bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2019‒10‒20
seventeen papers selected by
Ralitsa Radostinova Madsen
University College London Cancer Institute


  1. Cancers (Basel). 2019 Oct 17. pii: E1586. [Epub ahead of print]11(10):
    Kirstein AS, Augustin A, Penke M, Cea M, Körner A, Kiess W, Garten A.
      Germline mutations in the tumor suppressor gene PTEN cause PTEN Hamartoma Tumor Syndrome (PHTS). Pediatric patients with PHTS frequently develop lipomas. Treatment attempts with the mTORC1 inhibitor rapamycin were unable to reverse lipoma growth. Recently, lipomas associated with PIK3CA-related overgrowth syndrome were successfully treated with the novel PI3K inhibitor alpelisib. Here, we tested whether alpelisib has growth-restrictive effects and induces cell death in lipoma cells. We used PTEN-haploinsufficient lipoma cells from three patients and treated them with alpelisib alone or in combination with rapamycin. We tested the effect of alpelisib on viability, proliferation, cell death, induction of senescence, adipocyte differentiation, and signaling at 1-100 µM alpelisib. Alpelisib alone or in combination with rapamycin reduced proliferation in a concentration- and time-dependent manner. No cell death but an induction of senescence was detected after alpelisib incubation for 72 h. Alpelisib treatment led to a reduced phosphorylation of AKT, mTOR, and ribosomal protein S6. Rapamycin treatment alone led to increased AKT phosphorylation. This effect could be reversed by combining rapamycin with alpelisib. Alpelisib reduced the size of lipoma spheroids by attenuating adipocyte differentiation. Since alpelisib was well tolerated in first clinical trials, this drug alone or in combination with rapamycin is a potential new treatment option for PHTS-related adipose tissue overgrowth.
    Keywords:  AKT; PHTS; PROS; lipoma; mTOR; overgrowth; proliferation; rapamycin; ribosomal protein S6; spheroids
    DOI:  https://doi.org/10.3390/cancers11101586
  2. Adv Biol Regul. 2019 Sep 28. pii: S2212-4926(19)30078-8. [Epub ahead of print] 100657
    Rathinaswamy MK, Burke JE.
      The Class I phosphoinositide 3-kinases (PI3Ks) are a group of heterodimeric lipid kinases that regulate crucial cellular processes including proliferation, survival, growth, and metabolism. The diversity in functions controlled by the various catalytic isoforms (p110α, p110β, p110δ, and p110γ) depends on their abilities to be activated by distinct stimuli such as receptor tyrosine kinases (RTKs), G-protein coupled receptors (GPCRs), and the Ras family of small G-proteins. A major factor determining the ability of each p110 enzyme to be activated is the presence of regulatory binding partners. Given the overwhelming evidence for the involvement of PI3Ks in diseases such as cancer, inflammation, immunodeficiency and diabetes, an understanding of how these regulatory proteins influence PI3K function is essential. This article highlights research deciphering the role of regulatory subunits in PI3K signaling and their involvement in human disease.
    Keywords:  PI3K; PIK3CA; PIK3R1; Phosphoinositide 3-kinase; p110; p85
    DOI:  https://doi.org/10.1016/j.jbior.2019.100657
  3. PLoS Biol. 2019 Oct 15. 17(10): e3000509
    Borreguero-Muñoz N, Fletcher GC, Aguilar-Aragon M, Elbediwy A, Vincent-Mistiaen ZI, Thompson BJ.
