Histone deacetylase inhibition

625-45-6

RMIODHQZRUFFFF-UHFFFAOYSA-N

Methoxyacetic acid

Acetic acid, methoxy- 2-Methoxyacetic acid ACETIC ACID, METHOXY Acide methoxyacetique acido metoxiacetico Methoxy acetic acid Methoxyessigsaure Methoxyethanoic acid NSC 7300

DTXSID1031591

461-55-2

FERIUCNNQQJTOY-UHFFFAOYSA-M

Butyrate

DTXSID8040432

58880-19-6

RTKIYFITIVXBLE-QEQCGCAPSA-N

Trichostatin A

TSA

DTXSID6037063

99-66-1

NIJJYAXOARWZEE-UHFFFAOYSA-N

Valproic acid

VPA Pentanoic acid, 2-propyl- 2-Propylpentanoic acid 2-Propylvaleriansaure 2-propylvaleric acid 4-Heptanecarboxylic acid Acetic acid, dipropyl- acide 2-propylvalerique acido 2-propilvalerico Depakine Dipropylacetic acid Ergenyl Mylproin n-Dipropylacetic acid NSC 93819 VALERIC ACID, 2-PROPYL-

DTXSID6023733

149647-78-9

WAEXFXRVDQXREF-UHFFFAOYSA-N

Suberoylanilide hydroxamic acid

vorinostat Octanediamide, N-hydroxy-N'-phenyl- SAHA

DTXSID6041133

209783-80-2

INVTYAOGFAGBOE-UHFFFAOYSA-N

MS-275

DTXSID0041068

183506-66-3

JWOGUUIOCYMBPV-GMFLJSBRSA-N

JWOGUUIOCYMBPV-LQJYRIKDSA-N

Apicidin

(3S,6S,9S,15aR)-9-[(2S)-Butan-2-yl]-6-[(1-methoxy-1H-indol-3-yl)methyl]-3-(6-oxooctyl)octahydro-2H-pyrido[1,2-a][1,4,7,10]tetraazacyclododecine-1,4,7,10(3H,12H)-tetrone Apicidin Ia

DTXSID40274182

PR:000008478

PR histone deacetylase 1

CHEBI:15358

CHEBI histone

GO:0004857

GO enzyme inhibitor activity

GO:0031399

GO regulation of protein modification process

GO:0010467

GO gene expression

WIKI decreased

WIKI increased

WIKI abnormal

Methoxyacetic acid

2018-01-21T20:38:50

Butyrate

2018-01-21T20:39:19

Trichostatin A

2018-01-21T20:39:33

Valproic acid

2018-12-20T04:35:21

Suberoylanilide hydroxamic acid

2018-12-20T04:36:36

MS-275

2018-12-20T04:37:02

Apicidin

2018-12-20T04:37:15

Rocilinostat / Ricolinostat

2021-06-23T05:53:11

Ionizing Radiation Ionizing radiation can vary in energy, dose, charge, and in the spatial distributions of energy transferred to other matter (linear energy transfer per unit length or LET) (ICRU 1970). At the same dose, low and high LET both generate energy deposition events, including many higher energy events (Goodhead and Nikjoo 1989). However, they differ in the spatial distribution and upper range of intensity of energy deposited. Lower LET such as gamma rays sparsely deposit many individual excitations or small clusters of excitations of low energy (Goodhead 1988). In contrast, high LET such as alpha particles have fewer tracks but readily transfer their energy to matter and therefore deposit their energy over a much smaller area (Goodhead 1994). Consequently, alpha and other high LET particles penetrate less deeply into tissue, interactions are densely focused on a narrow track, and individual energy depositions can be large (Goodhead 1988). These different energy deposition patterns can lead to differences in radiation effects including the pattern of DNA damage.

Exposure to ionizing radiation can come from natural and industrial sources. Space and terrestrial radiation includes a range of LET particles, while diagnostic radiation methods such as X-ray imaging, mammography and CT scans use low LET X-rays. Radiation therapy can use an external beam to direct radiation on a focused tissue area, or deposit solid or liquid radioactive materials in the body that release (mostly gamma) radiation internally. External radiotherapy typically uses X-rays but is moving towards higher LET charged particles such as protons and heavy ions (Durante, Orecchia et al. 2017).

