Histone Lysine Residues Research Articles

DEVELOPMENT OF SMALL MOLECULE EPIGENETIC THERAPEUTICS FOR INFLAMMATORY BOWEL DISEASE

Abstract Long-term persistence of chronic inflammation in inflammatory bowel disease (IBD) including ulcerative colitis (UC) and Crohn’s disease (CD) is among the major factors contributing to neoplastic transformation and the development of colitis-associated colorectal cancer. There exists a lack of efficient medications for IBD, primarily due to emergence of resistance or side effects. Antibodies against tumor necrosis factor-α (anti-TNFα) are effective therapies in the armamentarium; however, up to 40% of patients become resistant to this therapy. Thus, target-based improved therapy with higher efficacy and enhanced safety profile is urgently needed to fill these gaps. We have demonstrated that bromodomain-containing protein 4 (BRD4), an epigenetic regulator, is required for stabilization of NFkB binding on the promoters of inflammatory genes, activation of RNA polymerase II, and histone H3 Lys122 acetylation (H3K122ac) to permit high levels of inflammatory gene expressions in sentinel immune cells, epithelial cells, and fibroblasts. Our compelling data using human IBD patient samples suggest that BRD4 activation is coincident with the initiation of colonic inflammation. Inhibition of the BRD4 activation is an attractive target for the development of superior therapeutics for IBD, especially for anti-TNFα-resistant patients. We have successfully identified proprietary highly potent and specific BRD4 inhibitors (patent WO 2018/112037 A1) with direct binding modes validated by the solved co-complex crystal structures. We observed that our lead compounds exhibit low toxicity both in vitro and in vivo. Therapeutic administration of our lead inhibitors ZL0516 and ZL0590 significantly reduces mucosal inflammation in several animal models of IBD and restores tissue architecture. Our data show that inhibition of BRD4 results in a decrease of key inflammatory cytokines associated with pathological responses in IBD such as TNFα, IL-6, IL-17A, and IL-1β expression in human colonic epithelial cells and peripheral blood mononuclear cells as well as several animal models of IBD colitis. Collectively, our data suggest that BRD4 activation is critical to the initiation of human colonic inflammation during IBD. BRD4 inhibition disrupts its protein-protein interactions with acetylated histone lysine residues, thereby blocking the pathological activation of the BRD4-NFκB signaling and suppressing colonic inflammation. Thus, BRD4 represents a unique drug target, and novel BRD4 inhibitors ZL0516 and ZL0590 have been identified as promising drug candidates towards the development of small molecule epigenetic therapeutics for the treatment of IBD and its chronic sequelae. Funding support: Crohn’s & Colitis Foundation Entrepreneurial Investing (EI) Initiative award, Litwin IBD Pioneers Program, and a research fellowship award from the Crohn’s & Colitis Foundation of America.

Epigenetic regulation of virulence and the transcription of ribosomal protein genes involves a YEATS family protein in Cryptococcus deneoformans

Epigenetic marks or post-translational modifications on histones have important regulatory roles in gene expression in eukaryotic organisms. The epigenetic regulation of gene expression in the pathogenic yeast Cryptococcus deneoformans remains largely undetermined. The YEATS domain proteins are readers of crotonylated lysine residues in histones. Here, we reported the identification of a single-copy gene putatively coding for a YEATS domain protein (Yst1) in C. deneoformans. To define its function, we created a mutant strain, yst1Δ, using CRISPR-Cas9 editing. yst1Δ exhibited defects in phenotype, for instance, it was hypersensitive to osmotic stress in the presence of 1.3M NaCl or KCl. Furthermore, it was hypersensitive to 1% Congo red, suggesting defects in the cell wall. Interestingly, RNA-seq data revealed that Yst1p was critical for the expression of genes encoding the ribosomal proteins, that is, most were expressed with significantly lower levels of mRNA in yst1Δ than in the wild-type strain. The mutant strain was hypersensitive to low temperature and anti-ribosomal drugs, which we putatively attribute to the impairment in ribosomal function. In addition, the yst1Δ strain was less virulent to Galleria mellonella. These results generally suggest that Yst1, as a histone modification reader, might be a key coordinator of the transcriptome of this human pathogen. Yst1 could be a potential target for novel antifungal drugs, which might lead to significant developments in the clinical treatment of cryptococcosis.

