H3K9 Hyperacetylation Research Articles

Pharmacological activation of STAT1-GSDME pyroptotic circuitry reinforces epigenetic immunotherapy for hepatocellular carcinoma.

Genomic screening uncovered interferon-gamma (IFNγ) pathway defects in tumours refractory to immune checkpoint blockade (ICB). However, its non-mutational regulation and reversibility for therapeutic development remain less understood. We aimed to identify ICB resistance-associated druggable histone deacetylases (HDACs) and develop a readily translatable combination approach for patients with hepatocellular carcinoma (HCC). We correlated the prognostic outcomes of HCC patients from a pembrolizumab trial (NCT03419481) with tumourous cell expressions of all HDAC isoforms by single-cell RNA sequencing. We investigated the therapeutic efficacy and mechanism of action of selective HDAC inhibition in 4 ICB-resistant orthotopic and spontaneous models using immune profiling, single-cell multiomics and chromatin immunoprecipitation-sequencing and verified by genetic modulations and co-culture systems. HCC patients showing higher HDAC1/2/3 expressions exhibited deficient IFNγ signalling and poorer survival on ICB therapy. Transient treatment of a selective class-I HDAC inhibitor CXD101 resensitised HDAC1/2/3high tumours to ICB therapies, resulting in CD8+T cell-dependent antitumour and memory T cell responses. Mechanistically, CXD101 synergised with ICB to stimulate STAT1-driven antitumour immunity through enhanced chromatin accessibility and H3K27 hyperacetylation of IFNγ-responsive genes. Intratumoural recruitment of IFNγ+GZMB+cytotoxic lymphocytes further promoted cleavage of CXD101-induced Gasdermin E (GSDME) to trigger pyroptosis in a STAT1-dependent manner. Notably, deletion of GSDME mimicked STAT1 knockout in abolishing the antitumour efficacy and survival benefit of CXD101-ICB combination therapy by thwarting both pyroptotic and IFNγ responses. Our immunoepigenetic strategy harnesses IFNγ-mediated network to augment the cancer-immunity cycle, revealing a self-reinforcing STAT1-GSDME pyroptotic circuitry as the mechanistic basis for an ongoing phase-II trial to tackle ICB resistance (NCT05873244).

Activation of AMPK inhibits cervical cancer growth by hyperacetylation of H3K9 through PCAF

BackgroundDysregulation in histone acetylation, a significant epigenetic alteration closely associated with major pathologies including cancer, promotes tumorigenesis, inactivating tumor-suppressor genes and activating oncogenic pathways. AMP-activated protein kinase (AMPK) is a cellular energy sensor that regulates a multitude of biological processes. Although a number of studies have identified the mechanisms by which AMPK regulates cancer growth, the underlying epigenetic mechanisms remain unknown.MethodsThe impact of metformin, an AMPK activator, on cervical cancer was evaluated through assessments of cell viability, tumor xenograft model, pan-acetylation analysis, and the role of the AMPK-PCAF-H3K9ac signaling pathway. Using label-free quantitative acetylproteomics and chromatin immunoprecipitation-sequencing (ChIP) technology, the activation of AMPK-induced H3K9 acetylation was further investigated.ResultsIn this study, we found that metformin, acting as an AMPK agonist, activates AMPK, thereby inhibiting the proliferation of cervical cancer both in vitro and in vivo. Mechanistically, AMPK activation induces H3K9 acetylation at epigenetic level, leading to chromatin remodeling in cervical cancer. This also enhances the binding of H3K9ac to the promoter regions of multiple tumor suppressor genes, thereby promoting their transcriptional activation. Furthermore, the absence of PCAF renders AMPK activation incapable of inducing H3K9 acetylation.ConclusionsIn conclusion, our findings demonstrate that AMPK mediates the inhibition of cervical cancer growth through PCAF-dependent H3K9 acetylation. This discovery not only facilitates the clinical application of metformin but also underscores the essential role of PCAF in AMPK activation-induced H3K9 hyperacetylation.

852P c-MAF-driven metabolic reprogramming mediates H3K27 hyperacetylation to regulate super enhancer-associated genes

852P c-MAF-driven metabolic reprogramming mediates H3K27 hyperacetylation to regulate super enhancer-associated genes

Modulation of Viability, Proliferation, and Stemness by Rosmarinic Acid in Medulloblastoma Cells: Involvement of HDACs and EGFR.