      The Hippo signalling pathway restricts cell proliferation in animal tissues by inhibiting Yes-associated protein (YAP or YAP1) and Transcriptional Activator with a PDZ domain (TAZ or WW-domain-containing transcriptional activator [WWTR1]), coactivators of the Scalloped (Sd or TEAD) DNA-binding transcription factor. Drosophila has a single YAP/TAZ homolog named Yorkie (Yki) that is regulated by Hippo pathway signalling in response to epithelial polarity and tissue mechanics during development. Here, we show that Yki translocates to the nucleus to drive Sd-mediated cell proliferation in the ovarian follicle cell epithelium in response to mechanical stretching caused by the growth of the germline. Importantly, mechanically induced Yki nuclear localisation also requires nutritionally induced insulin/insulin-like growth factor 1 (IGF-1) signalling (IIS) via phosphatidyl inositol-3-kinase (PI3K), phosphoinositide-dependent kinase 1 (PDK1 or PDPK1), and protein kinase B (Akt or PKB) in the follicular epithelium. We find similar results in the developing Drosophila wing, where Yki becomes nuclear in the mechanically stretched cells of the wing pouch during larval feeding, which induces IIS, but translocates to the cytoplasm upon cessation of feeding in the third instar stage. Inactivating Akt prevents nuclear Yki localisation in the wing disc, while ectopic activation of the insulin receptor, PI3K, or Akt/PKB is sufficient to maintain nuclear Yki in mechanically stimulated cells of the wing pouch even after feeding ceases. Finally, IIS also promotes YAP nuclear localisation in response to mechanical cues in mammalian skin epithelia. Thus, the Hippo pathway has a physiological function as an integrator of epithelial cell polarity, tissue mechanics, and nutritional cues to control cell proliferation and tissue growth in both Drosophila and mammals.
    DOI:  https://doi.org/10.1371/journal.pbio.3000509
  4. J Immunol. 2019 Oct 18. pii: ji1900749. [Epub ahead of print]
    Hawse WF, Cattley RT, Wendell SG.
      TCR signaling activates kinases including AKT/mTOR that engage metabolic networks to support the energetic demands of a T cell during an immune response. It is realized that CD4+ T cell subsets have different metabolic requirements. Yet, how TCR signaling is coupled to the regulation of intermediate metabolites and how changes in metabolite flux contribute to T cell differentiation are less established. We find that TCR signaling regulates acetyl-CoA metabolism via AKT in murine CD4+ T cells. Weak TCR signals promote AKT-catalyzed phosphorylation and inhibition of citrate synthase, elevated acetyl-CoA levels, and hyperacetylation of mitochondrial proteins. Genetic knockdown of citrate synthase promotes increased nuclear acetyl-CoA levels, increased histone acetylation at the FOXP3 promotor and induction of FOXP3 transcription. These data identify a circuit between AKT signaling and acetyl-CoA metabolism regulated via TCR signal strength and that transient fluctuations in acetyl-CoA levels function in T cell fate decisions.
    DOI:  https://doi.org/10.4049/jimmunol.1900749
  5. Nat Commun. 2019 Oct 17. 10(1): 4720
    Srikantan S, Deng Y, Cheng ZM, Luo A, Qin Y, Gao Q, Sande-Docor GM, Tao S, Zhang X, Harper N, Shannon CE, Fourcaudot M, Li Z, Kasinath BS, Harrison S, Ahuja S, Reddick RL, Dong LQ, Abdul-Ghani M, Norton L, Aguiar RCT, Dahia PLM.
      Understanding the molecular components of insulin signaling is relevant to effectively manage insulin resistance. We investigated the phenotype of the TMEM127 tumor suppressor gene deficiency in vivo. Whole-body Tmem127 knockout mice have decreased adiposity and maintain insulin sensitivity, low hepatic fat deposition and peripheral glucose clearance after a high-fat diet. Liver-specific and adipose-specific Tmem127 deletion partially overlap global Tmem127 loss: liver Tmem127 promotes hepatic gluconeogenesis and inhibits peripheral glucose uptake, while adipose Tmem127 downregulates adipogenesis and hepatic glucose production. mTORC2 is activated in TMEM127-deficient hepatocytes suggesting that it interacts with TMEM127 to control insulin sensitivity. Murine hepatic Tmem127 expression is increased in insulin-resistant states and is reversed by diet or the insulin sensitizer pioglitazone. Importantly, human liver TMEM127 expression correlates with steatohepatitis and insulin resistance. Our results suggest that besides tumor suppression activities, TMEM127 is a nutrient-sensing component of glucose/lipid homeostasis and may be a target in insulin resistance.
