Histone Methyltransferase Inhibitor Research Articles

Abstract 2066: Modulation of homologous recombination repair pathway gene expression by a dual EZH2 and EHMT2 histone methyltransferase inhibitor and synergy with PARP inhibitors in ovarian cancer

Abstract Defective DNA damage response (DDR) is a hallmark of high grade serous ovarian cancer (HGSOC). Genetic and epigenomic aberrations in DDR pathways including homologous recombination (BRCA1/BRCA2) and non-homologous end joining (PARP-1) make some HGSOC vulnerable to cisplatin and Poly (ADP-ribose) polymerase inhibitors (PARPi). However, mechanisms behind primary and acquired resistance to these agents remain unknown. We hypothesise aberrant epigenomic changes at DDR-associated genes contribute to PARPi resistance and can be reversed using a novel histone methyltransferase inhibitor (HKMT-1-005) which targets two histone methyltransferases (EZH2 and EHMT2) frequently upregulated in HGSOC. MTS assays were used to calculate the IC50 values for HKMT-1-005 and the PARPi Rucaparib in a panel of human HGSOC cell lines (n=8). Isobologram analysis using Combenefit software was used to determine synergy. RNA-seq and ATAC-seq was performed on cell lines derived from the same patient before (PEO1) and after acquired resistance to chemotherapy (PEO4) pre/post treatment with HKMT-1-005. Pathway analysis was used to identify pathways enriched in genes with altered expression and/or chromatin conformation after treatment with HKMT-1-005 and validated with qRT-PCR. Synergy between HKMT-1-005 and Rucaparib and changes in chromatin conformation with HKMT-1-005 treatment were further examined in CRIPSR modified ID8 murine ovarian cell lines with the genotypes: WT, P53-/-, P53-/-BRCA1-/- and P53-/-BRCA2-/-. Isobologram analysis revealed HKMT-1-005 in combination with Rucaparib was synergistic in multiple cell lines. Synergy was greater in PEO1 compared to PEO4. RNA-seq and ATAC-seq identified a significant (FDR <0.05) enrichment of genes associated with DDR pathways which had altered expression and/or chromatin accessibility in PEO1 compared to PEO4, including BRCA1 and BRCA2. qRT-PCR analysis confirmed treatment with HKMT-1-005 reduced expression of BRCA1 and BRCA2 in PEO1 but not PEO4. Synergy between HKMT-1-005 and Rucaparib was greater in P53-/-BRCA1-/- and P53-/-BRCA2-/- compared to WT or P53-/- ID8 mouse cell lines. ATAC-seq identified multiple DDR-associated genes had significantly (FDR <0.05) altered chromatin accessibility in P53-/-BRCA2-/- compared with P53-/- alone. HKMT-1-005 treatment in ID8 cell lines revealed changes in chromatin at multiple DDR-associated genes including BRCA2. HKMT-1-005 is synergistic with the PARP inhibitor Rucaparib and can modulate the expression and chromatin conformation of DDR-associated genes in multiple human and mouse ovarian cell lines. Depletion of BRCA2 may additionally regulate chromatin conformation of genes including those associated with DDR pathways and explain why greater synergy between HKMT-1-005 and Rucaparib was observed in BRCA deficient lines. Citation Format: Ian M. Garner, Zhuyan Su, Sawyer Hu, Yue Wu, Iain A. McNeish, Matthew J. Fuchter, Robert Brown. Modulation of homologous recombination repair pathway gene expression by a dual EZH2 and EHMT2 histone methyltransferase inhibitor and synergy with PARP inhibitors in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2066.

Abnormal H3K27 histone methylation of RASA1 gene leads to unexplained recurrent spontaneous abortion by regulating Ras-MAPK pathway in trophoblast cells.