Medicinska hemija inhibitora histon deacetilaza

Today, we are witnessing an explosion of scientific concepts in cancer chemotherapy. It has been considered for a long time that genetic instability in cancer should be treated with drugs that directly damage the DNA. Understanding the molecular basis of malignant diseases shed light on studying phenotypic plasticity. In the era of epigenetics, many efforts are being made to alter the aberrant homeostasis in cancer without modifying the DNA sequence. One such strategy is modulation of the lysine acetylome in human cancers. To remove the acetyl group from the histones, cells use the enzymes that are called histone deacetylases (HDACs). The disturbed equilibrium between acetylation and deacetylation on lysine residues of histones can be manipulated with histone deacetylase inhibitors (HDACi). Throughout the review, an effort will be made to present the mechanistic basis of targeting the HDAC isoforms, discovered selective HDAC inhibitors, and their therapeutical implications and expectations in modern drug discovery.

Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases.

The enzymes of the GCN5-related N-acetyltransferase (GNAT) superfamily count more than 870 000 members through all kingdoms of life and share the same structural fold. GNAT enzymes transfer an acyl moiety from acyl coenzyme A to a wide range of substrates including aminoglycosides, serotonin, glucosamine-6-phosphate, protein N-termini and lysine residues of histones and other proteins. The GNAT subtype of protein N-terminal acetyltransferases (NATs) alone targets a majority of all eukaryotic proteins stressing the omnipresence of the GNAT enzymes. Despite the highly conserved GNAT fold, sequence similarity is quite low between members of this superfamily even when substrates are similar. Furthermore, this superfamily is phylogenetically not well characterized. Thus functional annotation based on sequence similarity is unreliable and strongly hampered for thousands of GNAT members that remain biochemically uncharacterized. Here we used sequence similarity networks to map the sequence space and propose a new classification for eukaryotic GNAT acetyltransferases. Using the new classification, we built a phylogenetic tree, representing the entire GNAT acetyltransferase superfamily. Our results show that protein NATs have evolved more than once on the GNAT acetylation scaffold. We use our classification to predict the function of uncharacterized sequences and verify by in vitro protein assays that two fungal genes encode NAT enzymes targeting specific protein N-terminal sequences, showing that even slight changes on the GNAT fold can lead to change in substrate specificity. In addition to providing a new map of the relationship between eukaryotic acetyltransferases the classification proposed constitutes a tool to improve functional annotation of GNAT acetyltransferases.

DNA-Histone Cross-Links: Formation and Repair.

The nucleosome is a stretch of DNA wrapped around a histone octamer. Electrostatic interactions and hydrogen bonds between histones and DNA are vital for the stable organization of nucleosome core particles, and for the folding of chromatin into more compact structures, which regulate gene expression via controlled access to DNA. As a drawback of tight association, under genotoxic stress, DNA can accidentally cross-link to histone in a covalent manner, generating a highly toxic DNA-histone cross-link (DHC). DHC is a bulky lesion that can impede DNA transcription, replication, and repair, often with lethal consequences. The chemotherapeutic agent cisplatin, as well as ionizing and ultraviolet irradiations and endogenously occurring reactive aldehydes, generate DHCs by forming either stable or transient covalent bonds between DNA and side-chain amino groups of histone lysine residues. The mechanisms of DHC repair start to unravel, and certain common principles of DNA-protein cross-link (DPC) repair mechanisms that participate in the removal of cross-linked histones from DNA have been described. In general, DPC is removed via a two-step repair mechanism. First, cross-linked proteins are degraded by specific DPC proteases or by the proteasome, relieving steric hindrance. Second, the remaining DNA-peptide cross-links are eliminated in various DNA repair pathways. Delineating the molecular mechanisms of DHC repair would help target specific DNA repair proteins for therapeutic intervention to combat tumor resistance to chemotherapy and radiotherapy.

