Aberrant Histone Modifications Research Articles

Dysregulation of Apoptosis Caused by Aberrant Histone Modification Influences on the Recurrence of Meningiomas

Background: Alteration of apoptosis is related with progression and recurrence of atypical meningiomas (AMs). However, no comprehensive study has been conducted regarding histone modification regulating apoptosis in AMs. This study was aimed to determine the prognostic values of certain apoptosis-associated factors, and examine the role of histone modification on apoptosis in AMs. Materials and method: The medical records of 67 patients with AMs, as diagnosed during recent 13 years, were reviewed retrospectively. Immunohistochemical staining was performed on archived paraffin-embedded tissues for pro-apoptotic factors (CASP3, IGFBP, TRAIL-R1, BAX, and XAF1), anti-apoptotic factors (survivin, ERK, RAF1, MDM2, and BCL2), and the histone modifying enzymes (MLL2, RIZ, EZH1, NSD2, KDM5c, JMJD2a, UTX, and JMJD5). Results: Twenty-six (38.8%) patients recurred during the follow-up period (mean duration 47.7 months). In terms of time-to-recurrence (TTR), overexpression of CASP3, TRAIL-R1, and BAX had a longer TTR than underexpression, and overexpression of Survivin, MDM2, and BCL2 had a shorter TTR than underexpression (P<0.05). Additionally, overexpression of MLL2, UTX, and JMJ5 had shorter TTRs than underexpression, and overexpression of KDM5c had a longer TTR than underexpression. However, in the multi-variate analysis of predicting factors for recurrence, underexpression of CASP3 (P<0.001), and BAX (P<0.001), and overexpression of survivin (P=0.007), and MDM2 (P=0.037) were associated with recurrence independently, but any enzymes modifying histone were not associated with recurrence. Conclusion: This study suggests certain apoptosis-associated factors should be associated with recurrence of AMs, which may be regulated epigenetically by histone modifying enzymes.

Histone modification as a drug resistance driver in brain tumors ⁎

Abstract Patients with brain tumors, specifically, malignant forms such as glioblastoma, medulloblastoma and ependymoma, exhibit dismal survival rates despite advances in treatment strategies. Chemotherapeutics, the primary adjuvant treatment for human brain tumors following surgery, commonly lack efficacy due to either intrinsic or acquired drug resistance. New treatments targeting epigenetic factors are being explored. Post-translational histone modification provides a critical regulatory platform for processes such as chromosome condensation and segregation, apoptosis, gene transcription, and DNA replication and repair. This work reviews how aberrant histone modifications and alterations in histone-modifying enzymes can drive the acquisition of drug resistance in brain tumors. Elucidating these mechanisms should lead to new treatments for overcoming drug resistance.

A New Molecular Mechanism Underlying the Antitumor Effect of DNA Methylation Inhibitors via an Antiviral Immune Response.

Chromatin remodeling mediated by DNA methylation and histone modifications play critical roles in the transcriptional regulation of protein-coding genes, noncoding RNAs such as microRNAs, and endogenous retroviruses (ERVs). Many studies have shown that aberrant DNA methylation and histone modifications are associated with the initiation and progression of various malignancies. Epigenetic silencing of tumor suppressor genes in cancer is generally mediated by DNA hypermethylation of CpG island promoters and histone modifications such as histone deacetylation, methylation of histone H3 lysine 9 (H3K9), and trimethylation of H3K27. Chromatin-modifying drugs such as DNA methylation inhibitors and histone deacetylase inhibitors have clinical promise for cancer therapy. However, details of the mechanisms responsible for the antitumor effects of these drugs have been unclear. Recently, a new molecular mechanism for the antitumor effect of DNA methylation inhibitors has been proposed: induction of interferon-responsive genes via double-stranded RNAs derived from ERVs. We have also confirmed the same effect of DNA demethylation using a 3D culture system for stem cells known as organoid culture. Our findings indicated that DNA demethylation suppresses the proliferation of cancer-initiating cells by inducing an antiviral response, including activation of interferon-responsive genes. Treatment with DNA methylation inhibitors to activate a growth-inhibiting immune response may be an effective therapeutic approach for malignant disorders.