2019-05-03T12:36:36

2019-05-07T12:12:13

10116

NCBI rat

WCS_9606

common toxicological species human

10090

NCBI mouse

10090

NCBI Mus musculus

9606

NCBI Homo sapiens

10116

NCBI Rattus norvegicus

9986

NCBI Oryctolagus cuniculus

3708

NCBI Brassica napus

Histone deacetylase inhibition

Molecular

Nucleosomes consist of eight core histones, two of each histone H2A, H2B, H3, and H4 [Damaskos et al., 2017]. DNA strands (about 200 bp) wind around the core histones, which can be modified on their N-terminal ends. One possible modification is the acetylation of lysine residues, which decreases the binding strength between DNA and the core histone. Histone deacetylases (HDACs) hydrolyze the acetyl residues [Damaskos et al., 2017]. HDACs remove the acetyl groups from the lysine residues leading to the formation of a condensed and transcriptionally silenced chromatin. Thus, the inhibition of HDAC blocks this action and can result in hyperacetylation of histones associated mostly with increases in transcriptional activation. Histone deacetylase inhibitor (HDI) inhibits HDAC, causing increased acetylation of the histones and thereby facilitating binding of transcription factors [Taunton et al., 1996]. It is known that eukaryotic HDAC isoforms are classified into four classes: class I HDACs (isoforms 1, 2, 3, 8), class II HDACs (isoforms 4, 5, 6, 7, 9, 10), class III HDACs (the sirtuins), and HDAC11 [Gregoretti et al., 2004; Weichert, 2009; Barneda-Zahonero and Parra, 2012]. HDACs 1, 2, and 3 are ubiquitously expressed, whereas HDAC8 is predominantly expressed in cells with smooth muscle/myoepithelial differentiation [Weichert, 2009]. HDAC6 is not observed to be expressed in lymphocytes, stromal cells, and vascular endothelial cells [Weichert, 2009]. Class III HDACs, sirtuins, are widely expressed and localized in different cellular compartments [Barneda-Zahonero and Parra, 2012]. SirT1 is highly expressed in testis, thymus, and multiple types of germ cells [Bell et al., 2014]. HDAC11 expression is enriched in the kidney, brain, testis, heart, and skeletal muscle [Barneda-Zahonero and Parra, 2012]. The members of classes 1, 2, and 4 are dependent on a zinc ion and a water molecule at their active sites, for their deacetylase function. The Sirtuins of class 3 depend on NAD+ and are considered impervious to most known HDAC inhibitors [Drummond et al., 2005]. Several structurally distinct groups of compounds have been found to inhibit HDACs of class 1, 2, and 4, among others short-chain fatty acids (e.g. butyrate and VPA), hydroxamic acids (e.g. TSA and SAHA), and epoxyketones (e.g. Trapoxin) [Drummond et al., 2005]. The hydroxamic acids seem to exert their inhibitory action by mimicking the acetyl-lysine target of HDACs, chelating the zinc ion in the active site, and displacing the water molecule [Finnin et al., 1999]. Several high-resolution crystal structures support this mode of inhibition [Decroos et al., 2015; Luckhurst et al., 2016]. The mode of inhibition of epoxyketones seems to function in the formation of a stable transition state analog with the zinc ion in the active site [Porter and Christianson, 2017]. The inhibitory actions of the short-chain fatty acids are less well defined, but it has been speculated that VPA blocks access to the binding pocket [Göttlicher et al., 2001]. It has been shown that VPA exerts similar gene regulatory effects to TSA, on a panel of migration-related transcripts in neural crest cells [Dreser et al., 2015], supporting a mode of action similar to hydroxamic-acid type HDAC inhibitors. Some in silico methods including molecular modeling, virtual screening, and molecular dynamics are used to find the common HDAC inhibitor structures [Huang et al., 2016; Yanuar et al. 2016].

The measurement of HDAC inhibition monitors changes in histone acetylation. HDAC inhibition can be detected directly by the measurement of HDAC activity using commercially available colorimetric or fluorimetric kits or indirectly by the increase of histone acetylation as the detection of global histone acetylation changes by Western blot or mass spectrometry (MS)-based proteomics methods or as detection of site-specific histone acetylation changes using chromatin immunoprecipitation (ChIP) or ChIP-on-Chip. The measurement methods include the immunological detection of histone acetylation with anti-acetylated histone antibodies [Richon et al., 2004]. The histones are isolated from pellets of cells treated with HDIs, followed by acid-urea-triton gel electrophoresis, western blotting, and immunohistochemistry [Richon et al., 2003]. The HDAC activity is measured directly with ultra-high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UHPLC-ESI-MS/MS) by calculating the ratio of deacetylated peptide and acetylated peptide [Zwick et al., 2016]. HDAC inhibition can be predicted by perturbations in gene expression patterns as well; an 81-gene transcriptomic biomarker of HDAC inhibition, called TGx-HDACi, has shown to accurately predict HDAC inhibition after 4 hour exposures to HDI in TK6 human lymphoblastoid cells [Cho et al., 2021].