Histone Lysine Demethylase JMJD2D/KDM4D and Family Members Mediate Effects of Chronic Social Defeat Stress on Mouse Hippocampal Neurogenesis and Mood Disorders.

Depression, anxiety and related mood disorders are major psychiatric illnesses worldwide, and chronic stress appears to be one of the primary underlying causes. Therapeutics to treat these debilitating disorders without a relapse are limited due to the incomplete molecular understanding of their etiopathology. In addition to the well-studied genetic component, research in the past two decades has implicated diverse epigenetic mechanisms in mediating the negative effects of chronic stressful events on neural circuits. This includes the cognitive circuitry, where the dynamic hippocampal dentate gyrus (DG) neurogenesis gets affected in depression and related affective disorders. Most of these epigenetic studies have focused on the impact of acetylation/deacetylation and methylation of several histone lysine residues on neural gene expression. However, there is a dearth of investigation into the role of demethylation of these lysine residues in chronic stress-induced changes in neurogenesis that results in altered behaviour. Here, using the chronic social defeat stress (CSDS) paradigm to induce depression and anxiety in C57BL/6 mice and ex vivo DG neural stem/progenitor cell (NSCs/NPCs) culture we show the role of the members of the JMJD2/KDM4 family of histone lysine demethylases (KDMs) in mediating stress-induced changes in DG neurogenesis and mood disorders. The study suggests a critical role of JMJD2D in DG neurogenesis. Altered enrichment of JMJD2D on the promoters of Id2 (inhibitor of differentiation 2) and Sox2 (SRY-Box Transcription Factor 2) was observed during proliferation and differentiation of NSCs/NPCs obtained from the DG. This would affect the demethylation of repressive epigenetic mark H3K9, thus activating or repressing these and possibly other genes involved in regulating proliferation and differentiation of DG NSCs/NPCs. Treatment of the NSCs/NPCs culture with Dimethyloxallyl Glycine (DMOG), an inhibitor of JMJDs, led to attenuation in their proliferation capacity. Additionally, systemic administration of DMOG in mice for 10 days induced depression-like and anxiety-like phenotype without any stress exposure.

BRD4 Inhibitors Enhance the Anti-Tumor Activity of Targeted Therapy in Chronic Lymphocytic Leukemia