Prenatal Dexamethasone and Postnatal High-Fat Diet Decrease Interferon Gamma Production through an Age-Dependent Histone Modification in Male Sprague-Dawley Rats.

Overexposure to prenatal glucocorticoid (GC) disturbs hypothalamic-pituitary-adrenocortical axis-associated neuroendocrine metabolism and susceptibility to metabolic syndrome. A high-fat (HF) diet is a major environmental factor that can cause metabolic syndrome. We aimed to investigate whether prenatal GC plus a postnatal HF diet could alter immune programming in rat offspring. Pregnant Sprague-Dawley rats were given intraperitoneal injections of dexamethasone or saline at 14–21 days of gestation. Male offspring were then divided into four groups: vehicle, prenatal dexamethasone exposure, postnatal HF diet (VHF), and prenatal dexamethasone exposure plus a postnatal HF diet (DHF). The rats were sacrificed and adaptive immune function was evaluated. Compared to the vehicle, the DHF group had lower interferon gamma (IFN-γ) production by splenocytes at postnatal day 120. Decreases in H3K9 acetylation and H3K36me3 levels at the IFN-γ promoter correlated with decreased IFN-γ production. The impaired IFN-γ production and aberrant site-specific histone modification at the IFN-γ promoter by prenatal dexamethasone treatment plus a postnatal HF diet resulted in resilience at postnatal day 180. Prenatal dexamethasone and a postnatal HF diet decreased IFN-γ production through a site-specific and an age-dependent histone modification. These findings suggest a mechanism by which prenatal exposure to GC and a postnatal environment exert effects on fetal immunity programming.

Abstract LB-156: Delineating the pathological roles and molecular functions of histone methyltransferase G9a in hepatocellular carcinoma

Abstract Liver cancer, primarily hepatocellular carcinoma (HCC), is the third leading cause of cancer mortality worldwide. In HCC, epigenetic changes including aberrant DNA methylations and histone modifications occur far more frequently than genetic alternations. However, the underlying mechanism and specific gene targets are still unknown. Using RNA-Sequencing, we identified Euchromatic histone-lysine N-methyltransferase 2 (EHMT2/G9a) as one the most significantly deregulated epigenetic regulatory genes in human HCC. G9a is a SET domain containing histone methyltransferase specific for histone H3 lysine 9 methylation. However, little is known about the functional roles of G9a in human HCC. Herein, we showed that G9a expression was frequently up-regulated in primary HCC. Up-regulation of G9a was significantly associated with multiple clinicopathological features related to HCC metastasis. We demonstrated that the frequent G9a up-regulation in HCC was attributed to the G9a gene copy number gain. In addition, we identified miR-1 as a novel post-transcriptional regulator of G9a. Loss of miR-1 significantly contributed to G9a up-regulation in human HCC. Functionally, stable knockdown (by lenti-viral based shRNA) and genetic knock-out of G9a (by CRISPR/Cas9 gene editing system) significantly suppressed HCC cell proliferation, migration and colony formation. We also demonstrated that G9a specific inhibitors, UNC0638 and BIX01294, could effectively inhibit HCC cell growth. By utilizing nude mice model, we showed that depletion of G9a drastically inhibited in vivo tumorigenicity of HCC cells. Mechanistically, we found that up-regulation of G9a epigenetically silence the expression of tumor suppressive gene RARRES3 to promote HCC tumorigenicity and metastasis. In summary, our finding suggested that up-regulation of G9a contributed to the liver carcinogenesis and could be a therapeutic target for HCC treatment. Citation Format: Lei Wei, Felice Ho-Ching Tsang, Sandy Leung-Kuen Au, Joyce Lee, Carmen Wong, Irene Oi-Lin Ng, Chun-Ming Wong. Delineating the pathological roles and molecular functions of histone methyltransferase G9a in hepatocellular carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-156.

The many layers of epigenetic dysfunction in B-cell lymphomas.

