Histone Lysine Residues Research Articles

ACL and HAT1 form a nuclear module to acetylate histone H4K5 and promote cell proliferation

Acetyl-CoA utilized by histone acetyltransferases (HAT) for chromatin modification is mainly generated by ATP-citrate lyase (ACL) from glucose sources. How ACL locally establishes acetyl-CoA production for histone acetylation remains unclear. Here we show that ACL subunit A2 (ACLA2) is present in nuclear condensates, is required for nuclear acetyl-CoA accumulation and acetylation of specific histone lysine residues, and interacts with Histone AcetylTransferase1 (HAT1) in rice. The rice HAT1 acetylates histone H4K5 and H4K16 and its activity on H4K5 requires ACLA2. Mutations of rice ACLA2 and HAT1 (HAG704) genes impair cell division in developing endosperm, result in decreases of H4K5 acetylation at largely the same genomic regions, affect the expression of similar sets of genes, and lead to cell cycle S phase stagnation in the endosperm dividing nuclei. These results indicate that the HAT1-ACLA2 module selectively promotes histone lysine acetylation in specific genomic regions and unravel a mechanism of local acetyl-CoA production which couples energy metabolism with cell division.

Potential of Synthetic and Natural Compounds as Novel Histone Deacetylase Inhibitors for the Treatment of Hematological Malignancies.

Histone deacetylases (HDACs) and histone acetyltransferases (HATs) are enzymes that remove or add acetyl groups to lysine residues of histones, respectively. Histone deacetylation causes DNA to more snugly encircle histones and decreases gene expression, whereas acetylation has the opposite effect. Through these small alterations in chemical structure, HATs and HDACs regulate DNA expression. Recent research indicates histone deacetylase inhibitors (HDACis) may be used to treat malignancies, including leukemia, B-cell lymphoma, virus-associated tumors, and multiple myeloma. These data suggest that HDACis may boost the production of immune-related molecules, resulting in the growth of CD8-positive T-cells and the recognition of nonreactive tumor cells by the immune system, thereby diminishing tumor immunity. The argument for employing epigenetic drugs in the treatment of acute myeloid leukemia (AML) patients is supported by evidence that both epigenetic changes and mutations in the epigenetic machinery contribute to AML etiology. Although hypomethylating drugs have been licensed for use in AML, additional epigenetic inhibitors, such as HDACis, are now being tested in humans. Preclinical studies evaluating the efficacy of HDACis against AML have shown the ability of specific agents, such as anobinostat, vorinostat, and tricostatin A, to induce growth arrest, apoptosis, autophagy and cell death. However, these inhibitors do not seem to be successful as monotherapies, but instead achieve results when used in conjunction with other medications. In this article, we discuss the mounting evidence that HDACis promote extensive histone acetylation, as well as substantial increases in reactive oxygen species and DNA damage in hematological malignant cells. We also evaluate the potential of various natural product-based HDACis as therapeutic agents to combat hematological malignancies.

Knockdown of histone deacetylase 1 in fibroblasts and pericytes prevents renal interstitial fibrosis after ischemia-reperfusion injury.