Some studies suggest that the inactivation of the Ras-MAPK pathway in trophoblast cells can lead to recurrent abortion, but the molecular mechanism underlying the inactivation of this pathway in trophoblast cells is still unclear. This study aimed to explore the relationship between the mechanism of abnormal activation of RASA1, a regulatory protein of the Ras-MAPK pathway, and unexplained recurrent spontaneous abortion. RT-qPCR was used to detect the transcription levels of RASA1 gene. Immunohistochemistry and Western blot were used to detect the expression levels of the RASA1, Raf and MEK proteins. CCK-8, TUNEL and Transwell assays were used to detect the proliferative, apoptotic, and invasive capacities of HTR-8/SVneo cells. ChIP assays were used to detect the enrichment of H3K27me3 in RASA1 gene promoter. Abortion villi experiments showed that the enrichment of H3K27me3 in the RASA1 gene promoter was reduced, and that both RASA1 gene transcription and RASA1 protein expression were increased. Cell experiments confirmed that RASA1 could decrease the phosphorylated Raf and MEK proteins, inhibit the proliferation and invasion ability, and promote the apoptosis ability of HTR-8/SVneo cells. It was also found that the proliferation and invasion ability as well as the Ras-MAPK pathway activity of HTR-8/SVneo cells were inhibited when treated with histone methyltransferase inhibitor DZNep. RASA1 gene was abnormally activated in unexplained recurrent spontaneous abortion villi due to the decreased enrichment of H3K27me3 in the gene promoter. High expression of RASA1 could inhibit the activity of the Ras-MAPK pathway, and thus inhibit the proliferation and invasion ability of trophoblast cells.

Discovery of first-in-class inhibitors of ASH1L histone methyltransferase with anti-leukemic activity

ASH1L histone methyltransferase plays a crucial role in the pathogenesis of different diseases, including acute leukemia. While ASH1L represents an attractive drug target, developing ASH1L inhibitors is challenging, as the catalytic SET domain adapts an inactive conformation with autoinhibitory loop blocking the access to the active site. Here, by applying fragment-based screening followed by medicinal chemistry and a structure-based design, we developed first-in-class small molecule inhibitors of the ASH1L SET domain. The crystal structures of ASH1L-inhibitor complexes reveal compound binding to the autoinhibitory loop region in the SET domain. When tested in MLL leukemia models, our lead compound, AS-99, blocks cell proliferation, induces apoptosis and differentiation, downregulates MLL fusion target genes, and reduces the leukemia burden in vivo. This work validates the ASH1L SET domain as a druggable target and provides a chemical probe to further study the biological functions of ASH1L as well as to develop therapeutic agents.

Effects of Environmental Conditions on Nephron Number: Modeling Maternal Disease and Epigenetic Regulation in Renal Development.

A growing body of evidence suggests that low nephron numbers at birth can increase the risk of chronic kidney disease or hypertension later in life. Environmental stressors, such as maternal malnutrition, medication and smoking, can influence renal size at birth. Using metanephric organ cultures to model single-variable environmental conditions, models of maternal disease were evaluated for patterns of developmental impairment. While hyperthermia had limited effects on renal development, fetal iron deficiency was associated with severe impairment of renal growth and nephrogenesis with an all-proximal phenotype. Culturing kidney explants under high glucose conditions led to cellular and transcriptomic changes resembling human diabetic nephropathy. Short-term high glucose culture conditions were sufficient for long-term alterations in DNA methylation-associated epigenetic memory. Finally, the role of epigenetic modifiers in renal development was tested using a small compound library. Among the selected epigenetic inhibitors, various compounds elicited an effect on renal growth, such as HDAC (entinostat, TH39), histone demethylase (deferasirox, deferoxamine) and histone methyltransferase (cyproheptadine) inhibitors. Thus, metanephric organ cultures provide a valuable system for studying metabolic conditions and a tool for screening for epigenetic modifiers in renal development.

Chaetocin Affect Photosynthesis of Nicotiana tabacum under Abiotic Stress

Epigenetic regulation of gene expression plays an important role in plant growth, development, and response to various environmental stresses. Due to increasing pollution and global warming, the environmental condition is getting worse for living organisms and plants. The growth and productivity of crop plants worldwide are severely affected by abiotic stress condition. In present study, we studied the effect of histone methyltransferase inhibitor chaetocin in tobacco plant under different abiotic stresses like cold, heat, drought and salinity. In our present study, we have found that photosynthesis is lowered in control plants by chaetocin and it is further lowered under abiotic stresses in the presence of chaetocin. Our study will help understand the epigenetic regulation of genes involved in photosynthesis and identify stress-responsive genes to understand the mechanism that reduces crop yield.