Medulloblastoma (MB) is a heterogeneous group of malignant pediatric brain tumors, divided into molecular groups with distinct biological features and prognoses. Currently available therapy often results in poor long-term quality of life for patients, which will be afflicted by neurological, neuropsychiatric, and emotional sequelae. Identifying novel therapeutic agents capable of targeting the tumors without jeopardizing patients' quality of life is imperative. Rosmarinic acid (RA) is a plant-derived compound whose action against a series of diseases including cancer has been investigated, with no side effects reported so far. Previous studies have not examined whether RA has effects in MB. Here, we show RA is cytotoxic against human Daoy (IC50 = 168μM) and D283 (IC50 = 334μM) MB cells. Exposure to RA for 48h reduced histone deacetylase 1 (HDAC1) expression while increasing H3K9 hyperacetylation, reduced epidermal growth factor (EGFR) expression, and inhibited EGFR downstream targets extracellular-regulated kinase (ERK)1/2 and AKT in Daoy cells. These modifications were accompanied by increased expression of CDKN1A/p21, reduced expression of SOX2, and a decrease in proliferative rate. Treatment with RA also reduced cancer stem cell markers expression and neurosphere size. Taken together, our findings indicate that RA can reduce cell proliferation and stemness and induce cell cycle arrest in MB cells. Mechanisms mediating these effects may include targeting HDAC1, EGFR, and ERK signaling, and promoting p21 expression, possibly through an increase in H3K9ac and AKT deactivation. RA should be further investigated as a potential anticancer agent in experimental MB.

Altered Smooth Muscle Cell Histone Acetylome by the SPHK2/S1P Axis Promotes Pulmonary Hypertension.

Epigenetic regulation of vascular remodeling in pulmonary hypertension (PH) is poorly understood. Transcription regulating, histone acetylation code alters chromatin accessibility to promote transcriptional activation. Our goal was to identify upstream mechanisms that disrupt epigenetic equilibrium in PH. Human pulmonary artery smooth muscle cells (PASMCs), human idiopathic pulmonary arterial hypertension (iPAH):human PASMCs, iPAH lung tissue, failed donor lung tissue, human pulmonary microvascular endothelial cells, iPAH:PASMC and non-iPAH:PASMC RNA-seq databases, NanoString nCounter, and cleavage under targets and release using nuclease were utilized to investigate histone acetylation, hyperacetylation targets, protein and gene expression, sphingolipid activation, cell proliferation, and gene target identification. SPHK2 (sphingosine kinase 2) knockout was compared with control C57BL/6NJ mice after 3 weeks of hypoxia and assessed for indices of PH. We identified that Human PASMCs are vulnerable to the transcription-promoting epigenetic mediator histone acetylation resulting in alterations in transcription machinery and confirmed its pathological existence in PH:PASMC cells. We report that SPHK2 is elevated as much as 20-fold in iPAH lung tissue and is elevated in iPAH:PASMC cells. During PH pathogenesis, nuclear SPHK2 activates nuclear bioactive lipid S1P (sphingosine 1-phosphate) catalyzing enzyme and mediates transcription regulating histone H3K9 acetylation (acetyl histone H3 lysine 9 [Ac-H3K9]) through EMAP (endothelial monocyte activating polypeptide) II. In iPAH lungs, we identified a 4-fold elevation of the reversible epigenetic transcription modulator Ac-H3K9:H3 ratio. Loss of SPHK2 inhibited hypoxic-induced PH and Ac-H3K9 in mice. We discovered that pulmonary vascular endothelial cells are a priming factor of the EMAP II/SPHK2/S1P axis that alters the acetylome with a specificity for PASMC, through hyperacetylation of histone H3K9. Using cleavage under targets and release using nuclease, we further show that EMAP II-mediated SPHK2 has the potential to modify the local transcription machinery of pluripotency factor KLF4 (Krüppel-like factor 4) by hyperacetylating KLF4 Cis-regulatory elements while deletion and targeted inhibition of SPHK2 rescues transcription altering Ac-H3K9. SPHK2 expression and its activation of the reversible histone H3K9 acetylation in human pulmonary artery smooth muscle cell represent new therapeutic targets that could mitigate PH vascular remodeling.

Design, synthesis and biological evaluation of pyrimidine base hydroxamic acid derivatives as dual JMJD3 and HDAC inhibitors

The Jumonji domain-containing protein demethylase 3 (JMJD3) and histone deacetylase (HADC) are related to various cancers and regard as antitumor targets for drug discovery. In this study, based on rational drug design strategy, we designed and synthesized a series of pyrimidine derivatives with hydroxamic acid as novel dual JMJD3 and HDAC inhibitors for synergistic cancer treatment. Compound A5b exhibited inhibitory potency against JMJD3 and HDAC1/6 simultaneously and favorable cytotoxicity against human cancer cells such as A549 and U937. Furthermore, mechanistic studies showed that A5b treatment in A549 cells increased the hypermethylation of histone H3K27 and hyperacetylation of H3K9, suppressed clonogenicity, migration and invasion of cancer cells. Besides, A5b induced apoptosis via the cleavage of caspase-7 and PARP, and G1 cell cycle arrest via upregulated p21 expression. All these results suggested that A5b was the first dual inhibitor against JMJD3 and HDAC and can be a potential compound for cancer therapy.