    DOI:  https://doi.org/10.1038/s41467-019-12661-0
  6. Cell Rep. 2019 Oct 15. pii: S2211-1247(19)31172-6. [Epub ahead of print]29(3): 589-602.e6
    Bui T, Rennhack J, Mok S, Ling C, Perez M, Roccamo J, Andrechek ER, Moraes C, Muller WJ.
      Integrin receptors coordinate cell adhesion to the extracellular matrix (ECM) to facilitate many cellular processes during malignant transformation. Despite their pro-tumorigenic roles, therapies targeting integrins remain limited. Here, we provide genetic evidence supporting a functional redundancy between β1 and β3 integrin during breast cancer progression. Although ablation of β1 or β3 integrin alone has limited effects on ErbB2-driven mammary tumorigenesis, deletion of both receptors resulted in a significant delay in tumor onset with a corresponding impairment in lung metastasis. Mechanistically, stiff ECM cooperates with integrin receptors to recruit insulin receptors (IRs) to focal adhesion through the formation of integrin/IR complexes, thereby preventing their lysosomal degradation. β1/β3 integrin-deficient tumors that eventually emerged exhibit impaired Akt/mTORC1 activity. Murine and human breast cancers exhibiting enhanced integrin-dependent activity also display elevated IR/Akt/mTORC1 signaling activity. Together, these observations argue that integrin/IR crosstalk transduces mechanical cues from the tumor microenvironment to promote ErbB2-dependent breast cancer progression.
    Keywords:  Akt; ECM stiffness; ErbB2; breast cancer; insulin receptor; integrin; mTORC1; transgenic model
    DOI:  https://doi.org/10.1016/j.celrep.2019.09.004
  7. J Am Heart Assoc. 2019 Nov 05. 8(21): e013018
    Elmadani M, Khan S, Tenhunen O, Magga J, Aittokallio T, Wennerberg K, Kerkelä R.
      Background Small molecule kinase inhibitors (KIs) are a class of agents currently used for treatment of various cancers. Unfortunately, treatment of cancer patients with some of the KIs is associated with cardiotoxicity, and there is an unmet need for methods to predict their cardiotoxicity. Here, we utilized a novel computational method to identify protein kinases crucial for cardiomyocyte viability. Methods and Results One hundred forty KIs were screened for their toxicity in cultured neonatal cardiomyocytes. The kinase targets of KIs were determined based on integrated data from binding assays. The key kinases mediating the toxicity of KIs to cardiomyocytes were identified by using a novel machine learning method for target deconvolution that combines the information from the toxicity screen and from the kinase profiling assays. The top kinases identified by the model were phosphoinositide 3-kinase catalytic subunit alpha, mammalian target of rapamycin, and insulin-like growth factor 1 receptor. Knockdown of the individual kinases in cardiomyocytes confirmed their role in regulating cardiomyocyte viability. Conclusions Combining the data from analysis of KI toxicity on cardiomyocytes and KI target profiling provides a novel method to predict cardiomyocyte toxicity of KIs.
    Keywords:  cardiotoxicity; cell death; pharmacology
    DOI:  https://doi.org/10.1161/JAHA.119.013018
  8. Proc Natl Acad Sci U S A. 2019 Oct 17. pii: 201911385. [Epub ahead of print]
    Zammataro L, Lopez S, Bellone S, Pettinella F, Bonazzoli E, Perrone E, Zhao S, Menderes G, Altwerger G, Han C, Zeybek B, Bianchi A, Manzano A, Manara P, Cocco E, Buza N, Hui P, Wong S, Ravaggi A, Bignotti E, Romani C, Todeschini P, Zanotti L, Odicino F, Pecorelli S, Donzelli C, Ardighieri L, Angioli R, Raspagliesi F, Scambia G, Choi J, Dong W, Bilguvar K, Alexandrov LB, Silasi DA, Huang GS, Ratner E, Azodi M, Schwartz PE, Pirazzoli V, Stiegler AL, Boggon TJ, Lifton RP, Schlessinger J, Santin AD.