Background: The development of drugs targeting BTK and BCL2 has dramatically improved the therapeutic landscape in chronic lymphocytic leukemia (CLL). However, resistance to these agents has 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 regulates 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 two BRD4i, AZD5153 and PLX51107, and their cooperative role with the BCL2 inhibitor venetoclax and BTK inhibitor ibrutinib in CLL. Methods: Primary tumor cells were isolated from 36 CLL patients. Peripheral blood mononuclear cells were isolated via histopaque-1077 (Sigma-Aldrich, St Louis MO) from peripheral blood apheresis samples from consenting adults under RPCCC protocol CIC-01-16. B-cells were then isolated from enriched lymphocytes by MACS separation using a human B-cell Isolation Kit II. CLL cells were seeded at 3 x106/mL in a 384 well tissue culture plates and exposed to different doses of AZD5153 (1-20uM) or PLX51107 (1-20uM) as a single agent or in combination with venetoclax (1-100nM) or ibrutinib (50-1000nM) 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. In addition, CLL cells were plated in 6 well plates and exposed to AZD5153 or PLX51107 alone or in combination with either venetoclax or ibrutinib for 24 hrs. Induction of apoptosis and changes in B-cell receptor signaling, BCL2 and NF-kB pathway related proteins were evaluated by flow cytometry or Western blotting respectively. Results: The study included 33 treatment naïve and 3 relapsed/refractory CLL patients. Deletion 11q was detected in 6 patients and del 17p was seen in 1 patient. Both AZD5153 and PLX51107 displayed time and dose dependent induction of apoptosis of CLL cells. Activity was observed in both treatment naïve and relapsed/refractory samples. Moreover, activity was observed in del 17p or ATM deletion samples. Synergistic activity was observed between BRD4is and venetoclax. PLX51107 exhibited synergy with venetoclax in 83% of the samples tested. Similarly, AZD5153 exhibited synergistic effects when combined with venetoclax in 61% of the samples. To a lesser degree, BRD4is exhibited synergistic activity when combined with ibrutinib, (44% with PLX51107 and 39% with AZD5153). Induction of apoptosis was observed in CLL cells exposed to either BRD4i. Morevoer, an increase in the percentage of apoptosis was observed when BRD4i was combined with venetoclax. Western blotting showed a accumulation of p21, reduced levels of C-MYC, as well as modulation of BCL-2 family member proteins such as BCL2, MCL-1 following BRD4i ex vivo exposure. Conclusions: Our data indicate that BRD4 inhibition results in apoptosis of primary tumor cells isolated from patients with various subtypes of CLL. PLX51107 and AZD5153 exhibit synergistic effects when combined with venetoclax and to a lesser degree with ibrutinib. Modulation of BCL-2 family members following BRD4 inibition could play a role in the synergistic activity observed in our studies. A better understanding of the key signaling pathways involved in proliferation and survival of CLL cells impacted by BRD4i in combination with venetoclax and ibrutinib would provide a proof-of-concept rationale for studies validating BRD4i as epigenetic approach to target BCR signaling in CLL. Disclosures Hernandez-Ilizaliturri: Karyopharm: Consultancy; Celgene: Consultancy; Takeda: Consultancy; Amgen: Consultancy; Gilead: Consultancy; Pharmacyclics: Consultancy; Seattle Genetics: Consultancy; Astra Zeneca: Consultancy; Epyzome: Consultancy.

Role of histone acetyltransferase inhibitors in cancer therapy.

The development of cancer is a complex phenomenon driven by various extrinsic as well as intrinsic risk factors including epigenetic modifications. These post-translational modifications are encountered in diverse cancer cells and appear for a relatively short span of time. These changes can significantly affect various oncogenic genes and proteins involved in cancer initiation and progression. Histone lysine acetylation and deacetylation processes are controlled by two opposing classes of enzymes that modulate gene regulation either by adding an acetyl moiety on a histone lysine residue by histone lysine acetyltransferases (KATs) or via removing it by histone deacetylases (KDACs). Deregulated KAT activity has been implicated in the development of several diseases including cancer and can be targeted for the development of anti-neoplastic drugs. Here, we describe the predominant epigenetic changes that can affect key KAT superfamily members during carcinogenesis and briefly highlight the pharmacological potential of employing lysine acetyltransferase inhibitors (KATi) for cancer therapy.

The Roles of Histone Deacetylases and Their Inhibitors in Cancer Therapy.

Genetic mutations and abnormal gene regulation are key mechanisms underlying tumorigenesis. Nucleosomes, which consist of DNA wrapped around histone cores, represent the basic units of chromatin. The fifth amino group (Nε) of histone lysine residues is a common site for post-translational modifications (PTMs), and of these, acetylation is the second most common. Histone acetylation is modulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), and is involved in the regulation of gene expression. Over the past two decades, numerous studies characterizing HDACs and HDAC inhibitors (HDACi) have provided novel and exciting insights concerning their underlying biological mechanisms and potential anti-cancer treatments. In this review, we detail the diverse structures of HDACs and their underlying biological functions, including transcriptional regulation, metabolism, angiogenesis, DNA damage response, cell cycle, apoptosis, protein degradation, immunity and other several physiological processes. We also highlight potential avenues to use HDACi as novel, precision cancer treatments.

Tranylcypromine Based Lysine-Specific Demethylase 1 Inhibitor: Summary and Perspective.