Oncostatin M/Oncostatin M Receptor Signal Induces Radiation-Induced Heart Fibrosis by Regulating SMAD4 in Fibroblast

Radiation-induced heart fibrosis (RIHF) is a severe consequence of radiation-induced heart damage (RIHD) leading to impaired cardiac function. The involvement of oncostatin M (OSM) and its receptor (OSMR) in RIHD remains unclear. This study aimed to investigate the specific mechanism of OSM/OSMR in RIHF/RIHD. RNA sequencing was performed on heart tissues from a RIHD mouse model. OSM levels were assessed in serum samples obtained from patients receiving thoracic radiation therapy (RT), as well as in RIHF mouse heart tissues and serum using enzyme-linked immunosorbent assay. Fiber activation was evaluated through costimulation of primary cardiac fibroblasts and NIH3T3 cells with RT and OSM, using Western blotting, immunofluorescence, and quantitative Polymerase Chain Reaction (qPCR). Adeno-associated virus serotype 9-mediated overexpression or silencing of OSM specifically in the heart was performed in vivo to assess cardiac fibrosis levels by transthoracic echocardiography and pathologic examination. The regulatory mechanism of OSM on the transcription level of SMAD4 was further explored in vitro using mass spectrometric analysis, chromatin immunoprecipitation-qPCR, and DNA pull-down. OSM levels were elevated in the serum of patients after thoracic RT as well as in RIHF mouse cardiac endothelial cells and mouse serum. The OSM rate (post-RT/pre-RT) and the heart exposure dose in RT patients showed a positive correlation. Silencing OSMR in RIHF mice reduced fibrosis, while OSMR overexpression increased fibrotic responses. Furthermore, increased OSM promoted histone acetylation (H3K27ac) in the SMAD4 promoter region, influencing SMAD4 transcription and subsequently enhancing fibrotic response. The findings demonstrated that OSM/OSMR signaling promotes SMAD4 transcription in cardiac fibroblasts through H3K27 hyperacetylation, thereby promoting radiation-induced cardiac fibrosis and manifestations of RIHD.

Abstract 3681: c-MAF-driven metabolic reprogramming mediates H3K27 hyperacetylation to regulate super enhancer-associated genes

Abstract Overexpression of transcription factor c-MAF is found in about 50% of multiple myeloma cases, and associated with the prognostically unfavorable t(14;16) translocation subtype. Genetic alterations can modify the epigenome through metabolite availability that act as substrates in histone modifications, but how this translates into specificities in gene regulation is unclear. Here, we report a novel involvement of c-MAF in metabolically-driven histone acetylation, including the superenhancer mark H3K27ac, through altering acetyl-CoA metabolism. To sustain high levels of acetylation, c-MAF acquired the metabolic flexibility to utilize glutamine in addition to glucose, feeding into the tricarboxylic acid (TCA) cycle as acetyl-CoA sources. Loss-of-function studies indicated that c-MAF is important for citrate-derived acetyl-CoA and H3K27ac levels through metabolic enzymes citrate synthase (CS) and ATP-citrate lyase (ACLY). Furthermore, blocking citrate export from mitochondrial via CRISPR/Cas9 targeting of SLC25A1 reproduced the reductions in H3K27ac. Silencing of c-MAF also displayed defective mitochondrial oxidative phosphorylation attributed to reduced metabolic flux through TCA cycle and downregulation of electron transport chain complex I/II expression, without affecting mitochondrial DNA content. To identify c-MAF-regulated superenhancer genes, we overlapped our previously published H3K27ac ChIP-seq dataset on t(14;16) MM cell lines with c-MAF RNA-seq data. We found signal enrichment of H3K27ac at ZC3H3 locus responsible for its transcriptional upregulation, and knockdown of ZC3H3 inhibited cell growth specifically in the t(14;16) subtype. Altogether, we demonstrated a non-canonical c-MAF role in epigenetics that is connected to its altered metabolic state, and suggest metabolic disruptions as a new therapeutic direction in t(14;16) myeloma. Citation Format: Phyllis SY Chong, Sze Lynn Julia Lim, Jianbiao Zhou, Aaron Chung Yong Leow, Wee Joo Chng. c-MAF-driven metabolic reprogramming mediates H3K27 hyperacetylation to regulate super enhancer-associated genes. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3681.

