demonstrate there is metabolic suppression of oxidative phosphorylation and the tri-carboxylic acid (TCA) cycle in multiple organs with neutrophilia, lymphopenia and splenic atrophy mirroring human COVID-19 phenotypes. Animals had a significantly lower heart rate and electron microscopy demonstrated myofibrillar disarray and myocardial edema, a common pathogenic cardiac phenotype in human COVID-19. We perform metabolomic profiling of peripheral blood and identify a panel of TCA cycle metabolites that serve as biomarkers of depressed oxidative phosphorylation. Finally, we observed that SARS-CoV-2 induces epigenetic changes of DNA methylation, that affects expression of immune response genes and could in part contribute to COVID-19 pathogenesis. Our model suggests that SARS-CoV-2 induced metabolic reprogramming and epigenetic changes in internal organs could contribute to systemic toxicity and lethality in COVID-19.
    Keywords:  COVID-19; Epigenetics; Intermediary metabolism; Metabolism
    DOI:  https://doi.org/10.1172/jci.insight.145027