Histone lysine-specific demethylase 1 (LSD1/KDM1A) has become an important and promising anticancer target since it was first identified in 2004 and specially demethylates lysine residues of histone H3K4me1/2 and H3K9me1/2. LSD1 is ubiquitously overexpressed in diverse cancers, and abrogation of LSD1 results in inhibition of proliferation, invasion, and migration in cancer cells. Over the past decade, a number of biologically active small-molecule LSD1 inhibitors have been developed. To date, six trans-2-phenylcyclopropylamine (TCP)-based LSD1 inhibitors (including TCP, ORY-1001, GSK-2879552, INCB059872, IMG-7289, and ORY-2001) that covalently bind to the flavin adenine dinucleotide (FAD) within the LSD1 catalytic cavity have already entered into clinical trials. Here, we provide an overview about the structures, activities, and structure-activity relationship (SAR) of TCP-based LSD1 inhibitors that mainly covers the literature from 2008 to date. The opportunities, challenges, and future research directions in this emerging and promising field are also discussed.

Histone deacetylase inhibitors

The human genome is contained in chromatin, which is a complex macromolecular complex. It is made of DNA, histones and non-histone proteins. The structure of chromatin and the process of its rearrangement regulate the process of transcription, and hence gene expression. Deacetylase (HDAC) is a group of enzymes that catalyzes the cleavage of acetyl groups from lysine residues in histone and nonhistone proteins. This reaction is catalyzed by zinc or NAD + ions [3]. Histone deacetylases are present in the cytoplasm or nucleus of eukaryotes [4, 5]. These enzymes have been divided into 5 classes (I, IIa, IIb, III and IV) due to the similarity in structure and origin. Vorinostat is one of the most studied HDAC inhibitors. It belongs to the second generation polar-planar hydroxamic acid derivatives that inhibit class I and II histone deacetylases. Panobinostat and belinostat are HDAC inhibitors derived from hydroxamic acid that have also entered clinical trials. Valproic acid, from the group of aliphatic acids, belongs to inhibitors of class I and IIα deacetylases and is an established drug anticonvulsants. Histone deacetylase inhibitors may be useful in the treatment of neoplasms because they influence the action of factors related to cell proliferation, may cause cell cycle arrest, and coordinate the action of apoptotic factors and induce apoptosis. There are several deacetylase inhibitors available as drugs and are in different phases of clinical trials. They differ in potency and enzyme specificity. However, it is still unknown which deacetylases are essential for initiating and sustaining metabolic pathways leading to tumor development.

ATF3 Coordinates Antitumor Synergy between Epigenetic Drugs and Protein Disulfide Isomerase Inhibitors.

Histone deacetylase inhibitors (HDACi) are largely ineffective in the treatment of solid tumors. In this study, we describe a new class of protein disulfide isomerase (PDI) inhibitors that significantly and synergistically enhance the antitumor activity of HDACi in glioblastoma and pancreatic cancer preclinical models. RNA-sequencing screening coupled with gene silencing studies identified ATF3 as the driver of this antitumor synergy. ATF3 was highly induced by combined PDI and HDACi treatment as a result of increased acetylation of key histone lysine residues (acetylated histone 3 lysine 27 and histone 3 lysine 18) flanking the ATF3 promoter region. These chromatin marks were associated with increased RNA polymerase II recruitment to the ATF3 promoter, a synergistic upregulation of ATF3, and a subsequent apoptotic response in cancer cells. The HSP40/HSP70 family genes DNAJB1 and HSPA6 were found to be critical ATF3-dependent genes that elicited the antitumor response after PDI and HDAC inhibition. In summary, this study presents a synergistic antitumor combination of PDI and HDAC inhibitors and demonstrates a mechanistic and tumor suppressive role of ATF3. Combined treatment with PDI and HDACi offers a dual therapeutic strategy in solid tumors and the opportunity to achieve previously unrealized activity of HDACi in oncology. SIGNIFICANCE: This study uses a first-in-class PDI inhibitor entering clinical development to enhance the effects of epigenetic drugs in some of the deadliest forms of cancer.