Perturbation of the epigenome is emerging as a central driving force in the pathogenesis of diffuse large B-cell lymphomas (DLBCL) and follicular lymphoma. The purpose of this review is to explain how alteration of different layers of the epigenome contributes to the biology and clinical features of these tumors. Key new findings implicate DNA methylation heterogeneity as a core feature of DLBCL. Epigenetic diversity is linked to unfavorable clinical outcomes, clonal selection at relapse, and is driven at least in part because of the actions of activation-induced cytosine deaminase, which is a unique feature of B-cell lymphomas. Somatic mutations in histone modifier genes drive lymphomagenesis through the establishment of aberrant gene-specific histone modification signatures. For example, EZH2 somatic mutations drive silencing of bivalent gene promoters through histone 3 lysine 27 trimethylation, whereas KMT2D (MLL2) mutations disrupt specific sets of enhancers through depletion of histone 3 lysine 4 mono and dimethylation (H3K4me1/me2). Appreciation of the epigenome in determining lymphoma clonal heterogeneity and in driving lymphoma phenotypes through altered promoter and enhancer histone modification profiles is leading to a paradigm shift in how we understand and design therapies for DLBCL and follicular lymphoma.

Biphasic reduction of histone H3 phosphorylation in response to N-nitroso compounds induced DNA damage

BackgroundN-nitroso compounds (NOC) can cause cancers in a wide variety of animal species, and many of them are also potential human carcinogens. However, their underlying genotoxic mechanisms occurred within the context of chromatin, such as aberrant histone modifications, remained elusive. MethodsWe investigated the dynamic landscapes of histone modifications after N-nitroso compound N-methyl-N′-nitro-N-nitrosoguanidine (MNNG) and N-methyl-N-nitroso-urea (MNU) exposure. Among the altered histone modifications, we also investigated the control mechanisms of histone H3 phosphorylation changes and its possible implications on transcriptional repression. ResultsSignificantly, we find a specific biphasic reduction of histone H3 phosphorylation at serine 10 (H3S10ph) and serine 28 (H3S28ph), and a rapid decrease of histone H4 acetylation upon MNNG and MNU exposure. Further investigations reveal that the first hypophosphorylation of H3 occurs in a poly(ADP-ribosyl)ation enzyme PARP-1 (Poly(ADP-Ribose) Polymerase 1) dependent manner, whereas the second decline of H3 phosphorylation is at least partially under the control of histone kinase VRK1 (vaccinia-related kinase 1) and dependent on the tumor suppressor protein p53. In addition, DNA damage induced down-regulation of H3S10/S28 phosphorylation also functions in transcriptional repression of genes, such as cell-cycle regulators. ConclusionsAlkylating damage induced by NOC elicits a biphasic reduction of histone H3 phosphorylation with distinct control mechanisms, which is contributing to DNA damage responses such as the repair-facilitated transcriptional repression. General significanceIdentification of the dynamic changes and underlying mechanisms of histone modifications upon NOC exposure would be of great help in understanding the epigenetic regulations of NOC induced DNA damage responses.

Arsenic silences hepatic PDK4 expression through activation of histone H3K9 methylatransferase G9a

It is well established that increased liver cancer incidence is strongly associated with epigenetic silencing of tumor suppressor genes; the latter is contributed by the environmental exposure to arsenic. Pyruvate dehydrogenase kinase 4 (PDK4) is a mitochondrial protein that regulates the TCA cycle. However, the epigenetic mechanisms mediated by arsenic to control PDK4 expression remain elusive. In the present study, we showed that histone methyltransferase G9a- and Suv39H-mediated histone H3 lysine 9 (H3K9) methylations contributed to PDK4 silencing in hepatic cells. The PDK4 expression was induced by G9a inhibitor BRD4770 (BRD) and Suv39H inhibitor Chaetocin (CHA). In contrast, arsenic exposure decreased PDK4 expression by inducing G9a and increasing H3K9 di- and tri-methylations levels (H3K9me2/3). In addition, arsenic exposure antagonizes the effect of BRD by enhancing the enrichment of H3K9me2/3 in the PKD4 promoter. Moreover, knockdown of G9a using siRNA induced PDK4 expression in HCC cells. Furthermore, arsenic decreased hepatic PDK4 expression as well as diminished the induction of PDK4 by BRD in mouse liver and hepatocytes. Overall, the results suggest that arsenic causes aberrant repressive histone modification to silence PDK4 in both HCC cells and in mouse liver.