Ischemia-reperfusion injury (IRI), one form of acute kidney failure, often occurs after cardiovascular or renal surgery where there is a decline in blood flow through the kidney. This injury causes damage to renal cells and can lead to the formation of interstitial fibrosis, which will increase the risk of chronic kidney disease. The histone deacetylases (HDAC) protein family controls the expression of genes via epigenetic regulation of deacetylating histone lysine residues. We published that within an hour of bilateral IRI, in male mice, there was an increase of HDAC1 in the epithelium and interstitial cells. Moreover, inhibition of HDAC1 prior to IRI resulted in attenuated interstitial fibrosis. Myofibroblasts secrete collagen contributing significantly to wound healing as well as the development of interstitial fibrosis and these cells are predominantly differentiated fibroblasts and pericytes. We hypothesized that the knockdown of HDAC1 in fibroblasts and pericytes will attenuate interstitial fibrosis in the kidney after IRI. Male control (HDAC1fl/fl) and iFibroblastHDAC1KO (HDAC1fl/fl, Col1A2-CreER, hemizygous mice) were used in the experiment. The mice underwent bilateral renal artery and vein clamping for 18 minutes to induce IRI or sham surgery. Acute kidney injury was confirmed by serum creatinine measurements and determination of glomerular filtration rate (GFR) by transcutaneous FITC-sinistrin clearance 24 hours after injury. GFR was measured weekly for 4 weeks at which point the blood and kidneys were collected for analysis. Renal interstitial fibrosis was quantified by measuring the percentage coverage area of collagen stained by picrosirius red staining. 24 hours after surgery, IRI mice serum creatinine levels were greater in control mice 0.53 mg/dl ± 0.17, n = 9, and iFibHDAC1KO IRI mice 0.25 mg/dl ± 0.053, n = 10, compared to sham mice (control 0.084 mg/dl ± 0.008, n = 5, KO 0.098 mg/dl ± 0.006, n = 4, Pgenotype = 0.3, Psurgery = 0.028, Pinteraction = 0.25). This agreed with the measured GFR that was significantly reduced in the IRI mice (control IRI = 426 ul/min/100g ± 132, KO IRI = 529 ul/min/100g ± 116, Sham control = 1180 ul/min/100g ± 178, sham KO = 1188 ul/min/100g ± 156, Pgenotype = 0.71, Psurgery = 0.0003, Pinteraction = 0.75). The percentage of the collagen-positive area was significantly higher in control than in sham mice (p = 0.0011), while there was no noticeable difference (p = 0.9) between iFibHDAC1KO and sham mice (control IRI = 1.2 % ± 0.2, KO IRI = 0.47% ± 0.12, sham control = 0.35% ± 0.085, sham KO = 0.401% ± 0.073). In conclusion, HDAC1 is activated by IRI in the myofibroblast and promotes interstitial fibrosis. Funding resources: NIH NIDDK R01DK126664, UAB-UCSD O'Brien Center, and the Priya Nagar M.D. Foundation. This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

The role and prospect of lysine-specific demethylases in cancer chemoresistance.

Histone methylation plays a key function in modulating gene expression, and preserving genome integrity and epigenetic inheritance. However, aberrations of histone methylation are commonly observed in human diseases, especially cancer. Lysine methylation mediated by histone methyltransferases can be reversed by lysine demethylases (KDMs), which remove methyl marks from histone lysine residues. Currently, drug resistance is a main impediment for cancer therapy. KDMs have been found to mediate drug tolerance of many cancers via altering the metabolic profile of cancer cells, upregulating the ratio of cancer stem cells and drug-tolerant genes, and promoting the epithelial-mesenchymal transition and metastatic ability. Moreover, different cancers show distinct oncogenic addictions for KDMs. The abnormal activation or overexpression of KDMs can alter gene expression signatures to enhance cell survival and drug resistance in cancer cells. In this review, we describe the structural features and functions of KDMs, the KDMs preferences of different cancers, and the mechanisms of drug resistance resulting from KDMs. We then survey KDM inhibitors that have been used for combating drug resistance in cancer, and discuss the opportunities and challenges of KDMs as therapeutic targets for cancer drug resistance.

Correlating histone acetylation with nucleosome core particle dynamics and function

Epigenetic modifications of chromatin play a critical role in regulating the fidelity of the genetic code and in controlling the translation of genetic information into the protein components of the cell. One key posttranslational modification is acetylation of histone lysine residues. Molecular dynamics simulations, and to a smaller extent experiment, have established that lysine acetylation increases the dynamics of histone tails. However, a systematic, atomic resolution experimental investigation of how this epigenetic mark, focusing on one histone at a time, influences the structural dynamics of the nucleosome beyond the tails, and how this translates into accessibility of protein factors such as ligases and nucleases, has yet to be performed. Herein, using NMR spectroscopy of nucleosome core particles (NCPs), we evaluate the effects of acetylation of each histone on tail and core dynamics. We show that for histones H2B, H3, and H4, the histone core particle dynamics are little changed, even though the tails have increased amplitude motions. In contrast, significant increases to H2A dynamics are observed upon acetylation of this histone, with the docking domain and L1 loop particularly affected, correlating with increased susceptibility of NCPs to nuclease digestion and more robust ligation of nicked DNA. Dynamic light scattering experiments establish that acetylation decreases inter-NCP interactions in a histone-dependent manner and facilitates the development of a thermodynamic model for NCP stacking. Our data show that different acetylation patterns result in nuanced changes to NCP dynamics, modulating interactions with other protein factors, and ultimately controlling biological output.