      The prognosis of advanced/recurrent cervical cancer patients remains poor. We analyzed 54 fresh-frozen and 15 primary cervical cancer cell lines, along with matched-normal DNA, by whole-exome sequencing (WES), most of which harboring Human-Papillomavirus-type-16/18. We found recurrent somatic missense mutations in 22 genes (including PIK3CA, ERBB2, and GNAS) and a widespread APOBEC cytidine deaminase mutagenesis pattern (TCW motif) in both adenocarcinoma (ACC) and squamous cell carcinomas (SCCs). Somatic copy number variants (CNVs) identified 12 copy number gains and 40 losses, occurring more often than expected by chance, with the most frequent events in pathways similar to those found from analysis of single nucleotide variants (SNVs), including the ERBB2/PI3K/AKT/mTOR, apoptosis, chromatin remodeling, and cell cycle. To validate specific SNVs as targets, we took advantage of primary cervical tumor cell lines and xenografts to preclinically evaluate the activity of pan-HER (afatinib and neratinib) and PIK3CA (copanlisib) inhibitors, alone and in combination, against tumors harboring alterations in the ERBB2/PI3K/AKT/mTOR pathway (71%). Tumors harboring ERBB2 (5.8%) domain mutations were significantly more sensitive to single agents afatinib or neratinib when compared to wild-type tumors in preclinical in vitro and in vivo models (P = 0.001). In contrast, pan-HER and PIK3CA inhibitors demonstrated limited in vitro activity and were only transiently effective in controlling in vivo growth of PIK3CA-mutated cervical cancer xenografts. Importantly, combinations of copanlisib and neratinib were highly synergistic, inducing long-lasting regression of tumors harboring alterations in the ERBB2/PI3K/AKT/mTOR pathway. These findings define the genetic landscape of cervical cancer, suggesting that a large subset of cervical tumors might benefit from existing ERBB2/PIK3CA/AKT/mTOR-targeted drugs.
    Keywords:  HER2/neu; PIK3CA; cervical cancer; copanlisib; neratinib
    DOI:  https://doi.org/10.1073/pnas.1911385116
  9. Cold Spring Harb Perspect Biol. 2019 Oct 15. pii: a035634. [Epub ahead of print]
    White MD, Plachta N.
      Our understanding of how the first mammalian cell lineages arise has been shaped largely by studies of the preimplantation mouse embryo. Painstaking work over many decades has begun to reveal how a single totipotent cell is transformed into a multilayered structure representing the foundations of the body plan. Here, we review how the first lineage decision is initiated by epigenetic regulation but consolidated by the integration of morphological features and transcription factor activity. The establishment of pluripotent and multipotent stem cell lines has enabled deeper analysis of molecular and epigenetic regulation of cell fate decisions. The capability to assemble these stem cells into artificial embryos is an exciting new avenue of research that offers a long-awaited window into cell fate specification in the human embryo. Together, these approaches are poised to profoundly increase our understanding of how the first lineage decisions are made during mammalian embryonic development.
    DOI:  https://doi.org/10.1101/cshperspect.a035634
  10. PLoS Genet. 2019 Oct 17. 15(10): e1008424
    Meister J, Bone DBJ, Godlewski G, Liu Z, Lee RJ, Vishnivetskiy SA, Gurevich VV, Springer D, Kunos G, Wess J.