The inhibition of HDAC by HDIs is well conserved between species from lower organisms to mammals. <ul> <li>HDAC inhibition restores the rate of resorption of subretinal blebs in hyperglycemia in brown Norway rat and HDAC activity was inhibited with HDIs in human ARPE19 cells [Desjardins et al., 2016].</li> <li>Treatment of HDIs inducing HDAC inhibition showed anti-tumor effects in human non-small cell lung cancer cells [Ansari et al., 2016; Miyanaga et al., 2008].</li> <li>HDAC acetylation level was increased by HDIs in the MRL-lpr/lpr murine model of lupus splenocytes [Mishra et al., 2003].</li> <li>SAHA increased histone acetylation in the brain and spleen of mice [Hockly et al., 2003].</li> <li>MAA inhibits HDAC activity in HeLa cells and spleens from C57BL/6 mice [Jansen et al., 2004].</li> <li>It is also reported that MAA inhibits HDAC activity in testis cytosolic and nuclear extract of juvenile rats (27 days old) [Wade et al., 2008].</li> <li>VPA and TSA inhibit HDAC enzymatic activity in the mouse embryo and human HeLa cell nuclear extract [Di Renzo et al., 2007].</li> <li>The treatment with HDAC inhibitors, phenylbutyrate (PB) (2 mM) and TSA (200 nM), inhibits HDAC in adjuvant arthritis synovial cells derived from rats, causing higher acetylated histone [Chung et al., 2003].</li> </ul>

UBERON:0000062

UBERON organ

CL:0000000

CL cell

High Unspecific

Moderate

All life stages

High High High

Ansari, J. et al. (2016), "Epigenetics in non-small cell lung cancer: from basics to therapeutics", Transl Lung Cancer Res 5:155-171 Barneda-Zahonero, B. and Parra, M. (2012), "Histone deacetylases and cancer", Mol Oncol 6:579-589 Bell, E.L. et al. (2014), "SirT1 is required in the male germ cell for differentiation and fecundity in mice", Development 141:3495-3504 Cho, E. et al. (2021), "Development and validation of the TGx-HDACi transcriptomic biomarker to detect histone deacetylase inhibitors in human TK6 cells", Arch Toxicol 95:1631–1645 Chung, Y.L. et al. (2003), "A therapeutic strategy uses histone deacetylase inhibitors to modulate the expression of genes involved in the pathogenesis of rheumatoid arthritis", Mol Ther 8:707-717 Damaskos, C. et al. (2016), "Histone deacetylase inhibitors: a novel therapeutic weapon against medullary thyroid cancer?", Anticancer Res 36:5019-5024 Damaskos, C. et al. (2017), "Histone deacetylase inhibitors: an attractive therapeutic strategy against breast cancer", Anticancer Research 37:35-46 Decroos, C. et al. (2015), "Biochemical and structural characterization of HDAC8 mutants associated with cornelia de lange syndrome spectrum disorders", Biochemistry 54:6501–6513 Desjardins, D. et al. (2016), "Histone deacetylase inhibition restores retinal pigment epithelium function in hyperglycemia", PLoS ONE 11:e0162596 Di Renzo, F. et al. (2007), "Boric acid inhibits embryonic histone deacetylases: A suggested mechanism to explain boric acid-related teratogenicity", Toxicol and Appl Pharmacol 220:178-185 Dreser, N. et al. (2015), "Grouping of histone deacetylase inhibitors and other toxicants disturbing neural crest migration by transcriptional profiling", Neurotoxicology 50:56–70 Drummond, D.C. et al. (2005), "Clinical development of histone deacetylase inhibitors as anticancer agents", Annu Rev Pharmacol Toxicol 45:495–528 Finnin, M.S. et al. (1999), "Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors", Nature 401:188–193 Göttlicher, M. et al. (2001), "Valproic acid defines a novel class of HDAC inhibitors inducing differentiation of transformed cells", EMBO J 20:6969–6978 Gregoretti, I.V. et al. (2004), "Molecular evolution of the histone deacetylase family: functional implications of phylogenetic analysis", J Mol Biol 338:17–31 Hockly, E. et al. (2003), "Suberoylanilide hydroxamic acid, a histone deacetylase inhibitor, ameliorates motor deficits in a mouse model of Huntington’s disease", Proc Nat Acad Sci 100:2041-2046 Hu, E. et al. (2003), "Identification of novel isoform-selective inhibitors within class I histone deacetylases", J Pharmacol Exp Ther 307:720-728 Huang, Y.X. et al. (2016), "Virtual screening and experimental validation of novel histone deacetylase inhibitors", BMC Pharmacol Toxicol 17(1):32 Jansen, M.S. et al. (2014), "Short-chain fatty acids enhance nuclear receptor activity through mitogen-activated protein kinase activation and histone deacetylase inhibition", Proc Natl Acad Sci USA 101(18):7199-7204 Luckhurst, C.A. et al. (2016), "Potent, Selective, and CNS-Penetrant Tetrasubstituted Cyclopropane Class IIa Histone Deacetylase (HDAC) Inhibitors", ACS Med Chem Lett 7:34–39 Mishra, N. et al. (2003), "Histone deacetylase inhibitors modulate renal disease in the MRL-lpr/lpr mouse", J Clin Invest 111:539-552 Miyanaga, A. et al. (2008), "Antitumor activity of histone deacetylase inhibitors in non-small cell lung cancer cells: development of a molecular predictive model", Mol Cancer Ther 7:1923-1930 Ooi, J.Y.Y., et al. (2015), “HDAC inhibition attenuates cardiac hypertrophy by acetylation and deacetylation of target genes”, Epigenetics 10:418-430 Park M.J. and Sohrabi F. (2016), “The histone deacetylase inhibitor, sodium butyrate, exhibits neuroprotective effects for ischemic stroke in middle-aged female rats”, J Neuroinflammation 13:300 Porter, N.J., and Christianson, D.W. (2017), "Binding of the microbial cyclic tetrapeptide trapoxin A to the Class I histone deacetylase HDAC8", ACS Chem Biol 12:2281–2286 Richon, V.M. et al. (2003), "Histone deacetylase inhibitors: assays to assess effectiveness in vitro and in vivo", Methods Enzymol. 376:199-205 Ropero, S. and Esteller, M. (2007), "The role of histone deacetylases (HDACs) in human cancer", Mol Oncol 1:19-25 Sekhavat, A. et al. (2007), "Competitive inhibition of histone deacetylase activity by trichostatin A and butyrate", Biochemistry and Cell Biology 85:751-758 Taunton, J. et al. (1996), "A mammalian histone deacetylase related to the Yeast transcriptional regulator Rpd3p", Science 272:408-411 Villar-Garea, A. and Esteller, M. (2004), "Histone deacetylase inhibitors: understanding a new wave of anticancer agents", Int J Cancer 112:171-178 Wade, M.G. et al. (2008), "Methoxyacetic acid-induced spermatocyte death is associated with histone hyperacetylation in rats", Biol Reprod 78:822-831 Wagner F.F. et al. (2015), “Kinetically selective inhibitors of histone deacetylase 2 (HDAC2) as cognition enhances”, Chem Sci 6:804 Weichert, W. (2009) "HDAC expression and clinical prognosis in human malignancies", Cancer Letters 280:168-176 Yanuar, A. et al. (2016), "In silico approach to finding new active compounds from histone deacetylase (HDAC) family", Curr Pharm Des 22:3488-3497 Zwick, V. et al. (2016), "Cell-based multi-substrate assay coupled to UHPLC-ESI-MS/MS for a quick identification of class-specific HDAC inhibitors", J Enzyme Inhib Med Chem 31:209-214 AOPWiki 2018-01-21T20:07:19