Vitamin C Promotes Anti-Leukemia of DZNep in Acute Myeloid Leukemia

The epigenetic treatment by 3-Deazaneplanocin A (DZNep), a histone methyltransferase inhibitor, shows great potential to treat acute myeloid leukemia (AML). However, the variant sensitivity and incomplete response to DZNep are very common in different AML cell lines as well as primary leukemia cells from AML patients. Here, we reveal that vitamin C (Vc) dramatically promotes DZNep response in leukemia cells from different AML cell lines and primary AML patient. Vc enhances apoptosis and differentiation induced by DZNep in different AML cell lines in vitro and reduces leukemia progression in vivo. At the molecular level, Vc promotes downregulation of D-3-phosphoglycerate dehydrogenase (PHGDH), an enzyme for serine synthesis, and other anti-apoptotic genes, such as BCL2. Over-expression of PHGDH reverses the enhancing effect of Vc on the anti-leukemia effect of DZNep in AML cells. Together, our findings provide an effective approach to reduce the epigenetic treatment resistance by Vc and would be valuable in potential applications. Funding Information: This work was supported by the National Natural Science Foundation of China (81700149), Guangdong Basic and Applied Basic Research Foundation (No. 2020A1515010199), and the Fundamental Research Funds for the Central Universities (No. 20ykpy30). Declaration of Interests: The authors declare no competing financial interests. Ethics Approval Statement: All samples were collected after obtaining informed consent in accordance with the Declaration of Helsinki. The study was approved by the ethics committees of the Institutional Review Boards. All animal experiments were performed according to protocols approved by the institutional animal care and use committee.

The Effect of EZH2 Inhibition through DZNep on Epithelial-Mesenchymal Transition Mechanism.

Although the molecular pathogenesis of hepatocellular carcinoma (HCC) is uncertain, it is known that the epithelial-mesenchymal transition (EMT) mechanism and epigenetic changes have an important role. This study was focused on evaluating the relationship of 3-Deazaneplanocin A (DZNep) with the EMT mechanism, which is a histone methyltransferase inhibitor on HCC and is also known as an enhancer of zeste homolog 2 (EZH2) inhibitor. Cell viability of HepG2 cells (HCC cell line) assessed for DZNep over 72 hours with 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Additionally, colony-forming assay, apoptosis assay, RNA isolation, cDNA synthesis, and real-time PCR (RT-PCR) were performed to see the effect of DZNep on HepG2 cells. DZNep reduced cell proliferation for 72 hours, also significantly reduced colony formation in addition it increased the total apoptosis. DZNep on EZH2, E-cadherin, N-cadherin, and Vimentin (Vim) gene expressions was given different results by either decreasing or increasing the expressions. In this study, we observed a positive effect of DZNep on apoptosis and TIMP3 expression level and decreased colony formation. However, it gave complicated results with the level of gene expression E-cadherin and TIMP2, increase the level of Vim and MMP2 expression. Therefore, we think that further studies are necessary to clarify the role of DZNep.

Epigenetics, a new therapeutic target for fighting viral infections

Epigenetics play an important role in viral replication and in viral associated pathogenesis. In fact, viruses interact with epigenetic factors to promote the viral replication by stimulating the entry into the lytic cycle, but also by promoting viral latency. Furthermore, epigenetics control the immune response implemented by the host to counteract viral infections. Thus, epigenetic modifications are identified as potential therapeutic targets to control viral infections. Several studies have already shown the efficiency of inhibitors of histone deacetylases, demethylases, acetyltransferases and methyltransferases, as well as inhibitors of DNA methyltransferases in viral infections repression or in latency reactivation. In this review, we will examine the epigenetic regulation of viral infections by several DNA viruses, e.g. HSV, EBV, HCMV, KSHV, HBV, HPV and HAdV, and RNA viruses, e.g. HCV, HIV, IAV and CoV. Also, we will discuss the potential use of therapeutic approaches targeting epigenetics for the control of viral infections.