      Type 2 diabetes (T2D) has become a major health problem worldwide. Skeletal muscle (SKM) is the key tissue for whole-body glucose disposal and utilization. New drugs aimed at improving insulin sensitivity of SKM would greatly expand available therapeutic options. β-arrestin-1 and -2 (Barr1 and Barr2, respectively) are two intracellular proteins best known for their ability to mediate the desensitization and internalization of G protein-coupled receptors (GPCRs). Recent studies suggest that Barr1 and Barr2 regulate several important metabolic functions including insulin release and hepatic glucose production. Since SKM expresses many GPCRs, including the metabolically important β2-adrenergic receptor, the goal of this study was to examine the potential roles of Barr1 and Barr2 in regulating SKM and whole-body glucose metabolism. Using SKM-specific knockout (KO) mouse lines, we showed that the loss of SKM Barr2, but not of SKM Barr1, resulted in mild improvements in glucose tolerance in diet-induced obese mice. SKM-specific Barr1- and Barr2-KO mice did not show any significant differences in exercise performance. However, lack of SKM Barr2 led to increased glycogen breakdown following a treadmill exercise challenge. Interestingly, mice that lacked both Barr1 and Barr2 in SKM showed no significant metabolic phenotypes. Thus, somewhat surprisingly, our data indicate that SKM β-arrestins play only rather subtle roles (SKM Barr2) in regulating whole-body glucose homeostasis and SKM insulin sensitivity.
    DOI:  https://doi.org/10.1371/journal.pgen.1008424
  11. Am J Med Genet C Semin Med Genet. 2019 Oct 14.
    Macken WL, Tischkowitz M, Lachlan KL.
      PTEN hamartoma tumor syndrome (PHTS) is a highly variable autosomal dominant condition associated with intellectual disability, overgrowth, and tumor predisposition phenotypes, which often overlap. PHTS incorporates a number of historical clinical presentations including Bannayan-Riley-Ruvalcaba syndrome, Cowden syndrome, and a macrocephaly-autism/developmental delay syndrome. Many reviews in the literature focus on PHTS as an adult hamartoma and malignancy predisposition condition. Here, we review the current literature with a focus on pediatric presentations. The review starts with a summary of the main conditions encompassed within PHTS. We then discuss PHTS diagnostic criteria, and clinical features. We briefly address rarer PTEN associations, and the possible role of mTOR inhibitors in treatment. We acknowledge the limited understanding of the natural history of childhood-onset PHTS as a cancer predisposition syndrome and present a summary of important management considerations.
    Keywords:  Bannayan-Riley-Ruvalcaba syndrome; PHTS; PTEN hamartoma tumor syndrome; autism spectrum disorder; cowden syndrome
    DOI:  https://doi.org/10.1002/ajmg.c.31743
  12. J Biol Chem. 2019 Oct 18. pii: jbc.AW119.008146. [Epub ahead of print]
    Thompson CB, Bielska AA.
      How cells utilize nutrients to produce the ATP needed for bioenergetic homeostasis has been well characterized. What is less well studied is how resting cells metabolically shift from an ATP-producing catabolic metabolism to a metabolism that supports anabolic growth. In metazoan organisms, the discovery of growth factors and the ability of their receptors to induce new transcription and translation led to the hypothesis that the bioenergetic and synthetic demands of cell growth were primarily met through the replacement of nutrients consumed during net macromolecular synthesis, a demand-based system of nutrient uptake. Recent data have challenged this hypothesis. Instead there is increasing evidence that cellular nutrient uptake is a push system. Growth factor signaling has been linked to direct stimulation of nutrient uptake. The ability of growth factor signaling to increase the uptake of glucose, lipids, and amino acids to levels that exceed a cell's bioenergetic and synthetic needs has been documented in a wide variety of settings. In some tissues, this leads to the storage of the excess nutrients in the form of glycogen or fat. In others, the excess is secreted as lactate and certain non-essential amino acids. When growth factor signaling stimulates nutrient uptake to levels that exceed a cell's bioenergetic needs, adaptive changes in intermediate metabolism lead to the production of anabolic precursors that fuel the net synthesis of protein, lipids, and nucleic acids. Through the increased production of these precursors, growth factor signaling provides a supply side stimulation of cell growth and proliferation.