2022-07-14T16:18:05

Histone acetylation, increase

Cellular

Gene transcription is regulated with the balance between acetylation and deacetylation. A dynamic balance of histone acetylation and histone deacetylation is typically catalyzed by enzymes with histone acetyltransferase (HAT) and HDAC activities. Histone acetylation relaxes chromatin and makes it accessible to transcription factors, whereas deacetylation is associated with gene silencing. The balance can be disturbed also by targeting HAT, not only HDACs. At least theoretically, an activation of HAT might lead to an increase in histone acetylation. The acetylation and deacetylation are modulated on the NH3+ groups of lysine amino acid residues in histones. HDAC inhibition promotes hyperacetylation by inhibiting the deacetylation of histones with classes of H2A, H2B, H3, and H4 in nucleosomes. [Wade et al., 2008]. The inhibition of HDACs results in an accumulation of acetylated proteins such as tubulin or histones.

Histone acetylation is measured by the immunological detection of histone acetylation with anti-acetylated histone antibodies [Richon et al., 2004]. Histone acetylation on chromatin can be measured using the labeling method with sodium [3H]acetate [Gunjan et al., 2001]. The histone acetylation increase is detected as global histone acetylation changes by Western blot or mass spectrometry (MS)-based proteomics methods or as site-specific histone acetylation changes using chromatin immunoprecipitation (ChIP) or ChIP-on-Chip.

The histone acetylation increase by HDIs is well conserved between species from lower organisms to mammals. ・MAA, an HDAC inhibitor, induces acetylation of histones H3 and H4 in Sprague-Dawley rats (Rattus norvegicus) [Wade et al., 2008]. ・It is also reported that MAA promotes acetylation of H4 in HeLa cells (Homo sapiens) and spleens from C57BL/6 mice (Mus musculus) treated with MAA [Jansen et al., 2014]. ・VPA, an HDAC inhibitor, induces hyperacetylation of histone H4 in protein extract of mouse embryos (Mus musculus) exposed in utero for 1 hr to VPA [Di Renzo et al., 2007a]. ・Apicidin, MS-275 and sodium butyrate, HDAC inhibitors, induce hyperacetylation of histone H4 in homogenates from mouse embryos (Mus musculus) after the treatments [Di Renzo et al., 2007b]. ・MAA acetylates histones H3K9 and H4K12 in limbs of CD1 mice (Mus musculus) [Dayan and Hales, 2014].