Structural Basis of Sirtuin 6-Catalyzed Nucleosome Deacetylation.

The reversible acetylation of histone lysine residues is controlled by the action of acetyltransferases and deacetylases (HDACs), which regulate chromatin structure and gene expression. The sirtuins are a family of NAD-dependent HDAC enzymes, and one member, sirtuin 6 (Sirt6), influences DNA repair, transcription, and aging. Here, we demonstrate that Sirt6 is efficient at deacetylating several histone H3 acetylation sites, including its canonical site Lys9, in the context of nucleosomes but not free acetylated histone H3 protein substrates. By installing a chemical warhead at the Lys9 position of histone H3, we trap a catalytically poised Sirt6 in complex with a nucleosome and employ this in cryo-EM structural analysis. The structure of Sirt6 bound to a nucleosome reveals extensive interactions between distinct segments of Sirt6 and the H2A/H2B acidic patch and nucleosomal DNA, which accounts for the rapid deacetylation of nucleosomal H3 sites and the disfavoring of histone H2B acetylation sites. These findings provide a new framework for understanding how HDACs target and regulate chromatin.

The role of class IIa histone deacetylases in regulating endothelial function.

Vascular endothelial cells (ECs) are monolayer cells located in the inner layer of the blood vessel. Endothelial function is crucial in maintaining local and systemic homeostasis and is precisely regulated by sophisticated signaling pathways and epigenetic regulation. Endothelial dysfunctions are the main factors for the pathophysiological process of cardiovascular and cerebrovascular diseases like atherosclerosis, hypertension, and stroke. In these pathologic processes, histone deacetylases (HDACs) involve in epigenetic regulation by removing acetyl groups from lysine residues of histones and regulating downstream gene expression. Among all HDACs, Class IIa HDACs (HDAC4, 5, 7, 9) contain only an N-terminal regulatory domain, exert limited HDAC activity, and present tissue-specific gene regulation. Here, we discuss and summarize the current understanding of this distinct subfamily of HDACs in endothelial cell functions (such as angiogenesis and immune response) with their molecular underpinnings. Furthermore, we also present new thoughts for further investigation of HDAC inhibitors as a potential treatment in several vascular diseases.

Epigenetic modifications in the motor cortex caused by exercise or pharmacological inhibition of histone deacetylases (HDACs) after intracerebral hemorrhage (ICH)

Epigenetic regulation is expected to provide an enriched platform for neurorehabilitation of post-stroke patients. Acetylation of specific lysine residues in histones is a potent epigenetic target essential for transcriptional regulation. Exercise modulates histone acetylation and gene expression in neuroplasticity in the brain. This study sought to examine the effect of epigenetic treatment using a histone deacetylase (HDAC) inhibitor, sodium butyrate (NaB), and exercise on epigenetic markers in the bilateral motor cortex after intracerebral hemorrhage (ICH) to identify a more enriched neuronal condition for neurorehabilitation. Forty-one male Wistar rats were randomly divided into five groups: sham (n = 8), control (n = 9), NaB, exercise (n = 8), and NaB and exercise (n = 8). Intraperitoneal administration of an HDAC inhibitor (300 mg/kg NaB) and treadmill exercise (11 m/min for 30 min) was conducted five days a week for approximately-four weeks. ICH specifically decreased the acetylation level of histone H4 in the ipsilateral cortex, and HDAC inhibition with NaB increased the acetylation level of histone H4 over the sham level, accompanied by an improvement in motor function as assessed by the cylinder test. Exercise increased the acetylation levels of histones (H3 and H4) in the bilateral cortex. Synergistic effects of exercise and NaB were not observed during histone acetylation. Pharmacological treatment with a HDAC inhibitor and exercise can provide an enriched epigenetic platform for neurorehabilitation in an individual manner.

Salivary histone deacetylase in periodontal disease: A cross-sectional pilot study.