Absence of HDAC3 by Matrix Stiffness Promotes Chromatin Remodeling and Fibroblast Activation in Idiopathic Pulmonary Fibrosis

Idiopathic pulmonary fibrosis (IPF) is a chronic and fatal disease characterized by progressive and irreversible lung scarring associated with persistent activation of fibroblasts. Epigenetics could integrate diverse microenvironmental signals, such as stiffness, to direct persistent fibroblast activation. Histone modifications by deacetylases (HDAC) may play an essential role in the gene expression changes involved in the pathological remodeling of the lung. Particularly, HDAC3 is crucial for maintaining chromatin and regulating gene expression, but little is known about its role in IPF. In the study, control and IPF-derived fibroblasts were used to determine the influence of HDAC3 on chromatin remodeling and gene expression associated with IPF signature. Additionally, the cells were grown on hydrogels to mimic the stiffness of a fibrotic lung. Our results showed a decreased HDAC3 in the nucleus of IPF fibroblasts, which correlates with changes in nucleus size and heterochromatin loss. The inhibition of HDAC3 with a pharmacological inhibitor causes hyperacetylation of H3K9 and provokes an increased expression of Col1A1, ACTA2, and p21. Comparable results were found in hydrogels, where matrix stiffness promotes the loss of nuclear HDAC3 and increases the profibrotic signature. Finally, latrunculin b was used to confirm that changes by stiffness depend on the mechanotransduction signals. Together, these results suggest that HDAC3 could be a link between epigenetic mechanisms and the fibrotic microenvironment.

A Quadratic Phenotypic Optimization Drug Screening Platform (QPOP) Identified Chromatin Modification as a Potential Strategy to Target Radioresistant (RR) Head and Neck Cancers (HNC)

<h3>Purpose/Objective(s)</h3> Radiotherapy (RT) is a primary treatment modality for most HNC. However, locoregional recurrence post-RT remains a pertinent clinical problem, given that salvage therapeutic options are often limited and ineffective. Resistance to RT is thus an important unmet clinical need in HNC, but therapeutic strategies against radioresistance remain suboptimal, partly owing to the divergent tumor and microenvironmental factors underpinning radioresistance. We had previously developed a high-throughput drug screening method – QPOP that was applied successfully in drug-resistant multiple myeloma (Rashid M. et al., 2018). Here, we investigated the utility of QPOP for the discovery of novel drug combinations in RR-HNC models, and hypothesize that QPOP can accurately identify optimal drug combinations that resensitize RR cells. <h3>Materials/Methods</h3> <i>In vitro</i> isogenic models of RR-HNC were generated by exposing two wild-type (WT) HNC cell lines, FaDu and HK-1, to 90 Gy of 2 Gy irradiation (IR) (45 fr x 2 Gy/fr), and validated using clonogenic assays. QPOP is a complex system analytics platform that rapidly and efficiently ranks and compares all possible system-specific drug combinations from a large drug search set. Pre-experimental selection of drug candidates consisted of standard chemotherapy (cisplatin, carboplatin, and docetaxel), as well as small molecule inhibitors and targeted therapies specific to HNC. Validation of top and lowest QPOP-ranked drug combinations include synergy scoring (Bliss model), combination index theorem of Chou-Talalay, and apoptotic response (Annexin V assay). Drug targeting was validated by western blot analyses, and the Comet assay was used to quantify DNA damage. <h3>Results</h3> A preliminary QPOP-based combinatorial drug screen identified distinct drug sensitivities between WT- and RR-FaDu cells. Validation of the top 5 QPOP-ranked drug combinations revealed that co-treatment of panobinostat (HDAC inhibitor, Pano) and AZD7762 (CHK1 inhibitor) exhibited the most distinct and contrasting response between WT and RR cells. Response surface mapping highlighted Pano and AZD7762 synergy in RR-FaDu, further supported by Bliss synergy scoring that showed synergistic growth inhibition in RR (20.1, synergistic), but not in WT (8.3, additive) cells. These results were corroborated by H3K27 hyperacetylation, and increased downstream caspase-dependent apoptosis and DNA damage in RR-FaDu following combinatorial treatment, compared with single drug treatments. Next, we interrogated if Pano can re-sensitize RR-FaDu and RR-HK-1 to IR. Interestingly, exposure to Pano before 4 Gy IR led to radiosensitization of RR-HNC cells (radiosensitization ratio: FaDu=1.77 [<i>P</i>=0.06]; HK-1=1.81 [<i>P</i>=0.041]), but not WT-HNC cells (FaDu=0.90 [<i>P</i>=0.60]; HK-1=1.26 [<i>P</i>=0.29]). <h3>Conclusion</h3> Herein, QPOP identified the potential of chromatin modification using Pano, in combination with CHK1 blockade or re-IR for targeting RR-HNC.