UBERON:0000062

UBERON organ

CL:0000000

CL cell

High Unspecific

Moderate

Not Otherwise Specified

High High High

Dayan, C. and Hales, B.F. (2014), "Effects of ethylene glycol monomethyl ether and its metabolite, 2-methoxyacetic acid, on organogenesis stage mouse limbs in vitro", Birth Defects Res (Part B) 101:254-261 Di Renzo, F. et al. (2007a), "Boric acid inhibits embryonic histone deacetylases: A suggested mechanism to explain boric acid-related teratogenicity", Toxicol and Appl Pharmacol 220:178-185 Di Renzo, F. et al. (2007b), "Relationship between embryonic histonic hyperacetylation and axial skeletal defects in mouse exposed to the three HDAC inhibitors apicidin, MS-275, and sodium butyrate", Toxicol Sci 98:582-588 Gunjan, A. et al. (2001), "Core histone acetylation is regulated by linker histone stoichiometry in vivo", J Biol Chem 276:3635-3640 Jansen, M.S. et al. (2014), "Short-chain fatty acids enhance nuclear receptor activity through mitogen-activated protein kinase activation and histone deacetylase inhibition", Proc Natl Acad Sci USA 101:7199-7204 Richon, V.M. et al. (2004), "Histone deacetylase inhibitors: assays to assess effectiveness in vitro and in vivo", Methods Enzymol 376:199-205 Wade, M.G. et al. (2008), "Methoxyacetic acid-induced spermatocyte death is associated with histone hyperacetylation in rats", Biol Reprod 78:822-831 AOPWiki 2018-01-21T20:47:13

2021-07-28T00:10:22

Altered, Gene Expression

Molecular

It is well documented that alterations of histone acetylation have an impact on gene expression. Therefore if the acetylation status of the epigenetic set-up at the regulatory sequences of genes is altered, this leads to changes in gene expression.

Gene specific alterations in histone acetylation at gene regulatory seqences can be measured by chromatin immunoprecipitation (ChIPs) and gene expression analysis by RT-qPCR or whole transcriptomics (RNAseq, gene chips).

CL:0000255

CL eukaryotic cell

AOPWiki 2016-11-29T18:41:31

2019-03-06T10:03:28

Altered differentiation

Cellular

Proper differentiation during embryonic development is regulated by the expression of genes at the right time and space. If key regulator genes are not expressed or wrongly expressed this leads to a different cell type.

Differentiation can be measured e.g. by in vitro hESC or iPSC based differentiation systems. Pre-requisite for this is a well characterized and homogenous cell population. Then it can be measured by the analysis of altered genes by gene set enrichment analysis (GEA) comparing control with potentially disturbed differentiation. In the context of embryonic brain development, immunofluorescence on brain sections can be used with antibodies against neuronal differentiation markers such Tuj1, NeuN and betaIII-tubulin.

Embryonic development

Moderate Unspecific

Not Specified

Birth to < 1 month

Moderate

Pregnancy

Moderate AOPWiki 2018-12-20T08:30:57

2022-03-17T12:27:24

Neural tube defects

Tissue

Wrongly differentiated cells may not be able to perform the process of neural tube closure.

In vitro assays that follow rosettes formation In vivo animal models

AOPWiki 2018-12-20T08:31:33

2018-12-20T08:40:30

<upstream-id>90892966-37d0-48ff-8d96-fc590b749915</upstream-id> <downstream-id>295df882-6f9a-4ef9-a7fb-74a24b0b829b</downstream-id> The HDAC inhibitors (HDIs) inhibit deacetylation of the histone, leading to the increase in histone acetylation and gene transcription. HDACs deacetylate acetylated histone in epigenetic regulation [Falkenberg and Johnstone, 2014]. Histone acetylation is one of the major epigenetic mechanisms and belongs to the posttranslational modifications of histones. Histone acetyltransferase is setting the mark, and deacetylase (HDAC) is responsible for removing the acetyl group from specific lysine residues of the histones. It has been shown that the inhibition of HDACs leads to a hyperacetylation of histones and in general to an imbalance of other histone modifications.

HDACs are important proteins in the epigenetic regulation of gene transcription. Upon the inhibition of HDAC by HDIs, lysine in histone remains acetylated which leads to transcriptional activation or repression, changes in DNA replication, and DNA damage repair [Wade et al., 2008]. In all eukaryotes, the DNA containing the genetic information of an organism is organized in chromatin. The basic unit of chromatin is the nucleosome around which the naked DNA is wrapped. A nucleosome consists of two copies of each of the core histones H2A, H2B, H3, and H4 [Luger et al., 1997]. In order to dynamically regulate this highly complex structure several mechanisms are involved, including the posttranslational modifications of histones (reviewed in [Bannister and Kouzarides, 2011; Kouzarides, 2007]. For a long time, it is known that histones get acetylated and that this reaction is catalyzed by histone acetyltransferases (HAT) whereas the acetyl groups are removed by histone deacetylases (HDAC). Inhibition of HDACs by small-molecule compounds leads to hyperacetylation of the histones as the homeostasis of acetylation and deacetylation is disturbed (reviewed in [Gallinari et al., 2007]).