The histone methyltransferase inhibitor A-366 enhances hemoglobin expression in erythroleukemia cells upon co\u2010exposure with chemical inducers in culture

BackgroundErythroleukemia is caused by the uncontrolled multiplication of immature erythroid progenitor cells which fail to differentiate into erythrocytes. By directly targeting this class of malignant cells, the induction of terminal erythroid differentiation represents a vital therapeutic strategy for this disease. Erythroid differentiation involves the execution of a well-orchestrated gene expression program in which epigenetic enzymes play critical roles. In order to identify novel epigenetic mediators of differentiation, this study explores the effects of multiple, highly specific, epigenetic enzyme inhibitors, in murine and human erythroleukemia cell lines.ResultsWe used a group of compounds designed to uniquely target the following epigenetic enzymes: G9a/GLP, EZH1/2, SMYD2, PRMT3, WDR5, SETD7, SUV420H1 and DOT1L. The majority of the probes had a negative impact on both cell proliferation and differentiation. On the contrary, one of the compounds, A-366, demonstrated the opposite effect by promoting erythroid differentiation of both cell models. A-366 is a selective inhibitor of the G9a methyltransferase and the chromatin reader Spindlin1. Investigation of the molecular mechanism of action revealed that A-366 forced cells to exit from the cell cycle, a fact that favored erythroid differentiation. Further analysis led to the identification of a group of genes that mediate the A-366 effects and include CDK2, CDK4 and CDK6.ConclusionsA-366, a selective inhibitor of G9a and Spindlin1, demonstrates a compelling role in the erythroid maturation process by promoting differentiation, a fact that is highly beneficial for patients suffering from erythroleukemia. In conclusion, this data calls for further investigation towards the delivery of epigenetic drugs and especially A-366 in hematopoietic disorders.

Multiplexed Imaging of Posttranslational Modifications of Endogenous Proteins in Live Cells.

Posttranslational histone modifications are associated with the regulation of genome function. Some modifications are quite stable to maintain epigenome states of chromatin, and others can exhibit dynamic changes in response to internal and external stimuli. To track the local and global changes in histone modifications, multiplexed imaging in living cells is beneficial. Among live cell probes for detecting histone modifications, genetically encoded modification-specific intracellular antibodies, or mintbodies, are convenient and suitable tools for this purpose. We here describe the mintbody-based methods to monitor the changes in histone modification levels induced by histone methyltransferase and deacetylase inhibitors. By measuring the nuclear to cytoplasmic intensity ratios of mintbodies in living cells, changes in histone H4 lysine 20 methylation states and the increase in histone H3 acetylation were detected.

The epigenetic treatment remodel genome-wide histone H4 hyper-acetylation patterns and affect signaling pathways in acute promyelocytic leukemia cells

Although majority of acute promyelocytic leukemia (APL) patients achieve complete remission after the standard treatment, 5–10% of patients are shown to relapse or develop resistance to treatment. In such cases, medications that target epigenetic processes could become an appealing supplementary approach. In this study, we tested the anti-leukemic activity of histone deacetylase inhibitor Belinostat (PXD101) and histone methyltransferase inhibitor 3-Deazaneplanocin A combined with all-trans retinoic acid in APL cells NB4, promyelocytes resembling HL-60 cells and APL patients' cells. After HL-60 and NB4 cell treatment, ChIP-sequencing was performed using antibodies against hyper-acetylated histone H4. Hyper-acetylated histone H4 distribution peaks were compared in treated vs untreated HL-60 and NB4 cells. Results demonstrated that in treated HL-60 cells, the majority of peaks were distributed within the regions of proximal promoters, whereas in treated NB4 cells, hyper-acetylated histone H4 peaks were mainly localized in gene body regions. Further ChIP-seq data analysis revealed the changes in histone H4 hyper-acetylation in promoter/gene body regions of genes involved in cancer signaling pathways. In addition, quantitative gene expression analysis proved changes in various cellular pathways important for carcinogenesis. Epigenetic treatment down-regulated the expression of MTOR, LAMTOR1, WNT2B, VEGFR3, FGF2, FGFR1, TGFA, TGFB1, TGFBR1, PDGFA, PDGFRA and PDGFRB genes in NB4, HL-60 and APL patients’ cells. In addition, effect of epigenetic treatment on protein expression of aforementioned signaling pathways was confirmed with mass spectrometry analysis. Taken together, these results provide supplementary insights into molecular changes that occur during epigenetic therapy application in in vitro promyelocytic leukemia cell model.

