Histone Acetylation Pathways Research Articles

Epigenetic histone acetylation and Bdnf dysregulation in the hippocampus of rats exposed to repeated, low-dose diisopropylfluorophosphate

AimsDeployment-related exposures to organophosphate (OP) compounds are implicated for Gulf War Illness (GWI) development in First GW veterans. However, reasons for the persistence of GWI are not fully understood. Epigenetic modifications to chromatin are regulatory mechanisms that can adaptively or maladaptively respond to external stimuli. These include DNA methylation and histone acetylation. DNA methylation changes have been reported in GWI but the role of histone acetylation in GWI has been less explored, despite its importance as an epigenetic mechanism for neurological disorders. Main methodsMale Sprague-Dawley rats were exposed to OP diisopropyl fluorophosphate (DFP, 0.5 mg/kg s.c., 5-d) and 6-m later brains were dissected for hippocampus. Western blotting, activity assays and chromatin immunoprecipitation (ChIP) were utilized for epigenetic analyses. Behavior was assessed using the Forced Swim Test (FST) and the Elevated Plus Maze (EPM). Key findingsWe observed a significant upregulation in HDAC1 protein along with a significant increase in HDAC enzyme activity in the hippocampus of DFP rats. A locus-specific ChIP study revealed decreases in H3K9ac at the brain derived neurotrophic factor (Bdnf) promoter IV coupled with a significant decrease in BDNF protein in DFP rat hippocampus. Treatment with HDAC inhibitor valproic acid reduced HDAC activity and decreased the FST immobility time in DFP rats. SignificanceOur research suggests that epigenetic alterations to histone acetylation pathways and decreased BDNF expression could represent novel mechanisms for GWI symptomatology and may provide new targets for developing effective drugs for GWI treatment.

Dysregulation of histone acetylation pathways in hippocampus and frontal cortex of Alzheimer's disease patients

Memory impairment is the main feature of Alzheimer's disease (AD). Initial impairments originate in the temporal lobe area and propagate throughout the brain in a sequential manner. Epigenetic mechanisms, especially histone acetylation, regulate plasticity and memory processes. These may be dismantled during the disease. The aim of this work was to establish changes in the acetylation-associated pathway in two key brain regions affected in AD: the hippocampus and the F2 area of frontal cortex in end-stage AD patients and age-matched controls. We found that the F2 area was more affected than the hippocampus. Indeed, CREB-Binding Protein (CBP), P300/CBP-associated protein (PCAF), Histone Deacetylase 1 (HDAC1) and HDAC2 (but not HDAC3) levels were strongly decreased in F2 area of AD compared to controls patients, whereas only HDAC1 was decreased and CBP showed a downward trend in the hippocampus. At the histone level, we detected a substantial increase in total (H3 and H2B) histone levels in the frontal cortex, but these were decreased in nuclear extracts, pointing to a dysregulation in histone trafficking/catabolism in this brain region. Histone H3 acetylation levels were increased in cell nuclei mainly in the frontal cortex. These findings provide evidence for acetylation dysfunctions at the level of associated enzymes and of histones in AD brains, which may underlie transcriptional dysregulations and AD-related cognitive impairments. They further point to stronger dysregulations in the F2 area of the frontal cortex than in the hippocampus at an end-stage of the disease, suggesting a differential vulnerability and/or compensatory mechanisms efficiency towards epigenetic alterations.

Targeting histone acetylation in pulmonary hypertension and right ventricular hypertrophy.

Epigenetic mechanisms, including DNA methylation and histone post-translational modifications (PTMs), have been known to regulate chromatin structure and lineage-specific gene expression during cardiovascular development and disease. However, alterations in the landscape of histone PTMs and their contribution to the pathogenesis of incurable cardiovascular diseases such as pulmonary hypertension (PH) and associated right heart failure (RHF) remain largely unexplored. This review focusses on the studies in PH and RHF that investigated the gene families that write (histone acetyltransferases), read (bromodomain-containing proteins) or erase (histone deacetylases [HDACs] and sirtuins [SIRT]) acetyl moieties from the ε-amino group of lysine residues of histones and non-histone proteins. Analysis of cells and tissues isolated from the in vivo preclinical models of PH and human pulmonary arterial hypertension not only confirmed significant alterations in the expression levels of multiple HDACs, SIRT1, SIRT3 and BRD4 proteins but also demonstrated their strong association to proliferative, inflammatory and fibrotic phenotypes linked to the pathological vascular remodelling process. Due to the reversible nature of post-translational protein acetylation, the therapeutic efficacy of numerous small-molecule inhibitors (vorinostat, valproic acid, sodium butyrate, mocetinostat, entinostat, tubastatin A, apabetalone, JQ1 and resveratrol) have been evaluated in different preclinical models of cardiovascular disease, which revealed the promising therapeutic benefits of targeting histone acetylation pathways in the attenuation of cardiac hypertrophy, fibrosis, left heart dysfunction, PH and RHF. This review also emphasizes the need for deeper molecular insights into the contribution of epigenetic changes to PH pathogenesis and therapeutic evaluation of isoform-specific modulation in ex vivo and in vivo models of PH and RHF. LINKED ARTICLES: This article is part of a themed issue on Risk factors, comorbidities, and comedications in cardioprotection. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v178.1/issuetoc.