The objective of the study was to profile the expression level of histone deacetylase enzymes (HDACs) in human saliva in periodontal health, gingivitis and periodontitis. HDACs are epigenetic modulators and a group of enzymes that catalyse the removal of acetyl functional groups from the lysine residues of both histone and nonhistone proteins. HDACs have been detected in gingival tissues and may provide valuable insight into the periodontal inflammatory response. However, no studies have investigated the expression of HDACs in saliva from periodontitis-affected individuals and their capacity for periodontal diagnostics and screening. Whole unstimulated saliva was collected from 53 participants (17 healthy, 14 gingivitis and 22 stages III/IV periodontitis). The expression of 11 HDACs in saliva samples was determined using RT-qPCR and diagnostic power was calculated using the receiver operating characteristic (ROC) curves and area under the ROC Curve (AUC). Relative to health, the expression of HDAC4, 8 and 10 was downregulated in gingivitis, and the expression of HDAC4, 6, 8 and 9 was downregulated in periodontitis. Increased HDAC1 and decreased HDAC9 expression were observed in periodontitis compared to gingivitis. Higher HDAC1 and lower HDAC6 and 9 expression was observed in periodontitis compared to non-periodontitis (combining health and gingivitis). Expression of HDAC3, 4, 8, 9 and 10 was significantly decreased in periodontal disease (combining gingivitis and periodontitis) compared to health. HDAC4 and 8 exhibited an excellent diagnostic capacity for distinguishing gingivitis and periodontal disease from health (AUC 0.79-0.86). HDAC9 showed an acceptable power in discriminating periodontitis from health, gingivitis and non-periodontitis (AUC 0.76-0.80). Salivary HDAC enzyme activity showed no significant difference among the groups. This pilot study has demonstrated the differential expression of HDACs in human saliva for the first time and identified HDAC4, 8 and 9 as potential biomarkers in periodontal diagnosis.

Set7 methyltransferase roles in myocardial protection from chronic stressors.

Epigenome changes in chronic states of cardiovascular stress including diabetes, pressure overload and cardiomyopathies frequently involve changes in open chromatin and post-translation modifications of histone lysine residues at specific amino acid positions by acetylation, methylation and phosphorylation. Since the discovery of Set7 as an important regulator of histone H3 lysine 4 methylation state, there has been wide interest in its role in cardiovascular remodeling and cardiac dysfunction. Recent transcriptome and Fourier transform infrared spectroscopy analyses and in vivo assessments of cardiac function by Lunardon and colleagues now reveal a clear role of Set7 in the regulation of the extracellular matrix composition and cardiac hypertrophy in response to chronic isoproterenol induced cardiac stress.

Histone deacetylase (HDACs) inhibitors: Clinical applications.

Histone Deacetylases (HDACs) deacetylate lysine residues in histone and non-histone proteins. HDACs have been implicated in several diseases, including cancer, neurodegeneration, and cardiovascular disease. HDACs play an essential role in gene transcription, cell survival, growth, and proliferation, with histone hypoacetylation as one of the critical downstream signatures. HDAC inhibitors (HDACi) regulate gene expression epigenetically by restoring acetylation levels. Contrarily, only few HDACi have received FDA approval, and the majority are presently undergoing clinical trials to ascertain their effectiveness in the prevention and treatment of disease. In this book chapter, we give a detailed list of HDAC classes, and their functions in advancing diseases like cancer, cardiovascular, and neurodegeneration. Furthermore we touch upon novel and promising HDACi therapy approaches in the relevance of the current clinical scenario.

Histone lactylation promotes cell proliferation, migration and invasion through targeting HMGB1 in endometriosis.

Endometriosis is defined as a condition with endometrium-like tissues migrating outside of the pelvic cavity. However, the mechanism of endometriosis is still unclear. Lactate can be covalently modified to lysine residues of histones and other proteins, which is called lactylation. The results showed that the higher level of lactate and lactate dehydrogenase A enhanced the histone H3 lysine 18 lactylation (H3K18lac) in ectopic endometrial tissues and ectopic endometrial stromal cells than that in normal endometrial tissues and normal endometrial stromal cells. Lactate promoted cell proliferation, migration, and invasion in endometriosis. Mechanistically, lactate induced H3K18lac to promote the expression of high-mobility group box 1 (HMGB1) in endometriosis, and HMGB1 knockdown significantly reduced the cell proliferation, migration, and invasion of the lactate-treated cells through the phosphorylation of AKT. In conclusion, lactate could induce histone lactylation to promote endometriosis progression by upregulating the expression of HMGB1, which may provide a novel target for the prevention and treatment of endometriosis.

Structure based functional annotation of a MYND-less lysine methyl transferase inCandida albicans.