Abstract 1750: Combination of ZEN-3694 with CDK4/6 inhibitors reverses resistance in ER-positive breast cancer

Abstract CDK4/6 inhibitors have been shown to significantly prolong progression-free survival in patients with advanced hormone receptor (HR)-positive, HER2-negative breast cancer. In spite of the great successes with the currents lines of therapies, the patients still acquire resistance over time and, the development of additional novel therapeutic strategies is needed. The bromodomain and extra-terminal domain (BET) proteins are key epigenetic regulators that interact with acetylated lysine (AcLys) residues of histones or transcription factors, leading to the regulation of gene transcription. BET proteins have also been shown to be directly involved in the transcription of the estrogen receptor (ER) mRNA as well as cell cycle and therefore, BET inhibitors can potentially offer new strategies in the treatment of CDK4/6i- resistant and endocrine resistant ER+ breast cancer. ZEN-3694 is an orally bioavailable small molecule inhibitor of BET proteins currently being evaluated in Phase 1/2 clinical trials in metastatic castration-resistant prostate cancer (NCT02711956) and triple negative breast cancer (NCT03901469). We have shown previously that ZEN-3694 inhibits proliferation and induces apoptosis in ER+ cell lines. To assess the effects of ZEN-3694 in the combination with CDK4/6 inhibitors as a potential therapy in a CDK4/6i resistant population, we have developed a panel of ER+ cell lines resistant to palbociclib or abemaciclib by continuous stepwise exposure to increasing concentrations of CDK4/6 inhibitors. These cell lines have demonstrated cross-resistance to all three CDK4/6 inhibitors. Here, we describe that the combination treatment of ZEN-3694 with CDK4/6 inhibitors potently inhibits proliferation and induces apoptosis in all CDK4/6i resistant cell lines. The resistance to both palbociclib and abemaciclib was associated with the strong upregulation of CDK6 and CCND1protein levels in MCF7 which is consistent with their clinical mechanism of resistance. ZEN-3694 showed efficacy in all CDK4/6i-resistant models leading to downregulation of ER and CDK6 protein levels. Furthermore, our RNAseq data revealed several potential pathways involved in CDK4/6i resistance, including upregulation of cell cycle pathway and decrease of interferon signaling and demonstrated that the mechanisms of resistance to abemaciclib and palbociclib are similar but not identical. Additionally, we elucidated the mechanism of action of ZEN-3694 and in combinations with CDK4/6 inhibitors alleviating these resistance mechanisms. The pathway analysis demonstrated that the combination of ZEN-3694 with CDK4/6 inhibitors led to the strong downregulation of multiple pathways including cell cycle regulation, signaling by Rho family GTPases, STAT3, IL6 and other pathways. We conclude that ZEN-3694 has therapeutic potential in a combination with CDK4/6 inhibitors in ER+ breast cancer patients that developed resistance to endocrine therapies and/or CDK4/6 inhibitors. Citation Format: Olesya A. Kharenko, Reena G. Patel, Cyrus Calosing, Edward H. van der Horst. Combination of ZEN-3694 with CDK4/6 inhibitors reverses resistance in ER-positive breast cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1750.

Lysine Acetyltransferase Inhibitors From Natural Sources.

Acetylation of histone and non-histone protein lysine residues has been widely described as a critical modulator of several cell functions in humans. Lysine acetyltransferases (KATs) catalyse the transfer of acetyl groups on substrate proteins and are involved in multiple physiological processes such as cell signalling, metabolism, gene regulation, and apoptosis. Given the pivotal role of acetylation, the alteration of KATs enzymatic activity has been clearly linked to various cellular dysfunctions leading to several inflammatory, metabolic, neurological, and cancer diseases. Hence, the use KAT inhibitors (KATi) has been suggested as a potentially successful strategy to reverse or prevent these conditions. To date, only a few KATi have proven to be potential drug candidates, and there is still a keen interest in designing molecules showing drug-like properties from both pharmacodynamics and pharmacokinetics point of view. Increasing literature evidence has been highlighting natural compounds as a wide source of molecular scaffolds for developing therapeutic agents, including KATi. In fact, several polyphenols, catechins, quinones, and peptides obtained from natural sources (including nuts, oils, root extracts, and fungi metabolites) have been described as promising KATi. Here we summarize the features of this class of compounds, describing their modes of action, structure-activity relationships and (semi)-synthetic derivatives, with the aim of assisting the development of novel more potent, isoform selective and drug-like KATi.