Repurposing histone deacetylase inhibitors (HDACi) to treat Candida glabrata infections

Candida glabrata currently accounts for 25 % of all fungal cases in UK hospitals, second only to C. albicans. This number is expected to rise given the intrinsic anti-fungal resistance of this species and the difficulty in treating it. In an effort to identify novel-anti fungal targets in C. glabrata, we used comparative genomics within Saccharomycotina yeast to predict which genes are under positive selection in this species specifically. Such genes are predicted to have influenced the adaptation of C. glabrata from a free-living microbe to a human pathogen, potentially due to functional shift(s) of the proteins they encode. Our analysis predicts that histone acetylation pathways are under positive selection in C. glabrata. Thereforewe hypothesised that we could use histone deacetylase inhibitors (HDACi) to interfere with histone acetylation levels and impact C. glabrata virulence. By treating C. glabrata withbroad spectrum HDACis we show it has a reduced capacity to form biofilms, it is less well adapted to high salt conditions typically found within a human host, and most importantly, it reverts to a more anti-fungal sensitive state. RNAseq analysis indicates that HDACi treatment interferes with the C. glabrata transcriptional response to anti-fungal treatment, rendering it incapable of combating against these drugs. Furthermore, using an in vivo worm model of candidiasis, we show that HDACi treatment in conjunction with the anti-fungal fluconazole, can increase the survival rate of individuals with C. glabrata infections. Taken together our data suggest that the health threat posed by C. glabrata might be addressed by repurposing HDACi to treat this infection.

A role for ATP Citrate Lyase in cell cycle regulation during myeloid differentiation

Differentiation of myeloid progenitor cells into macrophages is accompanied by increased PU.1 concentration and increasing cell cycle length, culminating in cell cycle arrest. Induction of PU.1 expression in a cultured myeloid cell line expressing low PU.1 concentration results in decreased levels of mRNA encoding ATP-Citrate Lyase (ACL) and cell cycle arrest. ACL is an essential enzyme for generating acetyl-CoA, a key metabolite for the first step in fatty acid synthesis and for histone acetylation. We hypothesized that ACL may play a role in cell cycle regulation in the myeloid lineage. In this study, we found that acetyl-CoA or acetate supplementation was sufficient to rescue cell cycle progression in cultured BN cells treated with an ACL inhibitor or induced for PU.1 expression. Acetyl-CoA supplementation was also sufficient to rescue cell cycle progression in BN cells treated with a fatty acid synthase (FASN) inhibitor. We demonstrated that acetyl-CoA was utilized in both fatty acid synthesis and histone acetylation pathways to promote proliferation. Finally, we found that Acly mRNA transcript levels decrease during normal macrophage differentiation from bone marrow precursors. Our results suggest that regulation of ACL activity is a potentially important point of control for cell cycle regulation in the myeloid lineage.

Acetylation Reader Proteins: Linking Acetylation Signaling to Genome Maintenance and Cancer.

Chromatin-based DNA damage response (DDR) pathways are fundamental for preventing genome and epigenome instability, which are prevalent in cancer. Histone acetyltransferases (HATs) and histone deacetylases (HDACs) catalyze the addition and removal of acetyl groups on lysine residues, a post-translational modification important for the DDR. Acetylation can alter chromatin structure as well as function by providing binding signals for reader proteins containing acetyl-lysine recognition domains, including the bromodomain (BRD). Acetylation dynamics occur upon DNA damage in part to regulate chromatin and BRD protein interactions that mediate key DDR activities. In cancer, DDR and acetylation pathways are often mutated or abnormally expressed. DNA damaging agents and drugs targeting epigenetic regulators, including HATs, HDACs, and BRD proteins, are used or are being developed to treat cancer. Here, we discuss how histone acetylation pathways, with a focus on acetylation reader proteins, promote genome stability and the DDR. We analyze how acetylation signaling impacts the DDR in the context of cancer and its treatments. Understanding the relationship between epigenetic regulators, the DDR, and chromatin is integral for obtaining a mechanistic understanding of genome and epigenome maintenance pathways, information that can be leveraged for targeting acetylation signaling, and/or the DDR to treat diseases, including cancer.