SIRT1 mediates nutritional regulation of SREBP-1c-driven hepatic PNPLA3 transcription via modulation of H3k9 acetylation

BackgroundPatatin-like phospholipase domain containing 3 (PNPLA3) is the main nonalcoholic fatty liver disease (NAFLD) susceptibility. Its expression is regulated tightly by nutritional and energy status, but the mechanism of epigenetic regulation of PNPLA3 gene by nutritional dietary factors has not been reported. Here, we investigated the effect and mechanism of Sirtuin 1 (SIRT1) regulated H3K9 deacetylation on PNPLA3 transcriptional expression in vivo and in vitro.MethodsMouse models of fasting/re-feeding transition and nonalcoholic fatty liver induced by high Sucrose diet were constructed; and HepG2 cells were treated with serum- and glucose-free medium or exposed to high glucose and high insulin, to generate fasting and high-glucose-induced lipid deposition cell states. Enrichment levels of histone H3K9 acetylation and sterol responsive element binding protein-1c (SREBP-1c) at the PNPLA3 promoter were observed by ChIP-qPCR. PNPLA3 gene expression was detected by real-time PCR; SIRT1 protein expression was detected by western blot. And lipid deposition was detected by Oil Red O.ResultsH3K9ac levels at SRE regions of PNPLA3 promoter were found to be decreased in mice during fasting and increase during refeeding, and increased in mice with NAFLD induced by high-sucrose diet. The change pattern of PNPLA3 promoter H3K9Ac physiologically (fasting/refeeding) and pathologically was consistent with that of PNPLA3 gene expression, but opposite to that of SIRT1 protein expression. In HepG2 cells, overexpression of SIRT1 inhibited high-glucose induced hyper-acetylation of H3K9 at PNPLA3 promoter, and silent expression of SIRT1 suppressed fasting-induced hypo-acetylation of H3K9. Overexpression of SIRT1 prevented basal and SREBP-1c-driven PNPLA3 gene expression and also prevented the endogenous binding of SREBP-1c to PNPLA3.ConclusionsWe first preliminarily revealed SIRT1 may regulate PNPLA3 gene expression by affecting SREBP-1-driven transcription via acetylation modification of H3K9.

TAT-MeCP2 protein variants rescue disease phenotypes in human and mouse models of Rett syndrome

Rett syndrome (RTT) is a neurodevelopmental disorder caused by pathogenic variants leading to functional impairment of the MeCP2 protein. Here, we used purified recombinant MeCP2e1 and MeCP2e2 protein variants fused to a TAT protein transduction domain (PTD) to evaluate their transduction ability into RTT patient-derived fibroblasts and the ability to carry out their cellular function. We then assessed their transduction ability and therapeutic effects in a RTT mouse model. In vitro, TAT-MeCP2e2-eGFP reversed the pathological hyperacetylation of histones H3K9 and H4K16, a hallmark of abolition of MeCP2 function. In vivo, intraperitoneal administration of TAT-MeCP2e1 and TAT-MeCP2e2 extended the lifespan of Mecp2−/y mice by >50%. This was accompanied by rescue of hippocampal CA2 neuron size in animals treated with TAT-MeCP2e1. Taken together, these findings provide a strong indication that recombinant TAT-MeCP2 can reach mouse brains following peripheral injection and can ameliorate the phenotype of RTT mouse models. Thus, our study serves as a first step in the development of a potentially novel RTT therapy.

Thymic stromal lymphopoietin (TSLP) is a potent pro-inflammatory mediator which is epigenetically deregulated in endometriosis

ObjectiveEndometriosis is an estrogen-dependent disease characterized by the presence of endometriotic tissue outside the uterine cavity, the condition that immunological factors play important roles in its pathogenesis. Thymic stromal lymphopoietin (TSLP) is an interleukin 7–like cytokine that triggers dendritic cell–mediated T helper2 inflammatory responses. TSLP receptor, or cytokine receptor- like factor 2 (CRLF2), forms a functional heterodimeric complex with IL-7 receptor alpha (IL-7Rα) to bind with TSLP. The present study aimed to elucidate the expression and epigenetic alterations of TSLP gene parallel to TSLP receptor and IL-10 genes expression in endometrial tissues of patients with endometriosis compared to controls. Materials & methodsIn this case-control study, 45 women with and without endometriosis was enrolled. The relative expression of TSLP, TSLPR and IL-10 genes were examined using qPCR. Chromatin Immunoprecipitation (ChIP) was also used to monitor epigenetic marks of methylation and acetylation on lysine 9 of histone H3 (H3K9me/ac) and DNA methylation in TSLP promoter. Results and conclusionTSLP, TSLPR and IL-10 genes were overexpressed in ectopic endometriotic lesions compared to controls. In ectopic samples, significant H3K9 hyper-acetylation and hypo-methylation parallel to DNA hypo-methylation were detected in TSLP promoter compared to eutopic and control groups (p < 0.05). These epigenetic changes were aligned with TSLP gene expression profile. These data collectively identify TSLP and TSLPR as candidate genes critically involved in development of endometriosis beyond their role in promoting Th2 immune responses. In addition, acetylation and methylation of H3K9 may have effective roles in TSLP dysregulation in endometriosis.