The major empirical evidence came from the incubation of cell culture cells with small molecule compounds that inhibit HDAC enzymes followed by western blots or acid urea gel analysis. The first evidence was shown by Riggs et al. who showed that incubation of HeLa cells with n-butyrate leads to an accumulation of acetylated histone proteins [Riggs et al., 1977]. Later, it was shown that n-butyrate specifically increases the acetylation of histone by the incorporation of radioactive [3H]acetate and analysis of the histones on acid urea gels that allow the detection of acetylated histones [Cousens et al., 1979]. TSA was shown to be an HDAC inhibitor by acid urea gel analysis in 1990 [Yoshida et al., 1990] and good evidence for VPA as an HDAC inhibitor in vitro and in vivo was shown using acetyl-specific antibodies and western blot [Gottlicher et al., 2001]. There exist several pieces of evidence showing the link between histone deacetylase inhibition and increase in histone acetylation as follows: <ul> <li>Exposure of mouse embryos in utero to VPA and TSA (two well-known HDAC inhibitors) showed an increased histone acetylation level in whole embryo extracts and was also shown in situ immuno-stainings [Menegola et al., 2005].</li> <li>HDAC inhibition by HDIs leads to hyperacetylation of histone and a large number of cellular proteins such as NF-kappaB [Falkenberg and Johnstone, 2014; Chen et al., 2018].</li> <li>The concentrations of half-maximum inhibitory effect (IC50) for HDAC enzyme inhibition of 20 valproic acid derivatives correlated with teratogenic potential of the compounds, and HDAC inhibitory compounds showed hyperacetylation of core histone 4 in treated F9 cells [Eikel et al., 2006].</li> <li>HDIs increase histone acetylation in the brain [Schroeder et al., 2013].</li> <li>More acetylation sites on the histones H3 and H4 are responsive to SAHA than to MS-275 indicating that an HDI selectivity exists [Choudhary et al., 2009].</li> <li>HDI AR-42 induces acetylation of histone H3 in a dose-response manner in human pancreatic cancer cell lines [Henderson et al., 2016].</li> <li>MAA treatment in rats (650 mg/kg, for 4, 8, 12, and 24 hrs) induced hyperacetylation in histones H3 and H4 of testis nuclei [Wade et al., 2008].</li> <li>HDAC inhibition induced by valproic acid (VPA) leads to histone hyperacetylation in mouse teratocarcinoma cell line F9 [Eikel et al., 2006].</li> <li>Hyperacetylation of histone H3 was observed in HDAC1-deficient ES cells [Lagger et al., 2002].</li> <li>The treatment of MAA induced histone acetylation in H3K9Ac and H4K12Ac, as well as p53K379Ac [Dayan and Hales, 2014].</li> </ul>

HDACs affect a large number of cellular proteins including histones, which reminds us the HDAC inhibition by HDIs hyperacetylates cellular proteins other than histones and exhibit additional biological effects. It is also noted that HDAC functions as the catalytic subunits of the large protein complex, which suggests that the inhibition of HDAC by HDIs affects the function of the large multiprotein complexes of HDAC [Falkenberg and Johnstone, 2014].  Related-analysis are usually indirect or in purified systems, therefore a direct cause-consequence relation is difficult to obtain.

To quantify acetylation by HDAC, stable isotope labeling with amino acids in cell culture (SILAC) method is used [Choudhary et al., 2009].

SAHA or MS-275 treatment leads to an increase in acetylation of specific lysine residues on histones more than two-fold [Choudhary et al., 2009]. Acetylation of the variant histone H2AZ-a mark for DNA damage sites- was upregulated almost 20-fold by SAHA, whereas a number of sites on the core histones H3 and H4 are several times more highly regulated in response to SAHA than by MS-275 [Choudhary et al., 2009]. TSA (100 ng/ml) treatment leads to accumulation of the acetylated histones in a variety of mammalian cell lines, and the partially purified HDAC from wild-type FM3A cells was effectively inhibited by TSA (Ki = 3.4 nM) [Yoshida et al., 1990].

High Unspecific

Moderate

All life stages

High High High Moderate Moderate

The relationship between HDAC inhibition and increase in histone acetylation is conceivably well conserved among various species including mammals. <ul> <li>Hyperacetylation by HDIs such as SAHA and Cpd-60 are observed in mice (Mus musculus) [Schroeder et al., 2013].</li> <li>TSA induces acetylation of histone H4 in a time-dependent manner in mouse cell lines (Mus musculus) [Alberts et al., 1998].</li> <li>AR-42, a novel HDI, induces hyperacetylation in human pancreatic cancer cells (Homo sapiens) [Henderson et al., 2016].</li> <li>SAHA and MS-275 lead to the hyperacetylation of lysine residues of histones in human cell lines of epithelial (A549) and lymphoid origin (Jurkat) (Homo sapiens) [Choudhary et al., 2009].</li> <li>SAHA treatment induces the H3 and H4 histone acetylation in human corneal fibroblasts and conjunctiva from rabbits after glaucoma filtration surgery (Homo sapiens, Oryctolagus cuniculus) [Sharma et al., 2016].</li> <li>TSA induces the acetylation of histones H3 and H4 in Brassica napus microspore cultures (Brassica napu) [Li et al., 2014].</li> </ul>