Histone Demethylases and Their Roles in Cancer Epigenetics

The genetic abnormalities that drive tumorigenesis are usually coupled with epigenetic alterations, such as DNA methylation and aberrant histone modifications, which may help oncogenic drivers accelerate cancer progression, metastasis, and therapy resistance. The discovery of histone demethylases has provided us new insight for understanding the epigenetic landscape of the chromatin environment of cancer cells. This review aims to summarize the current knowledge on the human histone lysine demethylases and their functions in cancers, and recent advances in development of small molecule inhibitors to target histone demethylases in cancer treatment.

Relationship Between Noncoding RNA Dysregulation and Epigenetic Mechanisms in Cancer.

Epigenetic alterations, including aberrant DNA methylation and histone modification, play key roles in the dysregulation of tumor-related genes, thereby affecting numerous cellular processes, including cell proliferation, cell adhesion, apoptosis, and metastasis. In recent years, studies have demonstrated that short and long noncoding RNAs (ncRNAs) are key players in the initiation and progression of cancer, and epigenetic mechanisms are deeply involved in their dysregulation. Indeed, the growing list of microRNA (miRNA) genes aberrantly methylated in cancer suggests that a large number of miRNAs act as tumor suppressors or oncogenes. In addition, emerging evidence suggests that dysregulation of long ncRNAs (lncRNAs) plays critical roles in tumorigenesis. And because ncRNAs are involved in regulating gene expression through interaction with epigenetic modifiers, their dysregulation appears causally related to epigenetic alterations in cancer. Dissection of the interrelationships between ncRNAs and epigenetic alterations has the potential to reveal novel approaches to the diagnosis and treatment of cancer.

Combinatorial Epigenetic Aberration Propagates in Myelodysplastic Syndrome in the Setting of Concurrent Loss of Tet2 and Ezh2