Acetylation of H3K56 orchestrates UV-responsive chromatin events that generate DNA accessibility during Nucleotide Excision Repair

Histone modifications have long been related to DNA damage response. Nucleotide excision repair pathway that removes helix-distorting lesions necessitates DNA accessibility through chromatin modifications. Previous studies have linked H3 tail residue acetylation to UV-induced NER. Here we present evidences that acetylation of H3K56 is crucial for early phases of NER. Using H3K56 mutants K56Q and K56R, which mimic acetylated and unacetylated lysines respectively, we show that recruitment of the repair factor Rad16, a Swi/Snf family member is dependent on H3K56 acetylation. With constitutive H3K56 acetylation, Rad16 recruitment became UV-independent. Furthermore, H3K56 acetylation promoted UV-induced hyperacetylation of H3K9 and H3K14. Importantly, constitutive H3K56 acetylation prominently increased chromatin accessibility. During NER, lack of H3K56 acetylation that effectively aborted H3 tail residue acetylation and Rad16 recruitment, thus failed to impart essential chromatin modulations. The NER-responsive oscillation of chromatin structure observed in wild type, was distinctly eliminated in absence of H3K56 acetylation. In vitro assay with wild type and H3K56 mutant cell extracts further indicated that absence of H3K56 acetylation negatively affected DNA relaxation during NER. Overall, H3K56 acetylation regulates Rad16 redistribution and UV-induced H3 tail residue hyperacetylation, and the resultant modification code promotes chromatin accessibility and recruitment of subsequent repair factors during NER.

Mitochondrial dysfunction-induced H3K27 hyperacetylation perturbs enhancers in Parkinson's disease.

Mitochondrial dysfunction is a major pathophysiological contributor to the progression of Parkinson’s disease (PD); however, whether it contributes to epigenetic dysregulation remains unknown. Here, we show that both chemically and genetically driven mitochondrial dysfunctions share a common mechanism of epigenetic dysregulation. Under both scenarios, lysine 27 acetylation of likely variant H3.3 (H3.3K27ac) increased in dopaminergic neuronal models of PD, thereby opening that region to active enhancer activity via H3K27ac. These vulnerable epigenomic loci represent potential transcription factor motifs for PD pathogenesis. We further confirmed that mitochondrial dysfunction induces H3K27ac in ex vivo and in vivo (MitoPark) neurodegenerative models of PD. Notably, the significantly increased H3K27ac in postmortem PD brains highlights the clinical relevance to the human PD population. Our results reveal an exciting mitochondrial dysfunction-metabolism-H3K27ac-transcriptome axis for PD pathogenesis. Collectively, the mechanistic insights link mitochondrial dysfunction to epigenetic dysregulation in dopaminergic degeneration and offer potential new epigenetic intervention strategies for PD.

Prostaglandin E2 Protects HSC from DNA Damage Induced By Ionizing Radiation By Preventing Generation of Reactive Oxygen Species and Histone Acetylation