Covalent inhibition of NSD1 histone methyltransferase.

The NSD family of histone methyltransferases is associated with various malignancies, including aggressive acute leukemia with NUP98-NSD1 translocation. While NSD proteins represent attractive drug targets, their catalytic SET domains exist in autoinhibited conformation, presenting significant challenges for inhibitor development. Here, we employed a fragment-based screening strategy followed by chemical optimization, which resulted in development of the first-in-class irreversible small molecule inhibitors of the NSD1 SET domain. The crystal structure of NSD1 in complex with covalently bound ligand reveals conformational change in the autoinhibitory loop of the SET domain and formation of a channel-like pocket suitable for targeting with small molecules. Our covalent lead, compound BT5, demonstrates on-target activity in NUP98-NSD1 leukemia cells, including inhibition of H3K36 dimethylation and downregulation of target genes, and impairs colony formation in NUP98-NSD1 patient sample. This study will facilitate development of the next generation of potent and selective inhibitors of the NSD histone methyltransferases.

Long-Term Effect of Post-traumatic Stress in Adolescence on Dendrite Development and H3K9me2/BDNF Expression in Male Rat Hippocampus and Prefrontal Cortex.

Exposure to a harsh environment in early life increases in the risk of post-traumatic stress disorder (PTSD) of an individual. Brain derived neurotrophic factor (BDNF) plays an important role in neurodevelopment in developmental stages. Both chronic and traumatic stresses induce a decrease in the level of BDNF and reduce neural plasticity, which is linked to the pathogenesis of PTSD. Also, studies have shown that stress alters the epigenetic marker H3K9me2, which can bind to the promoter region of the Bdnf gene and reduce BDNF protein level. However, the long-term effects of traumatic stress during adolescence on H3K9me2, BDNF expression and dendrite development are not well-known. The present study established a model of PTSD in adolescent rats using an inescapable foot shock (IFS) procedure. Anxiety-like behaviors, social interaction behavior and memory function were assessed by the open field test, elevated plus maze test, three-chamber sociability test and Morris water maze test. In addition, neuronal development and H3K9me2/BDNF expression in hippocampus (HIP) and prefrontal cortex (PFC) were evaluated by Golgi staining, western blotting, qRT-PCR analysis and CHIP-qPCR analysis. Additionally, the Unc0642, a small molecule inhibitor of histone methyltransferase (EHMT2) was used for intervention. The results showed that the IFS procedure induced the PTSD-like behaviors in rats, resulted in fewer dendrite branches and shorter dendrite length in CA1 of HIP and PFC, increased H3K9me2 level and decreased BDNF expression in HIP and PFC. Also, although all the changes can persist to adulthood, Unc0642 administration relieved most of alterations. Our study suggests that traumatic stress in adolescence leads to immediate and long-term mental disorders, neuronal morphological changes, lower BDNF level and increased H3K9me2 level in the HIP and PFC, indicating that H3K9me2/BDNF dysfunction plays a key role in pathogenesis of PTSD.

Hypomethylating Agents in Lymphoma.

Epigenetic mutations are frequent and pathogenic in select subtypes of lymphoma, and agents modulating DNA and histone methylation-such as inhibitors of DNMT and EZH2, respectively-have demonstrated promise in treating these diseases. In particular, lymphomas derived from the germinal center-GC-DLBCL, FL, and AITL-are all characterized by epigenetic derangements. In an effort to target these derangements, DNMT inhibitors have been investigated as a means of improving responsiveness to chemotherapy in DLBCL patients, or as monotherapy or in combination with other epigenetic agents in the treatment of TCL. Histone methyltransferase inhibitors have demonstrated effectiveness in R/R FL patients with EZH2-activating mutations. New treatment options that target the pathogenesis of disease are needed. HDAC inhibitors have been in the clinic for over a decade for the treatment of lymphoma, and now methyltransferase inhibitors are finding their niche for this disease.