KAT7 is a genetic vulnerability of acute myeloid leukemias driven by MLL rearrangements.

Histone acetyltransferases (HATs) catalyze the transfer of an acetyl group from acetyl-CoA to lysine residues of histones and play a central role in transcriptional regulation in diverse biological processes. Dysregulation of HAT activity can lead to human diseases including developmental disorders and cancer. Through genome-wide CRISPR-Cas9 screens, we identified several HATs of the MYST family as fitness genes for acute myeloid leukaemia (AML). Here we investigate the essentiality of lysine acetyltransferase KAT7 in AMLs driven by the MLL-X gene fusions. We found that KAT7 loss leads to a rapid and complete loss of both H3K14ac and H4K12ac marks, in association with reduced proliferation, increased apoptosis and differentiation of AML cells. Acetyltransferase activity of KAT7 is essential for the proliferation of these cells. Mechanistically, our data propose that acetylated histones provide a platform for the recruitment of MLL-fusion-associated adaptor proteins such as BRD4 and AF4 to gene promoters. Upon KAT7 loss, these factors together with RNA polymerase II rapidly dissociate from several MLL-fusion target genes that are essential for AML cell proliferation, including MEIS1, PBX3 and SENP6. Our findings reveal that KAT7 is a plausible therapeutic target for this poor prognosis AML subtype.

Sirtuins in DNA repair

DNA repair involves number of processes required for detection and repair of DNA damage. The ability to repair existing damage is crucial for preservation of both physical integrity of the genome and fidelity of genetic information. Genetic insults may derive from either metabolic reactions inside the cell or come from exogenous environment. Sirtuins belong to the class of histone deacetylases that catalyze the removal of acetyl moieties from the lysine residues of both histone and nonhistone proteins. Furthermore, some sirtuins exhibit mono-ADP-ribosyltransferase activity that regulates activity of various proteins. The first sirtuin was identified in yeast (Saccharomyces cerevisiae), however both prokaryotic and eukaryotic homologs of sirtuins were later discovered. Seven mammalian homologs (SIRT1-SIRT7) exist. Sirtuins represent an emerging group of enzymes that coordinate DNA repair in respect of cellular metabolic status and may have a prominent role in neoplastic transformation, diabetes, ageing and age-related diseases such as neurodegeneration. The aim of this paper is to review recent research on the role of sirtuins in DNA repair processes.

Selective Class I HDAC Inhibitors Based on Aryl Ketone Zinc Binding Induce HIV-1 Protein for Clearance.

HIV persistence in latently infected, resting CD4+ T cells is broadly considered a barrier to eradicate HIV. Activation of the provirus using latency-reversing agents (LRAs) followed by immune-mediated clearance to purge reservoirs has been touted as a promising therapeutic approach. Histone deacetylases (HDACs) and histone acetyltransferases (HATs) control the acetylation level of lysine residues in histones to regulate the gene transcription. Several clinical HDAC inhibitors had been examined as LRAs, which induced HIV activation in vitro and in vivo. Here we report the discovery of a series of selective and potent class I HDAC inhibitors based on aryl ketones as a zinc binding group, which reversed HIV latency using a Jurkat model of HIV latency in 2C4 cells. The SAR led to the discovery of a highly selective class I HDAC inhibitor 10 with excellent potency. HDACi 10 induces the HIV gag P24 protein in patient latent CD4+ T cells.

Metabolic Ink Lactate Modulates Epigenomic Landscape: A Concerted Role of Pro-tumor Microenvironment and Macroenvironment During Carcinogenesis.