#<Reference::ActiveRecord_Associations_CollectionProxy:0x00007b430b5cb060> AOPWiki 2018-01-21T21:13:57

2021-08-05T19:32:19

<upstream-id>295df882-6f9a-4ef9-a7fb-74a24b0b829b</upstream-id> <downstream-id>8ff7c07a-abda-4b74-897e-3cf3e3556a5a</downstream-id> The structure of chromatin is a major component of gene regulation in eukaryotes by providing or preventing accessibility for the transcriptional machinery to the relevant regulatory DNA sequences. Histone acetylation is one of the major posttranslational modifications that are involved in the regulation of gene expression. Generally spoken, acetylation is correlated with actively transcribed genes, whereas hypoacetylation is involved in gene silencing.

In all eukaryotes, the DNA containing the genetic information of an organism is organized in chromatin. The basic unit of chromatin is the nucleosome around which the naked DNA is wrapped. A nucleosome consists of two copies of each of the core histones H2A, H2B, H3 and H4 (Luger et al., 1997). In general, chromatin is a permissive structure for all DNA-dependent processes such as DNA replication, recombination, repair, and transcription and therefore also for gene expression. However, chromatin structure is very dynamically regulated and can be made accessible for the transcriptional machinery and is, therefore, an important mechanism of gene regulation. One mechanism of chromatin structural regulation is the post-translational modifications of the histone proteins including the acetylation of lysine residues (reviewed in (Bannister and Kouzarides, 2011; Bannister et al., 2002; Kouzarides, 2007; Tessarz and Kouzarides, 2014)). These modifications serve as a docking station for further proteins and protein complexes that finally open or close the chromatin structure and allow or inhibit access of the transcriptional machinery (Musselman et al., 2012) or directly influence DNA histone interaction (reviewed in (Tessarz and Kouzarides, 2014). Histones get acetylated by histone acetyltransferases (HAT) and deacetylated by histone deacetylases (HDAC) (reviewed in (Gallinari et al., 2007; Bannister and Kouzarides, 2011; Kouzarides, 2007)). In general, it can be assumed, hyperacetylated histones are associated with actively transcribed genes, whereas hypoacetylation of histones is involved in gene silencing.

The first direct evidence that histone acetylation has an impact on gene expression came from mutation studies in yeast. Using ChIP on chip analysis showed that mutation or deletions of HDAC enzymes lead to changed gene expression levels on a subset of genes (Xu et al., 2005; Bernstein et al., 2000; Robyr et al., 2002). In the Drosophila cell line S2, it was shown that deregulation of transcription occurs only by know-down (RNAi) HDAC enzymes, that at least class 1 and 3 HDAC enzymes have an influence on gene expression (measured via gene chips). However, this study did not show a direct link between histone acetylation and gene expression (Foglietti et al., 2006). In mice knockout of HDACs are mostly embryonically lethal. However, the use of embryonic stem cells and the expression and acetylation profiles shows that also in mice an imbalance of histone acetylation may lead to changes in gene expression (Zupkovitz et al., 2006). Major gene expression changes were observed during the differentiation of hESC towards neuroectodermal progenitor cells. In these studies also the acetylation status of the deregulated genes was investigated by chromatin immunoprecipitation (Balmer et al., 2014; Balmer et al., 2012)

All above-mentioned analysis are indirect or in purified systems. Therefore a direct cause-consequence relation is difficult to obtain.

#<Reference::ActiveRecord_Associations_CollectionProxy:0x00007b430b5e45d8> AOPWiki 2018-12-20T08:32:46

2018-12-20T08:48:30

<upstream-id>8ff7c07a-abda-4b74-897e-3cf3e3556a5a</upstream-id> <downstream-id>daa175c6-fb1a-42ee-8bd2-2bab57fb7df4</downstream-id> During early embryonic development of the nervous system-specific developmental genes need to be activated in a highly regulated and concerted manner. Genes need to be expressed (or silenced) at the right time and space. If this concerted regulation is disturbed this may lead to severe malformations in the later fetus. The type of malformation depends strongly on the timing of disturbance, i.e. during which developmental stage the disturbance happened. For the development of neural tube defects, especially neural tube closure, the disturbance must happen before neurulation at the stage when neuroepithelial cells arise. Therefore, for this AOP the imbalance of gene expression must occur before neural tube closure. However, compare AOP23 the inhibition of neural crest migration by HDAC inhibition happens later in embryonic development.

Gene expression during embryonic development is a highly regulated process. The genes need to be expressed and silenced at the right time and place. Therefore, if cells that are determined to differentiate into e.g. NEP wrongly express neural crest marker genes this may lead to a failure of neural tube closure. One reason for this effect is that these cells lose their epithelial character and undergo an epithelial mesenchymal transition as neural crest cells do (Park and Gumbiner, 2010). In summary, imbalanced gene expression may lead to the differentiation of the wrong cell type at the wrong time and space.