Distinct Pattern Of Genomic Changes Associated With Smoking In Patients With Myelodysplastic Syndromes (MDS)

BackgroundSmoking is a risk factor for development of MDS and for overall survival. The pathogenesis of MDS is a multi-step process with both environmental and genetic influences. The link between smoking and MDS is thought to be mediated by organic solvents in tobacco. We identified specific molecular abnormalities associated with smoking exposure in MDS patients (pts). Methods151 MDS pts seen from 2000-2012 with complete smoking and molecular data were included. Correlations and univariable comparisons were performed using Fisher's Exact, Chi-square, Kruskal-Wallis, or Wilcoxon rank sum tests. Poisson regression models were used to assess associations between the number of mutations present and demographic and clinical factors. Analysis was performed using next-generation targeted deep gene sequencing with 22 common gene mutations, selected based on the frequency observed in a cohort of MDS patients analyzed by whole exome sequencing. Mutations were considered individually and in functional groups: methylation (TET2, IDH1, IDH2), histone modification (ASXL1, EZH2), and gene splicing (SRSF2, U2AF1, SF3B1). Paired DNA (tumor vs. CD3+ lymphocytes) produced raw sequence reads aligned using Burrows-Wheeler Aligner (BWA). Variants were detected using the Broad Institute's Best Practice Variant Detection GATK toolkit. ResultsMedian age at MDS diagnosis was 68 years (range 20-85); 42% were female; and 77% had de novo MDS. IPSS (low, Int-1, Int-2, high) and IPSS-R (very low, low, int, high, very high) categories were: 26%, 44%, 22%, 7% and 10%, 40%, 19%, 18%, 13%, respectively; IPSS-R cytogenetic categories were: very good (<1%), good (60%), int (14%), poor (12%), very poor (14%). Median survival was 42.6 months (95% C.I. 34.5-56.0). 54% of pts (81) were former (42%) or current (11%) smokers; median tobacco exposure was similar for both groups: 26 pack years (range 1.5-150) for former and 30 (10-60) for current smokers, p=0.22. More men than women ever smoked (p=0.03); all other clinical characteristics among never, ex-, and current smokers were similar. Overall 68% of pts (100) had at least one mutation of the 22 screened mutations: 32% (48) had a single mutation, 22% (33) had 2, and 13% (19) had 3 (n=10) to 6 (n=1) mutations. The most common mutations were in TET2 (19%), SF3B1 (15%), ASXL1 (14%), DNMT3A (11%), and U2AF1 (10%); 32% of pts had one or more mutation in genes involved in methylation, 19% in histone modification, and 32% with splicing. In univariable analyses, current/ex-smokers were more likely to have at least one of the common mutation than never smokers (75% vs. 52%, respectively, p=0.05). This was particularly true for genes involved in histone modification (25% vs. 11%, respectively, p=0.06). The number of mutations increased with smoking exposure (p=0.02, Figure 1), particularly with genes involved with histone modification, p=0.01. Certain mutations increased in prevalence with age, e.g.: pts<60 had fewer mutations overall than pts >60 (p=0.003), and in particular fewer mutations in methylation-associated genes (p=0.0001). In multivariable analysis that adjusted for IPSS-R cytogenetics, older age (p=0.0005) and greater smoking history/exposure (p=0.002) were both associated with more mutations. Current and ex-smokers and heavier smoking exposure (>20 pack years) were also associated with worse survival (p=.03 and .01, respectively), though current or ex-smokers with <20 pack years had similar survival to never smokers. Multivariable analyses confirmed smoking as a risk factor for survival (HR 1.63 (1.1-2.42); p=0.02). [Display omitted] ConclusionSmoking is associated with a greater number of molecular abnormalities in MDS pts, and may generate a distinct mutational signature pattern, particularly along histone acetylation pathways. This study identifies specific environmentally-mediated pathways in the multistep pathogenesis of MDS. Disclosures:No relevant conflicts of interest to declare.

Epigenetics and Hypertension

Epigenetics refers to mechanisms for environment-gene interactions (mainly by methylation of DNA and modification of histones) that do not alter the underlying base sequence of the gene. This article reviews evidence for epigenetic contributions to hypertension. For example, DNA methylation at CpG islands and histone acetylation pathways are known to limit nephron development, thereby unmasking hypertension associated with exposure to a high-salt diet. Maternal water deprivation and protein deficiency are shown to increase expression of renin-angiotensin system genes in the offspring. The methylation pattern of a serine protease inhibitor gene in human placentas is shown to be a marker for preeclampsia-associated hypertension. Mental stress induces phenylethanolamine n-methyltransferase, which may act as a DNA methylase and mimic the gene-silencing effects of methyl CpG binding protein-2 on the norepinephrine transporter gene, which, in turn, may exaggerate autonomic responsiveness. A disrupter of telomeric silencing (Dot1) is known to modulate the expression of a connective-tissue growth-factor gene associated with blood vessel remodeling, which could alter vascular compliance and elastance. Dot1a also interacts with the Af9 gene to produce high sodium channel permeability and silences the hydroxysteroid dehydrogenase-11β2 gene, thereby preventing metabolism of cortisol to cortisone and overstimulating aldosterone receptors. These findings indicate targets for environment-gene interactions in various hypertensive states and in essential hypertension.

Perturbation of gene expression of the chromatin remodeling pathway in premature newborns at risk for bronchopulmonary dysplasia

The expression profiles of umbilical cords from premature newborns reveal distinct patterns, including changes in the expression of chromatin remodeling factors, associated with the development of bronchopulmonary dysplasia.