    Keywords:  bioenergetics; cell growth; cell metabolism; cell proliferation; growth factor
    DOI:  https://doi.org/10.1074/jbc.AW119.008146
  13. iScience. 2019 Oct 01. pii: S2589-0042(19)30379-7. [Epub ahead of print]20 434-448
    Almacellas E, Pelletier J, Manzano A, Gentilella A, Ambrosio S, Mauvezin C, Tauler A.
      Cancer cells rely on mTORC1 activity to coordinate mitogenic signaling with nutrients availability for growth. Based on the metabolic function of E2F1, we hypothesize that glucose catabolism driven by E2F1 could participate on mTORC1 activation. Here, we demonstrate that glucose potentiates E2F1-induced mTORC1 activation by promoting mTORC1 translocation to lysosomes, a process that occurs independently of AMPK activation. We showed that E2F1 regulates glucose metabolism by increasing aerobic glycolysis and identified the PFKFB3 regulatory enzyme as an E2F1-regulated gene important for mTORC1 activation. Furthermore, PFKFB3 and PFK1 were found associated to lysosomes and we demonstrated that modulation of PFKFB3 activity, either by substrate accessibility or expression, regulates the translocation of mTORC1 to lysosomes by direct interaction with Rag B and subsequent mTORC1 activity. Our results support a model whereby a glycolytic metabolon containing phosphofructokinases transiently interacts with the lysosome acting as a sensor platform for glucose catabolism toward mTORC1 activity.
    Keywords:  Cell Biology; Molecular Genetics
    DOI:  https://doi.org/10.1016/j.isci.2019.09.040
  14. Hum Mol Genet. 2019 Oct 18. pii: ddz232. [Epub ahead of print]
    Conduit SE, Davies EM, Ooms LM, Gurung R, McGrath MJ, Hakim S, Cottle DL, Smyth IM, Dyson JM, Mitchell CA.
      Polycystic kidney disease (PKD) results in the formation of renal cysts that can impair function leading to renal failure. DNA damage accumulates in renal epithelial cells in PKD but the molecular mechanisms are unclear and are investigated here. Phosphoinositide 3- kinase (PI3K)/AKT signaling activates mammalian target of rapamycin complex 1 (mTORC1) and hyperactivation of mTORC1 is a common event in PKD, however, mTORC1 inhibitors have yielded disappointing results in clinical trials. Here we demonstrate AKT and mTORC1 hyperactivation in two representative murine PKD models (renal epithelial-specific Inpp5e knockout and collecting duct-specific Pkd1 deletion) and identify a downstream signaling network that contributes to DNA damage accumulation. Inpp5e- and Pkd1-null renal epithelial cells showed DNA damage including double-stranded DNA breaks associated with increased replication fork numbers, multinucleation and centrosome amplification. mTORC1 activated CAD, which promotes de novo pyrimidine synthesis, to sustain cell proliferation. AKT, but not mTORC1, inhibited the DNA repair/replication fork origin firing regulator TOPBP1, which impacts on DNA damage and cell proliferation. Notably, Inpp5e- and Pkd1-null renal epithelial cell spheroid formation defects were rescued by AKT inhibition. These data reveal that AKT hyperactivation contributes to DNA damage accumulation in multiple forms of PKD and cooperates with mTORC1 to promote cell proliferation. Hyperactivation of AKT may play a causal role in PKD by regulating DNA damage and cell proliferation, independent of mTORC1, and AKT inhibition may be a novel therapeutic approach for PKD.
    DOI:  https://doi.org/10.1093/hmg/ddz232
  15. Ann Oncol. 2019 Oct 18. pii: mdz440. [Epub ahead of print]
    Nunnery SE, Mayer IA.