Somatic loss-of-function mutations of epigenetic regulators are frequently found in MDS patients. Although DNA hypomethylating agents have been shown to improve the clinical outcomes in patients with MDS, it remains unknown how altered DNA methylation promotes the development of MDS. We have recently shown that concurrent loss of Tet2 and Ezh2 promotes the development of MDS in mice compared with the individual loss by utilizing hypomorphic Tet2 mice and Ezh2 conditional knockout mice. In this study, we transplanted Cre-ERT (WT), Tet2KD/KD, Cre-ERT;Ezh2fl/fl, and Tet2KD/KD;Cre-ERT;Ezh2fl/fl fetal liver cells into lethally irradiated recipient mice, and deleted Ezh2 at 4 weeks post-transplantation. To understand how DNA hypermethylation contributed to the development of MDS, we performed Reduced Representation Bisulfite Sequence (RRBS) in Lin- Sca1+ Kit+ (LSK) stem/progenitor cells isolated from WT, Tet2KD/KD, Ezh2Δ/Δ, and Tet2KD/KD Ezh2Δ/Δ mice. Both Tet2 loss and Ezh2 loss caused hypermethylation in CpG islands (CGIs) and promoter regions. However, the impact of Tet2 loss was much evident in the enhancer elements and ~20 % of them underwent hypermethylation upon Tet2 loss. Combined loss of Tet2 and Ezh2 caused hypermethylation in the transcriptional regulatory regions including both the promoter regions and enhancer elements. Importantly, the majority of hyper-differentially methylated regions (hyper-DMRs) in Tet2KD/KD Ezh2Δ/Δ -MDS LSK cells showed a distribution that was distinct from those of single mutant LSK cells and only the hyper-DMRs in the enhancer elements in Tet2KD/KD Ezh2Δ/Δ -MDS LSK cells correlated with a significant reduction in gene expression levels. Hyper-DMRs in MDS LSK cells were significantly enriched in genes involved in transcriptional regulation and cell differentiation by GO analysis. These findings suggest that combined loss of Tet2 and Ezh2 cooperatively remodeled DNA methylation to an extent not observed in either mutant allele alone and contributed to the pathogenesis of MDS. Notably, we found that 375 out of 780 hyper-DMRs in Tet2KD/KD Ezh2Δ/Δ MDS HSPCs were overlapped with DMRs in CD34+ HSPCs in patients with MDS (Maegawa S, et al. Genome Research 2014). We next focused on the 131 genes with hyper-DMRs that showed reduced expression levels in Tet2KD/KD Ezh2Δ/Δ -MDS LSK cells. Those included Gata2, Gata3, Evi1, and Nr4a2. Given that Nr4a2/Nurr1, a nuclear receptor transcription factor, restricts the proliferation of hematopoietic stem cells (HSCs), we transduced WT and Tet2KD/KD Ezh2Δ/Δ HSCs with an Nr4a2 retrovirus in vitro. We found that exogenous Nr4a2 severelyimpairs proliferative capacity of Tet2KD/KD Ezh2Δ/Δ HSCs but moderately that of WT HSCs, implying that MDS HSCs are more susceptible to activation of Nr4a2 compared to WT HSCs. Next, we sought to determine whether DMRs in CGIs were associated with altered histone modifications upon the deletion of Ezh2, we performed chromatin immunoprecipitation (ChIP) sequencing by using H3K27me3 and H3K4me3 antibodies. We defined canonical polycomb repressive complexes 2 (PRC2) targets by >2-fold enrichment of H3K27me3 and bivalent genes by enrichment of both H3K27me3 and H3K4me3 in WT LSK cells. We found that approximately half of the hyper-DMRs in CGIs were enriched in canonical PRC2 targets and bivalent genes in LSK cells of all mutant genotypes. Notably, these hyper-DMRs in PRC2 targets, including bivalent genes, were significantly associated with reduced expression levels only in Tet2KD/KD Ezh2Δ/Δ -MDS LSK cells but not in either single mutant alone. We also observed that these PRC2 targets with hyper-DMRs still retained reduced but higher levels of H3K27me3 compared to the others despite the absence of Ezh2, implying that both DNA hypermethylation and residual H3K27me3 by Ezh1 cooperate to repress the transcription of these genes critical for hematopoiesis. Finally, we examined the impact of decitabine, a demethylating agent in vivo. Although the treatment of decitabine did not improve the survival of Tet2KD/KD Ezh2Δ/Δ -MDS mice, it partly resolved hyper-DMRs at critical genes including Gata2, Gata3, and Nr4a2, followed by a significant elevation in platelets counts in vivo. Taken together, our study unveils the cooperative biological function of aberrant DNA methylation and histone modifications in the pathogenesis of MDS. DisclosuresNakaseko:BMS: Honoraria, Research Funding, Speakers Bureau; Pfizer: Honoraria, Research Funding, Speakers Bureau; Otsuka: Honoraria, Research Funding; Novartis: Honoraria, Research Funding, Speakers Bureau.

Recent progress in the treatment of infant acute lymphoblastic leukemia.

Treatment of infants with acute lymphoblastic leukemia (ALL), especially those with mixed lineage leukemia (MLL) rearrangement (MLL-r), which account for approximately 80% of cases, is still a major challenge for pediatric hematologists and oncologists worldwide. Continuing efforts by collaborative clinical study groups in Europe, North America, and Japan have rescued approximately half of the MLL-r ALL patients with intensive chemotherapy with or without allogeneic hematopoietic stem cell transplantation. Recent progress has clarified the unique mechanism of MLL-r ALL: the aberrant methylation and histone modifications via DOT1L and other related molecules by MLL fusion proteins lead to leukemogenetic gene expression, thus to overt leukemia. In order to overcome this dismal subtype of ALL, novel targeted therapy based on leukemia biology is urgently needed. Due to the extreme rarity of the disease, collaboration between the study groups in Europe (Interfant), North America (Children's Oncology Group), and Japan (Japanese Pediatric Leukemia/Lymphoma Study Group) is under way.