Tumor heterogeneity is influenced by various factors including genetic, epigenetic and axis of metabolic-epigenomic regulation. In recent years, metabolic-epigenomic reprogramming has been considered as one of the many tumor hallmarks and it appears to be driven by both microenvironment and macroenvironment factors including diet, microbiota and environmental pressures. Epigenetically, histone lysine residues are altered by various post-translational modifications (PTMs) such as acetylation, acylation, methylation and lactylation. Furthermore, lactylation is suggested as a new form of PTM that uses a lactate substrate as a metabolic ink for epigenetic writer enzyme that remodels histone proteins. Therefore, preclinical and clinical attempts are warranted to disrupt the pathway of metabolic-epigenomic reprogramming that will turn pro-tumor microenvironment into an anti-tumor microenvironment. This paper highlights the metabolicepigenomic regulation events including lactylation and its metabolic substrate lactate in the tumor microenvironment.

Radiosynthesis and in vivo evaluation of a new positron emission tomography radiotracer targeting bromodomain and extra-terminal domain (BET) family proteins

IntroductionBromodomain and extra-terminal domain (BET) family proteins play a vital role in the epigenetic regulation process by interacting with acetylated lysine (Ac-K) residues in histones. BET inhibitors have become promising candidates to treat various diseases through the inhibition of the interaction between BET bromodomains and Ac-K of histone tails. With a molecular imaging probe, noninvasive imaging such as positron emission tomography (PET) can visualize the distribution and roles of BET family proteins in vivo and enlighten our understanding of BET protein function in both healthy and diseased tissue. MethodsWe radiolabeled the potent BET inhibitor INCB054329 by N-methylation to make [11C]PB003 as a BET PET radiotracer. The bioactivity evaluation of unlabeled PB003 in vitro was performed to confirm its binding affinity for BRDs, then the PET/CT imaging in rodents was performed to evaluate the bioactivity of [11C]PB003 in vivo. ResultsIn our in vitro evaluation, PB003 showed a high BET binding affinity for BRDs (Kd = 2 nM, 1.2 nM, and 1.2 nM for BRD2, BRD3, and BRD4, respectively). In vivo PET/CT imaging demonstrated that [11C]PB003 has favorable uptake with appropriate kinetics and distributions in main peripheral organs. Besides, the blockade of [11C]PB003 binding was found in our blocking study which indicated the specificity of [11C]PB003. However, the BBB penetration and brain uptake of [11C]PB003 was limited, with only a maximum 0.2% injected dose/g at ~2 min post-injection. ConclusionThe imaging results in rodents in vivo demonstrate that [11C]PB003 binds to BET with high selectivity and specificity and has favorable uptake in peripheral organs. However, the low brain uptake of [11C]PB003 limits the visualization of brain regions indicating the efforts are still needed to discover the new BET imaging probes for brain visualization.

Formaldehyde Exposure and Epigenetic Effects: A Systematic Review

Formaldehyde (FA) is a general living and occupational pollutant, classified as carcinogenic for humans. Although genotoxicity is recognized as a FA mechanism of action, a potential contribution of epigenetic effects cannot be excluded. Therefore, aim of this review is to comprehensively assess possible epigenetic alterations induced by FA exposure in humans, animals, and cellular models. A systematic review of Pubmed, Scopus, and Isi Web of Science databases was performed. DNA global methylation changes were demonstrated in workers exposed to FA, and also in human bronchial cells. Histone alterations, i.e., the reduction in acetylation of histone lysine residues, in human lung cells were induced by FA. Moreover, a dysregulation of microRNA expression in human lung adenocarcinoma cells as well as in the nose, olfactory bulb and white blood cells of rodents and nonhuman primates was reported. Although preliminary, these findings suggest the role of epigenetic modifications as possible FA mechanisms of action that need deeper qualitative and quantitative investigation. This may allow to define the role of such alterations as indicators of early biological effect and the opportunity to include such information in future risk assessment and management strategies for public and occupationally FA-exposed populations.