It was shown that HDAC inhibition changes the gene expression pattern during the differentiation of hESC towards NEP cells. Furthermore, the changed differentiation track points to a wrong differentiation towards neural crest cells (Balmer et al., 2014). The differentiation track of hESC towards NEP is strongly disturbed in vitro by 6 different (structurally not related) HDAC inhibitors in a comparable manner (Rempel et al., 2015). TSA treated chicken embryos showed a disturbed gene expression pattern of the posterior neural tube, that points to a wrong differentiation track towards neural crest cells (Murko et al., 2013).

#<Reference::ActiveRecord_Associations_CollectionProxy:0x00007b430b5f9410> AOPWiki 2018-12-20T08:33:13

2018-12-20T08:53:06

<upstream-id>daa175c6-fb1a-42ee-8bd2-2bab57fb7df4</upstream-id> <downstream-id>255cbe26-6a5d-465a-b57f-4ff4ebd627df</downstream-id> During the process of neural tube closure, the cells at the dorsal boundary a new cell type arises, the neural crest cells. These cells undergo an epithelial to mesenchymal transition that enables them to migrate away from the neural tube. If the neuroepithelial cells of the neural tube express the wrong regulator genes it may happen that they acquire such neural crest characteristics, which prevents them from performing the closure of the neural tube.

Many HDAC inhibitors used as drugs have been shown to induce congenital malformations, including neural tube closure defects in humans and model organisms (Menegola et al., 1996; Nau, 1994). Most studies show that after treatment with HDAC inhibitors these malformations occur in the experimental animals, however direct evidence that neural tube closure defects result from wrongly differentiated neural tube cells.

TSA treated chicken embryos showed a disturbed gene expression pattern of the posterior neural tube, that points to a wrong differentiation track towards neural crest cells. This was shown by in situ immune staining using neural crest-specific antibodies (Murko et al., 2013). Further Menegola et al. showed direct evidence that HDAC inhibition is occurring in vivo in the neural tube of mice (Menegola et al., 2005).

Due to lacking studies directly showing that the neural tube cells are wrongly differentiated and that this may causative for closure defects the uncertainty of this KER is very high and based on correlation studies.

#<Reference::ActiveRecord_Associations_CollectionProxy:0x00007b430b61e3a0> AOPWiki 2018-12-20T08:33:26

2018-12-20T09:00:27

Histone deacetylase inhibition leads to neural tube defects

HDAC inhibition leads to neural tube defects

Allie Always

Tanja Waldmann

BY-SA

2.0

The expression and function of histone deacetylases (HDAC) are well known during embryonic development and especially plays a pivotal role in the development of the nervous system. HDAC inhibition during embryonic development has been correlated to several congenital malformations mainly affecting neurodevelopment. However, the kind of malformation strongly depends on the timing of disturbance, i.e. when during embryonic development the exposure occurred. This AOP concentrates on disturbances by HDAC inhibition during the first weeks of neurodevelopment, before or around the time point of neural tube closure. Therefore, this AOP suggests a mechanism how HDAC inhibitors could lead to the observed neural tube defects. It assumes that HDAC inhibition leads to an imbalance of histone modifications and eventually to altered gene expression. In the next KE altered gene expression may lead to a wrong differentiation of neuroectodermal cells that cannot close the neural tube anymore and therefore leads to neural tube closure defects. This AOP is linked to case study 2 that investigates the effects of VPA and its structural analogs the EU-ToxRisk DART (development and reproductive toxicology) test methods.

HDIs are classified according to chemical nature and mode of mechanism: the short-chain fatty acids (e.g., butyrate, valproate), hydroxamic acids (e.g., suberoylanilide hydroxamic acid or SAHA, Trichostatin A or TSA), cyclic tetrapeptides (e.g., FK-228), benzamides (e.g., N-acetyldinaline and MS-275) and epoxides (depeudecin, trapoxin A) [Richon et al., 2003; Ropero and Esteller, 2007; Villar-Garea et al., 2004]. There is a report showing that TSA and butyrate competitively inhibit HDAC activity [Sekhavat et al., 2007]. HDIs inhibit preferentially HDACs with some selectiveness [Hu et al., 2003]. TSA (Trichostatin A) inhibits class I and II of HDACs, while butyrate inhibits class I and IIa (HDACs 4, 5, 7, 9) of HDACs [Ooi et al., 2015; Park and Sohrabji, 2016; Wagner et al., 2015].  TSA inhibits HDAC1, 2, and 3 [Damaskos et al., 2016], whereas MS-27-275 has an inhibitory effect for HDAC1 and HDAC3 (IC50 value of ~0.3 microM and ~8 microM, respectively), but no effect for HDAC8 (IC50 value >100 microM) [Hu et al., 2003].

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AOPWiki 2018-12-20T08:24:47

2023-09-25T16:26:58