The Role of Dietary Extra Virgin Olive Oil and Corn Oil on the Alteration of Epigenetic Patterns in the Rat DMBA-Induced Breast Cancer Model.

Disruption of epigenetic patterns is a major change occurring in all types of cancers. Such alterations are characterized by global DNA hypomethylation, gene-promoter hypermethylation and aberrant histone modifications, and may be modified by environment. Nutritional factors, and especially dietary lipids, have a role in the etiology of breast cancer. Thus, we aimed to analyze the influence of different high fat diets on DNA methylation and histone modifications in the rat dimethylbenz(a)anthracene (DMBA)-induced breast cancer model. Female Sprague-Dawley rats were fed a low-fat, a high corn-oil or a high extra-virgin olive oil (EVOO) diet from weaning or from induction with DMBA. In mammary glands and tumors we analyzed global and gene specific (RASSF1A, TIMP3) DNA methylation by LUMA and bisulfite pyrosequencing assays, respectively. We also determined gene expression and enzymatic activity of DNA methyltransferases (DNMT1, DNMT3a and DNMT3b) and evaluated changes in histone modifications (H3K4me2, H3K27me3, H4K20me3 and H4K16ac) by western-blot. Our results showed variations along time in the global DNA methylation of the mammary gland displaying decreases at puberty and with aging. The olive oil-enriched diet, on the one hand, increased the levels of global DNA methylation in mammary gland and tumor, and on the other, changed histone modifications patterns. The corn oil-enriched diet increased DNA methyltransferase activity in both tissues, resulting in an increase in the promoter methylation of the tumor suppressor genes RASSF1A and TIMP3. These results suggest a differential effect of the high fat diets on epigenetic patterns with a relevant role in the neoplastic transformation, which could be one of the mechanisms of their differential promoter effect, clearly stimulating for the high corn-oil diet and with a weaker influence for the high EVOO diet, on breast cancer progression.

Aberrant Epigenetic Modifications of LPHN2 Function as a Potential Cisplatin-Specific Biomarker for Human Gastrointestinal Cancer.

PurposeEpigenetic alterations of specific genes have recently been identified as diagnostic biomarkers for human cancers. However, there are currently no standardized epigenetic biomarkers for drug sensitivity in human gastrointestinal cancer. Therefore, the aim of this study is to identify a novel epigenetic biomarker in gastrointestinal cancer.Materials and MethodsUsing bisulfite sequencing and pyrosequencing analysis, DNA methylation patterns of gastric, colon primary tissues and their cancer cells were analyzed, and histone modifications were analyzed using chromatin immunoprecipitation assay. In addition, cancer cells were exposed to cisplatin and treated with a DNA methyltransferase inhibitor.ResultsWe report that in human gastric and colon cancers, latrophilin 2 (LPHN2) is silenced by epigenetic modifications, including CpG island methylation and aberrant histone modifications. We also confirmed that LPHN2 was silenced by DNA hypermethylation in primary gastric and colon tumor tissues compared to their normal counterparts. Interestingly, we found that cancer cells with methylated LPHN2 showed higher sensitivity to cisplatin. Also, 5-aza- 2′-deoxycytidine combined with cisplatin decreased the cytotoxicity of cisplatin in cancer cells with methylated LPHN2. In addition, LPHN2 knockdown in cancer cells with high LPHN2 expression sensitized these cells to the anti-proliferative effects of cisplatin.ConclusionIn human gastrointestinal cancer, we found that LPHN2 is regulated by epigenetic modifications, and that cancer cells with lower LPHN2 expression show higher sensitivity to cisplatin. Therefore, the methylation status of LPHN2 is a potential novel epigenetic biomarker for cisplatin treatment in human gastric and colon cancers.