      Alterations in the PI3K/AKT pathway are frequently found in cancer and are especially common in breast cancer, where it is estimated that 70% of tumors have some type of genetic alteration that could lead to pathway hyperactivation. A variety of PI3K pathway inhibitors have been developed in an attempt to target this pathway and improve cancer control. One of the challenges in treating patients with PI3K/AKT pathway inhibitors is the associated toxicity from on-target and off-target effects. Such side effects are common, but reversible, and include hyperglycemia, rash, stomatitis, diarrhea, nausea, and fatigue. As a result, dose reductions, treatment delays, and treatment discontinuation are frequently reported. This impairs not only patients' quality of life but also treatment efficacy. Most side effects are reversible with drug interruption, since these drugs typically have a short half-life and are manageable with early intervention. An interdisciplinary approach with proactive management of patients receiving PI3K pathway inhibitors should include comprehensive education of patients about the range of toxicities, frequent monitoring, early toxicity recognition, active intervention, as well as prophylactic strategies.
    DOI:  https://doi.org/10.1093/annonc/mdz440
  16. Methods Enzymol. 2019 ;pii: S0076-6879(19)30293-9. [Epub ahead of print]626 1-21
    Trefely S, Doan MT, Snyder NW.
      Dynamic interplay between cellular metabolism and histone acetylation is a key mechanism underlying metabolic control of epigenetics. In particular, the central metabolite acetyl-coenzyme A (acetyl-CoA) acts as the acetyl-donor for histone acetylation in both an enzymatic and non-enzymatic manner. Since members of the family of histone acetyl transferases (HATs) that catalyze the acetylation of histone tails possess a Michaelis constant (Km) within the range of physiological cellular acetyl-CoA concentrations, changing concentrations of acetyl-CoA can restrict or promote enzymatic histone acetylation. Likewise, non-enzymatic histone acetylation occurs at physiological concentrations. These concepts implicate acetyl-CoA as a rheostat for nutrient availability acting, in part, by controlling histone acetylation. Histone acetylation is an important epigenetic modification that controls gene expression and acetyl-CoA dependent changes in both histone acetylation and gene expression have been shown in yeast and mammalian systems. However, quantifying the metabolic conditions required to achieve specific changes in histone acetylation is a major challenge. The relationship between acetyl-CoA and histone acetylation may be influenced by a variety of factors including sub-cellular location of metabolites and enzymes, relative quantities of metabolites, and substrate availability/preference. A diversity of substrates can contribute the two-carbon acyl-chain to acetyl-CoA, a number of pathways can create or degrade acetyl-CoA, and only a handful of potential mechanisms for the crosstalk between metabolism and histone acetylation have been explored. The centrality of acetyl-CoA in intermediary metabolism means that acetyl-CoA levels may change, or be resistant to change, in unexpected ways. Thus, quantification of relevant metabolites is critical evidence in understanding how the nutrient rheostat is set in normal and pathological contexts. Coupling metabolite quantitation with isotope tracing to examine fate of specific metabolites is critical to the crosstalk between metabolism and histone acetylation, including but not limited to acetyl-CoA provides necessary context. This chapter provides guidance on experimental design of quantification with isotope dilution and/or tracing of acetyl-CoA within a targeted or highly multiplexed multi-analyte workflow.
    Keywords:  Acetyl-coenzyme A; Acetylation; Liquid chromatography mass spectrometry; Metabolism
    DOI:  https://doi.org/10.1016/bs.mie.2019.07.013
  17. Front Endocrinol (Lausanne). 2019 ;10 629
    Brunetti A, Arcidiacono B, Foti DP, Semple RK.
      
    Keywords:  gene transcription; glucose homeostasis; insulin resistance; insulin signaling; microRNAs
    DOI:  https://doi.org/10.3389/fendo.2019.00629