Candida albicans is opportunistic pathogenic yeast that is widely distributed throughout the world and is classified as the most critical fungal pathogen group. Candida albicans is a common microbiota of healthy individuals but can cause superficial and invasive infections in immune compromised individuals. Protein Post-translational modifications involving methylation of lysine amino acids stand for a major regulator of eukaryotic transcription, and pathways controlling several cellular processes. SMYD makes up a SET (Su (Var) 3-9, Enhancer-of-zeste and Trithorax) and MYND (Myeloid, Nervy, and DEAF-1) domain containing lysine methyl transferase subfamily that transfers methyl groups from methyl donors onto lysine residues in histones (H3 and H4) and non-histone proteins. The SET domain is the methyltransferase catalytic domain, while MYND participates in both protein and DNA interactions. Well-studied examples of SMYD proteins are five human and two Saccharomyces cerevisiae, constituting examples of histone and non-histone protein lysine methyl transferase members. However, there is limited understanding of SET lysine methyltransferases, including the SMYD subfamily, in the pathogenic fungi Candida albicans. Using bioinformatics tools, we characterized the SMYD domain containing proteins in the important pathogen. We report the presence of an atypical SMYD member (CaO19.3863) as a new lysine methyltransferase that can be a target for antifungal therapy.

The role of histone deacetylases in embryonic development.

The basic units of chromatin are nucleosomes, that are made up of DNA wrapped around histone cores. Histone lysine residue is a common location for posttranslational modifications, with acetylation being the second most prevalent. Histone acetyltransferases (HATs/KATs) and histone deacetylases (HDACs/KDACs) regulate histone acetylation, which is important in gene expression control. HDACs/KDACsregulate gene expressions through the repression of the transcription machinery. HDAC/KDAC isoforms play a major role during various stages of embryo development and neurogenesis. In specific, class I and II HDACs/KDACs are involved in cardiac muscle differentiation and development. An insight into different pathways and genes associated with embryonic development, the effect of HDAC/KDAC activity during the embryonic stem cell differentiation, preimplantation, embryo development, gastrulation, and the role of different HDAC/KDAC inhibitors during the process of embryogenesis is summarized in the present review article.

Targeting Class I Histone Deacetylases in Human Uterine Leiomyosarcoma.

Uterine leiomyosarcoma (uLMS) is the most frequent subtype of uterine sarcoma that presents a poor prognosis, high rates of recurrence, and metastasis. Currently, the molecular mechanism of the origin and development of uLMS is unknown. Class I histone deacetylases (including HDAC1, 2, 3, and 8) are one of the major classes of the HDAC family and catalyze the removal of acetyl groups from lysine residues in histones and cellular proteins. Class I HDACs exhibit distinct cellular and subcellular expression patterns and are involved in many biological processes and diseases through diverse signaling pathways. However, the link between class I HDACs and uLMS is still being determined. In this study, we assessed the expression panel of Class I HDACs in uLMS and characterized the role and mechanism of class I HDACs in the pathogenesis of uLMS. Immunohistochemistry analysis revealed that HDAC1, 2, and 3 are aberrantly upregulated in uLMS tissues compared to adjacent myometrium. Immunoblot analysis demonstrated that the expression levels of HDAC 1, 2, and 3 exhibited a graded increase from normal and benign to malignant uterine tumor cells. Furthermore, inhibition of HDACs with Class I HDACs inhibitor (Tucidinostat) decreased the uLMS proliferation in a dose-dependent manner. Notably, gene set enrichment analysis of differentially expressed genes (DEGs) revealed that inhibition of HDACs with Tucidinostat altered several critical pathways. Moreover, multiple epigenetic analyses suggested that Tucidinostat may alter the transcriptome via reprogramming the oncogenic epigenome and inducing the changes in microRNA-target interaction in uLMS cells. In the parallel study, we also determined the effect of DL-sulforaphane on the uLMS. Our study demonstrated the relevance of class I HDACs proteins in the pathogenesis of malignant uLMS. Further understanding the role and mechanism of HDACs in uLMS may provide a promising and novel strategy for treating patients with this aggressive uterine cancer.