HMTase Inhibitors as a Potential Epigenetic-Based Therapeutic Approach for Friedreich's Ataxia.

Friedreich’s ataxia (FRDA) is a progressive neurodegenerative disorder caused by a homozygous GAA repeat expansion mutation in intron 1 of the frataxin gene (FXN), which instigates reduced transcription. As a consequence, reduced levels of frataxin protein lead to mitochondrial iron accumulation, oxidative stress, and ultimately cell death; particularly in dorsal root ganglia (DRG) sensory neurons and the dentate nucleus of the cerebellum. In addition to neurological disability, FRDA is associated with cardiomyopathy, diabetes mellitus, and skeletal deformities. Currently there is no effective treatment for FRDA and patients die prematurely. Recent findings suggest that abnormal GAA expansion plays a role in histone modification, subjecting the FXN gene to heterochromatin silencing. Therefore, as an epigenetic-based therapy, we investigated the efficacy and tolerability of two histone methyltransferase (HMTase) inhibitor compounds, BIX0194 (G9a-inhibitor) and GSK126 (EZH2-inhibitor), to specifically target and reduce H3K9me2/3 and H3K27me3 levels, respectively, in FRDA fibroblasts. We show that a combination treatment of BIX0194 and GSK126, significantly increased FXN gene expression levels and reduced the repressive histone marks. However, no increase in frataxin protein levels was observed. Nevertheless, our results are still promising and may encourage to investigate HMTase inhibitors with other synergistic epigenetic-based therapies for further preliminary studies.

The Promise for Histone Methyltransferase Inhibitors for Epigenetic Therapy in Clinical Oncology: A Narrative Review.

Epigenetic processes are essential for normal development and the maintenance of tissue-specific gene expression in mammals. Changes in gene expression and malignant cellular transformation can result from disruption of epigenetic mechanisms, and global disruption in the epigenetic landscape is a key feature of cancer. The study of epigenetics in cancer has revealed that human cancer cells harbor both genetic alterations and epigenetic abnormalities that interplay at all stages of cancer development. Unlike genetic mutations, epigenetic aberrations are potentially reversible through epigenetic therapy, providing a therapeutically relevant treatment option. Histone methyltransferase inhibitors are emerging as an epigenetic therapy approach with great promise in the field of clinical oncology. The recent accelerated approval of the enhancer of zeste homolog 2 (EZH2; also known as histone-lysine N-methyltransferase EZH2) inhibitor tazemetostat for metastatic or locally advanced epithelioid sarcoma marks the first approval of such a compound for the treatment of cancer. Many other histone methyltransferase inhibitors are currently in development, some of which are being tested in clinical studies. This review focuses on histone methyltransferase inhibitors, highlighting their potential in the treatment of cancer. We also discuss the role for such epigenetic drugs in overcoming epigenetically driven drug resistance mechanisms, and their value in combination with other therapeutic approaches such as immunotherapy.

A Histone Methyltransferase Inhibitor Can Reverse Epigenetically Acquired Drug Resistance in the Malaria Parasite Plasmodium falciparum.

Malaria parasites invade and replicate within red blood cells (RBCs), extensively modifying their structure and gaining access to the extracellular environment by placing the plasmodial surface anion channel (PSAC) into the RBC membrane. Expression of members of the cytoadherence linked antigen gene 3 (clag3) family is required for PSAC activity, a process that is regulated epigenetically. PSAC is a well-established route of uptake for large, hydrophilic antimalarial compounds, and parasites can acquire resistance by silencing clag3 gene expression, thereby reducing drug uptake. We found that exposure to sub-IC50 concentrations of the histone methyltransferase inhibitor chaetocin caused substantial changes in both clag3 gene expression and RBC permeability, and reversed acquired resistance to the antimalarial compound blasticidin S that is transported through PSACs. Chaetocin treatment also altered progression of parasites through their replicative cycle, presumably by changing their ability to modify chromatin appropriately to enable DNA replication. These results indicate that targeting histone modifiers could represent a novel tool for reversing epigenetically acquired drug resistance in P. falciparum.

Exon Skipping in Directly Reprogrammed Myotubes Obtained from Human Urine-Derived Cells.