Epigenetics, diseases and therapy in ophthalmology

Heritable changes in gene expression are regarded as epigenetics, which do not involve coding sequence modifications. The study of ophthalmology epigenetics is a rapidly growing area in biomedical research. Epigenetic mechanisms principally include DNA methylation, histone modification, chromatin remodeling and non-coding RNA. Aberrant DNA methylation and histone modification are linked to a number of age-related disorders, such as cancer, autoimmune and others. In recent years, the modulations of epigenetic changes on the pathogenesis of eye disorders and their roles in therapeutic interventions are drawing more and more attention, and these studies deepen the understanding of relevant diseases. Since the epigenetic alterations are reversible, modifying epigenetic marks contributing to eye diseases provide a new approach to the development of disease prevention, diagnosis and therapies. Herein we discuss the roles of epigenetic changes in eye disease development, hoping that ophthalmologists and researchers pay attention to these researching cues in pathogenesis of eye disorders caused by genetic expression alterations in response to environmental changes, importantly, to the implication for relevant eye disease therapy and prevention. Key words: Epigenesis, genetic; Eye/genetic; Eye disorder/therapy; DNA methylation; Histones; MicroRNA

Advances of Researches on the Role of Histone Modification in Hematological Neoplasms

As a crucial part of epigenetic regulation, the histone modification catalyzed by histone modification enzymes can alter the chromatin structure and modulate the gene expression. The role of histone modification in disease pathogenesis, especially in tumorigenesis, has become a research hotspot. The deregulation of histone modification, such as the overexpression and gain-of-function mutations of histone methyltransferase EZH2, the inactive mutations of histone methyltransferase MLL2, histone acetyltransferase CREBBP and EP300 are crucial for the development of hematological neoplasms. Some of Epi-drugs such as HDAC inhibitors, EZH2 inhibitors, are already clinically used, some are still in basic research stage, which are important field of new drug development for hematological neoplasms. In this review, the researches advances of basic medical sciences and clinical applications of aberrant histone modifications in hematological neoplasms are summarized.

An update on the epigenetics of psychotic diseases and autism.

The examination of potential roles of epigenetic alterations in the pathogenesis of psychotic diseases have become an essential alternative in recent years as genetic studies alone are yet to uncover major gene(s) for psychosis. Here, we describe the current state of knowledge from the gene-specific and genome-wide studies of postmortem brain and blood cells indicating that aberrant DNA methylation, histone modifications and dysregulation of micro-RNAs are linked to the pathogenesis of mental diseases. There is also strong evidence supporting that all classes of psychiatric drugs modulate diverse features of the epigenome. While comprehensive environmental and genetic/epigenetic studies are uncovering the origins, and the key genes/pathways affected in psychotic diseases, characterizing the epigenetic effects of psychiatric drugs may help to design novel therapies in psychiatry.

A role for epigenetics in the formation of chromosome translocations in acute leukemia

In general, the field of cancer genetics seems to have shifted its focus from cancer-associated genes to cancer-associated epigenetic activity. An abundance of evidence suggests that epigenetic malfunction, such as aberrant histone modification, and altered DNA methylation, is at the root of much, if not most aberrant gene expression associated with cancer. However, a role for epigenetics in physical DNA changes, such as chromosome rearrangements, is less obvious, and certainly less well understood. A growing body of evidence suggests that epigenetics may play a role in many of the steps of aberrant chromosome recombination, especially chromosome translocations, associated with cancers such as acute leukemias.

Emerging role of linker histone variant H1x as a biomarker with prognostic value in astrocytic gliomas. A multivariate analysis including trimethylation of H3K9 and H4K20.

Although epigenetic alterations play an essential role in gliomagenesis, the relevance of aberrant histone modifications and the respective enzymes has not been clarified. Experimental data implicates histone H3 lysine (K) methyltransferases SETDB1 and SUV39H1 into glioma pathobiology, whereas linker histone variant H1.0 and H4K20me3 reportedly affect prognosis. We investigated the expression of H3K9me3 and its methyltransferases along with H4K20me3 and H1x in 101 astrocytic tumors with regard to clinicopathological characteristics and survival. The effect of SUV39H1 inhibition by chaetocin on the proliferation, colony formation and migration of T98G cells was also examined. SETDB1 and cytoplasmic SUV39H1 levels increased from normal brain through low-grade to high-grade tumors, nuclear SUV39H1 correlating inversely with grade. H3K9me3 immunoreactivity was higher in normal brain showing no association with grade, whereas H1x and H4K20me3 expression was higher in grade 2 than in normal brain or high grades. These expression patterns of H1x, H4K20me3 and H3K9me3 were verified by Western immunoblotting. Chaetocin treatment significantly reduced proliferation, clonogenic potential and migratory ability of T98G cells. H1x was an independent favorable prognosticator in glioblastomas, this effect being validated in an independent set of 66 patients. Diminished nuclear SUV39H1 expression adversely affected survival in univariate analysis. In conclusion, H4K20me3 and H3K9 methyltransferases are differentially implicated in astroglial tumor progression. Deregulation of H1x emerges as a prognostic biomarker.