230 Investigating the role of histone deacetylases in human epidermis

Histone deacetylases (HDACs) remove acetyl moieties from lysine residues of histones and other proteins to induce epigenetic change to DNA, and hence are important regulators of gene expression. Within the skin, they play a role in regulating keratinocyte proliferation and differentiation. To date, four classes of the HDACs have been identified: Class I (HDAC1, HDAC2, HDAC3, and HDAC8), class II HDACs (HDAC4, HDAC5, HDAC6, HDAC7, HDAC9, and HDAC10), class III (SIRT1-7) and class IV (HDAC11) but their role in keratinocyte biology is largely unknown.

PLX51107 Enhances the Anti-Tumor Activity of Targeted Therapy in Chronic Lymphocytic Leukemia When Combined with Venetoclax

Background: The development of drugs targeting BTK and BCL2 have dramatically improved the therapeutic landscape in chronic lymphocytic leukemia (CLL). However, resistance to these agents have been reported due to non-recurrent changes in oncogenic pathways and gene expression signatures. The bromodomain and extra terminal (BET) family proteins (BRD2, BRD3, BRD4 and BRDT) are epigenetic reader proteins that recognize acetylated lysine residues in histones. They play a critical role in mediating gene transcription and have been considered as highly promising targets in several diseases including cancer. Of these, the BRD4 protein is highly enriched in super enhancers and regulate gene transcription of relevant oncogenes such as MYC, CDK genes, cyclin-D1, BCL2 and MCL-1. BRD4 inhibitors (BRD4i) block the transcription of these key oncogenes through the displacement of BRDs and other epigenetic modifiers from chromatin. In this study, we investigated the preclinical activity of BRD4i PLX51107, and their cooperative role with BCL2 inhibitor Venetoclax in CLL. Methods: 56 primary CLL cells were isolated via histopaque-1077 (Sigma-Aldrich, St Louis MO) from peripheral blood apheresis samples from consenting adults using Roswell Park Comprehensive Cancer Center protocol CIC-01-16. Peripheral blood mononuclear cells (PBMC) were seeded at 3 x106/mL in a 384 or 6 well tissue culture plates and exposed to different doses of PLX51107 (1-20uM) as a single agent or in combination with Venetoclax (1-100nM) for 48 and 72hrs (Selleck Chemicals, Houston TX). Cell viability was assessed using Cell Titer-glo (Promega, Madison WI) with all data being normalized to untreated controls. Synergy was calculated using Calcusyn (Cambridge, UK) software to determine Coefficient of Synergy (CI) values. Anti-tumor effect was also analyzed by induction of apoptosis using Annexin-V/PI staining by flow cytometry at 72hrs. Cells pellets were saved for western blotting to determine expression of BRD4 members and different members of the B-cell receptor, NF-kB pathway as also the BCL-2 family of proteins. Bcl-2 family profiling was performed via Milliplex Bcl-2 family protein panels 1 and 2 to look at overall changes in Bcl-2 family expression. Results: Single agent exposure to PLX51107 displayed time and dose dependent induction of apoptosis of CLL cells (Figure 1a). Next, we examined the interaction between the PLX51107 and Venetoclax. In 72hr exposure the combination of PLX51107 with Venetoclax with an ATM deletion was synergistic in 4 of 8 samples and 4 of 7 samples with p53 deletion. Annexin/PI staining yielded apoptotic cell death in the single agent and combination exposure with Venetoclax. Western blotting showed a modulation of both BRD4 proteins as well as Bcl-2 family member proteins (Figure 1b). Bcl-2 family profiling via Milliplex panels demonstrated the ratio of Bcl-2/Bcl x/L was much higher in samples with a high Venetoclax IC50 (136/1) compared to Venetoclax low IC50 (54/1). (Figure 1) -A) Samples with p53 deletion and corresponding synergy. (B) BCL2 family protein expression of CLL sample 214c. Conclusions: Our data indicates that a) PLX51107 has an antitumor effect in CLL cells; b) the combinational treatment of Venetoclax with PLX51107 highly improved the apoptotic effect of single agent treatments. A better understanding of the key signaling pathways for CLL cells' proliferation and survival impacted by BRD4i in combination with Venetoclax would provide a proof-of-concept rationale for studies validating BRD4i as epigenetic approach to target BCR signaling in CLL. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Optimization of Resveratrol Used as a Scaffold to Design Histone Deacetylase (HDAC-1 and HDAC-2) Inhibitors.