The hematopoietic system is highly radiosensitive; thus therapeutic and unwanted irradiation can produce significant/lethal acute and delayed bone marrow injury. In a murine hematopoietic-acute radiation syndrome (H-ARS) model, a single dose of 16,16 dimethyl Prostaglandin E2 (dmPGE2) given 15 min to 3 hrs before lethal (LD50/30-90/30) total body irradiation (TBI) results in 100% survival of mice at 30 days, with accelerated recovery of WBC, and hematopoietic stem and progenitor cell number and function.To explore mechanisms responsible for the radio-protective effect(s) of dmPGE2 we evaluated hematopoietic cells at early points post-TBI, focusing on oxidative pathways and epigenetic changes. Hematopoietic cells were isolated and evaluated at 1 hr and 1, 3 and 9 days post LD50 [853 cGy] TBI. Mitochondrial ROS and membrane potential were measured by flow cytometry in SLAM-SKL cells. Protein levels of gH2AX, LC3b, BNIP3, P16, P53, P62 acetylated H3K9 and H4K16 histones and SIRT1 were measured by flow cytometry. Acetylation of H3K9 and H4K16 at the KU70, Ku80, LC3b, Atg5, Atg7, Atg12, BNIP3, NF-kB and p53 promoters was evaluated by ChIP.Lethal radiation significantly increased HSC mitochondrial ROS and reduced membrane potential at 1,3 and 9 days post-TBI. Significant DNA damage was observed at 1 hour as measured by gH2AX. In contrast, mitochondrial ROS and DNA damage (gH2AX) were significantly lower in mice that received dmPGE2 before irradiation. In vehicle treated irradiated mice, we observed hyper-acetylated H3K9 and H4K16 at the Ku70/80 promoter, suggesting diminished capacity of Ku70/80 to repair DNA damage. In contrast, in mice treated with dmPGE2, H3K9 and H4K16 acetylation was significantly lower. Reduced mitochondrial membrane potential seen in vehicle treated mice was also prevented. The senescence markers SA-beta-gal and P16 in HSC were significantly reduced in PGE2 treated mice.The sirtuin family NAD-dependent deacetylase, SIRT1, has broad functions including gene silencing and DNA repair. In control irradiated mice SIRT1 levels dramatically decreased over 9 days post-irradiation, but remained significantly higher in dmPGE treated mice, which may account for the low acetylation levels of H3K9 and H4K16 in PGE treated mice. Consistent with elevated SIRT1 in PGE2 treated mice, we also observed global deacetylation of H3K9 and H4K16 in lineage negative and SLAM LSK cells at 1-3 days post-TBI. P53 is a key transcriptional regulator of genes involved in cell cycle, apoptosis and DNA repair and is acetylated after DNA damage. In control mice, irradiation resulted in robust acetylation of histone proteins at the p53 promoter, whereas dmPGE2 administration prevented acetylation of H4K16, but not H3K9. In addition, dmPGE2 blocked p53-mediated apoptosis via repression of p53 transcription.Since SIRT1 promotes autophagy, we evaluated autophagy related genes. CHIP analyses revealed low levels of acetylated-H3K9 at the LC3B, ATG7 and NF-KB promoters and deacetylated H4K16 at the LC3B, ATG7, BNIP3 and NF-kB promoters in PGE treated mice compared to vehicle controls. No effects on histone deacetylation of the Atg5 and Atg12 genes. BNIP3 is a mitophagy marker that when elevated downregulates mitochondrial mass and respiration. In irradiated control mice, BNIP3 levels were decreased at 1through 9 days, but remained elevated in mice treated with dmPGE2. The autophagy substrate P62 was significantly increased at 1 and 3 days post-irradiation in control mice, but was significantly lower in PGE2 treated mice. SIRT1 activation also leads to decreased binding of NFkB-p65 to DNA and attenuated oxidative stress through reduced transcription. CHIP data showed that TBI increased acetylation of H3K9 and H4K16 at the NF-kB p65 promoter in vehicle treated mice, whereas hyperacetylation of H3K9 and H4K16 and NF-kB transcription did not occur in mice treated with dmPGE2 before irradiation.These studies suggest that the radio protective effect of dmPGE2 and accelerated recovery of hematopoiesis following radiation exposure is mediated in part through reduction in oxidative stress and DNA damage induced in HSC and epigenetically, through prevention of histone acetylation of genes associated with DNA repair, autophagy and mitophagy, likely mediated through elevation of SIRT1. DisclosuresNo relevant conflicts of interest to declare.

Genome-wide histone acetylation analysis reveals altered transcriptional regulation in the Parkinson\u2019s disease brain

BackgroundParkinson’s disease (PD) is a complex, age-related neurodegenerative disorder of largely unknown etiology. PD is strongly associated with mitochondrial respiratory dysfunction, which can lead to epigenetic dysregulation and specifically altered histone acetylation. Nevertheless, and despite the emerging role of epigenetics in age-related brain disorders, the question of whether aberrant histone acetylation is involved in PD remains unresolved.MethodsWe studied fresh-frozen brain tissue from two independent cohorts of individuals with idiopathic PD (n = 28) and neurologically healthy controls (n = 21). We performed comprehensive immunoblotting to identify histone sites with altered acetylation levels in PD, followed by chromatin immunoprecipitation sequencing (ChIP-seq). RNA sequencing data from the same individuals was used to assess the impact of altered histone acetylation on gene expression.ResultsImmunoblotting analyses revealed increased acetylation at several histone sites in PD, with the most prominent change observed for H3K27, a marker of active promoters and enhancers. ChIP-seq analysis further indicated that H3K27 hyperacetylation in the PD brain is a genome-wide phenomenon with a strong predilection for genes implicated in the disease, including SNCA, PARK7, PRKN and MAPT. Integration of the ChIP-seq with transcriptomic data from the same individuals revealed that the correlation between promoter H3K27 acetylation and gene expression is attenuated in PD patients, suggesting that H3K27 acetylation may be decoupled from transcription in the PD brain. Strikingly, this decoupling was most pronounced among nuclear-encoded mitochondrial genes, corroborating the notion that impaired crosstalk between the nucleus and mitochondria is involved in the pathogenesis of PD. Our findings independently replicated in the two cohorts.ConclusionsOur findings strongly suggest that aberrant histone acetylation and altered transcriptional regulation are involved in the pathophysiology of PD. We demonstrate that PD-associated genes are particularly prone to epigenetic dysregulation and identify novel epigenetic signatures associated with the disease.

Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease.

The human placenta and its specialized cytotrophoblasts rapidly develop, have a compressed lifespan, govern pregnancy outcomes, and program the offspring's health. Understanding the molecular underpinnings of these behaviors informs development and disease. Profiling the extraembryonic epigenome and transcriptome during the 2nd and 3rd trimesters revealed H3K9 trimethylation overlapping deeply DNA hypomethylated domains with reduced gene expression and compartment-specific patterns that illuminated their functions. Cytotrophoblast DNA methylation increased, and several key histone modifications decreased across the genome as pregnancy advanced. Cytotrophoblasts from severe preeclampsia had substantially increased H3K27 acetylation globally and at genes that are normally downregulated at term but upregulated in this syndrome. In addition, some cases had an immature pattern of H3K27ac peaks, and others showed evidence of accelerated aging, suggesting subtype-specific alterations in severe preeclampsia. Thus, the cytotrophoblast epigenome dramatically reprograms during pregnancy, placental disease is associated with failures in this process, and H3K27 hyperacetylation is a feature of severe preeclampsia.

Design, synthesis and antitumor evaluations of nucleoside base hydroxamic acid derivatives as DNMT and HDAC dual inhibitors

DNA methyltransferase (DNMT) and histone deacetylase (HDAC) are well recognized epigenetic targets for discovery of antitumor agents. In this study, we designed and synthesized a series of nucleoside base hydroxamic acid derivatives as DNMT and HDAC dual inhibitors. MTT assays and enzymatic inhibitory activity tests indicated that compound 204 exhibited potent DNMT1 and HDAC1/6 inhibitory potency simultaneously in enzymatic levels and at cellular levels, inducing hypomethylation of p16 and hyperacetylation of histones H3K9 and H4K8. Besides, 204 remarkably inhibited proliferation against cancer cells U937 by prompting G0/G1 cell cycle arrest. Molecular docking models explained the functional mechanism of 204 inhibiting DNMT1 and HDAC. Preliminary studies on metabolic profiles revealed that 204 showed desirable stability in liver microsomes. Our study suggested that 204 inhibiting DNMT and HDAC concurrently can be a potential lead compound for epigenetic cancer therapy.

SIRT6 Protects Smooth Muscle Cells From Senescence and Reduces Atherosclerosis.

Vascular smooth muscle cell (VSMC) senescence promotes atherosclerosis and features of plaque instability, in part, through lipid-mediated oxidative DNA damage and telomere dysfunction. SIRT6 (Sirtuin 6) is a nuclear deacetylase involved in DNA damage response signaling, inflammation, and metabolism; however, its role in regulating VSMC senescence and atherosclerosis is unclear. We examined SIRT6 expression in human VSMCs, the role, regulation, and downstream pathways activated by SIRT6, and how VSMC SIRT6 regulates atherogenesis. SIRT6 protein, but not mRNA, expression was markedly reduced in VSMCs in human and mouse atherosclerotic plaques, and in human VSMCs derived from plaques or undergoing replicative or palmitate-induced senescence versus healthy aortic VSMCs. The ubiquitin ligase CHIP (C terminus of HSC70-interacting protein) promoted SIRT6 stability, but CHIP expression was reduced in human and mouse plaque VSMCs and by palmitate in a p38- and c-Jun N-terminal kinase-dependent manner. SIRT6 bound to telomeres, while SIRT6 inhibition using shRNA or a deacetylase-inactive mutant (SIRT6H133Y) shortened human VSMC lifespan and induced senescence, associated with telomeric H3K9 (histone H3 lysine 9) hyperacetylation and 53BP1 (p53 binding protein 1) binding, indicative of telomere damage. In contrast, SIRT6 overexpression preserved telomere integrity, delayed cellular senescence, and reduced inflammatory cytokine expression and changes in VSMC metabolism associated with senescence. SIRT6, but not SIRT6H133Y, promoted proliferation and lifespan of mouse VSMCs, and prevented senescence-associated metabolic changes. ApoE-/- (apolipoprotein E) mice were generated that overexpress SIRT6 or SIRT6H133Y in VSMCs only. SM22α-hSIRT6/ApoE-/- mice had reduced atherosclerosis, markers of senescence and inflammation compared with littermate controls, while plaques of SM22α-hSIRT6H133Y/ApoE-/- mice showed increased features of plaque instability. SIRT6 protein expression is reduced in human and mouse plaque VSMCs and is positively regulated by CHIP. SIRT6 regulates telomere maintenance and VSMC lifespan and inhibits atherogenesis, all dependent on its deacetylase activity. Our data show that endogenous SIRT6 deacetylase is an important and unrecognized inhibitor of VSMC senescence and atherosclerosis.