Histone Profiling in Leukemia Using LC-MS/MS

It has become increasingly evident that epigenetic changes, including aberrant histone modifications, play a crucial role in malignant transformation and may contribute to relapsed and refractory disease. There are over 160 known histone modifications, most of which remain poorly explored. Post-translational histone modifications (PTMs) have been shown to be altered in hematologic malignancies, and the protein network that regulates these PTMs offers potential therapeutic opportunities through pharmacologic inhibition. Prominent examples include aberrant histone acetylation in multiple malignancies, mutations in the histone acetyl transferase CEBBP in relapsed acute lymphoblastic leukemia (ALL), and activation mutations of the H3K27 lysine methyltransferase (KMT) EZH2 in lymphoma. Several histone deacetylase (HDAC) and KMT inhibitors are currently in clinical trials. Most mutations in the histone modifying enzymes have been identified by whole genome sequencing efforts. More recently, mass spectrometry has been proposed as a technique to identify patterns of histone modifications in cancer. Jaffe et al (Nature Genetics, 2013) developed a mass spectrometry approach to global chromatin profiling using leukemia cell lines. Their initial analysis focused on lysine methylation and acetylation, including some of the best characterized residues (H3K4, H3K9, H3K27, H3K36, H3K79). This proof of principle study showed that histone profiles matched what would be predicted based on our knowledge of genetic mutations. More importantly, profiles could serve as leads to discover previously unknown mutations in chromatin modifying enzymes.We adapted the methods established by Jaffe et al to histone modification profiling using small amounts of primary material from leukemia patients. Our work flow involves enrichment of blasts by ficoll centrifugation or fluorescent activated cell sorting, isolation highly purified histones from patient samples using a resin column followed by gel electrophoresis, digestion with ArgC and Trypsin, and nanoscale liquid chromatography followed by tandem mass spectrometry (nano LC-MS/MS). We established a leukemia cell line panel labeled with heavy (13C6) arginine and heavy (13C6) lysine for SILAC based internal standardization. Initially focusing our analysis on H3K27 and H3K36 methylation and using published retention times and m/z ratios, we were able to identify almost all major combinatorial acetylation and methylation states for the two residues (Table 1). We also identified methylation/acetylation states for H3K9 (ac), H3K14 (ac), H3K18 (ac, me), H3K23 (ac), and H3K79(me, me2) (data not shown). Preliminary experiments using a cell line with an activating NSD2 mutation correctly identified increased H3K36 dimethylation and decreased H2K27 trimethylation compared to the SILAC standard. We will use this method to correlate histone profiles of patient leukemia samples with clinical and molecular information as a means of interrogating the potential role for a number of known histone modifying enzymes in a single sample. In the future, we hope to extend our analysis to less well characterized histone PTMs. Table 1Lysine modifications found on histone H3.1 in Jurkat cell line. Percentages in BOLD = Arg-C digestion; Regular = Trypsin digestion.H3.1 ResidueCombinationsUnmodifiedAcetylMethylDimethylTrimethylK27 total K27unmod/K36 K27me1/K36 K27me2/K36 K27me3/K36 K27ac/K3614%/8% 71%66%33%100%/100%36%41%100% 22%60%31%/25% 29%33%44%40%14%/31%K36 total63%/44%6%/14%31%/20% DisclosuresNo relevant conflicts of interest to declare.