Histone deacetylases (HDAC) are epigenetic enzymes responsible for repressing gene expression through the deacetylation of histone lysine residues. Therefore, inhibition of HDACs has become an interesting approach for the treatment of several diseases, including cancer, hematology, neurodegenerative, immune diseases, bacterial infections, and more. Resveratrol (RVT) has pleiotropic effects, including pan-inhibition of HDAC isoforms; however, its ability to interfere with membranes requires additional optimization to eliminate nonspecific and off-target effects. Thus, to explore RVT as a scaffold, we designed a series of novel HDAC-1 and -2 inhibitors containing the 2-aminobenzamide subunit. Using molecular modeling, all compounds, except unsaturated compounds (4) and (7), exhibited a similar mode of interaction at the active sites of HDAC 1 and 2. The docking score values obtained from the study ranged from −12.780 to −10.967 Kcal/mol. All compounds were synthesized, with overall yields ranging from 33% to 67.3%. In an initial screening, compounds (4), (5), (7), and (20)–(26), showed enzymatic inhibitory effects ranging from 1 to 96% and 6 to 93% against HDAC-1 and HDAC-2, respectively. Compound (5), the most promising HDAC inhibitor in this series, was selected for IC50 assays, resulting in IC50 values of 0.44 µM and 0.37 µM against HDAC-1 and HDAC-2, respectively. In a panel of selectivity against HDACs 3–11, compound (5) presented selectivity towards Class I, mainly HDAC-1, 2, and 3. All compounds exhibited suitable physicochemical and ADMET properties as determined using in silico simulations. In conclusion, the optimization of the RVT structure allows the design of selective HDAC inhibitors, mainly targeting HDAC-1 and HDAC-2 isoforms.

THE REGULATORY MECHANISM OF HISTONE DEACETYLASES IN EPIGENETIC REGULATION: EMERGING PARADIGMS FROM HDAC INHIBITION STUDIES IN UTERINE LEIOMYOSARCOMA

Uterine leiomyosarcoma (LMS) is an aggressive and the most common type of uterine sarcoma that presents a poor prognosis, high rates of recurrence, and metastasis. Currently, there is limited information available concerning molecular mechanisms of LMS development and pathogenesis. Class I histone deacetylases (including HDAC1, 2, 3, and 8) are one of the major classes of the HDAC family, catalyzing the removal of acetyl groups from lysine residues in histones and cellular proteins. In this study, we aim to assess the transcriptome of LMS in the presence or absence of class I histone deacetylases (HDAC) inhibitor (HDACi, tucidinostatin), and characterized the regulatory mechanism of class I HDACs in the pathogenesis of LMS.

Development and validation of a microenvironment-related prognostic model for hepatocellular carcinoma patients based on histone deacetylase family

BackgroundHistone deacetylase (HDAC) family can remove acetyl groups from histone lysine residues, and their high expression is closely related to the poor prognosis of hepatocellular carcinoma (HCC) patients. Recently, it has been reported to play an immunosuppressive role in the microenvironment, but little is known about the mechanism. MethodsThrough machine learning, we trained and verified the prognostic model composed of HDACs. CIBERSORT was used to calculate the percentage of immune cells in the microenvironment. Based on co-expression network, potential targets of HDACs were screened. After that, qRT-PCR was employed to evaluate the expression of downstream genes of HDACs, while HPLC-CAD analysis was applied to detect the concentration of arachidonic acid (AA). Finally, Flow cytometry, WB and IHC experiments were used to detect CD86 expression in RAW246.7. ResultsWe constructed a great prognostic model composed of HDAC1 and HDAC11 that was significantly associated with overall survival. These HDACs were related to the abundance of macrophages, which might be attributed to their regulation of fatty-acid-metabolism related genes. In vitro experiments, the mRNA expression of ACSM2A, ADH1B, CYP2C8, CYP4F2 and SLC27A5 in HCC-LM3 was significantly down-regulated, and specific inhibitors of HDAC1 and HDAC11 significantly promoted the expression of these genes. HDAC inhibitors can promote the metabolism of AA, which may relieve the effect of AA on the polarization of M1 macrophages. ConclusionsOur study revealed the blocking effect of HDAC1 and HDAC11 on the polarization of macrophages M1 in the microenvironment by inhibiting fatty acid metabolism.