Duchenne muscular dystrophy (DMD), a progressive and fatal muscle disease, is caused by mutations in the DMD gene that result in the absence of dystrophin protein. To date, we have completed an investigator-initiated first-in-human study at the National Center of Neurology and Psychiatry based on the systemic injection of the morpholino oligonucleotides which are prone to exon-53 skipping. For the effective treatment of DMD, in vitro testing with myoblasts derived from DMD patients to screen drugs and assess patient eligibility before undertaking clinical trials is thought to be essential. Very recently, we reported a new MYOD1-converted urine-derived cell (UDC) treated with the histone methyltransferase inhibitor (3-deazaneplanocin A hydrochloride), as a cellular model of DMD. The new autologous UDC might show phenocopy of the disease-specific phenotypes of DMD, leading to the application of precision medicine in a variety of muscle-related diseases. In this article, we describe a detailed protocol for efficient modelling of DMD muscle cells using MYOD1-converted UDCs along with reverse transcriptase polymerase chain reaction (RT-PCR), Western blotting, and immunocytochemistry to evaluate the restoration of dystrophin mRNA and protein levels after exon skipping.

Epigenetically modifying the Foxp3 locus for generation of stable antigen-specific Tregs as cellular therapeutics.

Foxp3+ regulatory T cells (Tregs) are potent immunoregulatory cells, prompting strong interests in manipulating them for therapeutic purposes. However, significant challenges remain, including their heterogeneity and functional instability. Here we focused on the inducible Tregs (iTregs) and studied whether the Foxp3 locus can be epigenetically edited ex vivo to produce stable therapeutic iTregs. Under iTreg-inducing condition where activated CD4+ T effector cells were converted to Foxp3+ Tregs, we tested approximately 30 compounds and identified 3 chromatin-modifying chemical compounds (3C) consisting of sodium butyrate (a broad histone deacetylase inhibitor), UNC0646 (a histone methyltransferase inhibitor), and vitamin C (a TET dioxygenase co-activator), that together produced complete demethylation at the conserved noncoding sequence 2 (CNS2) region of Foxp3 locus. We found that iTregs induced in the presence of 3C (3C-iTregs) are stable, even after exposure to inflammatory cytokines. They expressed high levels of Foxp3 and exhibited potent suppressive activities both in vitro and in vivo. We showed that in models of autoimmunity and transplant rejection, adoptive transfer of antigen-specific 3C-iTregs prevented the induction of experimental autoimmune encephalitis and enabled long-term skin allograft survival. Our data demonstrate that the Foxp3 locus can be epigenetically edited ex vivo to generate stable therapeutic iTregs.

Small Molecules Targeting H3K9 Methylation Prevent Silencing of Reactivated FMR1 Alleles in Fragile X Syndrome Patient Derived Cells.

In fragile X syndrome (FXS), expansion of a CGG repeat tract in the 5′-untranslated region of the FMR1 gene to >200 repeats causes transcriptional silencing by inducing heterochromatin formation. Understanding the mechanism of FMR1 silencing is important as gene reactivation is a potential treatment approach for FXS. To date, only the DNA demethylating drug 5-azadeoxycytidine (AZA) has proved effective at gene reactivation; however, this drug is toxic. The repressive H3K9 methylation mark is enriched on the FMR1 gene in FXS patient cells and is thus a potential druggable target. However, its contribution to the silencing process is unclear. Here, we studied the effect of small molecule inhibitors of H3K9 methylation on FMR1 expression in FXS patient cells. Chaetocin showed a small effect on FMR1 gene reactivation and a synergistic effect on FMR1 mRNA levels when used in combination with AZA. Additionally, chaetocin, BIX01294 and 3-Deazaneplanocin A (DZNep) were able to significantly delay the re-silencing of AZA-reactivated FMR1 alleles. These data are consistent with the idea that H3K9 methylation precedes DNA methylation and that removal of DNA methylation is necessary to see the optimal effect of histone methyl-transferase (HMT) inhibitors on FMR1 gene expression. Nonetheless, our data also show that drugs targeting repressive H3K9 methylation marks are able to produce sustained reactivation of the FMR1 gene after a single dose of AZA.